Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus)

PubMed Central

2016-01-01

Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity. PMID:26865733

Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus).

PubMed

Ahrens, Collin W; James, Elizabeth A

2016-05-01

Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Isozymes and the genetic resources of forest trees

Treesearch

A. H. D. Brown; G. F. Moran

1981-01-01

Genetic data are an essential prerequisite for analysing the genetic structure of tree populations. The isozyme technique is the best currently available method for obtaining such data. Despite several shortcomings, isozyme data directly evaluate the genetic resources of forest trees, and can thus be used to monitor and manipulate these resources. For example,...

Genetic structure of Chinese indigenous goats and the special geographical structure in the Southwest China as a geographic barrier driving the fragmentation of a large population.

PubMed

Wei, Caihong; Lu, Jian; Xu, Lingyang; Liu, Gang; Wang, Zhigang; Zhao, Fuping; Zhang, Li; Han, Xu; Du, Lixin; Liu, Chousheng

2014-01-01

China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demographic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (H(S) of 0.644) and high population diversity at the species level (H(T) value of 0.737) were estimated. Significant moderate population differentiation was detected (F(ST) value of 0.129). Significant excess homozygosity (F(IS) of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human's migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats.

Genetic Structure of Chinese Indigenous Goats and the Special Geographical Structure in the Southwest China as a Geographic Barrier Driving the Fragmentation of a Large Population

PubMed Central

Xu, Lingyang; Liu, Gang; Wang, Zhigang; Zhao, Fuping; Zhang, Li; Han, Xu; Du, Lixin; Liu, Chousheng

2014-01-01

Background China has numerous native domestic goat breeds, however, extensive studies are focused on the genetic diversity within the fewer breeds and limited regions, the population demograogic history and origin of Chinese goats are still unclear. The roles of geographical structure have not been analyzed in Chinese goat domestic process. In this study, the genetic relationships of Chinese indigenous goat populations were evaluated using 30 microsatellite markers. Methodology/Principal Findings Forty Chinese indigenous populations containing 2078 goats were sampled from different geographic regions of China. Moderate genetic diversity at the population level (HS of 0.644) and high population diversity at the species level (HT value of 0.737) were estimated. Significant moderate population differentiation was detected (FST value of 0.129). Significant excess homozygosity (FIS of 0.105) and recent population bottlenecks were detected in thirty-six populations. Neighbour-joining tree, principal components analysis and Bayesian clusters all revealed that Chinese goat populations could be subdivided into at least four genetic clusters: Southwest China, South China, Northwest China and East China. It was observed that the genetic diversity of Northern China goats was highest among these clusters. The results here suggested that the goat populations in Southwest China might be the earliest domestic goats in China. Conclusions/Significance Our results suggested that the current genetic structure of Chinese goats were resulted from the special geographical structure, especially in the Western China, and the Western goat populations had been separated by the geographic structure (Hengduan Mountains and Qinling Mountains-Huaihe River Line) into two clusters: the Southwest and Northwest. It also indicated that the current genetic structure was caused by the geographical origin mainly, in close accordance with the human’s migration history throughout China. This study provides a fundamental genetic profile for the conservation of these populations and better to understand the domestication process and origin of Chinese goats. PMID:24718092

Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

PubMed

Pometti, Carolina; Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

2018-01-01

The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae)

PubMed Central

Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

2018-01-01

The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees. PMID:29389969

The Genetic Structure of an Invasive Pest, the Asian Citrus Psyllid Diaphorina citri (Hemiptera: Liviidae)

PubMed Central

Guidolin, Aline S.; Fresia, Pablo; Cônsoli, Fernando L.

2014-01-01

The Asian citrus psyllid Diaphorina citri is currently the major threat to the citrus industry as it is the vector of Candidatus Liberibacter, the causal agent of huanglongbing disease (HLB). D. citri is native to Asia and now colonizes the Americas. Although it has been known in some countries for a long time, invasion routes remain undetermined. There are no efficient control methods for the HLB despite the intensive management tools currently in use. We investigated the genetic variability and structure of populations of D. citri to aid in the decision making processes toward sustainable management of this species/disease. We employed different methods to quantify and compare the genetic diversity and structure of D. citri populations among 36 localities in Brazil, using an almost complete sequence of the cytochrome oxidase I (COI) gene. Our analyses led to the identification of two geographically and genetically structured groups. The indices of molecular diversity pointed to a recent population expansion, and we discuss the role of multiple invasion events in this scenario. We also argue that such genetic diversity and population structure may have implications for the best management strategies to be adopted for controlling this psyllid and/or the disease it vectors in Brazil. PMID:25545788

The genetic structure of an invasive pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae).

PubMed

Guidolin, Aline S; Fresia, Pablo; Cônsoli, Fernando L

2014-01-01

The Asian citrus psyllid Diaphorina citri is currently the major threat to the citrus industry as it is the vector of Candidatus Liberibacter, the causal agent of huanglongbing disease (HLB). D. citri is native to Asia and now colonizes the Americas. Although it has been known in some countries for a long time, invasion routes remain undetermined. There are no efficient control methods for the HLB despite the intensive management tools currently in use. We investigated the genetic variability and structure of populations of D. citri to aid in the decision making processes toward sustainable management of this species/disease. We employed different methods to quantify and compare the genetic diversity and structure of D. citri populations among 36 localities in Brazil, using an almost complete sequence of the cytochrome oxidase I (COI) gene. Our analyses led to the identification of two geographically and genetically structured groups. The indices of molecular diversity pointed to a recent population expansion, and we discuss the role of multiple invasion events in this scenario. We also argue that such genetic diversity and population structure may have implications for the best management strategies to be adopted for controlling this psyllid and/or the disease it vectors in Brazil.

The subtle role of climate change on population genetic structure in Canada lynx.

PubMed

Row, Jeffrey R; Wilson, Paul J; Gomez, Celine; Koen, Erin L; Bowman, Jeff; Thornton, Daniel; Murray, Dennis L

2014-07-01

Anthropogenically driven climatic change is expected to reshape global patterns of species distribution and abundance. Given recent links between genetic variation and environmental patterns, climate change may similarly impact genetic population structure, but we lack information on the spatial and mechanistic underpinnings of genetic-climate associations. Here, we show that current genetic variability of Canada lynx (Lynx canadensis) is strongly correlated with a winter climate gradient (i.e. increasing snow depth and winter precipitation from west-to-east) across the Pacific-North American (PNO) to North Atlantic Oscillation (NAO) climatic systems. This relationship was stronger than isolation by distance and not explained by landscape variables or changes in abundance. Thus, these patterns suggest that individuals restricted dispersal across the climate boundary, likely in the absence of changes in habitat quality. We propose habitat imprinting on snow conditions as one possible explanation for this unusual phenomenon. Coupling historical climate data with future projections, we also found increasingly diverging snow conditions between the two climate systems. Based on genetic simulations using projected climate data (2041-2070), we predicted that this divergence could lead to a threefold increase in genetic differentiation, potentially leading to isolated east-west populations of lynx in North America. Our results imply that subtle genetic structure can be governed by current climate and that substantive genetic differentiation and related ecological divergence may arise from changing climate patterns. © 2014 John Wiley & Sons Ltd.

Fine-scale genetic structure arises during range expansion of an invasive gecko.

PubMed

Short, Kristen Harfmann; Petren, Kenneth

2011-01-01

Processes of range expansion are increasingly important in light of current concerns about invasive species and range shifts due to climate change. Theoretical studies suggest that genetic structuring may occur during range expansion. Ephemeral genetic structure can have important evolutionary implications, such as propagating genetic changes along the wave front of expansion, yet few studies have shown evidence of such structure. We tested the hypothesis that genetic structure arises during range expansion in Hemidactylus mabouia, a nocturnal African gecko recently introduced to Florida, USA. Twelve highly variable microsatellite loci were used to screen 418 individuals collected from 43 locations from four sampling sites across Florida, representing a gradient from earlier (∼1990s) to very recent colonization. We found earlier colonized locations had little detectable genetic structure and higher allelic richness than more recently colonized locations. Genetic structuring was pronounced among locations at spatial scales of tens to hundreds of meters near the leading edge of range expansion. Despite the rapid pace of range expansion in this introduced gecko, dispersal is limited among many suitable habitat patches. Fine-scale genetic structure is likely the result of founder effects during colonization of suitable habitat patches. It may be obscured over time and by scale-dependent modes of dispersal. Further studies are needed to determine if such genetic structure affects adaptation and trait evolution in range expansions and range shifts.

The role of self-defined race/ethnicity in population structure control.

PubMed

Liu, X-Q; Paterson, A D; John, E M; Knight, J A

2006-07-01

Population-based association studies are powerful tools for the genetic mapping of complex diseases. However, this method is sensitive to potential confounding by population structure. While statistical methods that use genetic markers to detect and control for population structure have been the focus of current literature, the utility of self-defined race/ethnicity in controlling for population structure has been controversial. In this study of 1334 individuals, who self-identified as either African American, European American or Hispanic, we demonstrated that when the true underlying genetic structure and the self-defined racial/ethnic groups were roughly in agreement with each other, the self-defined race/ethnicity information was useful in the control of population structure.

Selection of RAPD markers for investigation of genetic population structure in fusiform rust fungus infecting loblolly pine

Treesearch

James H. Roberds; Thomas L. Kubisiak; Pauline C. Spaine; S.F. Covert; R.L. Doudrick

1997-01-01

research to determine patterns of genetic differentiation among and within field populations of Cronartium quercuum f. sp. fusiforme using RAPD markers is currently underway in the molecular genetics laboratory at the Southern Institute of Forest Genetics. Fungal tissue was collected as a drop of spermatia or scrapings of a...

Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia

PubMed Central

Balazik, Matthew T.; Farrae, Daniel J.; Darden, Tanya L.; Garman, Greg C.

2017-01-01

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were genetically evaluated using a powerful microsatellite marker suite to determine if they are genetically distinct. Specifically, this study evaluates the genetic structure, characterizes the genetic diversity, estimates effective population size, and measures inbreeding of Atlantic sturgeon in the James River. The results indicate that fall and spring spawning James River Atlantic sturgeon groups are genetically distinct (overall FST = 0.048, F’ST = 0.181) with little admixture between the groups. The observed levels of genetic diversity and effective population sizes along with the lack of detected inbreeding all indicated that the James River has two genetically healthy populations of Atlantic sturgeon. The study also demonstrates that samples from adult Atlantic sturgeon, with proper sample selection criteria, can be informative when creating reference population databases. The presence of two genetically-distinct spawning groups of Atlantic sturgeon within the James River raises concerns about the current genetic assignment used by managers. Other nearby rivers may also have dual spawning groups that either are not accounted for or are pooled in reference databases. Our results represent the second documentation of genetically distinct dual spawning groups of Atlantic sturgeon in river systems along the U.S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history. PMID:28686610

Past climate change drives current genetic structure of an endangered freshwater mussel species.

PubMed

Inoue, Kentaro; Lang, Brian K; Berg, David J

2015-04-01

Historical-to-recent climate change and anthropogenic disturbance affect species distributions and genetic structure. The Rio Grande watershed of the United States and Mexico encompasses ecosystems that are intensively exploited, resulting in substantial degradation of aquatic habitats. While significant anthropogenic disturbances in the Rio Grande are recent, inhospitable conditions for freshwater organisms likely existed prior to such disturbances. A combination of anthropogenic and past climate factors may contribute to current distributions of aquatic fauna in the Rio Grande basin. We used mitochondrial DNA and 18 microsatellite loci to infer evolutionary history and genetic structure of an endangered freshwater mussel, Popenaias popeii, throughout the Rio Grande drainage. We estimated spatial connectivity and gene flow across extant populations of P. popeii and used ecological niche models (ENMs) and approximate Bayesian computation (ABC) to infer its evolutionary history during the Pleistocene. structure results recovered regional and local population clusters in the Rio Grande. ENMs predicted drastic reductions in suitable habitat during the last glacial maximum. ABC analyses suggested that regional population structure likely arose in this species during the mid-to-late Pleistocene and was followed by a late Pleistocene population bottleneck in New Mexico populations. The local population structure arose relatively recently, perhaps due to anthropogenic factors. Popenaias popeii, one of the few freshwater mussel species native to the Rio Grande basin, is a case study for understanding how both geological and anthropogenic factors shape current population genetic structure. Conservation strategies for this species should account for the fragmented nature of contemporary populations. © 2015 John Wiley & Sons Ltd.

Genetic Analysis of Termite Colonies in Wisconsin

Treesearch

R.A. Arango; D.A. Marschalek; F. Green III; K.F. Raffa; M.E. Berres

2015-01-01

The objective of this study was to document current areas of subterranean termite activity in Wisconsin and to evaluate genetic characteristics of these northern, peripheral colonies. Here, amplified fragment-length polymorphism was used to characterize levels of inbreeding, expected heterozygosity, and percent polymorphism within colonies as well as genetic structure...

Genetic structure of nomadic Bedouin from Kuwait

PubMed Central

Mohammad, T.; Xue, Yali; Evison, M.; Tyler-Smith, Chris

2009-01-01

Bedouin are traditionally nomadic inhabitants of the Persian Gulf who claim descent from two male lineages: Adnani and Qahtani. We have investigated whether or not this tradition is reflected in the current genetic structure of a sample of 153 Bedouin males from six Kuwaiti tribes, including three tribes from each traditional lineage. Volunteers were genotyped using a panel of autosomal and Y-STRs, and Y-SNPs. The samples clustered with their geographical neighbours in both the autosomal and Y-chromosomal analyses, and showed strong evidence of genetic isolation and drift. Whilst there was no evidence of segregation into the two male lineages, other aspects of genetic structure were in accord with tradition. PMID:19639002

Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses

PubMed Central

Park, Danny S.; Brown, Brielin; Eng, Celeste; Huntsman, Scott; Hu, Donglei; Torgerson, Dara G.; Burchard, Esteban G.; Zaitlen, Noah

2015-01-01

Motivation: Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global ‘best guess’ reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Results: We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of ‘best guess’ reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing. Availability and implementation: Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix. Contact: noah.zaitlen@ucsf.edu PMID:26072481

Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change.

PubMed

Epps, Clinton W; Keyghobadi, Nusha

2015-12-01

Landscape genetics seeks to determine the effect of landscape features on gene flow and genetic structure. Often, such analyses are intended to inform conservation and management. However, depending on the many factors that influence the time to reach equilibrium, genetic structure may more strongly represent past rather than contemporary landscapes. This well-known lag between current demographic processes and population genetic structure often makes it challenging to interpret how contemporary landscapes and anthropogenic activity shape gene flow. Here, we review the theoretical framework for factors that influence time lags, summarize approaches to address this temporal disconnect in landscape genetic studies, and evaluate ways to make inferences about landscape change and its effects on species using genetic data alone or in combination with other data. Those approaches include comparing correlation of genetic structure with historical versus contemporary landscapes, using molecular markers with different rates of evolution, contrasting metrics of genetic structure and gene flow that reflect population genetic processes operating at different temporal scales, comparing historical and contemporary samples, combining genetic data with contemporary estimates of species distribution or movement, and controlling for phylogeographic history. We recommend using simulated data sets to explore time lags in genetic structure, and argue that time lags should be explicitly considered both when designing and interpreting landscape genetic studies. We conclude that the time lag problem can be exploited to strengthen inferences about recent landscape changes and to establish conservation baselines, particularly when genetic data are combined with other data. © 2015 John Wiley & Sons Ltd.

A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin

PubMed Central

Di Febbraro, Mirko; Imparato, Gennaro; Innangi, Michele; Véla, Errol; Menale, Bruno

2016-01-01

The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently—more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea daffodil especially during LGM because of strong variation in coastline caused by glaciations. PMID:27749920

Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda

PubMed Central

Tournebize, Rémi; Manel, Stéphanie; Vigouroux, Yves; Munoz, François; de Kochko, Alexandre

2017-01-01

Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion. PMID:28820899

Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning.

PubMed

Thomassen, Henri A; Harrigan, Ryan J; Semple Delaney, Kathleen; Riley, Seth P D; Serieys, Laurel E K; Pease, Katherine; Wayne, Robert K; Smith, Thomas B

2018-02-01

Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions. © 2017 Society for Conservation Biology.

Population structure, genetic variability, and gene flow of the bean leaf beetle, Cerotoma trifurcata, in the Midwestern United States

USDA-ARS?s Scientific Manuscript database

Bean leaf beetle, Cerotoma trifurcata (Forster) (Coleoptera: Chrysomelidae), is a common pest of soybean in the Midwest. However, there are currently no studies on the genetic variability of C. trifurcata. This study examined 15-30 individuals from 25 subpopulations to determine genetic variability ...

Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae)

Treesearch

Ken A. Sterling; David H. Reed; Brice P. Noonan; Melvin L. Warren

2012-01-01

The use of genetic methods to quantify the effects of anthropogenic habitat fragmentation on population structure has become increasingly common. However, in today’s highly fragmented habitats, researchers have sometimes concluded that populations are currently genetically isolated due to habitat fragmentation without testing the possibility that populations were...

Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers

PubMed Central

Janes, J K; Roe, A D; Rice, A V; Gorrell, J C; Coltman, D W; Langor, D W; Sperling, F A H

2016-01-01

An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure. PMID:26286666

Use of Population Genetics to Assess the Ecology, Evolution, and Population Structure of Coccidioides

PubMed Central

Teixeira, Marcus M.

2016-01-01

During the past 20 years, a general picture of the genetic diversity and population structure of Coccidioides, the causal agent of coccidioidomycosis (Valley fever), has emerged. The genus consists of 2 genetically diverse species, C. immitis and C. posadasii, each of which contains 1 or more distinct populations with limited gene flow. Genotypic data indicate that C. immitis is divided into 2 subpopulations (central and southern California populations) and C. posadasii is divided into 3 subpopulations (Arizona, Mexico, and Texas/South America populations). However, admixture within and among these populations and the current paucity of environmental isolates limit our understanding of the population genetics of Coccidioides. We assessed population structure of Coccidioides in Arizona by analyzing 495 clinical and environmental isolates. Our findings confirm the population structure as previously described and indicate a finer scale population structure in Arizona. Environmental isolates appear to have higher genetic diversity than isolates from human patients. PMID:27191589

A Participant-Oriented, Research-Based Approach for Design of a Biochemistry Workshop for Faculty at Undergraduate Institutions

ERIC Educational Resources Information Center

Owen, Rebecca L.; Breyer, Emelita D.

2005-01-01

The Molecular Genetics and Protein Structure and Function workshop is one of a series of workshops offered by the National Science Foundation-funded Center for Workshops in the Chemical Sciences. The workshop provides a hands-on introduction to current topics and techniques in molecular genetics and protein structure/function as applied to…

Does stand density affect mating system and population genetic structure in coast live oak?

Treesearch

Kathryn Beals; Richard S. Dodd

2006-01-01

Coast live oak (Quercus agrifolia) is a major species at risk in the current Phytophthora ramorum epidemic in California’s oak woodlands. To search effectively for resistant genotypes, it is imperative to have an understanding of the existing host population genetic structure in these forests, and how its reproductive capacity may...

Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic.

PubMed

Peacock, Elizabeth; Sonsthagen, Sarah A; Obbard, Martyn E; Boltunov, Andrei; Regehr, Eric V; Ovsyanikov, Nikita; Aars, Jon; Atkinson, Stephen N; Sage, George K; Hope, Andrew G; Zeyl, Eve; Bachmann, Lutz; Ehrich, Dorothee; Scribner, Kim T; Amstrup, Steven C; Belikov, Stanislav; Born, Erik W; Derocher, Andrew E; Stirling, Ian; Taylor, Mitchell K; Wiig, Øystein; Paetkau, David; Talbot, Sandra L

2015-01-01

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1-3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.

Implications of the Circumpolar Genetic Structure of Polar Bears for Their Conservation in a Rapidly Warming Arctic

PubMed Central

Peacock, Elizabeth; Sonsthagen, Sarah A.; Obbard, Martyn E.; Boltunov, Andrei; Regehr, Eric V.; Ovsyanikov, Nikita; Aars, Jon; Atkinson, Stephen N.; Sage, George K.; Hope, Andrew G.; Zeyl, Eve; Bachmann, Lutz; Ehrich, Dorothee; Scribner, Kim T.; Amstrup, Steven C.; Belikov, Stanislav; Born, Erik W.; Derocher, Andrew E.; Stirling, Ian; Taylor, Mitchell K.; Wiig, Øystein; Paetkau, David; Talbot, Sandra L.

2015-01-01

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat. PMID:25562525

Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic

USGS Publications Warehouse

Peacock, Elizabeth; Sonsthagen, Sarah A.; Obbard, Martyn E.; Boltunov, Andrei N.; Regehr, Eric V.; Ovsyanikov, Nikita; Aars, Jon; Atkinson, Stephen N.; Sage, George K.; Hope, Andrew G.; Zeyl, Eve; Bachmann, Lutz; Ehrich, Dorothee; Scribner, Kim T.; Amstrup, Steven C.; Belikov, Stanislav; Born, Erik W.; Derocher, Andrew E.; Stirling, Ian; Taylor, Mitchell K.; Wiig, Øystein; Paetkau, David; Talbot, Sandra L.

2015-01-01

We provide an expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat. We sought to evaluate whether their genetic diversity and structure have changed over this period of habitat decline, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate. Characterizing their circumpolar genetic structure using microsatellite data, we defined four clusters that largely correspond to current ecological and oceanographic factors: Eastern Polar Basin, Western Polar Basin, Canadian Archipelago and Southern Canada. We document evidence for recent (ca. last 1–3 generations) directional gene flow from Southern Canada and the Eastern Polar Basin towards the Canadian Archipelago, an area hypothesized to be a future refugium for polar bears as climate-induced habitat decline continues. Our data provide empirical evidence in support of this hypothesis. The direction of current gene flow differs from earlier patterns of gene flow in the Holocene. From analyses of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea subpopulation within the Eastern Polar Basin cluster did not show signals of population expansion, suggesting these areas may have served also as past interglacial refugia. Mismatch analyses of mitochondrial DNA data from polar and the paraphyletic brown bear (U. arctos) uncovered offset signals in timing of population expansion between the two species, that are attributed to differential demographic responses to past climate cycling. Mitogenomic structure of polar bears was shallow and developed recently, in contrast to the multiple clades of brown bears. We found no genetic signatures of recent hybridization between the species in our large, circumpolar sample, suggesting that recently observed hybrids represent localized events. Documenting changes in subpopulation connectivity will allow polar nations to proactively adjust conservation actions to continuing decline in sea-ice habitat.

A Clinician's primer in human genetics: what nurses need to know.

PubMed

Lea, D H

2000-09-01

This article provides nurses with general information about the structure and function of genes, metabolic and chromosomal disorders, and the inheritance of genetic conditions in families. It serves as a foundation for the remainder of this issue, which addresses the clinical application of genetic principles, genetic counseling and evaluation, and emerging genetic technologies. Nurses are present in all health care settings and care for individuals and families throughout their patient's life span. Nurses must therefore have adequate knowledge of human genetics so that they can identify individuals who may have a genetic condition or predisposition, and ensure that those individuals have access to the most current genetic diagnostics, treatment, and management therapeutics. With this knowledge, nurses can collect appropriate family histories, provide current genetic information, and support patients, families, and communities as they integrate this new information and technology into their daily lives.

Spatial and temporal variation in population genetic structure of wild Nile tilapia (Oreochromis niloticus) across Africa

PubMed Central

2011-01-01

Background Reconstructing the evolutionary history of a species is challenging. It often depends not only on the past biogeographic and climatic events but also the contemporary and ecological factors, such as current connectivity and habitat heterogeneity. In fact, these factors might interact with each other and shape the current species distribution. However, to what extent the current population genetic structure reflects the past and the contemporary factors is largely unknown. Here we investigated spatio-temporal genetic structures of Nile tilapia (Oreochromis niloticus) populations, across their natural distribution in Africa. While its large biogeographic distribution can cause genetic differentiation at the paleo-biogeographic scales, its restricted dispersal capacity might induce a strong genetic structure at micro-geographic scales. Results Using nine microsatellite loci and 350 samples from ten natural populations, we found the highest genetic differentiation among the three ichthyofaunal provinces and regions (Ethiopian, Nilotic and Sudano-Sahelian) (RST = 0.38 - 0.69). This result suggests the predominant effect of paleo-geographic events at macro-geographic scale. In addition, intermediate divergences were found between rivers and lakes within the regions, presumably reflecting relatively recent interruptions of gene flow between hydrographic basins (RST = 0.24 - 0.32). The lowest differentiations were observed among connected populations within a basin (RST = 0.015 in the Volta basin). Comparison of temporal sample series revealed subtle changes in the gene pools in a few generations (F = 0 - 0.053). The estimated effective population sizes were 23 - 143 and the estimated migration rate was moderate (m ~ 0.094 - 0.097) in the Volta populations. Conclusions This study revealed clear hierarchical patterns of the population genetic structuring of O. niloticus in Africa. The effects of paleo-geographic and climatic events were predominant at macro-geographic scale, and the significant effect of geographic connectivity was detected at micro-geographic scale. The estimated effective population size, the moderate level of dispersal and the rapid temporal change in genetic composition might reflect a potential effect of life history strategy on population dynamics. This hypothesis deserves further investigation. The dynamic pattern revealed at micro-geographic and temporal scales appears important from a genetic resource management as well as from a biodiversity conservation point of view. PMID:22151746

Genetic structure and natal origins of immature hawksbill turtles (Eretmochelys imbricata) in Brazilian waters.

PubMed

Proietti, Maira C; Reisser, Julia; Marins, Luis Fernando; Rodriguez-Zarate, Clara; Marcovaldi, Maria A; Monteiro, Danielle S; Pattiaratchi, Charitha; Secchi, Eduardo R

2014-01-01

Understanding the connections between sea turtle populations is fundamental for their effective conservation. Brazil hosts important hawksbill feeding areas, but few studies have focused on how they connect with nesting populations in the Atlantic. Here, we (1) characterized mitochondrial DNA control region haplotypes of immature hawksbills feeding along the coast of Brazil (five areas ranging from equatorial to temperate latitudes, 157 skin samples), (2) analyzed genetic structure among Atlantic hawksbill feeding populations, and (3) inferred natal origins of hawksbills in Brazilian waters using genetic, oceanographic, and population size information. We report ten haplotypes for the sampled Brazilian sites, most of which were previously observed at other Atlantic feeding grounds and rookeries. Genetic profiles of Brazilian feeding areas were significantly different from those in other regions (Caribbean and Africa), and a significant structure was observed between Brazilian feeding grounds grouped into areas influenced by the South Equatorial/North Brazil Current and those influenced by the Brazil Current. Our genetic analysis estimates that the studied Brazilian feeding aggregations are mostly composed of animals originating from the domestic rookeries Bahia and Pipa, but some contributions from African and Caribbean rookeries were also observed. Oceanographic data corroborated the local origins, but showed higher connection with West Africa and none with the Caribbean. High correlation was observed between origins estimated through genetics/rookery size and oceanographic/rookery size data, demonstrating that ocean currents and population sizes influence haplotype distribution of Brazil's hawksbill populations. The information presented here highlights the importance of national conservation strategies and international cooperation for the recovery of endangered hawksbill turtle populations.

Genetic Structure and Natal Origins of Immature Hawksbill Turtles (Eretmochelys imbricata) in Brazilian Waters

PubMed Central

Proietti, Maira C.; Reisser, Julia; Marins, Luis Fernando; Rodriguez-Zarate, Clara; Marcovaldi, Maria A.; Monteiro, Danielle S.; Pattiaratchi, Charitha; Secchi, Eduardo R.

2014-01-01

Understanding the connections between sea turtle populations is fundamental for their effective conservation. Brazil hosts important hawksbill feeding areas, but few studies have focused on how they connect with nesting populations in the Atlantic. Here, we (1) characterized mitochondrial DNA control region haplotypes of immature hawksbills feeding along the coast of Brazil (five areas ranging from equatorial to temperate latitudes, 157 skin samples), (2) analyzed genetic structure among Atlantic hawksbill feeding populations, and (3) inferred natal origins of hawksbills in Brazilian waters using genetic, oceanographic, and population size information. We report ten haplotypes for the sampled Brazilian sites, most of which were previously observed at other Atlantic feeding grounds and rookeries. Genetic profiles of Brazilian feeding areas were significantly different from those in other regions (Caribbean and Africa), and a significant structure was observed between Brazilian feeding grounds grouped into areas influenced by the South Equatorial/North Brazil Current and those influenced by the Brazil Current. Our genetic analysis estimates that the studied Brazilian feeding aggregations are mostly composed of animals originating from the domestic rookeries Bahia and Pipa, but some contributions from African and Caribbean rookeries were also observed. Oceanographic data corroborated the local origins, but showed higher connection with West Africa and none with the Caribbean. High correlation was observed between origins estimated through genetics/rookery size and oceanographic/rookery size data, demonstrating that ocean currents and population sizes influence haplotype distribution of Brazil's hawksbill populations. The information presented here highlights the importance of national conservation strategies and international cooperation for the recovery of endangered hawksbill turtle populations. PMID:24558419

The structural diversity of artificial genetic polymers

PubMed Central

Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

2016-01-01

Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson–Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata).

PubMed

Cox, Christian L; Chippindale, Paul T

2014-08-01

We evaluated the genetic diversity of a snake species with color polymorphism to understand the evolutionary processes that drive genetic structure across a large geographic region. Specifically, we analyzed genetic structure of the highly polymorphic ground snake, Sonora semiannulata, (1) among populations, (2) among color morphs (3) at regional and local spatial scales, using an amplified fragment length polymorphism dataset and multiple population genetic analyses, including FST-based and clustering analytical techniques. Based upon these methods, we found that there was moderate to low genetic structure among populations. However, this diversity was not associated with geographic locality at either spatial scale. Similarly, we found no evidence for genetic divergence among color morphs at either spatial scale. These results suggest that despite dramatic color polymorphism, this phenotypic diversity is not a major driver of genetic diversity within or among populations of ground snakes. We suggest that there are two mechanisms that could explain existing genetic diversity in ground snakes: recent range expansion from a genetically diverse founder population and current or recent gene flow among populations. Our findings have further implications for the types of color polymorphism that may generate genetic diversity in snakes.

Habitat continuity and stepping-stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea.

PubMed

Buonomo, Roberto; Assis, Jorge; Fernandes, Francisco; Engelen, Aschwin H; Airoldi, Laura; Serrão, Ester A

2017-02-01

Effective predictive and management approaches for species occurring in a metapopulation structure require good understanding of interpopulation connectivity. In this study, we ask whether population genetic structure of marine species with fragmented distributions can be predicted by stepping-stone oceanographic transport and habitat continuity, using as model an ecosystem-structuring brown alga, Cystoseira amentacea var. stricta. To answer this question, we analysed the genetic structure and estimated the connectivity of populations along discontinuous rocky habitat patches in southern Italy, using microsatellite markers at multiple scales. In addition, we modelled the effect of rocky habitat continuity and ocean circulation on gene flow by simulating Lagrangian particle dispersal based on ocean surface currents allowing multigenerational stepping-stone dynamics. Populations were highly differentiated, at scales from few metres up to thousands of kilometres. The best possible model fit to explain the genetic results combined current direction, rocky habitat extension and distance along the coast among rocky sites. We conclude that a combination of variable suitable habitat and oceanographic transport is a useful predictor of genetic structure. This relationship provides insight into the mechanisms of dispersal and the role of life-history traits. Our results highlight the importance of spatially explicit modelling of stepping-stone dynamics and oceanographic directional transport coupled with habitat suitability, to better describe and predict marine population structure and differentiation. This study also suggests the appropriate spatial scales for the conservation, restoration and management of species that are increasingly affected by habitat modifications. © 2016 John Wiley & Sons Ltd.

Uncovering the transmission dynamics of Plasmodium vivax using population genetics

PubMed Central

Barry, Alyssa E.; Waltmann, Andreea; Koepfli, Cristian; Barnadas, Celine; Mueller, Ivo

2015-01-01

Population genetic analysis of malaria parasites has the power to reveal key insights into malaria epidemiology and transmission dynamics with the potential to deliver tools to support control and elimination efforts. Analyses of parasite genetic diversity have suggested that Plasmodium vivax populations are more genetically diverse and less structured than those of Plasmodium falciparum indicating that P. vivax may be a more ancient parasite of humans and/or less susceptible to population bottlenecks, as well as more efficient at disseminating its genes. These population genetic insights into P. vivax transmission dynamics provide an explanation for its relative resilience to control efforts. Here, we describe current knowledge on P. vivax population genetic structure, its relevance to understanding transmission patterns and relapse and how this information can inform malaria control and elimination programmes. PMID:25891915

Contrasting Effects of Historical Sea Level Rise and Contemporary Ocean Currents on Regional Gene Flow of Rhizophora racemosa in Eastern Atlantic Mangroves.

PubMed

Ngeve, Magdalene N; Van der Stocken, Tom; Menemenlis, Dimitris; Koedam, Nico; Triest, Ludwig

2016-01-01

Mangroves are seafaring taxa through their hydrochorous propagules that have the potential to disperse over long distances. Therefore, investigating their patterns of gene flow provides insights on the processes involved in the spatial genetic structuring of populations. The coastline of Cameroon has a particular geomorphological history and coastal hydrology with complex contemporary patterns of ocean currents, which we hypothesize to have effects on the spatial configuration and composition of present-day mangroves within its spans. A total of 982 trees were sampled from 33 transects (11 sites) in 4 estuaries. Using 11 polymorphic SSR markers, we investigated genetic diversity and structure of Rhizophora racemosa, a widespread species in the region. Genetic diversity was low to moderate and genetic differentiation between nearly all population pairs was significant. Bayesian clustering analysis, PCoA, estimates of contemporary migration rates and identification of barriers to gene flow were used and complemented with estimated dispersal trajectories of hourly released virtual propagules, using high-resolution surface current from a mesoscale and tide-resolving ocean simulation. These indicate that the Cameroon Volcanic Line (CVL) is not a present-day barrier to gene flow. Rather, the Inter-Bioko-Cameroon (IBC) corridor, formed due to sea level rise, allows for connectivity between two mangrove areas that were isolated during glacial times by the CVL. Genetic data and numerical ocean simulations indicated that an oceanic convergence zone near the Cameroon Estuary complex (CEC) presents a strong barrier to gene flow, resulting in genetic discontinuities between the mangrove areas on either side. This convergence did not result in higher genetic diversity at the CEC as we had hypothesized. In conclusion, the genetic structure of Rhizophora racemosa is maintained by the contrasting effects of the contemporary oceanic convergence and historical climate change-induced sea level rise.

Contrasting Effects of Historical Sea Level Rise and Contemporary Ocean Currents on Regional Gene Flow of Rhizophora racemosa in Eastern Atlantic Mangroves

PubMed Central

Ngeve, Magdalene N.; Van der Stocken, Tom; Menemenlis, Dimitris; Koedam, Nico; Triest, Ludwig

2016-01-01

Mangroves are seafaring taxa through their hydrochorous propagules that have the potential to disperse over long distances. Therefore, investigating their patterns of gene flow provides insights on the processes involved in the spatial genetic structuring of populations. The coastline of Cameroon has a particular geomorphological history and coastal hydrology with complex contemporary patterns of ocean currents, which we hypothesize to have effects on the spatial configuration and composition of present-day mangroves within its spans. A total of 982 trees were sampled from 33 transects (11 sites) in 4 estuaries. Using 11 polymorphic SSR markers, we investigated genetic diversity and structure of Rhizophora racemosa, a widespread species in the region. Genetic diversity was low to moderate and genetic differentiation between nearly all population pairs was significant. Bayesian clustering analysis, PCoA, estimates of contemporary migration rates and identification of barriers to gene flow were used and complemented with estimated dispersal trajectories of hourly released virtual propagules, using high-resolution surface current from a mesoscale and tide-resolving ocean simulation. These indicate that the Cameroon Volcanic Line (CVL) is not a present-day barrier to gene flow. Rather, the Inter-Bioko-Cameroon (IBC) corridor, formed due to sea level rise, allows for connectivity between two mangrove areas that were isolated during glacial times by the CVL. Genetic data and numerical ocean simulations indicated that an oceanic convergence zone near the Cameroon Estuary complex (CEC) presents a strong barrier to gene flow, resulting in genetic discontinuities between the mangrove areas on either side. This convergence did not result in higher genetic diversity at the CEC as we had hypothesized. In conclusion, the genetic structure of Rhizophora racemosa is maintained by the contrasting effects of the contemporary oceanic convergence and historical climate change-induced sea level rise. PMID:26964094

Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

PubMed

Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

2017-01-01

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. Copyright © 2017 Montinaro et al.

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its tributaries, Colombia

PubMed Central

Berdugo, Gilberto Orozco; Narváez Barandica, Juan C.

2014-01-01

Prochilodus magdalenae is an endemic freshwater fish that occurs in the Magdalena, Sinú and Atrato hydrographic basins. It has an important economic role and is a food resource for the artisanal fishing communities. Its socioeconomic importance contrasts with the current status of its fisheries, where stocks are being depleted. Considering its importance and lack of information on its genetic structure, we used seven microsatellite markers to assess the genetic structure of wild populations of P. magdalenae. The genetic diversity was assessed and the population genetic structure was estimated through Fst, analysis of molecular variance and Bayesian analysis. A total of 290 alleles were found in all loci throughout all population. The high polymorphism contrasts with the levels of observed heterozygosity (Ho = 0.276), which are the lowest values recorded for the family. We found three populations of bocachico coexisting throughout the studied system, contradicting the hypothesis that freshwater migratory fish form panmictic populations. These results on the genetic structure of P. magdalenae constitute tools for a better understanding of the behavior and biology of this species, contributing to fish management and conservation programs. PMID:24688289

Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea

PubMed Central

Teacher, Amber GF; André, Carl; Jonsson, Per R; Merilä, Juha

2013-01-01

Marine fish often show little genetic structuring in neutral marker genes, and Atlantic herring (Clupea harengus) in the Baltic Sea are no exception; historically, very low levels of population differentiation (FST ≍ 0.002) have been found, despite a high degree of interpopulation environmental heterogeneity in salinity and temperature. Recent exome sequencing and SNP studies have however shown that many loci are under selection in this system. Here, we combined population genetic analyses of a large number of transcriptome-derived microsatellite markers with oceanographic modelling to investigate genetic differentiation and connectivity in Atlantic herring at a relatively fine scale within the Baltic Sea. We found evidence for weak but robust and significant genetic structuring (FST = 0.008) explainable by oceanographic connectivity. Genetic differentiation was also associated with site differences in temperature and salinity, with the result driven by the locus Her14 which appears to be under directional selection (FST = 0.08). The results show that Baltic herring are genetically structured within the Baltic Sea, and highlight the role of oceanography and environmental factors in explaining this structuring. The results also have implications for the management of herring fisheries, the most economically important fishery in the Baltic Sea, suggesting that the current fisheries management units may be in need of revision. PMID:23745145

Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera.

PubMed

Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

2017-01-10

Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. The unique life history characteristics of many marine invertebrates such as high dispersal rates, stochastic survival and variable recruitment are also likely to influence how populations are organised. To examine the microevolutionary forces influencing population structure, connectivity and adaptive variation in a highly-dispersive bivalve, populations of the black-lip pearl oyster Pinctada margaritifera were examined across its ~18,000 km Indo-Pacific distribution. Analyses utilising 9,624 genome-wide SNPs and 580 oysters, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (F st  = 0.2534-0.4177, p < 0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (F st  = 0.0007-0.1090, p < 0.001). Partitioning of genetic diversity (hierarchical AMOVA) attributed 18.1% of variance between ocean basins, whereas greater proportions were resolved within samples and populations (45.8% and 35.7% respectively). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively. Evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; F st  = 0.1012-0.4371, FDR = 0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations. It is evident that genetic structure and connectivity across the natural range of P. margaritifera is highly complex, and produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. Overall population organisation is far more elaborate than generalised CPH predictions, however valuable insights for regional fishery management, and a greater understanding of range-wide genetic structure in a highly-dispersive marine invertebrate have been gained.

Associations between forest fragmentation patterns and geneticstructure in Pfrimer’s Parakeet (Pyrrhura pfrimeri), an endangered endemic to central Brazil’s dry forests

USGS Publications Warehouse

Haig, Susan M.; Miller, Leonard F.; Bianchi, Carlos; Mullins, Thomas D.

2012-01-01

When habitat becomes fragmented, populations of species may become increasingly isolated. In the absence of habitat corridors, genetic structure may develop and populations risk reductions in genetic diversity from increased genetic drift and inbreeding. Deforestation of the Cerrado biome of Brazil, particularly of the dry forests within the Parana˜ River Basin, has incrementally occurred since the 1970s and increased forest fragmentation within the region. We performed landscape genetic analyses of Pfrimer’s parakeet (Pyrrhura pfrimeri), a globally endangered endemic to the region, to determine if forest fragmentation patterns were associated with genetic structuring in this species. We used previously generated satellite imagery that identified the locations of Parana˜ River Basin forest fragments in 1977, 1993/94, and 2008. Behavioral data quantifying the affinity of Pfrimer’s parakeet for forest habitat was used to parameterize empirically derived landscape conductance surfaces. Though genetic structure was observed among Pfrimer’s parakeet populations, no association between genetic and geographic distance was detected. Likewise, least cost path lengths, circuit theorybased resistance distances, and a new measure of least cost path length complexity could not be conclusively associated with genetic structure patterns. Instead, a new quantity that encapsulated connection redundancy from the 1977 forest fragmentation data provided the clearest associations with pairwise genetic differentiation patterns (Jost’s D: r = 0.72, P = 0.006; FST: r = 0.741, P = 0.001). Our analyses suggest a 35-year or more lag between deforestation and its effect on genetic structure. Because 66 % of the Parana˜ River Basin has been deforested since 1977, we expect that genetic structure will increase substantially among Pfrimer’s Parakeet populations in the future, especially if fragmentation continues at its current pace.

Landscape genetics in the subterranean rodent Ctenomys "chasiquensis" associated with highly disturbed habitats from the southeastern Pampas region, Argentina.

PubMed

Mora, Matías Sebastián; Mapelli, Fernando J; López, Aldana; Gómez Fernández, María Jimena; Mirol, Patricia M; Kittlein, Marcelo J

2017-12-01

Studies of genetic differentiation in fragmented environments help us to identify those landscape features that most affect gene flow and dispersal patterns. Particularly, the assessment of the relative significance of intrinsic biological and environmental factors affecting the genetic structure of populations becomes crucial. In this work, we assess the current dispersal patterns and population structure of Ctenomys "chasiquensis", a vulnerable and endemic subterranean rodent distributed on a small area in Central Argentina, using 9 polymorphic microsatellite loci. We use landscape genetics approaches to assess the relationship between genetic connectivity among populations and environmental attributes. Our analyses show that populations of C. "chasiquensis" are moderately to highly structured at a regional level. This pattern is most likely the outcome of substantial gene flow on the more homogeneous sand dune habitat of the Northwest of its distributional range, in conjunction with an important degree of isolation of eastern and southwestern populations, where the optimal habitat is surrounded by a highly fragmented landscape. Landscape genetics analysis suggests that habitat quality and longitude were the environmental factors most strongly associated with genetic differentiation/uniqueness of populations. In conclusion, our results indicate an important genetic structure in this species, even at a small spatial scale, suggesting that contemporary habitat fragmentation increases population differentiation.

Phylogeography of the Rock Shell Thais clavigera (Mollusca): Evidence for Long-Distance Dispersal in the Northwestern Pacific

PubMed Central

Jung, Daewui; Li, Qi; Kong, Ling-Feng; Ni, Gang; Nakano, Tomoyuki; Matsukuma, Akihiko; Kim, Sanghee; Park, Chungoo; Lee, Hyuk Je; Park, Joong-Ki

2015-01-01

The present-day genetic structure of a species reflects both historical demography and patterns of contemporary gene flow among populations. To precisely understand how these factors shape current population structure of the northwestern (NW) Pacific marine gastropod, Thais clavigera, we determined the partial nucleotide sequences of the mitochondrial COI gene for 602 individuals sampled from 29 localities spanning almost the whole distribution of T. clavigera in the NW Pacific Ocean (~3,700 km). Results from population genetic and demographic analyses (AMOVA, ΦST-statistics, haplotype networks, Tajima’s D, Fu’s FS, mismatch distribution, and Bayesian skyline plots) revealed a lack of genealogical branches or geographical clusters, and a high level of genetic (haplotype) diversity within each of studied population. Nevertheless, low but significant genetic structuring was detected among some geographical populations separated by the Changjiang River, suggesting the presence of geographical barriers to larval dispersal around this region. Several lines of evidence including significant negative Tajima’s D and Fu’s FS statistics values, the unimodally shaped mismatch distribution, and Bayesian skyline plots suggest a population expansion at marine isotope stage 11 (MIS 11; 400 ka), the longest and warmest interglacial interval during the Pleistocene epoch. The lack of genetic structure among the great majority of the NW Pacific T. clavigera populations may be attributable to high gene flow by current-driven long-distance dispersal of prolonged planktonic larval phase of this species. PMID:26171966

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

PubMed

Pissard, Audrey; Arbizu, Carlos; Ghislain, Marc; Faux, Anne-Michèle; Paulet, Sébastien; Bertin, Pierre

2008-01-01

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs.

PubMed

Viengkone, Michelle; Derocher, Andrew Edward; Richardson, Evan Shaun; Malenfant, René Michael; Miller, Joshua Moses; Obbard, Martyn E; Dyck, Markus G; Lunn, Nick J; Sahanatien, Vicki; Davis, Corey S

2016-12-01

Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single-nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine-scale structure. In Hudson Bay, Canada, three polar bear ( Ursus maritimus ) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark-recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine-scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western-including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern-individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast-individuals from SH (Akimiski Island in James Bay); and (iv) Northeast-individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine-scale population delineation in polar bears.

Ancient Humans Influenced the Current Spatial Genetic Structure of Common Walnut Populations in Asia

PubMed Central

Pollegioni, Paola; Woeste, Keith E.; Chiocchini, Francesca; Del Lungo, Stefano; Olimpieri, Irene; Tortolano, Virginia; Clark, Jo; Hemery, Gabriel E.; Mapelli, Sergio; Malvolti, Maria Emilia

2015-01-01

Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J. regia evolved over many centuries under the influence of human management and exploitation. We evaluated the hypothesis that the current distribution of natural genetic resources of common walnut in Asia is, at least in part, the product of ancient anthropogenic dispersal, human cultural interactions, and afforestation. Genetic analysis combined with ethno-linguistic and historical data indicated that ancient trade routes such as the Persian Royal Road and Silk Road enabled long-distance dispersal of J. regia from Iran and Trans-Caucasus to Central Asia, and from Western to Eastern China. Ancient commerce also disrupted the local spatial genetic structure of autochthonous walnut populations between Tashkent and Samarkand (Central-Eastern Uzbekistan), where the northern and central routes of the Northern Silk Road converged. A significant association between ancient language phyla and the genetic structure of walnut populations is reported even after adjustment for geographic distances that could have affected both walnut gene flow and human commerce over the centuries. Beyond the economic importance of common walnut, our study delineates an alternative approach for understanding how the genetic resources of long-lived perennial tree species may be affected by the interaction of geography and human history. PMID:26332919

Genetic signatures of historical dispersal of fish threatened by biological invasions: the case of galaxiids in South America

USGS Publications Warehouse

Vanhaecke, Delphine; Garcia de Leaniz, Carlos; Gajardo, Gonzalo; Dunham, Jason; Giannico, Guillermo; Consegura, Sofia

2015-01-01

Aim The ecological effects of biological invasions are well documented, but little is known about the effects of invaders on the genetic structure of native species. We examined the phylogeography, genetic variation and population structuring of two galaxiid fishes, Aplochiton zebraand A. taeniatus, threatened by non-native salmonids, and whose conservation is complicated by misidentification and limited knowledge of their genetic diversity. Location Chile and the Falkland Islands. Methods We combined microsatellite and mitochondrial DNA (16S rDNA and COI) markers to compare genetic diversity, effective population size and gene flow of Aplochiton spp. populations differentially affected by salmonid presence. Results We identified two 16S rDNA haplotypes among A. zebra – one dominant in coastal populations and another dominant in inland populations. Populations living on the island of Chiloé displayed a mixture of coastal and inland haplotypes, as well as high microsatellite diversity, as one would expect if the island had been a refugium during the Last Glacial Maximum, or a contact zone among populations. Microsatellite data revealed strong population structuring, indicative of current isolation patterns, and a negative correlation between the genetic diversity of A. zebra and the relative abundance of invasive salmonids. Main conclusions Our study indicates that population structuring of A. zebra reflects the influence of historical patterns of migration, but also the current levels of reduced gene flow among watersheds. Invasive salmonids, known to compete with and prey on native galaxiids, may have had negative impacts on the genetic diversity of Aplochiton spp. The low genetic variation found in some populations, coupled with potential biases in abundance estimates due to species misidentification, highlight the urgent need for more research into the conservation status of the two species of Aplochiton.

Current Genetic Discoveries and Education: "Strengths, Opportunities, and Limitations"

ERIC Educational Resources Information Center

Bates, Timothy C.

2008-01-01

This article notes that many key positive developments in education originated in research on the structure and genetics of abilities, providing primary evidence for ability in disadvantaged groups and playing a critical role in demonstrating the existence of developmental learning disorders and effective interventions. It is argued that new work…

Phylogeographic Structure in Benthic Marine Invertebrates of the Southeast Pacific Coast of Chile with Differing Dispersal Potential

PubMed Central

Haye, Pilar A.; Segovia, Nicolás I.; Muñoz-Herrera, Natalia C.; Gálvez, Francisca E.; Martínez, Andrea; Meynard, Andrés; Pardo-Gandarillas, María C.; Poulin, Elie; Faugeron, Sylvain

2014-01-01

The role of dispersal potential on phylogeographic structure, evidenced by the degree of genetic structure and the presence of coincident genetic and biogeographic breaks, was evaluated in a macrogeographic comparative approach along the north-central coast of Chile, across the biogeographic transition zone at 30°S. Using 2,217 partial sequences of the mitochondrial Cytochrome Oxidase I gene of eight benthic invertebrate species along ca. 2,600 km of coast, we contrasted dispersal potential with genetic structure and determined the concordance between genetic divergence between biogeographic regions and the biogeographic transition zone at 30°S. Genetic diversity and differentiation highly differed between species with high and low dispersal potential. Dispersal potential, sometimes together with biogeographic region, was the factor that best explained the genetic structure of the eight species. The three low dispersal species, and one species assigned to the high dispersal category, had a phylogeographic discontinuity coincident with the biogeographic transition zone at 30°S. Furthermore, coalescent analyses based on the isolation-with-migration model validate that the split between biogeographic regions north and south of 30°S has a historic origin. The signatures of the historic break in high dispersers is parsimoniously explained by the homogenizing effects of gene flow that have erased the genetic signatures, if ever existed, in high dispersers. Of the four species with structure across the break, only two had significant albeit very low levels of asymmetric migration across the transition zone. Historic processes have led to the current biogeographic and phylogeographic structure of marine species with limited dispersal along the north-central coast of Chile, with a strong lasting impact in their genetic structure. PMID:24586356

Multiscale Genetic Structure of Yellowstone Cutthroat Trout in the Upper Snake River Basin.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cegelski, Christine C.; Campbell, Matthew R.

2006-05-30

Populations of Yellowstone cutthroat trout Oncorhynchus clarkii bouvierii have declined throughout their native range as a result of habitat fragmentation, overharvest, and introductions of nonnative trout that have hybridized with or displaced native populations. The degree to which these factors have impacted the current genetic population structure of Yellowstone cutthroat trout populations is of primary interest for their conservation. In this study, we examined the genetic diversity and genetic population structure of Yellowstone cutthroat trout in Idaho and Nevada with data from six polymorphic microsatellite loci. A total of 1,392 samples were analyzed from 45 sample locations throughout 11 majormore » river drainages. We found that levels of genetic diversity and genetic differentiation varied extensively. The Salt River drainage, which is representative of the least impacted migration corridors in Idaho, had the highest levels of genetic diversity and low levels of genetic differentiation. High levels of genetic differentiation were observed at similar or smaller geographic scales in the Portneuf River, Raft River, and Teton River drainages, which are more altered by anthropogenic disturbances. Results suggested that Yellowstone cutthroat trout are naturally structured at the major river drainage level but that habitat fragmentation has altered this structuring. Connectivity should be restored via habitat restoration whenever possible to minimize losses in genetic diversity and to preserve historical processes of gene flow, life history variation, and metapopulation dynamics. However, alternative strategies for management and conservation should also be considered in areas where there is a strong likelihood of nonnative invasions or extensive habitat fragmentation that cannot be easily ameliorated.« less

Population genetic signatures of a climate change driven marine range extension.

PubMed

Ramos, Jorge E; Pecl, Gretta T; Moltschaniwskyj, Natalie A; Semmens, Jayson M; Souza, Carla A; Strugnell, Jan M

2018-06-22

Shifts in species distribution, or 'range shifts', are one of the most commonly documented responses to ocean warming, with important consequences for the function and structure of ecosystems, and for socio-economic activities. Understanding the genetic signatures of range shifts can help build our knowledge of the capacity of species to establish and persist in colonised areas. Here, seven microsatellite loci were used to examine the population connectivity, genetic structure and diversity of Octopus tetricus, which has extended its distribution several hundred kilometres polewards associated with the southwards extension of the warm East Australian Current along south-eastern Australia. The historical distribution and the range extension zones had significant genetic differences but levels of genetic diversity were comparable. The population in the range extension zone was sub-structured, contained relatively high levels of self-recruitment and was sourced by migrants from along the entire geographic distribution. Genetic bottlenecks and changes in population size were detected throughout the range extension axis. Persistent gene flow from throughout the historical zone and moderate genetic diversity may buffer the genetic bottlenecks and favour the range extension of O. tetricus. These characteristics may aid adaptation, establishment, and long-term persistence of the population in the range extension zone.

Stocking activities for the Arctic charr in Lake Geneva: Genetic effects in space and time.

PubMed

Savary, Romain; Dufresnes, Christophe; Champigneulle, Alexis; Caudron, Arnaud; Dubey, Sylvain; Perrin, Nicolas; Fumagalli, Luca

2017-07-01

Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In this study, we focus on the declining Arctic charr ( Salvelinus alpinus ) population from Lake Geneva (Switzerland and France), which has initially been restocked with allochtonous fishes in the early eighties, followed by supportive breeding. In this context, we conducted a genetic survey to document the evolution of the genetic diversity and structure throughout the last 50 years, before and after the initiation of hatchery supplementation, using contemporary and historical samples. We show that the introduction of exotic fishes was associated with a genetic bottleneck in the 1980-1990s, a break of Hardy-Weinberg Equilibrium (HWE), a reduction in genetic diversity, an increase in genetic structure among spawning sites, and a change in their genetic composition. Together with better environmental conditions, three decades of subsequent supportive breeding using local fishes allowed to re-establish HWE and the initial levels of genetic variation. However, current spawning sites have not fully recovered their original genetic composition and were extensively homogenized across the lake. Our study demonstrates the drastic genetic consequences of different restocking tactics in a comprehensive spatiotemporal framework and suggests that genetic alteration by nonlocal stocking may be partly reversible through supportive breeding. We recommend that conservation-based programs consider local diversity and implement adequate protocols to limit the genetic homogenization of this Arctic charr population.

The role of river drainages in shaping the genetic structure of capybara populations.

PubMed

Byrne, María Soledad; Quintana, Rubén Darío; Bolkovic, María Luisa; Cassini, Marcelo H; Túnez, Juan Ignacio

2015-12-01

The capybara, Hydrochoerus hydrochaeris, is an herbivorous rodent widely distributed throughout most of South American wetlands that lives closely associated with aquatic environments. In this work, we studied the genetic structure of the capybara throughout part of its geographic range in Argentina using a DNA fragment of the mitochondrial control region. Haplotypes obtained were compared with those available for populations from Paraguay and Venezuela. We found 22 haplotypes in 303 individuals. Hierarchical AMOVAs were performed to evaluate the role of river drainages in shaping the genetic structure of capybara populations at the regional and basin scales. In addition, two landscape genetic models, isolation by distance and isolation by resistance, were used to test whether genetic distance was associated with Euclidean distance (i.e. isolation by distance) or river corridor distance (i.e. isolation by resistance) at the basin scale. At the regional scale, the results of the AMOVA grouping populations by mayor river basins showed significant differences between them. At the basin scale, we also found significant differences between sub-basins in Paraguay, together with a significant correlation between genetic and river corridor distance. For Argentina and Venezuela, results were not significant. These results suggest that in Paraguay, the current genetic structure of capybaras is associated with the lack of dispersion corridors through permanent rivers. In contrast, limited structuring in Argentina and Venezuela is likely the result of periodic flooding facilitating dispersion.

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga).

PubMed

Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, Igor; Bilbao, Eider; Goñi, Nicolas; Santiago, Josu; Domingo, Andrés; Karakulak, Saadet; Oray, Işık; Estonba, Andone

2015-01-01

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

PubMed Central

Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, Igor; Bilbao, Eider; Goñi, Nicolas; Santiago, Josu; Domingo, Andrés; Karakulak, Saadet; Oray, Işık; Estonba, Andone

2015-01-01

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short- and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing. PMID:26090851

Mathematical methods for protein science

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hart, W.; Istrail, S.; Atkins, J.

1997-12-31

Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focusedmore » on two aspects of protein science: mathematical structure prediction, and inverse protein folding.« less

Genetics and biochemistry remain essential in the structural era of the spliceosome.

PubMed

Mayerle, Megan; Guthrie, Christine

2017-08-01

The spliceosome is not a single macromolecular machine. Rather it is a collection of dynamic heterogeneous subcomplexes that rapidly interconvert throughout the course of a typical splicing cycle. Because of this, for many years the only high resolution structures of the spliceosome available were of smaller, isolated protein or RNA components. Consequently much of our current understanding of the spliceosome derives from biochemical and genetic techniques. Now with the publication of multiple, high resolution structures of the spliceosome, some question the relevance of traditional biochemical and genetic techniques to the splicing field. We argue such techniques are not only relevant, but vital for an in depth mechanistic understanding of pre-mRNA splicing. Copyright © 2017 Elsevier Inc. All rights reserved.

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

USGS Publications Warehouse

Neville, Helen; Issacs, Frank B.; Thurow, Russel; Dunham, J.B.; Rieman, B.

2007-01-01

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

Diseases and Molecular Diagnostics: A Step Closer to Precision Medicine.

PubMed

Dwivedi, Shailendra; Purohit, Purvi; Misra, Radhieka; Pareek, Puneet; Goel, Apul; Khattri, Sanjay; Pant, Kamlesh Kumar; Misra, Sanjeev; Sharma, Praveen

2017-10-01

The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc., by mutation scanning and DNA chip technology. Further the functional genomics also exploring the expression genetics (hybridization-, PCR- and sequence-based technologies), two-hybrid technology, next generation sequencing with Bioinformatics and computational biology. Advances in microarray "chip" technology as microarrays have allowed the parallel analysis of gene expression patterns of thousands of genes simultaneously. Sequence information collected from the genomes of many individuals is leading to the rapid discovery of single nucleotide polymorphisms or SNPs. Further advances of genetic engineering have also revolutionized immunoassay biotechnology via engineering of antibody-encoding genes and the phage display technology. The Biotechnology plays an important role in the development of diagnostic assays in response to an outbreak or critical disease response need. However, there is also need to pinpoint various obstacles and issues related to the commercialization and widespread dispersal of genetic knowledge derived from the exploitation of the biotechnology industry and the development and marketing of diagnostic services. Implementation of genetic criteria for patient selection and individual assessment of the risks and benefits of treatment emerges as a major challenge to the pharmaceutical industry. Thus this field is revolutionizing current era and further it may open new vistas in the field of disease management.

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): Natural replicate tests of post-Pleistocene evolution

USGS Publications Warehouse

Morris-Pocock, J. A.; Taylor, S.A.; Birt, T.P.; Damus, M.; Piatt, John F.; Warheit, K.I.; Friesen, Vicki L.

2008-01-01

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east-west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east-west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa. ?? 2008 The Authors.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species.

PubMed

Murray-Dickson, Gillian; Ghazali, Muhammad; Ogden, Rob; Brown, Rafe; Auliya, Mark

2017-01-01

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds’ most traded snake species

PubMed Central

Ghazali, Muhammad; Ogden, Rob; Brown, Rafe; Auliya, Mark

2017-01-01

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins—which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python’s native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley’s modification of Wallace’s line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans. PMID:28817588

Population Genetic Structure and Demographic History of Atrina pectinata Based on Mitochondrial DNA and Microsatellite Markers

PubMed Central

Xue, Dong-Xiu; Wang, Hai-Yan; Zhang, Tao; Liu, Jin-Xian

2014-01-01

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata. PMID:24789175

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers

PubMed Central

Manechini, João Ricardo Vieira; da Costa, Juliana Borges; Pereira, Bruna Turcatto; Carlini-Garcia, Luciana Aparecida; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade

2018-01-01

The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: Φ^ST = 0.211 and S. spontaneum: Φ^ST = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny. PMID:29684082

Patterns of Deep-Sea Genetic Connectivity in the New Zealand Region: Implications for Management of Benthic Ecosystems

PubMed Central

Bors, Eleanor K.; Rowden, Ashley A.; Maas, Elizabeth W.; Clark, Malcolm R.; Shank, Timothy M.

2012-01-01

Patterns of genetic connectivity are increasingly considered in the design of marine protected areas (MPAs) in both shallow and deep water. In the New Zealand Exclusive Economic Zone (EEZ), deep-sea communities at upper bathyal depths (<2000 m) are vulnerable to anthropogenic disturbance from fishing and potential mining operations. Currently, patterns of genetic connectivity among deep-sea populations throughout New Zealand’s EEZ are not well understood. Using the mitochondrial Cytochrome Oxidase I and 16S rRNA genes as genetic markers, this study aimed to elucidate patterns of genetic connectivity among populations of two common benthic invertebrates with contrasting life history strategies. Populations of the squat lobster Munida gracilis and the polychaete Hyalinoecia longibranchiata were sampled from continental slope, seamount, and offshore rise habitats on the Chatham Rise, Hikurangi Margin, and Challenger Plateau. For the polychaete, significant population structure was detected among distinct populations on the Chatham Rise, the Hikurangi Margin, and the Challenger Plateau. Significant genetic differences existed between slope and seamount populations on the Hikurangi Margin, as did evidence of population differentiation between the northeast and southwest parts of the Chatham Rise. In contrast, no significant population structure was detected across the study area for the squat lobster. Patterns of genetic connectivity in Hyalinoecia longibranchiata are likely influenced by a number of factors including current regimes that operate on varying spatial and temporal scales to produce potential barriers to dispersal. The striking difference in population structure between species can be attributed to differences in life history strategies. The results of this study are discussed in the context of existing conservation areas that are intended to manage anthropogenic threats to deep-sea benthic communities in the New Zealand region. PMID:23185341

Population Genetics of Plasmodium vivax in Four Rural Communities in Central Vietnam

PubMed Central

Hong, Nguyen Van; Delgado-Ratto, Christopher; Thanh, Pham Vinh; Van den Eede, Peter; Guetens, Pieter; Binh, Nguyen Thi Huong; Phuc, Bui Quang; Duong, Tran Thanh; Van Geertruyden, Jean Pierre; D’Alessandro, Umberto; Erhart, Annette; Rosanas-Urgell, Anna

2016-01-01

Background The burden of malaria in Vietnam has drastically reduced, prompting the National Malaria Control Program to officially engage in elimination efforts. Plasmodium vivax is becoming increasingly prevalent, remaining a major problem in the country's central and southern provinces. A better understanding of P. vivax genetic diversity and structure of local parasite populations will provide baseline data for the evaluation and improvement of current efforts for control and elimination. The aim of this study was to examine the population genetics and structure of P. vivax isolates from four communities in Tra Leng commune, Nam Tra My district in Quang Nam, Central Vietnam. Methodology/Principal Findings P. vivax mono infections collected from 234 individuals between April 2009 and December 2010 were successfully analyzed using a panel of 14 microsatellite markers. Isolates displayed moderate genetic diversity (He = 0.68), with no significant differences between study communities. Polyclonal infections were frequent (71.4%) with a mean multiplicity of infection of 1.91 isolates/person. Low but significant genetic differentiation (FST value from -0.05 to 0.18) was observed between the community across the river and the other communities. Strong linkage disequilibrium (IAS = 0.113, p < 0.001) was detected across all communities, suggesting gene flow within and among them. Using multiple approaches, 101 haplotypes were grouped into two genetic clusters, while 60.4% of haplotypes were admixed. Conclusions/Significance In this area of Central Vietnam, where malaria transmission has decreased significantly over the past decade, there was moderate genetic diversity and high occurrence of polyclonal infections. Local human populations have frequent social and economic interactions that facilitate gene flow and inbreeding among parasite populations, while decreasing population structure. Findings provide important information on parasites populations circulating in the study area and are relevant to current malaria elimination efforts. PMID:26872387

Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers.

PubMed

Manechini, João Ricardo Vieira; da Costa, Juliana Borges; Pereira, Bruna Turcatto; Carlini-Garcia, Luciana Aparecida; Xavier, Mauro Alexandre; Landell, Marcos Guimarães de Andrade; Pinto, Luciana Rossini

2018-01-01

The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: [Formula: see text] = 0.211 and S. spontaneum: [Formula: see text] = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny.

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: Phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus)

USGS Publications Warehouse

Vandergast, A.G.; Bohonak, A.J.; Weissman, D.B.; Fisher, R.N.

2007-01-01

Habitat loss and fragmentation due to urbanization are the most pervasive threats to biodiversity in southern California. Loss of habitat and fragmentation can lower migration rates and genetic connectivity among remaining populations of native species, reducing genetic variability and increasing extinction risk. However, it may be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric fragmentation due to previous natural geological and climatic changes. To address these challenges, we examined the phylogenetic and population genetic structure of a flightless insect endemic to cismontane southern California, Stenopelmatus 'mahogani' (Orthoptera: Stenopelmatidae). Analyses of mitochondrial DNA sequence data suggest that diversification across southern California began during the Pleistocene, with most haplotypes currently restricted to a single population. Patterns of genetic divergence correlate with contemporary urbanization, even after correcting for (geographical information system) GIS-based reconstructions of fragmentation during the Pleistocene. Theoretical simulations confirm that contemporary patterns of genetic structure could be produced by recent urban fragmentation using biologically reasonable assumptions about model parameters. Diversity within populations was positively correlated with current fragment size, but not prehistoric fragment size, suggesting that the effects of increased drift following anthropogenic fragmentation are already being seen. Loss of genetic connectivity and diversity can hinder a population's ability to adapt to ecological perturbations commonly associated with urbanization, such as habitat degradation, climatic changes and introduced species. Consequently, our results underscore the importance of preserving and restoring landscape connectivity for long-term persistence of low vagility native species. Journal compilation ?? 2006 Blackwell Publishing Ltd.

Population genetic structure of eelgrass (Zostera marina) on the Korean coast: Current status and conservation implications for future management

PubMed Central

Kim, Jae Hwan; Kang, Ji Hyoun; Jang, Ji Eun; Choi, Sun Kyeong; Kim, Min Ji; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

Seagrasses provide numerous ecosystem services for coastal and estuarine environments, such as nursery functions, erosion protection, pollution filtration, and carbon sequestration. Zostera marina (common name “eelgrass”) is one of the seagrass bed-forming species distributed widely in the northern hemisphere, including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide, including Korea. We examined the current population genetic status of this species on the southern coast of Korea by estimating the levels of genetic diversity and genetic structure of 10 geographic populations using eight nuclear microsatellite markers. The level of genetic diversity was found to be significantly lower for populations on Jeju Island [mean allelic richness (AR) = 1.92, clonal diversity (R) = 0.51], which is located approximately 155 km off the southernmost region of the Korean Peninsula, than for those in the South Sea (mean AR = 2.69, R = 0.82), which is on the southern coast of the mainland. South Korean eelgrass populations were substantially genetically divergent from one another (FST = 0.061–0.573), suggesting that limited contemporary gene flow has been taking place among populations. We also found weak but detectable temporal variation in genetic structure within a site over 10 years. In additional depth comparisons, statistically significant genetic differentiation was observed between shallow (or middle) and deep zones in two of three sites tested. Depleted genetic diversity, small effective population sizes (Ne) and limited connectivity for populations on Jeju Island indicate that these populations may be vulnerable to local extinction under changing environmental conditions, especially given that Jeju Island is one of the fastest warming regions around the world. Overall, our work will inform conservation and restoration efforts, including transplantation for eelgrass populations at the southern tip of the Korean Peninsula, for this ecologically important species. PMID:28323864

Population genetic structure of eelgrass (Zostera marina) on the Korean coast: Current status and conservation implications for future management.

PubMed

Kim, Jae Hwan; Kang, Ji Hyoun; Jang, Ji Eun; Choi, Sun Kyeong; Kim, Min Ji; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

Seagrasses provide numerous ecosystem services for coastal and estuarine environments, such as nursery functions, erosion protection, pollution filtration, and carbon sequestration. Zostera marina (common name "eelgrass") is one of the seagrass bed-forming species distributed widely in the northern hemisphere, including the Korean Peninsula. Recently, however, there has been a drastic decline in the population size of Z. marina worldwide, including Korea. We examined the current population genetic status of this species on the southern coast of Korea by estimating the levels of genetic diversity and genetic structure of 10 geographic populations using eight nuclear microsatellite markers. The level of genetic diversity was found to be significantly lower for populations on Jeju Island [mean allelic richness (AR) = 1.92, clonal diversity (R) = 0.51], which is located approximately 155 km off the southernmost region of the Korean Peninsula, than for those in the South Sea (mean AR = 2.69, R = 0.82), which is on the southern coast of the mainland. South Korean eelgrass populations were substantially genetically divergent from one another (FST = 0.061-0.573), suggesting that limited contemporary gene flow has been taking place among populations. We also found weak but detectable temporal variation in genetic structure within a site over 10 years. In additional depth comparisons, statistically significant genetic differentiation was observed between shallow (or middle) and deep zones in two of three sites tested. Depleted genetic diversity, small effective population sizes (Ne) and limited connectivity for populations on Jeju Island indicate that these populations may be vulnerable to local extinction under changing environmental conditions, especially given that Jeju Island is one of the fastest warming regions around the world. Overall, our work will inform conservation and restoration efforts, including transplantation for eelgrass populations at the southern tip of the Korean Peninsula, for this ecologically important species.

New Genes and New Insights from Old Genes: Update on Alzheimer Disease

PubMed Central

Ringman, John M.; Coppola, Giovanni

2013-01-01

Purpose of Review: This article discusses the current status of knowledge regarding the genetic basis of Alzheimer disease (AD) with a focus on clinically relevant aspects. Recent Findings: The genetic architecture of AD is complex, as it includes multiple susceptibility genes and likely nongenetic factors. Rare but highly penetrant autosomal dominant mutations explain a small minority of the cases but have allowed tremendous advances in understanding disease pathogenesis. The identification of a strong genetic risk factor, APOE, reshaped the field and introduced the notion of genetic risk for AD. More recently, large-scale genome-wide association studies are adding to the picture a number of common variants with very small effect sizes. Large-scale resequencing studies are expected to identify additional risk factors, including rare susceptibility variants and structural variation. Summary: Genetic assessment is currently of limited utility in clinical practice because of the low frequency (Mendelian mutations) or small effect size (common risk factors) of the currently known susceptibility genes. However, genetic studies are identifying with confidence a number of novel risk genes, and this will further our understanding of disease biology and possibly the identification of therapeutic targets. PMID:23558482

Model invariance across genders of the Broad Autism Phenotype Questionnaire.

PubMed

Broderick, Neill; Wade, Jordan L; Meyer, J Patrick; Hull, Michael; Reeve, Ronald E

2015-10-01

ASD is one of the most heritable neuropsychiatric disorders, though comprehensive genetic liability remains elusive. To facilitate genetic research, researchers employ the concept of the broad autism phenotype (BAP), a milder presentation of traits in undiagnosed relatives. Research suggests that the BAP Questionnaire (BAPQ) demonstrates psychometric properties superior to other self-report measures. To examine evidence regarding validity of the BAPQ, the current study used confirmatory factor analysis to test the assumption of model invariance across genders. Results of the current study upheld model invariance at each level of parameter constraint; however, model fit indices suggested limited goodness-of-fit between the proposed model and the sample. Exploratory analyses investigated alternate factor structure models but ultimately supported the proposed three-factor structure model.

Phylogeography in Galaxias maculatus (Jenyns, 1848) along Two Biogeographical Provinces in the Chilean Coast

PubMed Central

González-Wevar, Claudio A.; Salinas, Pilar; Hüne, Mathias; Segovia, Nicolás I.; Vargas-Chacoff, Luis; Astorga, Marcela; Cañete, Juan I.; Poulin, Elie

2015-01-01

Major geologic and climatic changes during the Quaternary exerted a major role in shaping past and contemporary distribution of genetic diversity and structure of aquatic organisms in southern South America. In fact, the northern glacial limit along the Pacific coast, an area of major environmental changes in terms of topography, currents, and water salinity, represents a major biogeographic transition for marine and freshwater species. We used mitochondrial DNA sequences (D-loop) to investigate the consequences of Quaternary glacial cycles over the pattern of genetic diversity and structure of G. maculatus (Pisces: Galaxiidae) along two biogeographical provinces in the Chilean coast. Extreme levels of genetic diversity and strong phylogeographic structure characterize the species suggesting a low amount of influence of the last glacial cycle over its demography. However, we recognized contrasting patterns of genetic diversity and structure between main biogeographical areas here analyzed. Along the Intermediate Area (38°–41° S) each estuarine population constitutes a different unit. In contrast, Magellanic populations (43°–53° S) exhibited low levels of genetic differentiation. Contrasting patterns of genetic diversity and structure recorded in the species between the analyzed biogeographic areas are consistent with the marked differences in abiotic factors (i.e., different coastal configurations, Quaternary glacial histories, and oceanographic regimes) and to inherent characteristics of the species (i.e., salt-tolerance, physiology, and reproductive behavior). PMID:26161896

The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines.

PubMed

Williams, Rachel C; Jackson, Benjamin C; Duvaux, Ludovic; Dawson, Deborah A; Burke, Terry; Sinclair, William

2015-07-01

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST  = 0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST  = 0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. © 2015 John Wiley & Sons Ltd.

Genetic structure among greater white-fronted goose populations of the Pacific Flyway

USGS Publications Warehouse

Ely, Craig R.; Wilson, Robert E.; Talbot, Sandra L.

2017-01-01

An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.

Genetic structure and demographic history of the endangered and endemic schizothoracine fish Gymnodiptychus pachycheilus in Qinghai-Tibetan Plateau.

PubMed

Su, Junhu; Ji, Weihong; Wei, Yanming; Zhang, Yanping; Gleeson, Dianne M; Lou, Zhongyu; Ren, Jing

2014-08-01

The endangered schizothoracine fish Gymnodiptychus pachycheilus is endemic to the Qinghai-Tibetan Plateau (QTP), but very little genetic information is available for this species. Here, we accessed the current genetic divergence of G. pachycheilus population to evaluate their distributions modulated by contemporary and historical processes. Population structure and demographic history were assessed by analyzing 1811-base pairs of mitochondrial DNA from 61 individuals across a large proportion of its geographic range. Our results revealed low nucleotide diversity, suggesting severe historical bottleneck events. Analyses of molecular variance and the conventional population statistic FST (0.0435, P = 0.0215) confirmed weak genetic structure. The monophyly of G. pachycheilus was statistically well-supported, while two divergent evolutionary clusters were identified by phylogenetic analyses, suggesting a microgeographic population structure. The consistent scenario of recent population expansion of two clusters was identified based on several complementary analyses of demographic history (0.096 Ma and 0.15 Ma). This genetic divergence and evolutionary process are likely to have resulted from a series of drainage arrangements triggered by the historical tectonic events of the region. The results obtained here provide the first insights into the evolutionary history and genetic status of this little-known fish.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

Inferring human history in East Asia from Y chromosomes.

PubMed

Wang, Chuan-Chao; Li, Hui

2013-06-03

East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.

Inferring human history in East Asia from Y chromosomes

PubMed Central

2013-01-01

East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history. PMID:23731529

Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

PubMed Central

Han, Qingxiang; Higashi, Hiroyuki; Mitsui, Yuki; Setoguchi, Hiroaki

2015-01-01

Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands. PMID:26247202

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

PubMed

Mayol, Maria; Palau, Carles; Rosselló, Josep A; González-Martínez, Santiago C; Molins, Arántzazu; Riba, Miquel

2012-02-01

Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands.

Genetic patterns of habitat fragmentation and past climate-change effects in the Mediterranean high-mountain plant Armeria caespitosa (Plumbaginaceae).

PubMed

García-Fernández, Alfredo; Iriondo, Jose M; Escudero, Adrián; Aguilar, Javier Fuertes; Feliner, Gonzalo Nieto

2013-08-01

Mountain plants are among the species most vulnerable to global warming, because of their isolation, narrow geographic distribution, and limited geographic range shifts. Stochastic and selective processes can act on the genome, modulating genetic structure and diversity. Fragmentation and historical processes also have a great influence on current genetic patterns, but the spatial and temporal contexts of these processes are poorly known. We aimed to evaluate the microevolutionary processes that may have taken place in Mediterranean high-mountain plants in response to changing historical environmental conditions. Genetic structure, diversity, and loci under selection were analyzed using AFLP markers in 17 populations distributed over the whole geographic range of Armeria caespitosa, an endemic plant that inhabits isolated mountains (Sierra de Guadarrama, Spain). Differences in altitude, geographic location, and climate conditions were considered in the analyses, because they may play an important role in selective and stochastic processes. Bayesian clustering approaches identified nine genetic groups, although some discrepancies in assignment were found between alternative analyses. Spatially explicit analyses showed a weak relationship between genetic parameters and spatial or environmental distances. However, a large proportion of outlier loci were detected, and some outliers were related to environmental variables. A. caespitosa populations exhibit spatial patterns of genetic structure that cannot be explained by the isolation-by-distance model. Shifts along the altitude gradient in response to Pleistocene climatic oscillations and environmentally mediated selective forces might explain the resulting structure and genetic diversity values found.

RAPD variation and population genetic structure of Physalaemus cuvieri (Anura: Leptodactylidae) in Central Brazil.

PubMed

Telles, Mariana Pires de Campos; Bastos, Rogério Pereira; Soares, Thannya Nascimento; Resende, Lucileide Vilela; Diniz-Filho, José Alexandre Felizola

2006-01-01

Studies about the organization of the genetic variability and population structure in natural populations are used either to understand microevolutionary processes or the effects of isolation by human-inducted landscape modifications. In this paper, we analyzed patterns of genetic population structure using 126 RAPD loci scored for 214 individuals of Physalaemus cuvieri, sampled from 18 local populations. Around 97% of these loci were polymorphic. The among-population variation component (Phi(ST)) obtained by AMOVA was equal to 0.101 and theta B obtained using a Bayesian approach for dominant markers was 0.103. Genetic divergence, analyzed by Mantel spatial correlogram, revealed only a short-distance significant correlation between genetic and geographic distances. This is expected if low levels of population differentiation, due to high abundance buffering the effect of stochastic processes, are combined with low spatially restricted gene flow. Although this may be consistent with the current knowledge of species' biology, the spatial distribution of local populations observed in this study also suggest that, at least in part, recent human occupation and habitat fragmentation may also explain part of the interpopulational component of the genetic variation.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats.

PubMed

Wereszczuk, Anna; Leblois, Raphaël; Zalewski, Andrzej

2017-12-22

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species' ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago

PubMed Central

Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M.; Jerry, Dean R.

2015-01-01

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock. PMID:25951344

Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

PubMed

Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M; Jerry, Dean R

2015-01-01

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

Genetic Diversity and Population Parameters of Sea Otters, Enhydra lutris, before Fur Trade Extirpation from 1741–1911

PubMed Central

Larson, Shawn; Jameson, Ron; Etnier, Michael; Jones, Terry; Hall, Roberta

2012-01-01

All existing sea otter, Enhydra lutris, populations have suffered at least one historic population bottleneck stemming from the fur trade extirpations of the eighteenth and nineteenth centuries. We examined genetic variation, gene flow, and population structure at five microsatellite loci in samples from five pre-fur trade populations throughout the sea otter's historical range: California, Oregon, Washington, Alaska, and Russia. We then compared those values to genetic diversity and population structure found within five modern sea otter populations throughout their current range: California, Prince William Sound, Amchitka Island, Southeast Alaska and Washington. We found twice the genetic diversity in the pre-fur trade populations when compared to modern sea otters, a level of diversity that was similar to levels that are found in other mammal populations that have not experienced population bottlenecks. Even with the significant loss in genetic diversity modern sea otters have retained historical structure. There was greater gene flow before extirpation than that found among modern sea otter populations but the difference was not statistically significant. The most dramatic effect of pre fur trade population extirpation was the loss of genetic diversity. For long term conservation of these populations increasing gene flow and the maintenance of remnant genetic diversity should be encouraged. PMID:22403635

Population Genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) across Multiple Spatial Scales

PubMed Central

Unger, Shem D.; Rhodes, Olin E.; Sutton, Trent M.; Williams, Rod N.

2013-01-01

Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical) scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (Fst values ranged from 0.001 between rivers within a single watershed to 0.218 between states). We identified two genetically differentiated groups at the range-wide scale: 1) the Ohio River drainage and 2) the Tennessee River drainage. An analysis of molecular variance (AMOVA) based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94–98%) occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD) at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species. PMID:24204565

Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa.

PubMed

Lyam, Paul Terwase; Duque-Lazo, Joaquín; Durka, Walter; Hauenschild, Frank; Schnitzler, Jan; Michalak, Ingo; Ogundipe, Oluwatoyin Temitayo; Muellner-Riehl, Alexandra Nora

2018-01-01

Climate change is predicted to impact species' genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species' ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species' adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change.

Genetic diversity and distribution of Senegalia senegal (L.) Britton under climate change scenarios in West Africa

PubMed Central

Duque-Lazo, Joaquín; Durka, Walter; Hauenschild, Frank; Schnitzler, Jan; Michalak, Ingo; Ogundipe, Oluwatoyin Temitayo; Muellner-Riehl, Alexandra Nora

2018-01-01

Climate change is predicted to impact species’ genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species’ ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species’ adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change. PMID:29659603

Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

PubMed Central

Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

2011-01-01

Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

Small-scale genetic structure in an endangered wetland specialist: possible effects of landscape change and population recovery

USGS Publications Warehouse

van Rees, Charles B.; Reed, J. Michael; Wilson, Robert E.; Underwood, Jared G.; Sonsthagen, Sarah A.

2018-01-01

The effects of anthropogenic landscape change on genetic population structure are well studied, but the temporal and spatial scales at which genetic structure can develop, especially in taxa with high dispersal capabilities like birds, are less well understood. We investigated population structure in the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered wetland specialist bird on the island of O`ahu (Hawai`i, USA). Hawaiian gallinules have experienced a gradual population recovery from near extinction in the 1950s, and have recolonized wetlands on O`ahu in the context of a rapidly urbanizing landscape. We genotyped 152 Hawaiian gallinules at 12 microsatellite loci and sequenced a 520 base-pair fragment of the ND2 region of mitochondrial DNA (mtDNA) from individuals captured at 13 wetland locations on O`ahu in 2014–2016. We observed moderate to high genetic structuring (overall microsatellite FST = 0.098, mtDNA FST = 0.248) among populations of Hawaiian gallinules occupying wetlands at very close geographic proximity (e.g., 1.5–55 km). Asymmetry in gene flow estimates suggests that Hawaiian gallinules may have persisted in 2–3 strongholds which served as source populations that recolonized more recently restored habitats currently supporting large numbers of birds. Our results highlight that genetic structure can develop in taxa that are expanding their range after severe population decline, and that biologically significant structuring can occur over small geographic distances, even in avian taxa.

Population structure and genetic variation of the endangered species Elaeagnus mollis Diels (Elaeagnaceae).

PubMed

Zhang, J M; Zhang, F

2015-06-01

Elaeagnus mollis Diels is a group of shrubs and dwarf trees endemic to China and are endangered plants. However, the reason why these plants are endangered remains controversial. The current study aimed to explore the endangered status of E. mollis from a genetic perspective and to propose conservation strategies for this species. Using 16 polymorphic allozyme loci, the population genetic structure was investigated for three populations representing the taxa and variants. The variants exhibited relatively high levels of genetic variation compared to other woody shrubs with similar geographic distributions. The overall genetic diversity (HE = 0.352) was elevated compared to long-lived woody angiosperms. The average number of alleles per locus (A), percentage polymorphic loci (P), and observed heterozygosity (HO) were 2.0, 85.2, and 0.371, respectively. Furthermore, gene flow estimates within the population groups were also elevated. The life history and habitats of E. mollis play major roles in the levels of genetic diversity. The results of this study may help to device strategies for preserving the genetic diversity of E. mollis and for promoting planting.

Recent advances in primary ciliary dyskinesia genetics

PubMed Central

Kurkowiak, Małgorzata; Ziętkiewicz, Ewa; Witt, Michał

2015-01-01

Primary ciliary dyskinesia (PCD) is a rare genetically heterogeneous disorder caused by the abnormal structure and/or function of motile cilia. The PCD diagnosis is challenging and requires a well-described clinical phenotype combined with the identification of abnormalities in ciliary ultrastructure and/or beating pattern as well as the recognition of genetic cause of the disease. Regarding the pace of identification of PCD-related genes, a rapid acceleration during the last 2–3 years is notable. This is the result of new technologies, such as whole-exome sequencing, that have been recently applied in genetic research. To date, PCD-causative mutations in 29 genes are known and the number of causative genes is bound to rise. Even though the genetic causes of approximately one-third of PCD cases still remain to be found, the current knowledge can already be used to create new, accurate genetic tests for PCD that can accelerate the correct diagnosis and reduce the proportion of unexplained cases. This review aims to present the latest data on the relations between ciliary structure aberrations and their genetic basis. PMID:25351953

Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.

PubMed

Reig-Valiente, Juan L; Viruel, Juan; Sales, Ester; Marqués, Luis; Terol, Javier; Gut, Marta; Derdak, Sophia; Talón, Manuel; Domingo, Concha

2016-12-01

After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes. A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results. Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.

The impact of selection on population genetic structure in the clam Meretrix petechialis revealed by microsatellite markers.

PubMed

Lu, Xia; Wang, Hongxia; Li, Yan; Liu, Baozhong

2016-02-01

The aim of our work is to evaluate the impact of mass selection on genetic structure in artificially closed populations of the clam Meretrix petechialis. In the present study, we performed mass selection over four generations (from 2004 to 2010) on two clam populations [shell features of purple lines (SP) and black dots (SB)] and analyzed their temporal genetic variation and structure using microsatellite makers. The two closed populations originated from the natural Shandong population (SD); thus, a natural SD population (10SD) was used to detect the current genetic structure after 6 years of natural selection. The results showed that the genetic diversity of the four generations of SB and SP was gradually reduced but remained at relatively high levels (SB, A = 18.9.4-16.8, Ho = 0.7389-0.6971, and He = 0.8897-0.8591; SP, A = 20.0-17.8, Ho = 0.7512-0.7043, and He = 0.8938-0.8625), which has not been reduced compared with that of the 10SD population (A = 17.8, Ho = 0.6803, and He = 0.8302). The Ne estimates for the two populations were almost at the same levels as the actual numbers of parental individuals. In addition, a low inbreeding coefficient was detected in the two populations (SB, 0.00201-0.00639; SP, 0.00176-0.00541). Based on the results, the present mass selection has not made a large impact on the population genetic structure of the closed populations. The present investigation provides important information for the development of management strategies for genetic breeding of the clam.

Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs.

PubMed

Llorens, Tanya M; Ayre, David J; Whelan, Robert J

2018-04-01

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F' ST  = 0.615 and 0.454; S p  = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long-term effects of inbreeding in self-compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self-compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation. © 2018 John Wiley & Sons Ltd.

Sex-specific genetic analysis indicates low correlation between demographic and genetic connectivity in the Scandinavian brown bear (Ursus arctos).

PubMed

Schregel, Julia; Kopatz, Alexander; Eiken, Hans Geir; Swenson, Jon E; Hagen, Snorre B

2017-01-01

The degree of gene flow within and among populations, i.e. genetic population connectivity, may closely track demographic population connectivity. Alternatively, the rate of gene flow may change relative to the rate of dispersal. In this study, we explored the relationship between genetic and demographic population connectivity using the Scandinavian brown bear as model species, due to its pronounced male dispersal and female philopatry. Thus, we expected that females would shape genetic structure locally, whereas males would act as genetic mediators among regions. To test this, we used eight validated microsatellite markers on 1531 individuals sampled noninvasively during country-wide genetic population monitoring in Sweden and Norway from 2006 to 2013. First, we determined sex-specific genetic structure and substructure across the study area. Second, we compared genetic differentiation, migration/gene flow patterns, and spatial autocorrelation results between the sexes both within and among genetic clusters and geographic regions. Our results indicated that demographic connectivity was not a reliable indicator of genetic connectivity. Among regions, we found no consistent difference in long-term gene flow and estimated current migration rates between males and females. Within regions/genetic clusters, only females consistently displayed significant positive spatial autocorrelation, indicating male-biased small-scale dispersal. In one cluster, however, males showed a dispersal pattern similar to females. The Scandinavian brown bear population has experienced substantial recovery over the last decades; however, our results did not show any changes in its large-scale population structure compared to previous studies, suggesting that an increase in population size and dispersal of individuals does not necessary lead to increased genetic connectivity. Thus, we conclude that both genetic and demographic connectivity should be estimated, so as not to make false assumptions about the reality of wildlife populations.

Population genetic structure of endangered Mongolian racerunner (Eremias argus) from the Korean Peninsula.

PubMed

Park, Han-Chan; Suk, Ho Young; Jeong, Eu-Jin; Park, Dae-Sik; Lee, Hang; Min, Mi-Sook

2014-11-01

The Mongolian racerunner (Eremias argus) is a small lacertid lizard species, and its distribution range encompasses the Korean Peninsula, Mongolia, China and Russia. Eremias argus is widespread, but populations on the Korean Peninsula are small and declining, provoking concerns that genetic diversity is being lost. This species is currently listed under the Protection of Wild Fauna and Flora Act in South Korea. In this study, nine novel microsatellites for E. argus were developed with a biotin-enrichment method and used to understand its population genetic structure and delineate conservation units on the Korean Peninsula. Overall, low intrapopulation genetic diversity was observed (mean number of alleles per locus = 2.463; mean H E = 0.398) from 10 populations investigated (n = 110). Two populations (among five with n≥ 10) showed an excess of heterozygosity expected under HWE relative to that expected at mutation-drift equilibrium, indicating severe reduction in population sizes. With only a few exceptions, the overall genetic differentiation among populations was substantial with the high levels of pairwise-F ST (0.006-0.746) and -R ST (0.034-0.940) values. The results of Bayesian STRUCTURE analysis showed that E. argus populations on the Korean Peninsula were most likely partitioned into three genetic clusters. Taken all together, such low levels of gene flow and strong genetic structuring have critical implications for the conservation of this endangered species and its management.

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

PubMed

Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

2006-10-11

Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

PubMed Central

Tani, Naoki; Yoshimaru, Hiroshi; Kawahara, Takayuki; Hoshi, Yoshio; Nobushima, Fuyuo; Yasui, Takaya

2006-01-01

Background Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. Results Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. Conclusion The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species. PMID:17034624

Congruent population structure inferred from dispersal behaviour and intensive genetic surveys of the threatened Florida scrub-jay (Aphelocoma cœrulescens)

USGS Publications Warehouse

Coulon, A.; Fitzpatrick, J.W.; Bowman, R.; Stith, B.M.; Makarewich, C.A.; Stenzler, L.M.; Lovette, I.J.

2008-01-01

The delimitation of populations, defined as groups of individuals linked by gene flow, is possible by the analysis of genetic markers and also by spatial models based on dispersal probabilities across a landscape. We combined these two complimentary methods to define the spatial pattern of genetic structure among remaining populations of the threatened Florida scrub-jay, a species for which dispersal ability is unusually well-characterized. The range-wide population was intensively censused in the 1990s, and a metapopulation model defined population boundaries based on predicted dispersal-mediated demographic connectivity. We subjected genotypes from more than 1000 individual jays screened at 20 microsatellite loci to two Bayesian clustering methods. We describe a consensus method for identifying common features across many replicated clustering runs. Ten genetically differentiated groups exist across the present-day range of the Florida scrub-jay. These groups are largely consistent with the dispersal-defined metapopulations, which assume very limited dispersal ability. Some genetic groups comprise more than one metapopulation, likely because these genetically similar metapopulations were sundered only recently by habitat alteration. The combined reconstructions of population structure based on genetics and dispersal-mediated demographic connectivity provide a robust depiction of the current genetic and demographic organization of this species, reflecting past and present levels of dispersal among occupied habitat patches. The differentiation of populations into 10 genetic groups adds urgency to management efforts aimed at preserving what remains of genetic variation in this dwindling species, by maintaining viable populations of all genetically differentiated and geographically isolated populations.

Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

PubMed

Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P < 0.01). This algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P < 0.05), whereas it shows results not significantly different to 3D-COFFEE (P > 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

Elevational patterns of genetic variation in the cosmopolitan moss Bryum argenteum (Bryaceae).

PubMed

Pisa, Sergio; Werner, Olaf; Vanderpoorten, Alain; Magdy, Mahmoud; Ros, Rosa M

2013-10-01

The Baas Becking tenet posits that 'everything is everywhere, but the environment selects' to explain cosmopolitan distributions in highly vagile taxa. Bryophyte species show wider distributions than vascular plants and include examples of truly cosmopolitan ranges, which have been interpreted as a result of high dispersal capacities and ecological plasticity. In the current study, we documented patterns of genetic structure and diversity in the cosmopolitan moss Bryum argenteum along an elevational gradient to determine if genetic diversity and structure is homogenized by intense migrations in the lack of ecological differentiation. • 60 specimens were collected in the Sierra Nevada Mountains (Spain) between 100 and 2870 m and sequenced for ITS and rps4. Comparative analyses, genetic diversity estimators, and Mantel's tests were employed to determine the relationship between genetic variation, elevation, and geographic distance and to look for signs of demographic shifts. • Genetic diversity peaked above 1900 m and no signs of demographic shifts were detected at any elevation. There was a strong phylogenetic component in elevational variation. Genetic variation was significantly correlated with elevation, but not with geographic distance. • The results point to the long-term persistence of Bryum argenteum in a range that was glaciated during the Late Pleistocene. Evidence for an environmentally driven pattern of genetic differentiation suggests adaptive divergence. This supports the Baas Becking tenet and indicates that ecological specialization might play a key role in explaining patterns of genetic structure in cosmopolitan mosses.

Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla)

USGS Publications Warehouse

Miller, Mark P.; Gratto-Trevor, Cheri; Haig, Susan M.; Mizrahi, David S.; Mitchell, Melanie M.; Mullins, Thomas D.

2013-01-01

Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to western, central, and eastern breeding groups exist. In this study, mitochondrial control region sequences and nuclear microsatellite loci were used to analyze DNA of birds (microsatellites: n = 120; mtDNA: n = 114) sampled from seven North American locations. Analyses designed to quantify genetic structure and diversity patterns, evaluate genetic evidence for population size changes, and determine if genetic data support the existence of Semipalmated Sandpiper subspecies were performed. Genetic structure based only on the mtDNA data was observed, whereas the microsatellite loci provided no evidence of genetic differentiation. Differentiation among locations and regions reflected allele frequency differences rather than separate phylogenetic groups, and similar levels of genetic diversity were noted. Combined, the two data sets provided no evidence to support the existence of subspecies and were not useful for determining migratory connectivity between breeding sites and wintering grounds. Birds from western and central groups displayed signatures of population expansions, whereas the eastern group was more consistent with a stable overall population. Results of this analysis suggest that the eastern group was the source of individuals that colonized the central and western regions currently utilized by Semipalmated Sandpipers.

Population genetics of Enterocytozoon bieneusi in captive giant pandas of China.

PubMed

Li, Wei; Song, Yuan; Zhong, Zhijun; Huang, Xiangming; Wang, Chengdong; Li, Caiwu; Yang, Haidi; Liu, Haifeng; Ren, Zhihua; Lan, Jingchao; Wu, Kongju; Peng, Guangneng

2017-10-18

Most studies on Enterocytozoon bieneusi are conducted based on the internal transcribed spacer (ITS) region of the rRNA gene, whereas some have examined E. bieneusi population structures. Currently, the population genetics of this pathogen in giant panda remains unknown. The objective of this study was to determine the E. bieneusi population in captive giant pandas in China. We examined 69 E. bieneusi-positive specimens from captive giant pandas in China using five loci (ITS, MS1, MS3, MS4 and MS7) to infer E. bieneusi population genetics. For multilocus genotype (MLG) analysis of E. bieneusi-positive isolates, the MS1, MS3, MS4, and MS7 microsatellite and minisatellite loci were amplified and sequenced in 48, 45, 50 and 47 specimens, respectively, generating ten, eight, nine and five types. We successfully amplified 36 specimens and sequenced all five loci, forming 24 MLGs. Multilocus sequence analysis revealed a strong and significant linkage disequilibrium (LD), indicating a clonal population. This result was further supported by measurements of pairwise intergenic LD and a standardized index of association (I S A ) from allelic profile data. The analysis in STRUCTURE suggested three subpopulations in E. bieneusi, further confirmed using right's fixation index (F ST ). Subpopulations 1 and 2 exhibited an epidemic structure, whereas subpopulation 3 had a clonal structure. Our results describe E. bieneusi population genetics in giant pandas for the first time, improving the current understanding E. bieneusi epidemiology in the studied region. These data also benefit future studies exploring potential transmission risks from pandas to other animals, including humans.

Surviving in mountain climate refugia: new insights from the genetic diversity and structure of the relict shrub Myrtus nivellei (Myrtaceae) in the Sahara Desert.

PubMed

Migliore, Jérémy; Baumel, Alex; Juin, Marianick; Fady, Bruno; Roig, Anne; Duong, Nathalie; Médail, Frédéric

2013-01-01

The identification of past glacial refugia has become a key topic for conservation under environmental change, since they contribute importantly to shaping current patterns of biodiversity. However, little attention has been paid so far to interglacial refugia despite their key role for the survival of relict species currently occurring in climate refugia. Here, we focus on the genetic consequences of range contraction on the relict populations of the evergreen shrub Myrtus nivellei, endemic in the Saharan mountains since at least the end of the last Green Sahara period, around 5.5 ka B.P. Multilocus genotypes (nuclear microsatellites and AFLP) were obtained from 215 individuals collected from 23 wadis (temporary rivers) in the three main mountain ranges in southern Algeria (the Hoggar, Tassili n'Ajjer and Tassili n'Immidir ranges). Identical genotypes were found in several plants growing far apart within the same wadis, a pattern taken as evidence of clonality. Multivariate analyses and Bayesian clustering revealed that genetic diversity was mainly structured among the mountain ranges, while low isolation by distance was observed within each mountain range. The range contraction induced by the last episode of aridification has likely increased the genetic isolation of the populations of M. nivellei, without greatly affecting the genetic diversity of the species as a whole. The pattern of genetic diversity observed here suggests that high connectivity may have prevailed during humid periods, which is consistent with recent paleoenvironmental reconstructions.

Population structure and genetic diversity of wild Helianthus species from Mozambique.

PubMed

Ribeiro, A; Gouveia, M; Bessa, A; Ferreira, A; Magumisse, A T; Manjate, M; Faria, T

2010-08-01

The production of sunflower suffered a major decline in Mozambique after its independence in 1975. Civil war, human activities and environmental damage subjected the species to an ecological stress contributing to reduce the number and size of wild populations. As this reduction is often related to a loss of genetic variation we estimated the genetic diversity within and among populations of wild Helianthus from five districts of Mozambique using RAPD markers. The 44 accessions studied grouped into four major clusters exhibiting structured variability with regard to geographic origin. A high level of genetic diversity (He = 0.350 and I = 0.527) was retained at the population level. The genetic variation among populations was high (59.7%), which is consistent with low gene flow (Nm = 0.338). The proportion of total genetic diversity residing among these populations should be kept in mind to devise different conservation strategies in order to preserve these populations. Currently wild Helianthus genetic resources present in Maputo and Sofala are on the edge of extinction mainly due to excessive urbanization. Therefore, conservation of what remains of this plant genetic diversity is essential for sustainable utilization and can be useful for breeding programs.

Are electronic health records ready for genomic medicine?

PubMed

Scheuner, Maren T; de Vries, Han; Kim, Benjamin; Meili, Robin C; Olmstead, Sarah H; Teleki, Stephanie

2009-07-01

The goal of this project was to assess genetic/genomic content in electronic health records. Semistructured interviews were conducted with key informants. Questions addressed documentation, organization, display, decision support and security of family history and genetic test information, and challenges and opportunities relating to integrating genetic/genomics content in electronic health records. There were 56 participants: 10 electronic health record specialists, 18 primary care clinicians, 16 medical geneticists, and 12 genetic counselors. Few clinicians felt their electronic record met their current genetic/genomic medicine needs. Barriers to integration were mostly related to problems with family history data collection, documentation, and organization. Lack of demand for genetics content and privacy concerns were also mentioned as challenges. Data elements and functionality requirements that clinicians see include: pedigree drawing; clinical decision support for familial risk assessment and genetic testing indications; a patient portal for patient-entered data; and standards for data elements, terminology, structure, interoperability, and clinical decision support rules. Although most said that there is little impact of genetics/genomics on electronic records today, many stated genetics/genomics would be a driver of content in the next 5-10 years. Electronic health records have the potential to enable clinical integration of genetic/genomic medicine and improve delivery of personalized health care; however, structured and standardized data elements and functionality requirements are needed.

Climatic drivers of leaf traits and genetic divergence in the tree Annona crassiflora: a broad spatial survey in the Brazilian savannas.

PubMed

Ribeiro, Priciane C; Souza, Matheus L; Muller, Larissa A C; Ellis, Vincenzo A; Heuertz, Myriam; Lemos-Filho, José P; Lovato, Maria Bernadete

2016-11-01

The Cerrado is the largest South American savanna and encompasses substantial species diversity and environmental variation. Nevertheless, little is known regarding the influence of the environment on population divergence of Cerrado species. Here, we searched for climatic drivers of genetic (nuclear microsatellites) and leaf trait divergence in Annona crassiflora, a widespread tree in the Cerrado. The sampling encompassed all phytogeographic provinces of the continuous area of the Cerrado and included 397 individuals belonging to 21 populations. Populations showed substantial genetic and leaf trait divergence across the species' range. Our data revealed three spatially defined genetic groups (eastern, western and southern) and two morphologically distinct groups (eastern and western only). The east-west split in both the morphological and genetic data closely mirrors previously described phylogeographic patterns of Cerrado species. Generalized linear mixed effects models and multiple regression analyses revealed several climatic factors associated with both genetic and leaf trait divergence among populations of A. crassiflora. Isolation by environment (IBE) was mainly due to temperature seasonality and precipitation of the warmest quarter. Populations that experienced lower precipitation summers and hotter winters had heavier leaves and lower specific leaf area. The southwestern area of the Cerrado had the highest genetic diversity of A. crassiflora, suggesting that this region may have been climatically stable. Overall, we demonstrate that a combination of current climate and past climatic changes have shaped the population divergence and spatial structure of A. crassiflora. However, the genetic structure of A. crassiflora reflects the biogeographic history of the species more strongly than leaf traits, which are more related to current climate. © 2016 John Wiley & Sons Ltd.

Molecular genetic analysis of podocyte genes in focal segmental glomerulosclerosis--a review.

PubMed

Löwik, M M; Groenen, P J; Levtchenko, E N; Monnens, L A; van den Heuvel, L P

2009-11-01

This review deals with podocyte proteins that play a significant role in the structure and function of the glomerular filter. Genetic linkage studies has identified several genes involved in the development of nephrotic syndrome and contributed to the understanding of the pathophysiology of glomerular proteinuria and/or focal segmental glomerulosclerosis. Here, we describe already well-characterized genetic diseases due to mutations in nephrin, podocin, CD2AP, alpha-actinin-4, WT1, and laminin beta2 chain, as well as more recently identified genetic abnormalities in TRPC6, phospholipase C epsilon, and the proteins encoded by the mitochondrial genome. In addition, the role of the proteins which have shown to be important for the structure and functions by gene knockout studies in mice, are also discussed. Furthermore, some rare syndromes with glomerular involvement, in which molecular defects have been recently identified, are briefly described. In summary, this review updates the current knowledge of genetic causes of congenital and childhood nephrotic syndrome and provides new insights into mechanisms of glomerular dysfunction.

Analysis of mitochondrial genetic diversity of Ustilago maydis in Mexico.

PubMed

Jiménez-Becerril, María F; Hernández-Delgado, Sanjuana; Solís-Oba, Myrna; González Prieto, Juan M

2018-01-01

The current understanding of the genetic diversity of the phytopathogenic fungus Ustilago maydis is limited. To determine the genetic diversity and structure of U. maydis, 48 fungal isolates were analyzed using mitochondrial simple sequence repeats (SSRs). Tumours (corn smut or 'huitlacoche') were collected from different Mexican states with diverse environmental conditions. Using bioinformatic tools, five microsatellites were identified within intergenic regions of the U. maydis mitochondrial genome. SSRMUM4 was the most polymorphic marker. The most common repeats were hexanucleotides. A total of 12 allelic variants were identified, with a mean of 2.4 alleles per locus. An estimate of the genetic diversity using analysis of molecular variance (AMOVA) revealed that the highest variance component is within states (84%), with moderate genetic differentiation between states (16%) (F ST  = 0.158). A dendrogram generated using the unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure grouped the U. maydis isolates into two subgroups (K = 2) based on their shared SSRs.

Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

PubMed

Milanesi, P; Holderegger, R; Bollmann, K; Gugerli, F; Zellweger, F

2017-02-01

Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting β values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality. © 2016 by the Ecological Society of America.

Genetic and Environmental Associations Between Procrastination and Internalizing/Externalizing Psychopathology.

PubMed

Gustavson, Daniel E; du Pont, Alta; Hatoum, Alexander S; Hyun Rhee, Soo; Kremen, William S; Hewitt, John K; Friedman, Naomi P

2017-09-01

Recent work on procrastination has begun to unravel the genetic and environmental correlates of this problematic behavior. However, little is known about how strongly procrastination is associated with internalizing and externalizing psychopathology, and the extent to which shared genetic/environmental factors or relevant personality constructs (e.g., fear of failure, impulsivity, and neuroticism) can inform the structure of these associations. The current study examined data from 764 young adult twins who completed questionnaires assessing procrastination and personality and structured interviews regarding psychopathology symptoms. Results indicated that procrastination was positively correlated with both internalizing and externalizing latent variables, and that these correlations were driven by shared genetic influences. Moreover, the association between procrastination and internalizing was accounted for by fear of failure and neuroticism, whereas the association between procrastination and externalizing was primarily explained by impulsivity. The role of procrastination in psychopathology is discussed using a framework that highlights common and broadband-specific variance.

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations

PubMed Central

Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

2015-01-01

Background and Aims Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Methods Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Key Results Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. Conclusions This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. PMID:26113618

A collection of popcorn as a reservoir of genes for the generation of lineages.

PubMed

de Carvalho, Misael Severino Nunes; Mangolin, Claudete Aparecida; Scapim, Carlos Alberto; da Silva, Teresa Aparecida; Machado, Maria de Fátima Pires da Silva

2013-03-01

In the present study, we analyze the genetic structure and diversity among accessions of popcorn obtained from the CIMMYT International Maize and Wheat Improvement Center that represent the diversity available for current use by breeding programs. The main objectives were to identify SSR loci that were the best indicators of genetic diversity, to measure the genetic diversity within popcorn genotypes, and to analyze the genetic structure of the promising populations destined for use in breeding programs. The mean gene diversity of all SSR loci was 0.6352. An extremely high population differentiation level was detected (F(st) = 0.3152) with F(st) for each locus ranging from 0.1125 (Umc1229) to 0.4870 (Umc1755). Analyzing the genetic structure of eight popcorn accessions was especially important for identifying both SSR loci with high levels of heterozygosity and genotypes showing high heterozygosity (BOYA462 and ARZM13 050). This analysis should be the medium and long-term selection goal for the generation of inbred lines and the future production of new cultivars. Plant accessions ARZM05 083, ARZM13 050, and URUG298 may also be useful varieties that exhibit important agronomic characteristics that can be used through crosses to broaden the genetic basis of popcorn.

Connectivity of the habitat-forming kelp, Ecklonia radiata within and among estuaries and open coast.

PubMed

Coleman, Melinda A

2013-01-01

With marine protected areas being established worldwide there is a pressing need to understand how the physical setting in which these areas are placed influences patterns of dispersal and connectivity of important marine organisms. This is particularly critical for dynamic and complex nearshore marine environments where patterns of genetic structure of organisms are often chaotic and uncoupled from broad scale physical processes. This study determines the influence of habitat heterogeneity (presence of estuaries) on patterns of genetic structure and connectivity of the common kelp, Ecklonia radiata. There was no genetic differentiation of kelp between estuaries and the open coast and the presence of estuaries did not increase genetic differentiation among open coast populations. Similarly, there were no differences in level of inbreeding or genetic diversity between estuarine and open coast populations. The presence of large estuaries along rocky coastlines does not appear to influence genetic structure of this kelp and factors other than physical heterogeneity of habitat are likely more important determinants of regional connectivity. Marine reserves are currently lacking in this bioregion and may be designated in the future. Knowledge of the factors that influence important habitat forming organisms such as kelp contribute to informed and effective marine protected area design and conservation initiatives to maintain resilience of important marine habitats.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

Evaluation of genetic population structure of smallmouth bass in the Susquehanna River basin, Pennsylvania

USGS Publications Warehouse

Schall, Megan K.; Bartron, Meredith L.; Wertz, Timothy; Niles, Jonathan M.; Shaw, Cassidy H.; Wagner, Tyler

2017-01-01

The Smallmouth Bass Micropterus dolomieu was introduced into the Susquehanna River basin, Pennsylvania, nearly 150 years ago. Since introduction, it has become an economically and ecologically important species that supports popular recreational fisheries. It is also one of the most abundant top predators in the system. Currently, there is no information on the level of genetic diversity or genetic structuring that may have occurred since introduction. An understanding of genetic diversity is important for the delineation of management units and investigation of gene flow at various management scales. The goals of this research were to investigate population genetic structure of Smallmouth Bass at sites within the Susquehanna River basin and to assess genetic differentiation relative to Smallmouth Bass at an out-of-basin site (Allegheny River, Pennsylvania) located within the species’ native range. During spring 2015, fin clips (n = 1,034) were collected from adults at 11 river sites and 13 tributary sites in the Susquehanna River basin and at one site on the Allegheny River. Fin clips were genotyped at 12 polymorphic microsatellite loci. Based on our results, adults sampled throughout the Susquehanna River basin did not represent separate genetic populations. There were only subtle differences in genetic diversity among sites (mean pairwise genetic differentiation index FST = 0.012), and there was an overall lack of population differentiation (K = 3 admixed populations). The greatest genetic differentiation was observed between fish collected from the out-of-basin site and those from the Susquehanna River basin sites. Knowledge that separate genetic populations of Smallmouth Bass do not exist in the Susquehanna River basin is valuable information for fisheries management in addition to providing baseline genetic data on an introduced sport fish population.

Genetic structuring of northern myotis (Myotis septentrionalis) at multiple spatial scales

USGS Publications Warehouse

Johnson, Joshua B.; Roberts, James H.; King, Timothy L.; Edwards, John W.; Ford, W. Mark; Ray, David A.

2014-01-01

Although groups of bats may be genetically distinguishable at large spatial scales, the effects of forest disturbances, particularly permanent land use conversions on fine-scale population structure and gene flow of summer aggregations of philopatric bat species are less clear. We genotyped and analyzed variation at 10 nuclear DNA microsatellite markers in 182 individuals of the forest-dwelling northern myotis (Myotis septentrionalis) at multiple spatial scales, from within first-order watersheds scaling up to larger regional areas in West Virginia and New York. Our results indicate that groups of northern myotis were genetically indistinguishable at any spatial scale we considered, and the collective population maintained high genetic diversity. It is likely that the ability to migrate, exploit small forest patches, and use networks of mating sites located throughout the Appalachian Mountains, Interior Highlands, and elsewhere in the hibernation range have allowed northern myotis to maintain high genetic diversity and gene flow regardless of forest disturbances at local and regional spatial scales. A consequence of maintaining high gene flow might be the potential to minimize genetic founder effects following population declines caused currently by the enzootic White-nose Syndrome.

Obstructive Sleep Apnea Syndrome: From Phenotype to Genetic Basis

PubMed Central

Casale, M; Pappacena, M; Rinaldi, V; Bressi, F; Baptista, P; Salvinelli, F

2009-01-01

Obstructive sleep apnea syndrome (OSAS) is a complex chronic clinical syndrome, characterized by snoring, periodic apnea, hypoxemia during sleep, and daytime hypersomnolence. It affects 4-5% of the general population. Racial studies and chromosomal mapping, familial studies and twin studies have provided evidence for the possible link between the OSAS and genetic factors and also most of the risk factors involved in the pathogenesis of OSAS are largely genetically determined. A percentage of 35-40% of its variance can be attributed to genetic factors. It is likely that genetic factors associated with craniofacial structure, body fat distribution and neural control of the upper airway muscles interact to produce the OSAS phenotype. Although the role of specific genes that influence the development of OSAS has not yet been identified, current researches, especially in animal model, suggest that several genetic systems may be important. In this chapter, we will first define the OSAS phenotype, the pathogenesis and the risk factors involved in the OSAS that may be inherited, then, we will review the current progress in the genetics of OSAS and suggest a few future perspectives in the development of therapeutic agents for this complex disease entity. PMID:19794884

Matching genetics with oceanography: directional gene flow in a Mediterranean fish species.

PubMed

Schunter, C; Carreras-Carbonell, J; Macpherson, E; Tintoré, J; Vidal-Vijande, E; Pascual, A; Guidetti, P; Pascual, M

2011-12-01

Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts. © 2011 Blackwell Publishing Ltd.

Population Genetic Structure of the Cayo Santiago Colony of Rhesus Macaques (Macaca mulatta).

PubMed

Kanthaswamy, Sreetharan; Oldt, Robert F; Ng, Jillian; Ruiz-Lambides, Angelina V; Maldonado, Elizabeth; Martínez, Melween I; Sariol, Carlos A

2017-07-01

The rhesus macaque population at Cayo Santiago increases annually and is in urgent need of control. In-depth assessments of the colony's population genetic and pedigree structures provide a starting point for improving the colony's long-term management program. We evaluated the degree of genetic variation and coefficients of inbreeding and kinship of the Cayo Santiago colony by using pedigree and short tandem repeat (STR) data from 4738 rhesus macaques, which represent 7 extant social groups and a group of migrant males. Information on each animal's parentage, sex, birth date, and date of death or removal from the island were used to generate estimates of mean kinship, kinship value, gene value, genome uniqueness (GU), founder equivalents (fe), and founder genome equivalents (fg). Pedigree and STR analyses revealed that the social groups have not differentiated genetically from each other due to male-mediated gene flow (that is, FST estimates were in the negative range) and exhibit sufficient genetic variation, with mean estimates of allele numbers and observed and expected heterozygosity of 6.57, 0.72, and 0.70, respectively. Estimates of GU, fe, and fg show that a high effective number of founders has affected the colony's current genetic structure in a positive manner. As demographic changes occur, genetic and pedigree matrices need to be monitored consistently to ensure the health and wellbeing of the Cayo Santiago colony.

Genetic population structure of Shoal Bass within their native range

USGS Publications Warehouse

Taylor, Andrew T.; Tringali, Michael D.; Sammons, Steven M.; Ingram, Travis R.; O'Rouke, Patrick M.; Peterson, Douglas L.; Long, James M.

2018-01-01

Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites (N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is conserved and overall adaptability of the species is maintained.

Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation.

PubMed

Ochoa, Luz Eneida; Pereira, Luiz Henrique G; Costa-Silva, Guilherme Jose; Roxo, Fábio F; Batista, Jacqueline S; Formiga, Kyara; Foresti, Fausto; Oliveira, Claudio

2015-05-01

Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for F ST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2-2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2-2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin.

Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation

PubMed Central

Ochoa, Luz Eneida; Pereira, Luiz Henrique G; Costa-Silva, Guilherme Jose; Roxo, Fábio F; Batista, Jacqueline S; Formiga, Kyara; Foresti, Fausto; Oliveira, Claudio

2015-01-01

Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for FST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2–2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2–2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin. PMID:26045952

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

PubMed Central

Mayol, Maria; Palau, Carles; Rosselló, Josep A.; González-Martínez, Santiago C.; Molins, Arántzazu; Riba, Miquel

2012-01-01

Background and Aims Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Methods Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Key Results Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Conclusions Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands. PMID:22167790

Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA

PubMed Central

Casas-Marce, Mireia; Marmesat, Elena; Soriano, Laura; Martínez-Cruz, Begoña; Lucena-Perez, Maria; Nocete, Francisco; Rodríguez-Hidalgo, Antonio; Canals, Antoni; Nadal, Jordi; Detry, Cleia; Bernáldez-Sánchez, Eloísa; Fernández-Rodríguez, Carlos; Pérez-Ripoll, Manuel; Stiller, Mathias; Hofreiter, Michael; Rodríguez, Alejandro; Revilla, Eloy; Delibes, Miguel; Godoy, José A.

2017-01-01

Abstract There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions. PMID:28962023

Chromosomal disorders and male infertility

PubMed Central

Harton, Gary L; Tempest, Helen G

2012-01-01

Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain largely undiscovered. Nevertheless, more and more genetic factors associated with infertility are being identified. This review will focus on our current understanding of the chromosomal basis of male infertility specifically: chromosomal aneuploidy, structural and numerical karyotype abnormalities and Y chromosomal microdeletions. Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans. Aneuploidy is predominantly maternal in origin, but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts. Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm. Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed, as well as the application of preimplantation genetic diagnosis (PGD) in such cases. Clinical recommendations where possible will be made, as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility. PMID:22120929

Chromosomal disorders and male infertility.

PubMed

Harton, Gary L; Tempest, Helen G

2012-01-01

Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain largely undiscovered. Nevertheless, more and more genetic factors associated with infertility are being identified. This review will focus on our current understanding of the chromosomal basis of male infertility specifically: chromosomal aneuploidy, structural and numerical karyotype abnormalities and Y chromosomal microdeletions. Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans. Aneuploidy is predominantly maternal in origin, but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts. Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm. Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed, as well as the application of preimplantation genetic diagnosis (PGD) in such cases. Clinical recommendations where possible will be made, as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility.

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

PubMed Central

Yan, Yu-Bin; Duke, Norm C.; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees. PMID:27746790

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species.

PubMed

Yan, Yu-Bin; Duke, Norm C; Sun, Mei

2016-01-01

Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata , and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa , suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees.

Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas.

PubMed

Boissin, E; Micu, D; Janczyszyn-Le Goff, M; Neglia, V; Bat, L; Todorova, V; Panayotova, M; Kruschel, C; Macic, V; Milchakova, N; Keskin, Ç; Anastasopoulou, A; Nasto, I; Zane, L; Planes, S

2016-05-01

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level. © 2016 John Wiley & Sons Ltd.

The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe

PubMed Central

2014-01-01

Background Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown. Results To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia. Conclusions The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia. PMID:24411008

The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854

PubMed Central

Wrange, Anna-Lisa; Charrier, Gregory; Thonig, Anne; Alm Rosenblad, Magnus; Blomberg, Anders; Havenhand, Jonathan N.; Jonsson, Per R.; André, Carl

2016-01-01

Understanding the ecological and evolutionary forces that determine the genetic structure and spread of invasive species is a key component of invasion biology. The bay barnacle, Balanus improvisus (= Amphibalanus improvisus), is one of the most successful aquatic invaders worldwide, and is characterised by broad environmental tolerance. Although the species can spread through natural larval dispersal, human-mediated transport through (primarily) shipping has almost certainly contributed to the current global distribution of this species. Despite its worldwide distribution, little is known about the phylogeography of this species. Here, we characterize the population genetic structure and model dispersal dynamics of the barnacle B. improvisus, and describe how human-mediated spreading via shipping as well as natural larval dispersal may have contributed to observed genetic variation. We used both mitochondrial DNA (cytochrome c oxidase subunit I: COI) and nuclear microsatellites to characterize the genetic structure in 14 populations of B. improvisus on a global and regional scale (Baltic Sea). Genetic diversity was high in most populations, and many haplotypes were shared among populations on a global scale, indicating that long-distance dispersal (presumably through shipping and other anthropogenic activities) has played an important role in shaping the population genetic structure of this cosmopolitan species. We could not clearly confirm prior claims that B. improvisus originates from the western margins of the Atlantic coasts; although there were indications that Argentina could be part of a native region. In addition to dispersal via shipping, we show that natural larval dispersal may play an important role for further colonisation following initial introduction. PMID:26821161

Genetic diversity and population structure of a Sichuan sika deer (Cervus sichuanicus) population in Tiebu Nature Reserve based on microsatellite variation

PubMed Central

HE, Ya; WANG, Zheng-Huan; WANG, Xiao-Ming

2014-01-01

Cervus sichuanicus is a species of sika deer (Cervus nippon Group). To date, research has mainly focused on quantity surveying and behavior studies, with genetic information on this species currently deficient. To provide scientific evidence to assist in the protection of this species, we collected Sichuan sika deer fecal samples from the Sichuan Tiebu Nature Reserve (TNR) and extracted DNA from those samples. Microsatellite loci of bovine were used for PCR amplification. After GeneScan, the genotype data were used to analyze the genetic diversity and population structure of the Sichuan sika deer in TNR. Results showed that the average expected heterozygosity of the Sichuan sika deer population in TNR was 0.562, equivalent to the average expected heterozygosity of endangered animals, such as Procapra przewalskii. Furthermore, 8 of 9 microsatellite loci significantly deviated from the Hardy-Weinberg equilibrium and two groups existed within the Sichuan sika deer TNR population. This genetic structure may be caused by a group of Manchurian sika deer (Cervus hortulorum) released in TNR. PMID:25465089

Genetic diversity and population structure of a Sichuan sika deer (Cervus sichuanicus) population in Tiebu Nature Reserve based on microsatellite variation.

PubMed

He, Ya; Wang, Zheng-Huan; Wang, Xiao-Ming

2014-11-18

Cervus sichuanicus is a species of sika deer (Cervus nippon Group). To date, research has mainly focused on quantity surveying and behavior studies, with genetic information on this species currently deficient. To provide scientific evidence to assist in the protection of this species, we collected Sichuan sika deer fecal samples from the Sichuan Tiebu Nature Reserve (TNR) and extracted DNA from those samples. Microsatellite loci of bovine were used for PCR amplification. After GeneScan, the genotype data were used to analyze the genetic diversity and population structure of the Sichuan sika deer in TNR. Results showed that the average expected heterozygosity of the Sichuan sika deer population in TNR was 0.562, equivalent to the average expected heterozygosity of endangered animals, such as Procapra przewalskii. Furthermore, 8 of 9 microsatellite loci significantly deviated from the Hardy-Weinberg equilibrium and two groups existed within the Sichuan sika deer TNR population. This genetic structure may be caused by a group of Manchurian sika deer (Cervus hortulorum) released in TNR.

Genetic diversity and divergence at the Arbutus unedo L. (Ericaceae) westernmost distribution limit.

PubMed

Ribeiro, Maria Margarida; Piotti, Andrea; Ricardo, Alexandra; Gaspar, Daniel; Costa, Rita; Parducci, Laura; Vendramin, Giovanni Giuseppe

2017-01-01

Mediterranean forests are fragile ecosystems vulnerable to recent global warming and reduction of precipitation, and a long-term negative effect is expected on vegetation with increasing drought and in areas burnt by fires. We investigated the spatial distribution of genetic variation of Arbutus unedo in the western Iberia Peninsula, using plastid markers with conservation and provenance regions design purposes. This species is currently undergoing an intense domestication process in the region, and, like other species, is increasingly under the threat from climate change, habitat fragmentation and wildfires. We sampled 451 trees from 15 natural populations from different ecological conditions spanning the whole species' distribution range in the region. We applied Bayesian analysis and identified four clusters (north, centre, south, and a single-population cluster). Hierarchical AMOVA showed higher differentiation among clusters than among populations within clusters. The relatively low within-clusters differentiation can be explained by a common postglacial history of nearby populations. The genetic structure found, supported by the few available palaeobotanical records, cannot exclude the hypothesis of two independent A. unedo refugia in western Iberia Peninsula during the Last Glacial Maximum. Based on the results we recommend a conservation strategy by selecting populations for conservation based on their allelic richness and diversity and careful seed transfer consistent with current species' genetic structure.

Genetic diversity and divergence at the Arbutus unedo L. (Ericaceae) westernmost distribution limit

PubMed Central

Ribeiro, Maria Margarida; Piotti, Andrea; Ricardo, Alexandra; Gaspar, Daniel; Costa, Rita; Parducci, Laura; Vendramin, Giovanni Giuseppe

2017-01-01

Mediterranean forests are fragile ecosystems vulnerable to recent global warming and reduction of precipitation, and a long-term negative effect is expected on vegetation with increasing drought and in areas burnt by fires. We investigated the spatial distribution of genetic variation of Arbutus unedo in the western Iberia Peninsula, using plastid markers with conservation and provenance regions design purposes. This species is currently undergoing an intense domestication process in the region, and, like other species, is increasingly under the threat from climate change, habitat fragmentation and wildfires. We sampled 451 trees from 15 natural populations from different ecological conditions spanning the whole species’ distribution range in the region. We applied Bayesian analysis and identified four clusters (north, centre, south, and a single-population cluster). Hierarchical AMOVA showed higher differentiation among clusters than among populations within clusters. The relatively low within-clusters differentiation can be explained by a common postglacial history of nearby populations. The genetic structure found, supported by the few available palaeobotanical records, cannot exclude the hypothesis of two independent A. unedo refugia in western Iberia Peninsula during the Last Glacial Maximum. Based on the results we recommend a conservation strategy by selecting populations for conservation based on their allelic richness and diversity and careful seed transfer consistent with current species’ genetic structure. PMID:28384294

Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control.

PubMed

Zalewski, Andrzej; Zalewska, Hanna; Lunneryd, Sven-Gunnar; André, Carl; Mikusiński, Grzegorz

2016-01-01

Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison) to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55), genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.

Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear.

PubMed

Xenikoudakis, G; Ersmark, E; Tison, J-L; Waits, L; Kindberg, J; Swenson, J E; Dalén, L

2015-07-01

The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution. © 2015 John Wiley & Sons Ltd.

Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat.

PubMed

Wingen, Luzie U; Orford, Simon; Goram, Richard; Leverington-Waite, Michelle; Bilham, Lorelei; Patsiou, Theofania S; Ambrose, Mike; Dicks, Jo; Griffiths, Simon

2014-08-01

A high level of genetic diversity was found in the A. E. Watkins bread wheat landrace collection. Genotypic information was used to determine the population structure and to develop germplasm resources. In the 1930s A. E. Watkins acquired landrace cultivars of bread wheat (Triticum aestivum L.) from official channels of the board of Trade in London, many of which originated from local markets in 32 countries. The geographic distribution of the 826 landrace cultivars of the current collection, here called the Watkins collection, covers many Asian and European countries and some from Africa. The cultivars were genotyped with 41 microsatellite markers in order to investigate the genetic diversity and population structure of the collection. A high level of genetic diversity was found, higher than in a collection of modern European winter bread wheat varieties from 1945 to 2000. Furthermore, although weak, the population structure of the Watkins collection reveals nine ancestral geographical groupings. An exchange of genetic material between ancestral groups before commercial wheat-breeding started would be a possible explanation for this. The increased knowledge regarding the diversity of the Watkins collection was used to develop resources for wheat research and breeding, one of them a core set, which captures the majority of the genetic diversity detected. The understanding of genetic diversity and population structure together with the availability of breeding resources should help to accelerate the detection of new alleles in the Watkins collection.

Environmental Awareness: Relating Current Issues to Biology.

ERIC Educational Resources Information Center

DeFina, Anthony

1995-01-01

Presents examples of incorporating environmental issues into lesson plans to raise the level of students' environmental awareness. Topics include: ecology, taxonomy, biochemistry, energy reactions, cell structure and function, genetics and development, and human biology. (JRH)

Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China.

PubMed

Li, Jing-Jing; Hu, Zi-Min; Sun, Zhong-Min; Yao, Jian-Ting; Liu, Fu-Li; Fresia, Pablo; Duan, De-Lin

2017-12-07

Long-term survival in isolated marginal seas of the China coast during the late Pleistocene ice ages is widely believed to be an important historical factor contributing to population genetic structure in coastal marine species. Whether or not contemporary factors (e.g. long-distance dispersal via coastal currents) continue to shape diversity gradients in marine organisms with high dispersal capability remains poorly understood. Our aim was to explore how historical and contemporary factors influenced the genetic diversity and distribution of the brown alga Sargassum thunbergii, which can drift on surface water, leading to long-distance dispersal. We used 11 microsatellites and the plastid RuBisCo spacer to evaluate the genetic diversity of 22 Sargassum thunbergii populations sampled along the China coast. Population structure and differentiation was inferred based on genotype clustering and pairwise F ST and allele-frequency analyses. Integrated genetic analyses revealed two genetic clusters in S. thunbergii that dominated in the Yellow-Bohai Sea (YBS) and East China Sea (ECS) respectively. Higher levels of genetic diversity and variation were detected among populations in the YBS than in the ECS. Bayesian coalescent theory was used to estimate contemporary and historical gene flow. High levels of contemporary gene flow were detected from the YBS (north) to the ECS (south), whereas low levels of historical gene flow occurred between the two regions. Our results suggest that the deep genetic divergence in S. thunbergii along the China coast may result from long-term geographic isolation during glacial periods. The dispersal of S. thunbergii driven by coastal currents may facilitate the admixture between southern and northern regimes. Our findings exemplify how both historical and contemporary forces are needed to understand phylogeographical patterns in coastal marine species with long-distance dispersal.

Genetic structure in the southernmost populations of black-and-gold howler monkeys (Alouatta caraya) and its conservation implications

PubMed Central

Miño, Carolina Isabel; Fernández, Gabriela; Caputo, Mariela; Corach, Daniel

2017-01-01

Black-and-gold howler monkeys Alouatta caraya, are arboreal primates, inhabitants of Neotropical forests, highly susceptible to the yellow fever virus, considered early 'sentinels' of outbreaks, and thus, of major epidemiological importance. Currently, anthropogenic habitat loss and modifications threatens their survival. Habitat modification can prevent, reduce or change dispersal behavior, which, in turn, may influence patterns of gene flow. We explored past and contemporary levels of genetic diversity, elucidated genetic structure and identified its possible drivers, in ten populations (n = 138) located in the southernmost distribution range of the species in South America, in Argentina and Paraguay. Overall, genetic variability was moderate (ten microsatellites: 3.16 ± 0.18 alleles per locus, allelic richness of 2.93 ± 0.81, 0.443±0.025 unbiased expected heterozygosity; 22 haplotypes of 491-bp mitochondrial Control Region, haplotypic diversity of 0.930 ± 0.11, and nucleotide diversity of0.01± 0.007). Significant evidence of inbreeding was found in a population that was, later, decimated by yellow fever. Population-based gene flow measures (FST = 0.13; θST = 018), hierarchical analysis of molecular variance and Bayesian clustering methods revealed significant genetic structure, grouping individuals into four clusters. Shared haplotypes and lack of mitochondrial differentiation (non-significant θST) among some populations seem to support the hypothesis of historical dispersal via riparian forests. Current resistance analyses revealed a significant role of landscape features in modeling contemporary gene flow: continuous forest and riparian forests could promote genetic exchange, whereas disturbed forests or crop/grassland fields may restrict it. Estimates of effective population size allow anticipating that the studied populations will lose 75% of heterozygosity in less than 50 generations. Our findings suggest that anthropogenic modifications on native forests, increasingly ongoing in Northeastern Argentina, Southern Paraguay and Southeastern Brazil, might prevent the dispersal of howlers, leading to population isolation. To ensure long-term viability and maintain genetic connectivity of A. caraya remnant populations, we recommend preserving and restoring habitat continuity. To conserve the species genetic pool, as well, the four genetic clusters identified here should be considered separate Management Units and given high conservation priority. In light of our findings and considering complementary non-genetic information, we suggest upgrading the international conservation status of A. caraya to “Vulnerable”. PMID:28968440

Alu polymorphic insertions reveal genetic structure of north Indian populations.

PubMed

Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

2008-10-01

The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

Rocky Mountain Center for Conservation Genetics and Systematics

USGS Publications Warehouse

Oyler-McCance, S.J.; Quinn, T.W.

2005-01-01

The use of molecular genetic tools has become increasingly important in addressing conservation issues pertaining to plants and animals. Genetic information can be used to augment studies of population dynamics and population viability, investigate systematic, refine taxonomic definitions, investigate population structure and gene flow, and document genetic diversity in a variety of plant and animal species. Further, genetic techniques are being used to investigate mating systems through paternity analysis, and analyze ancient DNA samples from museum specimens, and estimate population size and survival rates using DNA as a unique marker. Such information is essential for the sound management of small, isolated populations of concern and is currently being used by universities, zoos, the U.S. Fish and Wildlife Service, and numerous state fish and wildlife agencies.

The dimensional structure of psychopathology in 22q11.2 Deletion Syndrome.

PubMed

Niarchou, Maria; Moore, Tyler M; Tang, Sunny X; Calkins, Monica E; McDonald-McGuinn, Donna M; Zackai, Elaine H; Emanuel, Beverly S; Gur, Ruben C; Gur, Raquel E

2017-09-01

22q11.2 Deletion Syndrome (22q11.2DS) is one of the strongest known genetic risk factors for developing schizophrenia. Individuals with 22q11.2DS have high rates of neurodevelopmental disorders in childhood, while in adulthood ∼25% develop schizophrenia. Similar to the general population, high rates of comorbidity are common in 22q11.2DS. Employing a dimensional approach where psychopathology is examined at the symptom-level as complementary to diagnostic categories in a population at such high genetic risk for schizophrenia can help gain a better understanding of how psychopathology is structured as well as its genetic underpinnings. This is the first study to examine the dimensional structure of a wide spectrum of psychopathology in the context of a homogeneous genetic etiology like 22q11.2DS. We evaluated 331 individuals with 22q11.2DS, mean age (SD) = 16.9(8.7); 51% males, who underwent prospective comprehensive phenotyping. We sought to replicate previous findings by examining a bi-factor model that derives a general factor of psychopathology in addition to more specific dimensions of psychopathology (i.e., internalizing, externalizing and thought disorder). Psychopathology in 22q11.2DS was divided into one 'general psychopathology' factor and four specific dimensions (i.e., 'anxiety', 'mood', 'ADHD' and 'psychosis'). The 'psychosis' symptoms loaded strongly on the 'general psychopathology' factor. The similarity of the symptom structure of psychopathology between 22q11.2DS and community and clinical populations without the deletion indicate that 22q11.2DS can provide a model to explore alternative approaches to our current nosology. Our findings add to a growing literature indicating the need to reorganize current diagnostic classification systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander.

PubMed

Velo-Antón, G; Parra, J L; Parra-Olea, G; Zamudio, K R

2013-06-01

Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans-Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico. © 2013 John Wiley & Sons Ltd.

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us.

PubMed

El Baidouri, Fouad; Diancourt, Laure; Berry, Vincent; Chevenet, François; Pratlong, Francine; Marty, Pierre; Ravel, Christophe

2013-01-01

Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease.

Postglacial expansion pathways of red mangrove, Rhizophora mangle, in the Caribbean Basin and Florida.

PubMed

Kennedy, John Paul; Pil, Maria W; Proffitt, C Edward; Boeger, Walter A; Stanford, Alice M; Devlin, Donna J

2016-02-01

The Last Glacial Maximum (LGM) was a period of massive range contraction. Post-LGM, water-dispersed coastal species, including the red mangrove (Rhizophora mangle), expanded poleward as propagules were transported by ocean currents. We assessed postglacial marine expansion pathways for R. mangle within the Caribbean Basin and Florida. Six microsatellite loci were used to genotype 237 individuals from nine R. mangle populations in the Caribbean, Florida, and Northwest Africa. We evaluated genetic variation, population structure, gene flow along alternative post-LGM expansion pathways to Florida, and potential long-distance dispersal (LDD) from West Africa to Caribbean islands. These R. mangle populations had substantial genetic structure (FST = 0.37, P < 0.0001) with three discrete population clusters (Caribbean mainland, Caribbean islands, and Florida). Genetic connectivity along the mainland pathway (Caribbean mainland to Florida) vs. limited gene dispersal along the Antilles Island pathway (Caribbean islands to Florida) supported Florida recolonization from Caribbean mainland sources. Genetic similarity of Northwest Africa and two Caribbean islands provided evidence for trans-Atlantic LDD. We did not find a pattern of decreasing genetic diversity with latitude. We outline a complex expansion history for R. mangle, with discrete pathways of recolonization for Florida and Caribbean islands. Contrary to expectation, connectivity to putative Caribbean mainland refugial populations via ocean currents, and not latitude, appears to dictate genetic diversity within Caribbean island and Florida R. mangle. These findings provide a framework for further investigation of additional water-dispersed neotropical species, and insights for management initiatives. © 2016 Botanical Society of America.

Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus).

PubMed

Schield, Drew R; Adams, Richard H; Card, Daren C; Corbin, Andrew B; Jezkova, Tereza; Hales, Nicole R; Meik, Jesse M; Perry, Blair W; Spencer, Carol L; Smith, Lydia L; García, Gustavo Campillo; Bouzid, Nassima M; Strickland, Jason L; Parkinson, Christopher L; Borja, Miguel; Castañeda-Gaytán, Gamaliel; Bryson, Robert W; Flores-Villela, Oscar A; Mackessy, Stephen P; Castoe, Todd A

2018-06-15

The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene. Copyright © 2018 Elsevier Inc. All rights reserved.

Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove.

PubMed

Calderón, Luciano; Campagna, Leonardo; Wilke, Thomas; Lormee, Hervé; Eraud, Cyril; Dunn, Jenny C; Rocha, Gregorio; Zehtindjiev, Pavel; Bakaloudis, Dimitrios E; Metzger, Benjamin; Cecere, Jacopo G; Marx, Melanie; Quillfeldt, Petra

2016-11-07

Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.

ParallelStructure: A R Package to Distribute Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core Computers

PubMed Central

Besnier, Francois; Glover, Kevin A.

2013-01-01

This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/. PMID:23923012

Different Histories, Different Destinies‒Impact of Evolutionary History and Population Genetic Structure on Extinction Risk of the Adriatic Spined Loaches (Genus Cobitis; Cypriniformes, Actinopterygii).

PubMed

Buj, Ivana; Ćaleta, Marko; Marčić, Zoran; Šanda, Radek; Vukić, Jasna; Mrakovčić, Milorad

2015-01-01

The region of Balkans is often considered as an ichthyologic "hot spot", with a great number of species and high portion of endemics living in fresh waters in a relatively small area. The Adriatic watershed in Croatia and Herzegovina is inhabited by six spined loach species (genus Cobitis) whose extinction risk estimations were based solely on their extent of occurrence (and/or area of occupancy) and its fragmentation, and conservation proposals do not consider diversity below species level. In this investigation we employed molecular genetic methods to describe present genetic structure of the Adriatic spined loaches and reveal their demographic history. The divergence of the Adriatic lineages inside the genus Cobitis started in Miocene and lasted until Pleistocene epoch. Geological events responsible for shaping recent diversity of spined loaches in the Adriatic basin are: the Dinarid Mountains upwelling, the evolution of Dinaric Lake system, local tectonic activity, river connections during glaciations and differences in sea level. Even though all the investigated species inhabit karstic rivers located in the same geographic area and that were subject of similar geological events, the results obtained reveal great differences in their genetic diversity and structure and point out the necessity of different conservation measures to ensure their future viability. High level of genetic polymorphism is characteristic for species located more to the south. Two species comprised of more than one population have completely different intraspecific structure; populations of C. illyrica are genetically distinct and represent separate evolutionary significant units, whereas intraspecific structure of C. narentana corresponds to metapopulational pattern. Without population genetic data, evolutionary significant units could be easily misidentified. Furthermore, the obtained results affirm that population genetic measurements are able to detect differences among closely located and related species and estimate extinction risk even more accurately than currently applied IUCN criteria.

Evolutionary origins and genetic variation of the Seychelles treefrog, Tachycnemis seychellensis (Duméril and Bibron, 1841) (Amphibia: Anura: Hyperoliidae).

PubMed

Maddock, Simon T; Day, Julia J; Nussbaum, Ronald A; Wilkinson, Mark; Gower, David J

2014-06-01

The hyperoliid frog Tachycnemis seychellensis, the only species of its genus, is endemic to the four largest granitic islands of the Seychelles archipelago and is reliant on freshwater bodies for reproduction. Its presence in the Seychelles is thought to be the product of a transoceanic dispersal, diverging from the genus Heterixalus, its closest living relative (currently endemic to Madagascar), between approximately 10-35Ma. A previous study documented substantial intraspecific morphological variation among island populations and also among populations within the largest island (Mahé). To assess intraspecific genetic variation and to infer the closest living relative(s) of T. seychellensis, DNA sequence data were generated for three mitochondrial and four nuclear markers. These data support a sister-group relationship between T. seychellensis and Heterixalus, with the divergence between the two occurring between approximately 11-19Ma based on cytb p-distances. Low levels of genetic variation were found among major mitochondrial haplotype clades of T. seychellensis (maximum 0.7% p-distance concatenated mtDNA), and samples from each of the islands (except La Digue) comprised multiple mitochondrial haplotype clades. Two nuclear genes (rag1 and tyr) showed no variation, and the other two (rho and pomc) lacked any notable geographic structuring, counter to patterns observed within presumably more vagile Seychelles taxa such as lizards. The low levels of genetic variation and phylogeographic structure support an interpretation that there is a single but morphologically highly variable species of Seychelles treefrog. The contrasting genetic and morphological intraspecific variation may be attributable to relatively recent admixture during low sea-level stands, ecophenotypic plasticity, local adaptation to different environmental conditions, and/or current and previously small population sizes. Low genetic phylogeographic structure but substantial morphological variation is unusual within anurans. Copyright © 2014 Elsevier Inc. All rights reserved.

Phylogeography and postglacial expansion of the endangered semi-aquatic mammal Galemys pyrenaicus

PubMed Central

2013-01-01

Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-aquatic mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range, but its genetic structure is currently unknown. While the stringent ecological demands derived from its aquatic habitat might have caused a partition of the genetic diversity among river basins, Pleistocene glaciations would have generated a genetic pattern related to glacial refugia. Results To study the relative importance of historical and ecological factors in the genetic structure of G. pyrenaicus, we used mitochondrial and intronic sequences of specimens covering most of the species range. We show, first, that the Pyrenean desman has very low levels of genetic diversity compared to other mammals. In addition, phylogenetic and dating analyses of the mitochondrial sequences reveal a strong phylogeographic structure of a Middle Pleistocene origin, suggesting that the main lineages arose during periods of glacial isolation. Furthermore, both the spatial distribution of nuclear and mitochondrial diversity and the results of species distribution modeling suggest the existence of a major glacial refugium in the northwestern part of the Iberian Peninsula. Finally, the main mitochondrial lineages show a striking parapatric distribution without any apparent exchange of mitochondrial haplotypes between the lineages that came into secondary contact (although with certain permeability to nuclear genes), indicating incomplete mixing after the post-glacial recolonization. On the other hand, when we analyzed the partition of the genetic diversity among river basins, the Pyrenean desman showed a lower than expected genetic differentiation among main rivers. Conclusions The analysis of mitochondrial and intronic markers in G. pyrenaicus showed the predominant effects of Pleistocene glaciations on the genetic structure of this species, while the distribution of the genetic diversity was not greatly influenced by the main river systems. These results and, particularly, the discovery of a marked phylogeographic structure, may have important implications for the conservation of the Pyrenean desman. PMID:23738626

Genetic relationships among some subspecies of the Peregrine Falcon (Falco peregrinus L.), inferred from mitochondrial DNA control-region sequences

USGS Publications Warehouse

White, Clayton M.; Sonsthagen, Sarah A.; Sage, George K.; Anderson, Clifford; Talbot, Sandra L.

2013-01-01

The ability to successfully colonize and persist in diverse environments likely requires broad morphological and behavioral plasticity and adaptability, and this may partly explain why the Peregrine Falcon (Falco peregrinus) exhibits a large range of morphological characteristics across their global distribution. Regional and local differences within Peregrine Falcons were sufficiently variable that ∼75 subspecies have been described; many were subsumed, and currently 19 are generally recognized. We used sequence information from the control region of the mitochondrial genome to test for concordance between genetic structure and representatives of 12 current subspecies and from two areas where subspecies distributions overlap. Haplotypes were broadly shared among subspecies, and all geographic locales shared a widely distributed common haplotype (FalconCR2). Haplotypes were distributed in a star-like phylogeny, consistent with rapid expansion of a recently derived species, with observed genetic patterns congruent with incomplete lineage sorting and/or differential rates of evolution on morphology and neutral genetic characters. Hierarchical analyses of molecular variance did not uncover genetic partitioning at the continental level, despite strong population-level structure (FST = 0.228). Similar analyses found weak partitioning, albeit significant, among subspecies (FCT = 0.138). All reconstructions placed the hierofalcons' (Gyrfalcon [F. rusticolus] and Saker Falcon [F. cherrug]) haplotypes in a well-supported clade either basal or unresolved with respect to the Peregrine Falcon. In addition, haplotypes representing Taita Falcon (F. fasciinucha) were placed within the Peregrine Falcon clade.

Historical explanation of genetic variation in the Mediterranean horseshoe bat Rhinolophus euryale (Chiroptera: Rhinolophidae) inferred from mitochondrial cytochrome-b and D-loop genes in Iran.

PubMed

Najafi, Nargess; Akmali, Vahid; Sharifi, Mozafar

2018-04-26

Molecular phylogeography and species distribution modelling (SDM) suggest that late Quaternary glacial cycles have portrayed a significant role in structuring current population genetic structure and diversity. Based on phylogenetic relationships using Bayesian inference and maximum likelihood of 535 bp mtDNA (D-loop) and 745 bp mtDNA (Cytb) in 62 individuals of the Mediterranean Horseshoe Bat, Rhinolophus euryale, from 13 different localities in Iran we identified two subspecific populations with differing population genetic structure distributed in southern Zagros Mts. and northern Elburz Mts. Analysis of molecular variance (AMOVA) obtained from D-loop sequences indicates that 21.18% of sequence variation is distributed among populations and 10.84% within them. Moreover, a degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.68, p = .005). The positive and significant correlation between geographic and genetic distances (R 2  = 0.28, r = 0.529, p = .000) is obtained following controlling for environmental distance. Spatial distribution of haplotypes indicates that marginal population of the species in southern part of the species range have occupied this section as a glacial refugia. However, this genetic variation, in conjunction with results of the SDM shows a massive postglacial range expansion for R. euryale towards higher latitudes in Iran.

Population genetic studies of the polar bear (Ursus maritimus): A summary of available data and interpretation of results

USGS Publications Warehouse

Scribner, Kim T.; Garner, G.W.; Amstrup, Steven C.; Cronin, M.A.; Dizon, Andrew E.; Chivers, Susan J.; Perrin, William F.

1997-01-01

A summary of existing population genetics literature is presented for polar bears (Ursus maritimus) and interpreted in the context of the species' life-history characteristics and regional heterogeneity in environmental regimes and movement patterns. Several nongenetic data sets including morphology, contaminant levels, geographic variation in reproductive characteristics, and the location and distribution of open-water foraging habitat suggest some degree of spatial structuring. Eleven populations are recognized by the IUCN Polar Bear Specialist Group. Few genetics studies exist for polar bears. Interpretation and generalizations of regional variation in intra- and interpopulation levels of genetic variability are confounded by the paucity of data from many regions and by the fact that no single informative genetic marker has been employed in multiple regions. Early allozyme studies revealed comparatively low levels of genetic variability and no compelling evidence of spatial structuring. Studies employing mitochondrial DNA (mtDNA) also found low levels of genetic variation, a lack of phylogenetic structure, and no significant evidence for spatial variation in haplotype frequency. In contrast, microsatellite variable number of tandem repeat (VNTR) loci have revealed significant heterogeneity in allele frequency among populations in the Canadian Arctic. These regions are characterized by archipelgic patterns of sea-ice movements. Further studies using highly polymorphic loci are needed in regions characterized by greater polar bear dependency on pelagic sea-ice movements and in regions for which no data currently exist (i.e., Laptev and Novaya Zemlya/Franz Josef).

Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

PubMed

Faulks, L K; Östman, Ö

2016-04-01

This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended. © 2016 The Fisheries Society of the British Isles.

Educational priorities and current involvement in genetic practice: a survey of midwives in the Netherlands, UK and Sweden.

PubMed

Benjamin, Caroline M; Anionwu, Elizabeth N; Kristoffersson, Ulf; ten Kate, Leo P; Plass, Anne Marie C; Nippert, Irmgard; Julian-Reynier, Claire; Harris, Hilary J; Schmidtke, Joerg; Challen, Kirsty; Calefato, Jean Marc; Waterman, Christine; Powell, Eileen; Harris, Rodney

2009-10-01

to investigate whether practising midwives are adequately prepared to integrate genetic information into their practice. a cross-sectional, postal, structured questionnaire survey was sent to practising midwives. practising midwives from the Netherlands (NL), Sweden (SE) and the United Kingdom (UK). 1021 replies were received, achieving a response rate of 62%. 79% (799/1015) of midwives reported attending courses with some 'genetic content' during their initial training. Sixty-eight per cent (533/784) judged this to have been useful for clinical practice. Variation was seen between countries in the amount of genetic content in post-registration training (SE 87%, NL 44%, UK 17%) and most was considered useful. Questions assessing clinical activity identified a current need for genetic knowledge. Midwives described low levels of self-reported confidence both in overtly genetic procedures and in everyday tasks that were underpinned by genetic knowledge. For eight of the 12 procedures, fewer than 20% of midwives considered themselves to be confident. Differences were apparent between countries. Midwives identified psychosocial, screening and risk assessment aspects of genetic education as being important to them, rather than technical aspects or genetic science. given the low reported confidence with genetic issues in clinical practice, it is essential that this is addressed in terms of the amount, content and targeting of genetic education. This is especially important to ensure the success of national antenatal and baby screening programmes. The results of this study suggest that midwives would welcome further training in genetics, addressing genetic topics most relevant to their clinical practice.

Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA.

PubMed

Casas-Marce, Mireia; Marmesat, Elena; Soriano, Laura; Martínez-Cruz, Begoña; Lucena-Perez, Maria; Nocete, Francisco; Rodríguez-Hidalgo, Antonio; Canals, Antoni; Nadal, Jordi; Detry, Cleia; Bernáldez-Sánchez, Eloísa; Fernández-Rodríguez, Carlos; Pérez-Ripoll, Manuel; Stiller, Mathias; Hofreiter, Michael; Rodríguez, Alejandro; Revilla, Eloy; Delibes, Miguel; Godoy, José A

2017-11-01

There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839).

PubMed

Gonzalez, Elena G; Beerli, Peter; Zardoya, Rafael

2008-09-17

Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects past events of isolation and secondary contact. Given the inferred relatively low number of immigrants per generation around the Cape of Good Hope, the proportions of the mitochondrial clades in the different oceans may keep stable, and it seems plausible that the presence of individuals belonging to the mt Clade I in the Atlantic Ocean may be due to extensive migrations that predated the last glaciation.

Patterns of Post-Glacial Genetic Differentiation in Marginal Populations of a Marine Microalga

PubMed Central

Tahvanainen, Pia; Alpermann, Tilman J.; Figueroa, Rosa Isabel; John, Uwe; Hakanen, Päivi; Nagai, Satoshi; Blomster, Jaanika; Kremp, Anke

2012-01-01

This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F ST) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms. PMID:23300940

Patterns of post-glacial genetic differentiation in marginal populations of a marine microalga.

PubMed

Tahvanainen, Pia; Alpermann, Tilman J; Figueroa, Rosa Isabel; John, Uwe; Hakanen, Päivi; Nagai, Satoshi; Blomster, Jaanika; Kremp, Anke

2012-01-01

This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F(ST)) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.

Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

PubMed

Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

2016-02-01

The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

Population structure and relatedness among female Northern Pintails in three California wintering regions

USGS Publications Warehouse

Fleskes, Joseph P.; Fowler, Ada C.; Casazza, Michael L.; Eadie, John M.

2010-01-01

Female Northern Pintails (Anas acuta) were sampled in California's three main Central Valley wintering regions (Sacramento Valley, Suisun Marsh, San Joaquin Valley) during September–October before most regional movements occur and microsatellite and mitochondrial DNA were analyzed to examine population structure and relatedness. Despite reportedly high rates of early-fall pairing and regional fidelity, both sets of markers indicated that there was little overall genetic structuring by region. Pintails from Suisun Marsh did exhibit higher relatedness among individuals and capture groups than in the Sacramento or San Joaquin Valleys, likely reflecting a sample comprised of a greater proportion of local breeders. The lack of genetic structuring among regions indicates that a high degree of movement and interchange occurs among pintails wintering in the Central Valley. Thus, although maintaining the existing distribution of pintails among Central Valley regions is important for other reasons, it does not appear to be critical to retain current patterns of population genetic variation. Because of potential lack of independence among highly related study individuals, researchers should consider regional differences in relatedness when designing sampling schemes and interpreting research findings.

Population genetic structure and Wolbachia infection in an endangered butterfly, Zizina emelina (Lepidoptera, Lycaenidae), in Japan.

PubMed

Sakamoto, Y; Hirai, N; Tanikawa, T; Yago, M; Ishii, M

2015-04-01

Zizina emelina (de l'Orza) is listed on Japan's Red Data List as an endangered species because of loss of its principal food plant and habitat. We compared parts of the mitochondrial and nuclear genes of this species to investigate the level of genetic differentiation among the 14 extant populations. We also examined infection of the butterfly with the bacterium Wolbachia to clarify the bacterium's effects on the host population's genetic structure. Mitochondrial and nuclear DNA analyses revealed that haplotype composition differed significantly among most of the populations, and the fixation index F ST was positively correlated with geographic distance. In addition, we found three strains of Wolbachia, one of which was a male killer; these strains were prevalent in several populations. There was linkage between some host mitochondrial haplotypes and the three Wolbachia strains, although no significant differences were found in a comparison of host mitochondrial genetic diversity with nuclear genetic diversity in Wolbachia-infected or -uninfected populations. These genetic analyses and Wolbachia infection findings show that Z. emelina has little migratory activity and that little gene flow occurs among the current populations.

Direct-to-consumer genetic testing in Slovenia: availability, ethical dilemmas and legislation.

PubMed

Vrecar, Irena; Peterlin, Borut; Teran, Natasa; Lovrecic, Luca

2015-01-01

Over the last few years, many private companies are advertising direct-to-consumer genetic testing (DTC GT), mostly with no or only minor clinical utility and validity of tests and without genetic counselling. International professional community does not approve provision of DTC GT and situation in some EU countries has been analysed already. The aim of our study was to analyse current situation in the field of DTC GT in Slovenia and related legal and ethical issues. Information was retrieved through internet search, performed independently by two authors, structured according to individual private company and the types of offered genetic testing. Five private companies and three Health Insurance Companies offer DTC GT and it is provided without genetic counselling. Available tests include testing for breast cancer, tests with other health-related information (complex diseases, drug responses) and other tests (nutrigenetic, ancestry, paternity). National legislation is currently being developed and Council of Experts in Medical Genetics has issued an opinion about Genetic Testing and Commercialization of Genetic Tests in Slovenia. Despite the fact that Slovenia has signed the Additional protocol to the convention on human rights and biomedicine, concerning genetic testing for health purposes, DTC GT in Slovenia is present and against all international recommendations. There is lack of or no medical supervision, clinical validity and utility of tests and inappropriate genetic testing of minors is available. There is urgent need for regulation of ethical, legal, and social aspects. National legislation on DTC GT is being prepared.

Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

PubMed Central

Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C.; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M.; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

2014-01-01

The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry. PMID:25254375

Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 individuals.

PubMed

Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Victor; Quinto-Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; de Avila, Francisco; Gómez-Valdés, Jorge; León-Mimila, Paola; Hunemeier, Tábita; Ramallo, Virginia; Silva de Cerqueira, Caio C; Burley, Mari-Wyn; Konca, Esra; de Oliveira, Marcelo Zagonel; Veronez, Mauricio Roberto; Rubio-Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schuler-Faccini, Lavinia; Salzano, Francisco M; Bortolini, Maria-Cátira; Canizales-Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David; Gonzalez-José, Rolando

2014-09-01

The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence.

PubMed

Lin, Long-Hui; Qu, Yan-Fu; Li, Hong; Zhou, Kai-Ya; Ji, Xiang

2012-01-01

An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a "star" cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization.

Genetic structure of the date palm (Phoenix dactylifera) in the Old World reveals a strong differentiation between eastern and western populations.

PubMed

Zehdi-Azouzi, Salwa; Cherif, Emira; Moussouni, Souhila; Gros-Balthazard, Muriel; Abbas Naqvi, Summar; Ludeña, Bertha; Castillo, Karina; Chabrillange, Nathalie; Bouguedoura, Nadia; Bennaceur, Malika; Si-Dehbi, Farida; Abdoulkader, Sabira; Daher, Abdourahman; Terral, Jean-Frederic; Santoni, Sylvain; Ballardini, Marco; Mercuri, Antonio; Ben Salah, Mohamed; Kadri, Karim; Othmani, Ahmed; Littardi, Claudio; Salhi-Hannachi, Amel; Pintaud, Jean-Christophe; Aberlenc-Bertossi, Frédérique

2015-07-01

Date palms (Phoenix dactylifera, Arecaceae) are of great economic and ecological value to the oasis agriculture of arid and semi-arid areas. However, despite the availability of a large date palm germplasm spreading from the Atlantic shores to Southern Asia, improvement of the species is being hampered by a lack of information on global genetic diversity and population structure. In order to contribute to the varietal improvement of date palms and to provide new insights on the influence of geographic origins and human activity on the genetic structure of the date palm, this study analysed the diversity of the species. Genetic diversity levels and population genetic structure were investigated through the genotyping of a collection of 295 date palm accessions ranging from Mauritania to Pakistan using a set of 18 simple sequence repeat (SSR) markers and a plastid minisatellite. Using a Bayesian clustering approach, the date palm genotypes can be structured into two different gene pools: the first, termed the Eastern pool, consists of accessions from Asia and Djibouti, whilst the second, termed the Western pool, consists of accessions from Africa. These results confirm the existence of two ancient gene pools that have contributed to the current date palm diversity. The presence of admixed genotypes is also noted, which points at gene flows between eastern and western origins, mostly from east to west, following a human-mediated diffusion of the species. This study assesses the distribution and level of genetic diversity of accessible date palm resources, provides new insights on the geographic origins and genetic history of the cultivated component of this species, and confirms the existence of at least two domestication origins. Furthermore, the strong genetic structure clearly established here is a prerequisite for any breeding programme exploiting the effective polymorphism related to each gene pool. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Under the Influence of Genetics: How Transdisciplinarity Leads Us to Rethink Social Pathways to Illness

PubMed Central

Pescosolido, Bernice A.; Perry, Brea L.; Long, J. Scott; Martin, Jack K.; Nurnberger, John I.; Hesselbrock, Victor

2015-01-01

To extend our understanding of how social structures and social processes impact behavior, sociologists have been challenged to incorporate the potential explanatory role of genetics in their models. Here, we draw propositions from three major understandings of illness causation offered by social theory – fundamental causes, social stress processes, and social safety net theories. We tailor hypotheses to the case of alcohol dependence, long considered a multifaceted problem, defying simple explanation and having both biological and social roots. After briefly reviewing current appeals for transdisciplinary research, we describe both sociological and genetic theories, and derive propositions expected under each and under a transdisciplinary theoretical frame. Analyses of a later wave of the preeminent medical science study, the Collaborative Study on the Genetics of Alcoholism (COGA), reveals a complex interplay of how the GABRA2 gene works with and against social structural factors to produce cases meeting DSM/ICD diagnoses. When both genetic and social factors are controlled, virtually equivalent effects of each remain; and, only modest evidence suggests that genetic influence works through social structural conditions and experiences. Further exploratory analyses using multiplicative terms reveal enhanced gene-environment interactions: 1) women are largely unaffected in their risk for alcohol dependence by allele status at this candidate gene; 2) family support attenuates genetic influence; 3) childhood deprivation exacerbates genetic predispositions. We discuss how these findings lead us to consider the essential intradisciplinary tension in sociological theories (i.e., the role of proximal and distal influences in social processes). Overall, our findings point to the promise of theories blending social and genetic influences by focusing directly on dynamic, networked sequences that produce different pathways to health and illness. PMID:19569404

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords.

PubMed

Canales-Aguirre, Cristian B; Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Hernández, Cristián E

2016-01-01

Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA.

Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba

PubMed Central

2011-01-01

Background Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill Euphausia superba using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range. Results MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter g (a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60 000 - 40 000 years ago) for the expansion. Conclusions The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, versus sedentary benthic shelf species. EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species. PMID:21486439

Genetic Diversity of an Imperiled Neotropical Catfish and Recommendations for Its Restoration

PubMed Central

Fonseca, Fernando S.; Domingues, Rodrigo R.; Hallerman, Eric M.; Hilsdorf, Alexandre W. S.

2017-01-01

The long-whiskered catfish Steindachneridion parahybae (Family Pimelodidae) is endemic to the Paraíba do Sul River basin in southeastern Brazil. This species was heavily exploited by artisanal fisheries and faces challenges posed by dams, introduced species, and deterioration of critical habitat. The remaining populations are small and extirpated from some locales, and the species is listed as critically endangered in Brazil. Screening variation at a partial mitochondrial control region sequence (mtCR) and 20 microsatellite loci, we: (i) describe the patterns of genetic diversity along its current distributional range; (ii) test the null hypothesis of panmixia; (iii) investigate the main factors driving its current population structure, and (iv) propose management of broodstock for fostering recovery of wild populations through genetically cognizant restocking. Our microsatellite data for 70 individuals from five collections indicate moderate levels of heterozygosity (HO = 0.45) and low levels of inbreeding (FIS = 0.016). Individual-based cluster analyses showed clear genetic structure, with three clusters of individuals over the collection area with no mis-assigned individuals, suggesting no recent migration among the three clusters. Pairwise DEST values showed moderate and significant genetic differentiation among all populations so identified. The MUR population may have suffered a recent demographic reduction. mtCRs for 70 individuals exhibited 36 haplotypes resulting from 38 polymorphic sites. Overall, mitochondrial haplotype diversity was 0.930 (±0.023) and nucleotide diversity was 0.011 (±0.002). Significant population structure was observed, with ϕST = 0.226. Genetic markers could be used in a hatchery-based restoration program emphasizing breeding of pairs with low kinship values in order to promote retention of genetic diversity and avoid inbreeding. Individual average kinship relationships showed 87.3% advised matings, 11.0% marginal matings, and 1.7% advised against. While these results comprise a contribution toward planning better breeding management and monitoring, parallel actions to be undertaken include surveying healthy riverine habits for reintroduction and continued searching for wild individuals to introduce new variation into the captive broodstock to avoid adaptation to captivity and to minimize inbreeding. PMID:29312433

Genetic Diversity of an Imperiled Neotropical Catfish and Recommendations for Its Restoration.

PubMed

Fonseca, Fernando S; Domingues, Rodrigo R; Hallerman, Eric M; Hilsdorf, Alexandre W S

2017-01-01

The long-whiskered catfish Steindachneridion parahybae (Family Pimelodidae) is endemic to the Paraíba do Sul River basin in southeastern Brazil. This species was heavily exploited by artisanal fisheries and faces challenges posed by dams, introduced species, and deterioration of critical habitat. The remaining populations are small and extirpated from some locales, and the species is listed as critically endangered in Brazil. Screening variation at a partial mitochondrial control region sequence (mtCR) and 20 microsatellite loci, we: (i) describe the patterns of genetic diversity along its current distributional range; (ii) test the null hypothesis of panmixia; (iii) investigate the main factors driving its current population structure, and (iv) propose management of broodstock for fostering recovery of wild populations through genetically cognizant restocking. Our microsatellite data for 70 individuals from five collections indicate moderate levels of heterozygosity ( H O = 0.45) and low levels of inbreeding ( F IS = 0.016). Individual-based cluster analyses showed clear genetic structure, with three clusters of individuals over the collection area with no mis-assigned individuals, suggesting no recent migration among the three clusters. Pairwise D EST values showed moderate and significant genetic differentiation among all populations so identified. The MUR population may have suffered a recent demographic reduction. mtCRs for 70 individuals exhibited 36 haplotypes resulting from 38 polymorphic sites. Overall, mitochondrial haplotype diversity was 0.930 (±0.023) and nucleotide diversity was 0.011 (±0.002). Significant population structure was observed, with ϕ ST = 0.226. Genetic markers could be used in a hatchery-based restoration program emphasizing breeding of pairs with low kinship values in order to promote retention of genetic diversity and avoid inbreeding. Individual average kinship relationships showed 87.3% advised matings, 11.0% marginal matings, and 1.7% advised against. While these results comprise a contribution toward planning better breeding management and monitoring, parallel actions to be undertaken include surveying healthy riverine habits for reintroduction and continued searching for wild individuals to introduce new variation into the captive broodstock to avoid adaptation to captivity and to minimize inbreeding.

Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

PubMed Central

Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

2010-01-01

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

Combining Population Structure with Historic Abitoic Processes to Better Understand Species and Community Range Shifts in Response to Climate Change

NASA Astrophysics Data System (ADS)

Graham, N. M.

2015-12-01

The evolution and speciation of plants is directly tied to the environment as the constrained stages of dispersal creates strong genetic differentiation among populations. This can result in differing genetic patterns between nuclear and chloroplast loci, where genes are inherited differently and dispersed via separate vectors. By developing distribution models based on genetic patterns found within a species, it is possible to begin understanding the influence of historic geomorphic and/or climatic processes on population evolution. If genetic patterns of the current range correlate with specific patterns of climate variability within the Pleistocene, it is possible that future shifts in species distribution in response to climate change can be more accurately modelled due to the historic signature that is found within inherited genes. Preliminary genetic analyses of Linanthus dichotomus, an annual herb distributed across California, suggests that the current taxonomic treatment does not accurately depict how this species is evolving. Genetic patterns of chloroplast genes suggest that populations are more correlated with biogeography than what the current nomenclature states. Additionally, chloroplast and nuclear genes show discrepancies in the dispersal across the landscape, suggesting pollinator driven gene flow overcoming seed dispersal boundaries. By comparing discrepancies between pollinator and seed induced gene flow we may be able to gain insight into historical pollinator communities within the Pleistocene. This information can then be applied to projected climate models to more accurately understand how species and/or communities will respond to a changing environment.

Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

PubMed Central

Burns, Lynne E; Frasier, Timothy R; Broders, Hugh G

2014-01-01

Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics for multiple bat species. We characterized population genetic structure of the little brown bat, Myotis lucifugus, at swarming sites in southeastern Canada using 9 nuclear microsatellites and a 292-bp region of the mitochondrial genome. Analyses of FST, ΦST, and Bayesian clustering (STRUCTURE) found weak levels of genetic structure among swarming sites for the nuclear and mitochondrial genome (Global FST = 0.001, P < 0.05, Global ΦST = 0.045, P < 0.01, STRUCTURE K = 1) suggesting high contemporary gene flow. Hierarchical AMOVA also suggests little structuring at a regional (provincial) level. Metrics of nuclear genetic structure were not found to differ between males and females suggesting weak asymmetries in gene flow between the sexes. However, a greater degree of mitochondrial structuring does support male-biased dispersal long term. Demographic analyses were consistent with past population growth and suggest a population expansion occurred from approximately 1250 to 12,500 BP, following Pleistocene deglaciation in the region. Our study suggests high gene flow and thus a high degree of connectivity among bats that visit swarming sites whereby mainland areas of the region may be best considered as one large gene pool for management and conservation. PMID:25505539

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation.

PubMed

Shinada, Hiroshi; Yamamoto, Toshio; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Matsuba, Shuichi; Fujino, Kenji

2014-04-01

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world. Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.

Patenting human genetic material: refocusing the debate

PubMed Central

Caulfield, Timothy; Gold, E. Richard; Cho, Mildred K.

2008-01-01

The biotechnology industry has become firmly established over the past twenty years and gene patents have played an important part in this phenomenon. However, concerns have been raised over the patentability of human genetic material, through public protests and international statements, but to little effect. Here we discuss some of these concerns, the patent authorities’ response to them, and ways in which to address these issues and to move the debate forward using current legal structures. PMID:11252752

Climate Change and Genetic Structure of Leading Edge and Rear End Populations in a Northwards Shifting Marine Fish Species, the Corkwing Wrasse (Symphodus melops).

PubMed

Knutsen, Halvor; Jorde, Per Erik; Gonzalez, Enrique Blanco; Robalo, Joana; Albretsen, Jon; Almada, Vitor

2013-01-01

One mechanism by which marine organisms may respond to climate shifts is range shifts. The corkwing wrasse (Symphodus melops) is a temperate fish species, inhabiting the coasts of Europe, that show strong indications of current as well as historical (ice-age) range shifts towards the north. Nine neutral microsatellite DNA markers were screened to study genetic signatures and spatial population structure over the entire geographic and thermal gradient of the species from Portugal to Norway. A major genetic break (F ST  = 0.159 average among pairs) was identified between Scandinavian and more southern populations, with a marked reduction (30% or more) in levels of genetic variability in Scandinavia. The break is probably related to bottleneck(s) associated with post-glacial colonization of the Scandinavian coasts, and indicates a lack of present gene flow across the North Sea. The lack of gene flow can most likely be attributed to the species' need for rocky substrate for nesting and a relatively short pelagic larval phase, limiting dispersal by ocean currents. These findings demonstrate that long-distance dispersal may be severely limited in the corkwing wrasse, and that successful range-shifts following present climate change may be problematic for this and other species with limited dispersal abilities, even in the seemingly continuous marine environment.

Using Vocal Dialects to Assess the Population Structure of Bigg's Killer Whales in Alaska

NASA Astrophysics Data System (ADS)

Sharpe, D. L.; Wade, P. R.; Castellote, M.; Cornick, L. A.

2016-02-01

Apex predators are important indicators of ecosystem health, but little is known about the population structure of Bigg's killer whales (Orcinus orca; i.e. "transient" ecotype) in western Alaska. Currently, all Bigg's killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about group-specific killer whale vocal dialects in other locations, we sought to evaluate and refine Bigg's killer whale population structure by using acoustic recordings to examine the spatial distribution of call types in western Alaska. Digital audio recordings were collected from 34 encounters with Bigg's killer whales throughout the Aleutian and Pribilof Islands in the summers of 2001-2007 and 2009-2010, then visually and aurally reviewed using the software Adobe Audition. High quality calls were identified and classified into discrete call types based on spectrographic characteristics and aural uniqueness. A comparative analysis of call types recorded throughout the study area revealed spatial segregation of call types, corresponding well with proposed genetic delineations. These results suggest that Bigg's killer whales exhibit regional vocal dialects, which can be used to help refine the putative sub-populations that have been genetically identified throughout western Alaska. Our findings support the proposal to restructure current stock designations.

[Research progress in chemical communication among insect-resistant genetically modified plants, insect pests and natural enemies].

PubMed

Liu, Qing-Song; Li, Yun-He; Chen, Xiu-Ping; Peng, Yu-Fa

2014-08-01

Semiochemicals released by plants or insects play an important role in the communication among plants, phytophagous insects and their natural enemies. They thus form a chemical information network which regulates intra- and inter-specific behaviors and sustains the composition and structure of plant and insect communities. The application of insect-resistant genetically modified (IRGM) crops may affect the chemical communication within and among the tritrophic levels, and thus cause disturbances to the biotic community structure and the stability of the farmland ecosystem. This has raised concerns about the environmental safety of IRGM crops and triggered research worldwide. In the current article we provided a brief summary of the chemical communication among plants, herbivores and natural enemies; analyzed the potential of IRGM crops to affect the chemical communication between plants and arthropods and the related mechanisms; and discussed the current research progress and the future prospects in this field. We hope that this will promote the research in this field by Chinese scientists and increase our understanding of the potential effects of growing of IRGM crops on the arthropod community structure.

Genetic structure of eelgrass Zostera marina meadows in an embayment with restricted water flow

USGS Publications Warehouse

Munoz-Salazar, R.; Talbot, S.L.; Sage, G.K.; Ward, D.H.; Cabello-Pasini, Alejandro

2006-01-01

Genetic structure of the seagrass Zostera marina in a coastal lagoon with restricted water flow, and with heterogeneous water residence times and oceanographic characteristics, was assessed using 8 polymorphic microsatellite loci. Analyses of genetic differentiation (??) and Bayesian clustering suggested that the Z. marina population in San Quintin Bay (SQB) is genetically substructured, with at least 4 genetically different groups: (1) West Head, (2) Mouth, (3) East Arm, and (4) East Head. The greatest ?? value was observed between the most distant sites (?? = 0.095). The lowest values were found among sites closest to the mouth of the coastal lagoon (?? = 0.000 to 0.009). The maximum likelihood approach showed that the sites at the mouth have a mixed pattern of gene flow without a unidirectional pattern. In contrast, there was a clear pattern of asymmetrical gene flow from the mouth towards the West Head. These results suggested that the restriction of water flow at the heads, current pattern, and the distance between sites can reduce genetic flow and promote genetic differences within Z. marina meadows in small water embayments such as SQB. Though the population is genetically substructured and a 14 % decline in cover has been detected, this study did not show evidence of a recent genetic bottleneck. In contrast, mouth sites have experienced a recent expansion in their population size, and also perhaps a recent influx of rare alleles from genetically distinct immigrants. ?? Inter-Research 2006.

Social network analysis of the genetic structure of Pacific islanders.

PubMed

Terrell, John Edward

2010-05-01

Social network analysis (SNA) is a body of theory and a set of relatively new computer-aided techniques used in the analysis and study of relational data. Recent studies of autosomal markers from over 40 human populations in the south-western Pacific have further documented the remarkable degree of genetic diversity in this part of the world. I report additional analysis using SNA methods contributing new controlled observations on the structuring of genetic diversity among these islanders. These SNA mappings are then compared with model-based network expectations derived from the geographic distances among the same populations. Previous studies found that genetic divergence among island Melanesian populations is organised by island, island size/topography, and position (coastal vs. inland), and that similarities observed correlate only weakly with an isolation-by-distance model. Using SNA methods, however, improves the resolution of among population comparison, and suggests that isolation by distance constrained by social networks together with position (coastal/inland) accounts for much of the population structuring observed. The multilocus data now available is also in accord with current thinking on the impact of major biogeographical transformations on prehistoric colonisation and post-settlement human interaction in Oceania.

Genetic Structure of Aedes aegypti in Australia and Vietnam Revealed by Microsatellite and Exon Primed Intron Crossing Markers Suggests Feasibility of Local Control Options

PubMed Central

ENDERSBY, N. M.; HOFFMANN, A. A.; WHITE, V. L.; LOWENSTEIN, S.; RITCHIE, S.; JOHNSON, P. H.; RAPLEY, L. P.; RYAN, P. A.; NAM, V. S.; YEN, N. T.; KITTIYAPONG, P.; WEEKS, A. R.

2009-01-01

The distribution of Aedes aegypti (L.) in Australia is currently restricted to northern Queensland, but it has been more extensive in the past. In this study, we evaluate the genetic structure of Ae. aegypti populations in Australia and Vietnam and consider genetic differentiation between mosquitoes from these areas and those from a population in Thailand. Six microsatellites and two exon primed intron crossing markers were used to assess isolation by distance across all populations and also within the Australian sample. Investigations of founder effects, amount of molecular variation between and within regions and comparison of FST values among Australian and Vietnamese populations were made to assess the scale of movement of Ae. aegypti. Genetic control methods are under development for mosquito vector populations including the dengue vector Ae. aegypti. The success of these control methods will depend on the population structure of the target species including population size and rates of movement among populations. Releases of modified mosquitoes could target local populations that show a high degree of isolation from surrounding populations, potentially allowing new variants to become established in one region with eventual dispersal to other regions. PMID:19769038

Characterisation of genetic structure of the Mayan population in Guatemala by autosomal STR analysis.

PubMed

Martinez-Gonzalez, L J; Alvarez-Cubero, M J; Saiz, M; Alvarez, J C; Martinez-Labarga, C; Lorente, J A

2016-09-01

Currently, the Guatemalan population comprises genetically isolated groups due to geographic, linguistic and cultural factors. For example, Mayan groups within the Guatemala population have preserved their own language, culture and religion. These practices have limited genetic admixture and have maintained the genetic identity of Mayan populations. This study is designed to define the genetic structure of the Mayan-Guatemalan groups Kaqchiquel, K'iche', Mam and Q'eqchi' through autosomal short tandem repeat (STR) polymorphisms and to analyse the genetic relationships between them and with other Mayan groups. Fifteen STR polymorphisms were analysed in 200 unrelated donors belonging to the Kaqchiquel (n = 50), K'iche' (n = 50), Mam (n = 50) and Q'eqchi' (n = 50) groups living in Guatemala. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between population groups. Within the Mayan population, the STRs D18S51 and FGA were the most informative markers and TH01 was the least informative. AMOVA and genetic distance analyses showed that the Guatemalan-Native American populations are highly similar to Mayan populations living in Mexico. The Mayan populations from Guatemala and other Native American groups display high genetic homogeneity. Genetic relationships between these groups are more affected by cultural and linguistic factors than geographical and local flow. This study represents one of the first steps in understanding Mayan-Guatemalan populations, the associations between their sub-populations and differences in gene diversity with other populations. This article also demonstrates that the Mestizo population shares most of its ancestral genetic components with the Guatemala Mayan populations.

Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia).

PubMed

Pannacciulli, Federica G; Maltagliati, Ferruccio; de Guttry, Christian; Achituv, Yair

2017-01-01

The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the 'isolation with migration' model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms.

Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia)

PubMed Central

Pannacciulli, Federica G.; de Guttry, Christian; Achituv, Yair

2017-01-01

The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the ‘isolation with migration’ model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms. PMID:28594840

Does the seed bank contribute to the build-up of a genetic extinction debt in the grassland perennial Campanula rotundifolia?

PubMed

Plue, Jan; Vandepitte, Katrien; Honnay, Olivier; Cousins, Sara A O

2017-09-01

Habitat fragmentation threatens global biodiversity. Many plant species persist in habitat fragments via persistent life cycle stages such as seed banks, generating a species extinction debt. Here, seed banks are hypothesized to cause a temporal delay in the expected loss of genetic variation, which can be referred to as a genetic extinction debt, as a possible mechanism behind species extinction debts. Fragmented grassland populations of Campanula rotundifolia were examined for evidence of a genetic extinction debt, investigating if the seed bank contributed to the extinction debt build-up. The genetic make-up of 15 above- and below-ground populations was analysed in relation to historical and current levels of habitat fragmentation, both separately and combined. Genetic diversity was highest in above-ground populations, though below-ground populations contained 8 % of unique alleles that were absent above-ground. Above-ground genetic diversity and composition were related to historical patch size and connectivity, but not current patch characteristics, suggesting the presence of a genetic extinction debt in the above-ground populations. No such relationships were found for the below-ground populations. Genetic diversity measures still showed a response to historical but not present landscape characteristics when combining genetic diversity of the above- and below-ground populations. The fragmented C. rotundifolia populations exhibited a genetic extinction debt. However, the role of the seed banks in the build-up of this extinction debt is probably small, since the limited, unique genetic diversity of the seed bank alone seems unable to counter the detrimental effects of habitat fragmentation on the population genetic structure of C. rotundifolia. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

AFLP Approach Reveals Variability in Phragmites australis: Implications for Its Die-Back and Evidence for Genotoxic Effects

PubMed Central

Coppi, Andrea; Lastrucci, Lorenzo; Cappelletti, David; Cerri, Martina; Ferranti, Francesco; Ferri, Valentina; Foggi, Bruno; Gigante, Daniela; Venanzoni, Roberto; Viciani, Daniele; Selvaggi, Roberta; Reale, Lara

2018-01-01

Phragmites australis is a subcosmopolitan species typical of wetlands being studied in Europe for its disappearance from natural stands, a phenomenon called reed die-back syndrome (RDBS). Although it is conjectured that low genetic variability contributes to RDBS, this aspect remains neglected to this day. Using a molecular fingerprinting approach and a sequence analysis of the trnT-trnL/rbcL-psaI regions of cpDNA, this study aimed to compare the genetic structure of stable vs. RDBS-affected P. australis stands from five wetlands of central Italy. Beforehand, in order to characterize the health condition of reed populations, the occurrence of the main macromorphological descriptors for RDBS was considered on 40 reed stands. Soil samples were also collected to examine the total content of heavy metals. The current study analyzed cpDNA in 19 samples and AFLP profiles in 381 samples to investigate the genetic structure of Phragmites populations. Based on the multinomial-Dirichlet model, an analysis of candidate loci under selective pressure was also performed. The relationships among AFLP data, RDBS descriptors and chemicals were evaluated with the use of Linear Mixed Models. The analysis of the cpDNA shows the occurrence of the haplotypes M (the most widespread), and K here recorded for the first time in Italy. Three new haplotypes were also described. The DNA fingerprinting analysis has produced a total of 322 loci (98% polymorphic) and shows the medium-to-high amount of genetic diversity. The significant genetic differentiation among wetlands (Fst = 0.337) suggests either low gene flow or small effective population size. Moreover, the low amount of outlier loci (only 5; l.5% of the total), seems to indicate the scarce occurrence of selective pressure upon the reed’s genome. Genetic diversity increased in relationship to the decrease in diameter and of flowering buds of the reed, two of the trends associated with the die-back. The current study rejects the hypothesis that genetic diversity massively contributed to RDBS. Moreover, significant relationships between genetic diversity and the total concentration of some heavy metals (Cr, Cu, and Zn) were highlighted, indicating possible genotoxic effects on P. australis. The current study represents a fact-finding background useful for the conservation of common reed. PMID:29632544

Genetic algorithm based fuzzy control of spacecraft autonomous rendezvous

NASA Technical Reports Server (NTRS)

Karr, C. L.; Freeman, L. M.; Meredith, D. L.

1990-01-01

The U.S. Bureau of Mines is currently investigating ways to combine the control capabilities of fuzzy logic with the learning capabilities of genetic algorithms. Fuzzy logic allows for the uncertainty inherent in most control problems to be incorporated into conventional expert systems. Although fuzzy logic based expert systems have been used successfully for controlling a number of physical systems, the selection of acceptable fuzzy membership functions has generally been a subjective decision. High performance fuzzy membership functions for a fuzzy logic controller that manipulates a mathematical model simulating the autonomous rendezvous of spacecraft are learned using a genetic algorithm, a search technique based on the mechanics of natural genetics. The membership functions learned by the genetic algorithm provide for a more efficient fuzzy logic controller than membership functions selected by the authors for the rendezvous problem. Thus, genetic algorithms are potentially an effective and structured approach for learning fuzzy membership functions.

Population-level genetic variation and climate change in a biodiversity hotspot

PubMed Central

2017-01-01

Introduction Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. Factors influencing the distribution of genetic variation Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant–insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. Regional priorities and examples A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. Conclusions, Solutions and Recommendations The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California’s plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species. PMID:28069633

Synthetic genetic polymers capable of heredity and evolution.

PubMed

Pinheiro, Vitor B; Taylor, Alexander I; Cozens, Christopher; Abramov, Mikhail; Renders, Marleen; Zhang, Su; Chaput, John C; Wengel, Jesper; Peak-Chew, Sew-Yeu; McLaughlin, Stephen H; Herdewijn, Piet; Holliger, Philipp

2012-04-20

Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.

The epigenetic landscape of aneuploidy: constitutional mosaicism leading the way?

PubMed

Davidsson, Josef

2014-02-01

The role of structural genetic changes in human disease has received substantial attention in recent decades, but surprisingly little is known about numerical chromosomal abnormalities, even though they have been recognized since the days of Boveri as partaking in different cellular pathophysiological processes such as cancer and genomic disorders. The current knowledge of the genetic and epigenetic consequences of aneuploidy is reviewed herein, with a special focus on using mosaic genetic syndromes to study the DNA methylation footprints and expressional effects associated with whole-chromosomal gains. Recent progress in understanding the debated role of aneuploidy as a driver or passenger in malignant transformation, as well as how the cell responds to and regulates excess genetic material in experimental settings, is also discussed in detail.

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

USGS Publications Warehouse

Meece, J.K.; Anderson, J.L.; Fisher, M.C.; Henk, D.A.; Sloss, Brian L.; Reed, K.D.

2011-01-01

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n = 112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and ??-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species. ?? 2011, American Society for Microbiology.

Population genetic structure of clinical and environmental isolates of Blastomyces dermatitidis based on 27 polymorphic microsatellite markers

USGS Publications Warehouse

Meece, Jennifer K.; Anderson, Jennifer L.; Fisher, Matthew C.; Henk, Daniel A.; Sloss, Brian L.; Reed, Kurt D.

2011-01-01

Blastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure of B. dermatitidis would improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates of B. dermatitidis. We developed 27 microsatellite markers and genotyped B. dermatitidis isolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designated B. dermatitidis includes a cryptic subspecies or perhaps a separate species.

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology

PubMed Central

Brudey, Karine; Driscoll, Jeffrey R; Rigouts, Leen; Prodinger, Wolfgang M; Gori, Andrea; Al-Hajoj, Sahal A; Allix, Caroline; Aristimuño, Liselotte; Arora, Jyoti; Baumanis, Viesturs; Binder, Lothar; Cafrune, Patricia; Cataldi, Angel; Cheong, Soonfatt; Diel, Roland; Ellermeier, Christopher; Evans, Jason T; Fauville-Dufaux, Maryse; Ferdinand, Séverine; de Viedma, Dario Garcia; Garzelli, Carlo; Gazzola, Lidia; Gomes, Harrison M; Guttierez, M Cristina; Hawkey, Peter M; van Helden, Paul D; Kadival, Gurujaj V; Kreiswirth, Barry N; Kremer, Kristin; Kubin, Milan; Kulkarni, Savita P; Liens, Benjamin; Lillebaek, Troels; Ly, Ho Minh; Martin, Carlos; Martin, Christian; Mokrousov, Igor; Narvskaïa, Olga; Ngeow, Yun Fong; Naumann, Ludmilla; Niemann, Stefan; Parwati, Ida; Rahim, Zeaur; Rasolofo-Razanamparany, Voahangy; Rasolonavalona, Tiana; Rossetti, M Lucia; Rüsch-Gerdes, Sabine; Sajduda, Anna; Samper, Sofia; Shemyakin, Igor G; Singh, Urvashi B; Somoskovi, Akos; Skuce, Robin A; van Soolingen, Dick; Streicher, Elisabeth M; Suffys, Philip N; Tortoli, Enrico; Tracevska, Tatjana; Vincent, Véronique; Victor, Tommie C; Warren, Robin M; Yap, Sook Fan; Zaman, Khadiza; Portaels, Françoise; Rastogi, Nalin; Sola, Christophe

2006-01-01

Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress. PMID:16519816

Population Genetics of Plasmodium vivax in Four High Malaria Endemic Areas in Thailand.

PubMed

Congpuong, Kanungnit; Ubalee, Ratawan

2017-10-01

Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.

Genetic Population Structure in the Antarctic Benthos: Insights from the Widespread Amphipod, Orchomenella franklini

PubMed Central

Baird, Helena Phoenix; Miller, Karen Joy; Stark, Jonathan Sean

2012-01-01

Currently there is very limited understanding of genetic population structure in the Antarctic benthos. We conducted one of the first studies of microsatellite variation in an Antarctic benthic invertebrate, using the ubiquitous amphipod Orchomenella franklini (Walker, 1903). Seven microsatellite loci were used to assess genetic structure on three spatial scales: sites (100 s of metres), locations (1–10 kilometres) and regions (1000 s of kilometres) sampled in East Antarctica at Casey and Davis stations. Considerable genetic diversity was revealed, which varied between the two regions and also between polluted and unpolluted sites. Genetic differentiation among all populations was highly significant (F ST = 0.086, R ST = 0.139, p<0.001) consistent with the brooding mode of development in O. franklini. Hierarchical AMOVA revealed that the majority of the genetic subdivision occurred across the largest geographical scale, with Nem≈1 suggesting insufficient gene flow to prevent independent evolution of the two regions, i.e., Casey and Davis are effectively isolated. Isolation by distance was detected at smaller scales and indicates that gene flow in O. franklini occurs primarily through stepping-stone dispersal. Three of the microsatellite loci showed signs of selection, providing evidence that localised adaptation may occur within the Antarctic benthos. These results provide insights into processes of speciation in Antarctic brooders, and will help inform the design of spatial management initiatives recently endorsed for the Antarctic benthos. PMID:22479613

Genome-wide characterization of genetic diversity and population structure in Secale

PubMed Central

2014-01-01

Background Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Results Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. Conclusions Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies. PMID:25085433

Molecular Population Genetic Structure in the Piping Plover

USGS Publications Warehouse

Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

2009-01-01

The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect differences in spatiotemporal stability of Piping Plover nesting habitat between regions.

"Genetically Engineered" Nanoelectronics

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Salazar-Lazaro, Carlos H.; Stoica, Adrian; Cwik, Thomas

2000-01-01

The quantum mechanical functionality of nanoelectronic devices such as resonant tunneling diodes (RTDs), quantum well infrared-photodetectors (QWIPs), quantum well lasers, and heterostructure field effect transistors (HFETs) is enabled by material variations on an atomic scale. The design and optimization of such devices requires a fundamental understanding of electron transport in such dimensions. The Nanoelectronic Modeling Tool (NEMO) is a general-purpose quantum device design and analysis tool based on a fundamental non-equilibrium electron transport theory. NEW was combined with a parallelized genetic algorithm package (PGAPACK) to evolve structural and material parameters to match a desired set of experimental data. A numerical experiment that evolves structural variations such as layer widths and doping concentrations is performed to analyze an experimental current voltage characteristic. The genetic algorithm is found to drive the NEMO simulation parameters close to the experimentally prescribed layer thicknesses and doping profiles. With such a quantitative agreement between theory and experiment design synthesis can be performed.

Ancient DNA reveals that the genetic structure of the northern Han Chinese was shaped prior to 3,000 years ago.

PubMed

Zhao, Yong-Bin; Zhang, Ye; Zhang, Quan-Chao; Li, Hong-Jie; Cui, Ying-Qiu; Xu, Zhi; Jin, Li; Zhou, Hui; Zhu, Hong

2015-01-01

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.

Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

PubMed Central

Zhang, Quan-Chao; Li, Hong-Jie; Cui, Ying-Qiu; Xu, Zhi; Jin, Li; Zhou, Hui; Zhu, Hong

2015-01-01

The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area. PMID:25938511

Development of a Genetic Algorithm to Automate Clustering of a Dependency Structure Matrix

NASA Technical Reports Server (NTRS)

Rogers, James L.; Korte, John J.; Bilardo, Vincent J.

2006-01-01

Much technology assessment and organization design data exists in Microsoft Excel spreadsheets. Tools are needed to put this data into a form that can be used by design managers to make design decisions. One need is to cluster data that is highly coupled. Tools such as the Dependency Structure Matrix (DSM) and a Genetic Algorithm (GA) can be of great benefit. However, no tool currently combines the DSM and a GA to solve the clustering problem. This paper describes a new software tool that interfaces a GA written as an Excel macro with a DSM in spreadsheet format. The results of several test cases are included to demonstrate how well this new tool works.

The Genetics of Non-conventional Wine Yeasts: Current Knowledge and Future Challenges.

PubMed

Masneuf-Pomarede, Isabelle; Bely, Marina; Marullo, Philippe; Albertin, Warren

2015-01-01

Saccharomyces cerevisiae is by far the most widely used yeast in oenology. However, during the last decade, several other yeasts species has been purposed for winemaking as they could positively impact wine quality. Some of these non-conventional yeasts (Torulaspora delbrueckii, Metschnikowia pulcherrima, Pichia kluyveri, Lachancea thermotolerans, etc.) are now proposed as starters culture for winemakers in mixed fermentation with S. cerevisiae, and several others are the subject of various studies (Hanseniaspora uvarum, Starmerella bacillaris, etc.). Along with their biotechnological use, the knowledge of these non-conventional yeasts greatly increased these last 10 years. The aim of this review is to describe the last updates and the current state-of-art of the genetics of non-conventional yeasts (including S. uvarum, T. delbrueckii, S. bacillaris, etc.). We describe how genomics and genetics tools provide new data into the population structure and biodiversity of non-conventional yeasts in winemaking environments. Future challenges will lie on the development of selection programs and/or genetic improvement of these non-conventional species. We discuss how genetics, genomics and the advances in next-generation sequencing will help the wine industry to develop the biotechnological use of non-conventional yeasts to improve the quality and differentiation of wines.

Structure and function of the homeotic gene complex (HOM-C) in the beetle, Tribolium castaneum

NASA Technical Reports Server (NTRS)

Beeman, R. W.; Stuart, J. J.; Brown, S. J.; Denell, R. E.; Spooner, B. S. (Principal Investigator)

1993-01-01

The powerful combination of genetic, developmental and molecular approaches possible with the fruit fly, Drosophila melanogaster, has led to a profound understanding of the genetic control of early developmental events. However, Drosophila is a highly specialized long germ insect, and the mechanisms controlling its early development may not be typical of insects or Arthropods in general. The beetle, Tribolium castaneum, offers a similar opportunity to integrate high resolution genetic analysis with the developmental/molecular approaches currently used in other organisms. Early results document significant differences between insect orders in the functions of genes responsible for establishing developmental commitments.

Structure and function of the homeotic gene complex (HOM-C) in the beetle, Tribolium castaneum.

PubMed

Beeman, R W; Stuart, J J; Brown, S J; Denell, R E

1993-07-01

The powerful combination of genetic, developmental and molecular approaches possible with the fruit fly, Drosophila melanogaster, has led to a profound understanding of the genetic control of early developmental events. However, Drosophila is a highly specialized long germ insect, and the mechanisms controlling its early development may not be typical of insects or Arthropods in general. The beetle, Tribolium castaneum, offers a similar opportunity to integrate high resolution genetic analysis with the developmental/molecular approaches currently used in other organisms. Early results document significant differences between insect orders in the functions of genes responsible for establishing developmental commitments.

Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis

PubMed Central

Zhao, Wei; Wang, Xiao-Ru

2013-01-01

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species’ range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China. PMID:23840668

Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis.

PubMed

Wang, Baosheng; Mao, Jian-Feng; Zhao, Wei; Wang, Xiao-Ru

2013-01-01

Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.

Genetic perspectives on northern population cycles: bridging the gap between theory and empirical studies.

PubMed

Norén, Karin; Angerbjörn, Anders

2014-05-01

Many key species in northern ecosystems are characterised by high-amplitude cyclic population demography. In 1924, Charles Elton described the ecology and evolution of cyclic populations in a classic paper and, since then, a major focus has been the underlying causes of population cycles. Elton hypothesised that fluctuations reduced population genetic variation and influenced the direction of selection pressures. In concordance with Elton, present theories concern the direct consequences of population cycles for genetic structure due to the processes of genetic drift and selection, but also include feedback models of genetic composition on population dynamics. Most of these theories gained mathematical support during the 1970s and onwards, but due to methodological drawbacks, difficulties in long-term sampling and a complex interplay between microevolutionary processes, clear empirical data allowing the testing of these predictions are still scarce. Current genetic tools allow for estimates of genetic variation and identification of adaptive genomic regions, making this an ideal time to revisit this subject. Herein, we attempt to contribute towards a consensus regarding the enigma described by Elton almost 90 years ago. We present nine predictions covering the direct and genetic feedback consequences of population cycles on genetic variation and population structure, and review the empirical evidence. Generally, empirical support for the predictions was low and scattered, with obvious gaps in the understanding of basic population processes. We conclude that genetic variation in northern cyclic populations generally is high and that the geographic distribution and amount of diversity are usually suggested to be determined by various forms of context- and density-dependent dispersal exceeding the impact of genetic drift. Furthermore, we found few clear signatures of selection determining genetic composition in cyclic populations. Dispersal is assumed to have a strong impact on genetic structuring and we suggest that the signatures of other microevolutionary processes such as genetic drift and selection are weaker and have been over-shadowed by density-dependent dispersal. We emphasise that basic biological and demographical questions still need to be answered and stress the importance of extensive sampling, appropriate choice of tools and the value of standardised protocols. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

Pedigree analysis in the Austrian Noriker draught horse: genetic diversity and the impact of breeding for coat colour on population structure.

PubMed

Druml, T; Baumung, R; Sölkner, J

2009-10-01

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average co-ancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.

Loss of Genetic Diversity Means Loss of Geological Information: The Endangered Japanese Crayfish Exhibits Remarkable Historical Footprints

PubMed Central

Koizumi, Itsuro; Usio, Nisikawa; Kawai, Tadashi; Azuma, Noriko; Masuda, Ryuichi

2012-01-01

Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall F ST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events. PMID:22470505

Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes.

PubMed

Zinck, John W R; Rajora, Om P

2016-03-02

Knowledge of the historical distribution and postglacial phylogeography and evolution of a species is important to better understand its current distribution and population structure and potential fate in the future, especially under climate change conditions, and conservation of its genetic resources. We have addressed this issue in a wide-ranging and heavily exploited keystone forest tree species of eastern North America, eastern white pine (Pinus strobus). We examined the range-wide population genetic structure, tested various hypothetical population history and evolutionary scenarios and inferred the location of glacial refugium and post-glacial recolonization routes. Our hypothesis was that eastern white pine survived in a single glacial refugium and expanded through multiple post-glacial recolonization routes. We studied the range-wide genetic diversity and population structure of 33 eastern white pine populations using 12 nuclear and 3 chloroplast microsatellite DNA markers. We used Approximate Bayesian Computation approach to test various evolutionary scenarios. We observed high levels of genetic diversity, and significant genetic differentiation (F ST = 0.104) and population structure among eastern white pine populations across its range. A south to north trend of declining genetic diversity existed, consistent with repeated founder effects during post-glaciation migration northwards. We observed broad consensus from nuclear and chloroplast genetic markers supporting the presence of two main post-glacial recolonization routes that originated from a single southern refugium in the mid-Atlantic plain. One route gave rise to populations at the western margin of the species' range in Minnesota and western Ontario. The second route gave rise to central-eastern populations, which branched into two subgroups: central and eastern. We observed minimal sharing of chloroplast haplotypes between recolonization routes but there was evidence of admixture between the western and west-central populations. Our study reveals a single southern refugium, two recolonization routes and three genetically distinguishable lineages in eastern white pine that we suggest to be treated as separate Evolutionarily Significant Units. Like many wide-ranging North American species, eastern white pine retains the genetic signatures of post-glacial recolonization and evolution, and its contemporary population genetic structure reflects not just the modern distribution and effects of heavy exploitation but also routes northward from its glacial refugium.

Adaptive genetic potential of coniferous forest tree species under climate change: implications for sustainable forest management

NASA Astrophysics Data System (ADS)

Mihai, Georgeta; Birsan, Marius-Victor; Teodosiu, Maria; Dumitrescu, Alexandru; Daia, Mihai; Mirancea, Ionel; Ivanov, Paula; Alin, Alexandru

2017-04-01

Mountain ecosystems are extremely vulnerable to climate change. The real potential for adaptation depends upon the existence of a wide genetic diversity in trees populations, upon the adaptive genetic variation, respectively. Genetic diversity offers the guarantee that forest species can survive, adapt and evolve under the influence of changing environmental conditions. The aim of this study is to evaluate the genetic diversity and adaptive genetic potential of two local species - Norway spruce and European silver fir - in the context of regional climate change. Based on data from a long-term provenance experiments network and climate variables spanning over more than 50 years, we have investigated the impact of climatic factors on growth performance and adaptation of tree species. Our results indicate that climatic and geographic factors significantly affect forest site productivity. Mean annual temperature and annual precipitation amount were found to be statistically significant explanatory variables. Combining the additive genetic model with the analysis of nuclear markers we obtained different images of the genetic structure of tree populations. As genetic indicators we used: gene frequencies, genetic diversity, genetic differentiation, genetic variance, plasticity. Spatial genetic analyses have allowed identifying the genetic centers holding high genetic diversity which will be valuable sources of gene able to buffer the negative effects of future climate change. Correlations between the marginal populations and in the optimal vegetation, between the level of genetic diversity and ecosystem stability, will allow the assessment of future risks arising from current genetic structure. Therefore, the strategies for sustainable forest management have to rely on the adaptive genetic variation and local adaptation of the valuable genetic resources. This work was realized within the framework of the project GENCLIM (Evaluating the adaptive potential of the main coniferous species for a sustainable forest management in the context of climate change), financed by the Executive Agency for Higher Education, Research, Development and Innovation Funding, grant number PN-II-PC-PCCA-2013-4-0695.

Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea.

PubMed

De Groote, Annelies; Hauquier, Freija; Vanreusel, Ann; Derycke, Sofie

2017-07-01

There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic. Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (Φ ST  = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow. The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

High genetic structure and low mitochondrial diversity in bottlenose dolphins of the Archipelago of Bocas del Toro, Panama: A population at risk?

PubMed Central

Tezanos-Pinto, Gabriela; Islas-Villanueva, Valentina; Correa-Cárdenas, Camilo A.

2017-01-01

The current conservation status of the bottlenose dolphin (Tursiops truncatus) under the IUCN is ‘least concern’. However, in the Caribbean, small and localized populations of the ‘inshore form’ may be at higher risk of extinction than the ‘worldwide distributed form’ due to a combination of factors including small population size, high site fidelity, genetic isolation, and range overlap with human activities. Here, we study the population genetic structure of bottlenose dolphins from the Archipelago of Bocas del Toro in Panama. This is a small population characterized by high site fidelity and is currently heavily-impacted by the local dolphin-watching industry. We collected skin tissue samples from 25 dolphins to study the genetic diversity and structure of this population. We amplified a portion of the mitochondrial Control Region (mtDNA-CR) and nine microsatellite loci. The mtDNA-CR analyses revealed that dolphins in Bocas del Toro belong to the ‘inshore form’, grouped with the Bahamas-Colombia-Cuba-Mexico population unit. They also possess a unique haplotype new for the Caribbean. The microsatellite data indicated that the Bocas del Toro dolphin population is highly structured, likely due to restricted movement patterns. Previous abundance estimates obtained with mark-recapture methods reported a small population of 80 dolphins (95% CI = 72–87), which is similar to the contemporary effective population size estimated in this study (Ne = 73 individuals; CI = 18.0 - ∞; 0.05). The combination of small population size, high degree of genetic isolation, and intense daily interactions with dolphin-watching boats puts the Bocas del Toro dolphin to at high risk of extinction. Despite national guidelines to regulate the dolphin-watching industry in Bocas del Toro and ongoing educational programs for tour operators, only in 2012 seven animals have died due to boat collisions. Our results suggest that the conservation status of bottlenose dolphins in Bocas del Toro should be elevated to ‘endangered’ at the national level, as a precautionary measure while population and viability estimates are conducted. PMID:29236757

Global Genetics and Invasion History of the Potato Powdery Scab Pathogen, Spongospora subterranea f.sp. subterranea

PubMed Central

Gau, Rebecca D.; Merz, Ueli; Falloon, Richard E.; Brunner, Patrick C.

2013-01-01

Spongospora subterranea f. sp. subterranea (Sss) causes two diseases on potato (Solanum tuberosum), lesions on tubers and galls on roots, which are economically important worldwide. Knowledge of global genetic diversity and population structure of pathogens is essential for disease management including resistance breeding. A combination of microsatellite and DNA sequence data was used to investigate the structure and invasion history of Sss. South American populations (four countries, 132 samples) were consistently more diverse than those from all other regions (15 countries, 566 samples), in agreement with the hypothesis that Sss originated in South America where potato was domesticated. A substantial genetic differenciation was found between root and tuber-derived samples from South America. Estimates of past and recent gene flow suggested that Sss was probably introduced from South America into Europe. Subsequently, Europe is likely to have been the recent source of migrants of the pathogen, acting as a “bridgehead” for further global dissemination. Quarantine measures must continue to be focussed on maintaining low global genetic diversity and avoiding exchange of genetic material between the native and introduced regions. Nevertheless, the current low global genetic diversity of Sss allows potato breeders to select for resistance, which is likely to be durable. PMID:23840791

Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA.

PubMed

Putra, I Nyoman Giri; Syamsuni, Yuliana Fitri; Subhan, Beginer; Pharmawati, Made; Madduppa, Hawis

2018-01-01

The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on D A distance and Bayesian clustering revealed three major clusters of E. acoroides . Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides .

Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA

PubMed Central

Putra, I Nyoman Giri; Syamsuni, Yuliana Fitri; Subhan, Beginer; Pharmawati, Made

2018-01-01

The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides. PMID:29576933

Geographic structure of European anchovy: A nuclear-DNA study

NASA Astrophysics Data System (ADS)

Bouchenak-Khelladi, Yanis; Durand, Jean-Dominique; Magoulas, Antonios; Borsa, Philippe

2008-08-01

Atlantic-Mediterranean anchovies were genetically characterized at two polymorphic nuclear loci (intron 6 of two creatine-kinase genes) and compared to reference Engraulis albidus and E. encrasicolus samples from the northern Western Mediterranean to provide new insights into their geographic structure. Northeastern Atlantic anchovy, represented by one sample from the Canary archipelago and one sample from the Alboran Sea, were genetically distinct from Mediterranean E. encrasicolus (Weir and Cockerham's ^θ = 0.027-0.311), indicating geographic isolation from either side of the Almería-Oran oceanographic front. Generally smaller genetic differences were evident among anchovy populations from different sub-basins in the Mediterranean ( ^θ = - 0.019-0.116), the genetic differences between Black Sea and Ionian Sea/Aegean Sea anchovies being the strongest ( ^θ = 0.002-0.116). There was no evidence of the presence of E. albidus in our samples outside Camargue (northern shore of the Western Mediterranean). However, a sample from the southern Western Mediterranean appeared to be genetically intermediate between E. albidus and Mediterranean E. encrasicolus, indicating possible hybridization. Anchovy from the Benguela current system off southern Africa possessed allele frequencies characteristic of E. albidus at one locus and Northeastern Atlantic anchovy at the other locus, suggesting past introgression.

Oceanography promotes self-recruitment in a planktonic larval disperser.

PubMed

Teske, Peter R; Sandoval-Castillo, Jonathan; van Sebille, Erik; Waters, Jonathan; Beheregaray, Luciano B

2016-09-30

The application of high-resolution genetic data has revealed that oceanographic connectivity in marine species with planktonic larvae can be surprisingly limited, even in the absence of major barriers to dispersal. Australia's southern coast represents a particularly interesting system for studying planktonic larval dispersal, as the hydrodynamic regime of the wide continental shelf has potential to facilitate onshore retention of larvae. We used a seascape genetics approach (the joint analysis of genetic data and oceanographic connectivity simulations) to assess population genetic structure and self-recruitment in a broadcast-spawning marine gastropod that exists as a single meta-population throughout its temperate Australian range. Levels of self-recruitment were surprisingly high, and oceanographic connectivity simulations indicated that this was a result of low-velocity nearshore currents promoting the retention of planktonic larvae in the vicinity of natal sites. Even though the model applied here is comparatively simple and assumes that the dispersal of planktonic larvae is passive, we find that oceanography alone is sufficient to explain the high levels of genetic structure and self-recruitment. Our study contributes to growing evidence that sophisticated larval behaviour is not a prerequisite for larval retention in the nearshore region in planktonic-developing species.

A Mesoamerican origin of cherimoya (Annona cherimola Mill.): Implications for the conservation of plant genetic resources.

PubMed

Larranaga, N; Albertazzi, F J; Fontecha, G; Palmieri, M; Rainer, H; van Zonneveld, M; Hormaza, J I

2017-08-01

Knowledge on the structure and distribution of genetic diversity is a key aspect to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1,765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the Neotropics and used as a food source by pre-Columbian cultures, was collected from six different countries across the American continent and amplified with nine highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops. © 2017 John Wiley & Sons Ltd.

Population-level genetic variation and climate change in a biodiversity hotspot.

PubMed

Schierenbeck, Kristina A

2017-01-01

Estimated future climate scenarios can be used to predict where hotspots of endemism may occur over the next century, but life history, ecological and genetic traits will be important in informing the varying responses within myriad taxa. Essential to predicting the consequences of climate change to individual species will be an understanding of the factors that drive genetic structure within and among populations. Here, I review the factors that influence the genetic structure of plant species in California, but are applicable elsewhere; existing levels of genetic variation, life history and ecological characteristics will affect the ability of an individual taxon to persist in the presence of anthropogenic change. Persistence in the face of climate change is likely determined by life history characteristics: dispersal ability, generation time, reproductive ability, degree of habitat specialization, plant-insect interactions, existing genetic diversity and availability of habitat or migration corridors. Existing levels of genetic diversity in plant populations vary based on a number of evolutionary scenarios that include endemism, expansion since the last glacial maximum, breeding system and current range sizes. A number of well-documented examples are provided from the California Floristic Province. Some predictions can be made for the responses of plant taxa to rapid environmental changes based on geographic position, evolutionary history, existing genetic variation, and ecological amplitude. The prediction of how species will respond to climate change will require a synthesis drawing from population genetics, geography, palaeontology and ecology. The important integration of the historical factors that have shaped the distribution and existing genetic structure of California's plant taxa will enable us to predict and prioritize the conservation of species and areas most likely to be impacted by rapid climate change, human disturbance and invasive species. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic Analysis of Termite Colonies in Wisconsin.

PubMed

Arango, R A; Marschalek, D A; Green, F; Raffa, K F; Berres, M E

2015-06-01

The objective of this study was to document current areas of subterranean termite activity in Wisconsin and to evaluate genetic characteristics of these northern, peripheral colonies. Here, amplified fragment-length polymorphism was used to characterize levels of inbreeding, expected heterozygosity, and percent polymorphism within colonies as well as genetic structure among populations sampled. Genetic analysis revealed two species of termites occur in Wisconsin, Reticulitermes flavipes (Kollar) and Reticulitermes tibialis Banks, both found in the southern half of the state. Colonies of both species in Wisconsin are thought to represent the northern boundary of their current distributions. Measurements of within colony genetic variation showed the proportion of polymorphic loci to be between 52.9-63.9% and expected heterozygosity to range from 0.122-0.189. Consistent with geographical isolation, strong intercolony genetic differences were observed, with over 50% of FST values above 0.25 and the remaining showing moderate levels of genetic differentiation. Combined with low levels of inbreeding in most collection locations (FIS 0.042-0.123), we hypothesize termites were introduced numerous times in the state, likely by anthropogenic means. We discuss the potential effects of these genetic characteristics on successful colony establishment of termites along the northern boundary compared with termites in the core region of their distribution. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

The genetics of obstructive sleep apnoea.

PubMed

Mukherjee, Sutapa; Saxena, Richa; Palmer, Lyle J

2018-01-01

Obstructive sleep apnoea (OSA) is a common chronic disease and is associated with high social and economic costs. OSA is heritable, and there is evidence of both direct genetic contributions to OSA susceptibility and indirect contributions via 'intermediate' phenotypes such as obesity, craniofacial structure, neurological control of upper airway muscles and of sleep and circadian rhythm. Investigation of the genetics of OSA is an important research area and may lead to improved understanding of disease aetiology, pathogenesis, adverse health consequences and new preventive strategies and treatments. Genetic studies of OSA have lagged behind other chronic diseases; however recent gene discovery efforts have been successful in finding genetic loci contributing to OSA-associated intermediate phenotypes. Nevertheless, many of the seminal questions relating to the genetic epidemiology of OSA and associated factors remain unanswered. This paper reviews the current state of knowledge of the genetics of OSA, with a focus on genomic approaches to understanding sleep apnoea. © 2017 Asian Pacific Society of Respirology.

Calculating expected DNA remnants from ancient founding events in human population genetics

PubMed Central

Stacey, Andrew; Sheffield, Nathan C; Crandall, Keith A

2008-01-01

Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible. PMID:18928554

Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA.

PubMed

Hu, Yibo; Guo, Yu; Qi, Dunwu; Zhan, Xiangjiang; Wu, Hua; Bruford, Michael W; Wei, Fuwen

2011-07-01

Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence-based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai-Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above-mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite-based Bayesian clustering clearly identified three groups (Qionglai-Liangshan, Xiaoxiangling and Gaoligong-Tibet). A significant isolation-by-distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large-scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai-Tibetan Plateau, subspecies classification and conservation of red pandas are discussed. © 2011 Blackwell Publishing Ltd.

Inferring Genetic Variation and Demographic History of Michelia yunnanensis Franch. (Magnoliaceae) from Chloroplast DNA Sequences and Microsatellite Markers

PubMed Central

Zhang, Xue; Shen, Shikang; Wu, Fuqin; Wang, Yuehua

2017-01-01

Michelia yunnanensis Franch., is a traditional ornamental, aromatic, and medicinal shrub that endemic to Yunnan Province in southwest China. Although the species has a large distribution pattern and is abundant in Yunnan Province, the populations are dramatically declining because of overexploitation and habitat destruction. Studies on the genetic variation and demography of endemic species are necessary to develop effective conservation and management strategies. To generate such knowledge, we used 3 pairs of universal cpDNA markers and 10 pairs of microsatellite markers to assess the genetic diversity, genetic structure, and demographic history of 7 M. yunnanensis populations. We calculated a total of 88 alleles for 10 polymorphic loci and 10 haplotypes for a combined 2,089 bp of cpDNA. M. yunnanensis populations showed high genetic diversity (Ho = 0.551 for nuclear markers and Hd = 0.471 for cpDNA markers) and low genetic differentiation (FST = 0.058). Geographical structure was not found among M. yunnanensis populations. Genetic distance and geographic distance were not correlated (P > 0.05), which indicated that geographic isolation is not the primary cause of the low genetic differentiation of M. yunnanensis. Additionally, M. yunnanensis populations contracted ~20,000–30,000 years ago, and no recent expansion occurred in current populations. Results indicated that the high genetic diversity of the species and within its populations holds promise for effective genetic resource management and sustainable utilization. Thus, we suggest that the conservation and management of M. yunnanensis should address exotic overexploitation and habitat destruction. PMID:28484472

Pathway-based discovery of genetic interactions in breast cancer

PubMed Central

Xu, Zack Z.; Boone, Charles; Lange, Carol A.

2017-01-01

Breast cancer is the second largest cause of cancer death among U.S. women and the leading cause of cancer death among women worldwide. Genome-wide association studies (GWAS) have identified several genetic variants associated with susceptibility to breast cancer, but these still explain less than half of the estimated genetic contribution to the disease. Combinations of variants (i.e. genetic interactions) may play an important role in breast cancer susceptibility. However, due to a lack of statistical power, the current tests for genetic interactions from GWAS data mainly leverage prior knowledge to focus on small sets of genes or SNPs that are known to have an association with breast cancer. Thus, many genetic interactions, particularly among novel variants, remain understudied. Reverse-genetic interaction screens in model organisms have shown that genetic interactions frequently cluster into highly structured motifs, where members of the same pathway share similar patterns of genetic interactions. Based on this key observation, we recently developed a method called BridGE to search for such structured motifs in genetic networks derived from GWAS studies and identify pathway-level genetic interactions in human populations. We applied BridGE to six independent breast cancer cohorts and identified significant pathway-level interactions in five cohorts. Joint analysis across all five cohorts revealed a high confidence consensus set of genetic interactions with support in multiple cohorts. The discovered interactions implicated the glutathione conjugation, vitamin D receptor, purine metabolism, mitotic prometaphase, and steroid hormone biosynthesis pathways as major modifiers of breast cancer risk. Notably, while many of the pathways identified by BridGE show clear relevance to breast cancer, variants in these pathways had not been previously discovered by traditional single variant association tests, or single pathway enrichment analysis that does not consider SNP-SNP interactions. PMID:28957314

FDA toxicity databases and real-time data entry.

PubMed

Arvidson, Kirk B

2008-11-15

Structure-searchable electronic databases are valuable new tools that are assisting the FDA in its mission to promptly and efficiently review incoming submissions for regulatory approval of new food additives and food contact substances. The Center for Food Safety and Applied Nutrition's Office of Food Additive Safety (CFSAN/OFAS), in collaboration with Leadscope, Inc., is consolidating genetic toxicity data submitted in food additive petitions from the 1960s to the present day. The Center for Drug Evaluation and Research, Office of Pharmaceutical Science's Informatics and Computational Safety Analysis Staff (CDER/OPS/ICSAS) is separately gathering similar information from their submissions. Presently, these data are distributed in various locations such as paper files, microfiche, and non-standardized toxicology memoranda. The organization of the data into a consistent, searchable format will reduce paperwork, expedite the toxicology review process, and provide valuable information to industry that is currently available only to the FDA. Furthermore, by combining chemical structures with genetic toxicity information, biologically active moieties can be identified and used to develop quantitative structure-activity relationship (QSAR) modeling and testing guidelines. Additionally, chemicals devoid of toxicity data can be compared to known structures, allowing for improved safety review through the identification and analysis of structural analogs. Four database frameworks have been created: bacterial mutagenesis, in vitro chromosome aberration, in vitro mammalian mutagenesis, and in vivo micronucleus. Controlled vocabularies for these databases have been established. The four separate genetic toxicity databases are compiled into a single, structurally-searchable database for easy accessibility of the toxicity information. Beyond the genetic toxicity databases described here, additional databases for subchronic, chronic, and teratogenicity studies have been prepared.

Cityscape genetics: structural vs. functional connectivity of an urban lizard population.

PubMed

Beninde, Joscha; Feldmeier, Stephan; Werner, Maike; Peroverde, Daniel; Schulte, Ulrich; Hochkirch, Axel; Veith, Michael

2016-10-01

Functional connectivity is essential for the long-term persistence of populations. However, many studies assess connectivity with a focus on structural connectivity only. Cityscapes, namely urban landscapes, are particularly dynamic and include numerous potential anthropogenic barriers to animal movements, such as roads, traffic or buildings. To assess and compare structural connectivity of habitats and functional connectivity of gene flow of an urban lizard, we here combined species distribution models (SDMs) with an individual-based landscape genetic optimization procedure. The most important environmental factors of the SDMs are structural diversity and substrate type, with high and medium levels of structural diversity as well as open and rocky/gravel substrates contributing most to structural connectivity. By contrast, water cover was the best model of all environmental factors following landscape genetic optimization. The river is thus a major barrier to gene flow, while of the typical anthropogenic factors only buildings showed an effect. Nonetheless, using SDMs as a basis for landscape genetic optimization provided the highest ranked model for functional connectivity. Optimizing SDMs in this way can provide a sound basis for models of gene flow of the cityscape, and elsewhere, while presence-only and presence-absence modelling approaches showed differences in performance. Additionally, interpretation of results based on SDM factor importance can be misleading, dictating more thorough analyses following optimization of SDMs. Such approaches can be adopted for management strategies, for example aiming to connect native common wall lizard populations or disconnect them from non-native introduced populations, which are currently spreading in many cities in Central Europe. © 2016 John Wiley & Sons Ltd.

Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica

PubMed Central

Kimura, Megumi K.; Uchiyama, Kentaro; Nakao, Katsuhiro; Moriguchi, Yoshinari; San Jose-Maldia, Lerma; Tsumura, Yoshihiko

2014-01-01

Background and Aims Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM). Methods Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis. Key Results STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia. Conclusions The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis. PMID:25355521

Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract

NASA Astrophysics Data System (ADS)

Debiasse, M. B.; Richards, V. P.; Shivji, M. S.

2010-03-01

The genetic population structure of the common branching vase sponge, Callyspongia vaginalis, was determined along the entire length (465 km) of the Florida reef system from Palm Beach to the Dry Tortugas based on sequences of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Populations of C. vaginalis were highly structured (overall ΦST = 0.33), in some cases over distances as small as tens of kilometers. However, nonsignificant pairwise ΦST values were also found between a few relatively distant sampling sites suggesting that some long distance larval dispersal may occur via ocean currents or transport in sponge fragments along continuous, shallow coastlines. Indeed, sufficient gene flow appears to occur along the Florida reef tract to obscure a signal of isolation by distance, but not to homogenize COI haplotype frequencies. The strong genetic differentiation among most of the sampling locations suggests that recruitment in this species is largely local source-driven, pointing to the importance of further elucidating general connectivity patterns along the Florida reef tract to guide the spatial scale of management efforts.

Rivers influence the population genetic structure of bonobos (Pan paniscus).

PubMed

Eriksson, J; Hohmann, G; Boesch, C; Vigilant, L

2004-11-01

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.

Genetic Divergence among Regions Containing the Vulnerable Great Desert Skink (Liopholis kintorei) in the Australian Arid Zone

PubMed Central

Dennison, Siobhan; McAlpin, Steve; Chapple, David G.; Stow, Adam J.

2015-01-01

Knowledge of genetic structure and patterns of connectivity is valuable for implementation of effective conservation management. The arid zone of Australia contains a rich biodiversity, however this has come under threat due to activities such as altered fire regimes, grazing and the introduction of feral herbivores and predators. Suitable habitats for many species can be separated by vast distances, and despite an apparent lack of current geographical barriers to dispersal, habitat specialisation, which is exhibited by many desert species, may limit connectivity throughout this expansive region. We characterised the genetic structure and differentiation of the great desert skink (Liopholis kintorei), which has a patchy, but widespread distribution in the western region of the Australian arid zone. As a species of cultural importance to local Aboriginal groups and nationally listed as Vulnerable, it is a conservation priority for numerous land managers in central Australia. Analysis of mitochondrial ND4 sequence data and ten nuclear microsatellite loci across six sampling localities through the distribution of L. kintorei revealed considerable differentiation among sites, with mitochondrial FST and microsatellite F′ST ranging from 0.047-0.938 and 0.257-0.440, respectively. The extent of differentiation suggests three main regions that should be managed separately, in particular the southeastern locality of Uluru. Current genetic delineation of these regions should be maintained if future intervention such as translocation or captive breeding is to be undertaken. PMID:26061141

A review on neuroimaging studies of genetic and environmental influences on early brain development.

PubMed

Gao, Wei; Grewen, Karen; Knickmeyer, Rebecca C; Qiu, Anqi; Salzwedel, Andrew; Lin, Weili; Gilmore, John H

2018-04-16

The past decades witnessed a surge of interest in neuroimaging study of normal and abnormal early brain development. Structural and functional studies of normal early brain development revealed massive structural maturation as well as sequential, coordinated, and hierarchical emergence of functional networks during the infancy period, providing a great foundation for the investigation of abnormal early brain development mechanisms. Indeed, studies of altered brain development associated with either genetic or environmental risks emerged and thrived. In this paper, we will review selected studies of genetic and environmental risks that have been relatively more extensively investigated-familial risks, candidate risk genes, and genome-wide association studies (GWAS) on the genetic side; maternal mood disorders and prenatal drug exposures on the environmental side. Emerging studies on environment-gene interactions will also be reviewed. Our goal was not to perform an exhaustive review of all studies in the field but to leverage some representative ones to summarize the current state, point out potential limitations, and elicit discussions on important future directions. Copyright © 2018 Elsevier Inc. All rights reserved.

The Vredefort Dome: Review of geology and deformation phenomena and status report on current knowledge and remaining problematics (five years after the cryptoexplosion workshop)

NASA Technical Reports Server (NTRS)

Reimold, W. U.

1992-01-01

The Vredefort structure located in the center of the Witwatersrand basin in South Africa and the Sudbury structure in Canada are widely considered the two oldest and largest impact structures still evident on Earth. Both structures are very similar in a number of geological aspects (e.g., association with major economic ore deposits, similar ages of ca. 2 Ga, abundant pseudotachylite as well as shatter cone occurrences, overturned collar). However, whereas the geological community generally accepts an impact origin for the Sudbury structure, a number of researchers are still reluctant to accept this for the Vredefort Dome. Therefore, the aim of this review is to present new data, highlight the most obvious shortcomings in the current database, and to summarize the major arguments in the genetic controversy.

Up and down the blind alley: population divergence with scant gene flow in an endangered tropical lineage of Andean palms (Ceroxylon quindiuense clade: Ceroxyloideae).

PubMed

Sanín, María José; Zapata, Patricia; Pintaud, Jean-Christophe; Galeano, Gloria; Bohórquez, Adriana; Tohme, Joseph; Hansen, Michael Møller

2017-02-10

Given the geographical complexity of the Andes, species distributions hold interesting information regarding the history of isolation and gene flow across geographic barriers and ecological gradients. Moreover, current threats to the region’s enormous plant diversity pose an additional challenge to the understanding of these patterns. We explored the geographic structure of genetic diversity within the Ceroxylon quindiuense species complex (wax palms) at a regional scale, using a model-based approach to disentangle the historical mechanisms by which these species have dispersed over a range encompassing 17° of latitude in the tropical Andes. A total of 10 microsatellite loci were cross-amplified in 8 populations of the 3 species comprising the C. quindiuense complex. Analyses performed include estimates of molecular diversity and genetic structure, testing for genetic bottlenecks and an evaluation of the colonization scenario under approximate Bayesian computation. We showed that there was a geographical diversity gradient reflecting the orogenetic pattern of the northern Andes and its end at the cordilleras facing the Caribbean Sea. A general pattern of diversity suggests that the cordilleras of Colombia have served as historical recipients of gene flow occurring only scantly along the northern Andes. We provided evidence of important isolation between the largest populations of this complex, suggesting that both historical constraints to dispersal but also current anthropogenic effects might explain the high levels of population structuring. We provide a list of advisable measures for conservation stakeholders.

Diversity and structure of landraces of Agave grown for spirits under traditional agriculture: A comparison with wild populations of A. angustifolia (Agavaceae) and commercial plantations of A. tequilana.

PubMed

Vargas-Ponce, Ofelia; Zizumbo-Villarreal, Daniel; Martínez-Castillo, Jaime; Coello-Coello, Julián; Colunga-Garcíamarín, Patricia

2009-02-01

Traditional farming communities frequently maintain high levels of agrobiodiversity, so understanding their agricultural practices is a priority for biodiversity conservation. The cultural origin of agave spirits (mezcals) from west-central Mexico is in the southern part of the state of Jalisco where traditional farmers cultivate more than 20 landraces of Agave angustifolia Haw. in agroecosystems that include in situ management of wild populations. These systems, rooted in a 9000-year-old tradition of using agaves as food in Mesoamerica, are endangered by the expansion of commercial monoculture plantations of the blue agave variety (A. tequilana Weber var. Azul), the only agave certified for sale as tequila, the best-known mezcal. Using intersimple sequence repeats and Bayesian estimators of diversity and structure, we found that A. angustifolia traditional landraces had a genetic diversity (H(BT) = 0.442) similar to its wild populations (H(BT) = 0.428) and a higher genetic structure ((B) = 0.405; (B) =0. 212). In contrast, the genetic diversity in the blue agave commercial system (H(B) = 0.118) was 73% lower. Changes to agave spirits certification laws to allow the conservation of current genetic, ecological and cultural diversity can play a key role in the preservation of the traditional agroecosystems.

A high-resolution cattle CNV map by population-scale genome sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) are common genomic structural variations that have been linked to human diseases and phenotypic traits. CNVs represent an important type of genetic variation among cattle breeds and even individual animals; however, only low-resolution maps of cattle CNVs currently exis...

Population genetics of seaside Sparrow (Ammodramus maritimus) subspecies along the gulf of Mexico.

PubMed

Woltmann, Stefan; Stouffer, Philip C; Bergeon Burns, Christine M; Woodrey, Mark S; Cashner, Mollie F; Taylor, Sabrina S

2014-01-01

Seaside Sparrows (Ammodramus maritimus) along the Gulf of Mexico are currently recognized as four subspecies, including taxa in Florida (A. m. juncicola and A. m. peninsulae) and southern Texas (Ammodramus m. sennetti), plus a widespread taxon between them (A. m. fisheri). We examined population genetic structure of this "Gulf Coast" clade using microsatellite and mtDNA data. Results of Bayesian analyses (Structure, GeneLand) of microsatellite data from nine locations do not entirely align with current subspecific taxonomy. Ammodramus m. sennetti from southern Texas is significantly differentiated from all other populations, but we found evidence of an admixture zone with A. m. fisheri near Corpus Christi. The two subspecies along the northern Gulf Coast of Florida are significantly differentiated from both A. m. sennetti and A. m. fisheri, but are not distinct from each other. We found a weak signal of isolation by distance within A. m. fisheri, indicating this population is not entirely panmictic throughout its range. Although continued conservation concern is warranted for all populations along the Gulf Coast, A. m. fisheri appears to be more secure than the far smaller populations in south Texas and the northern Florida Gulf Coast. In particular, the most genetically distinct populations, those in Texas south of Corpus Christi, occupy unique habitats within a very small geographic range.

Population structure of the giant garter snake, Thamnophis gigas

USGS Publications Warehouse

Paquin, M.M.; Wylie, G.D.; Routman, E.J.

2006-01-01

The giant garter snake, Thamnophis gigas, is a threatened species endemic to California's Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas. ?? Springer 2006.

Phylogeography of a Habitat Specialist with High Dispersal Capability: The Savi’s Warbler Locustella luscinioides

PubMed Central

Neto, Júlio M.; Arroyo, José L.; Bargain, Bruno; Monrós, Juan S.; Mátrai, Norbert; Procházka, Petr; Zehtindjiev, Pavel

2012-01-01

In order to describe the influence of Pleistocene glaciations on the genetic structure and demography of a highly mobile, but specialized, passerine, the Savi’s Warbler (Locustella luscinioides), mitochondrial DNA sequences (ND2) and microsatellites were analysed in c.330 individuals of 17 breeding and two wintering populations. Phylogenetic, population genetics and coalescent methods were used to describe the genetic structure, determine the timing of the major splits and model the demography of populations. Savi’s Warblers split from its sister species c.8 million years ago and have two major haplotype groups that diverged in the early/middle Pleistocene. One of these clades originated in the Balkans and is currently widespread, showing strong evidence for population expansion; whereas the other is restricted to Iberia and remained stable. Microsatellites agreed with a genetic break around the Pyrenees, but showed considerable introgression and a weaker genetic structure. Both genetic markers showed an isolation-by-distance pattern associated with the population expansion of the eastern clade. Breeding populations seem to be segregated at the wintering sites, but results on migratory connectivity are preliminary. Savi’s Warbler is the only known migratory bird species in which Iberian birds did not expand beyond the Pyrenees after the last glaciation. Despite the long period of independent evolution of western and eastern populations, complete introgression occurred when these groups met in Iberia. Mitochondrial sequences indicated the existence of refugia-within-refugia in the Iberian Peninsula during the last glacial period, which is surprising given the high dispersal capacity of this species. Plumage differences of eastern subspecies seemed to have evolved recently through natural selection, in agreement with the glacial expansion hypothesis. This study supports the great importance of the Iberian Peninsula and its role for the conservation of genetic variation. PMID:22701653

Genetic variability and structure of jaguar (Panthera onca) in Mexican zoos.

PubMed

Rueda-Zozaya, Pilar; Mendoza-Martínez, Germán D; Martínez-Gómez, Daniel; Monroy-Vilchis, Octavio; Godoy, José Antonio; Sunny, Armando; Palomares, Francisco; Chávez, Cuauhtémoc; Herrera-Haro, José

2016-02-01

Genealogical records of animals (studbook) are created to avoid reproduction between closely related individuals, which could cause inbreeding, particularly for such endangered species as the Panthera onca (Linnaeus, 1758). Jaguar is the largest felid in the Americas and is considered an important ecological key species. In Mexico, wild jaguar populations have been significantly reduced in recent decades, and population decline typically accompany decreases in genetic variation. There is no current census of captive jaguars in Mexico, and zoos do not follow a standardized protocol in breeding programs based on genetic studies. Here, we emphasise the importance of maintaining an adequate level of genetic variation and propose the implementation of standardised studbooks for jaguars in Mexico, mainly to avoid inbreeding. In addition, achieving the aims of studbook registration would provide a population genetic characterisation that could serve as a basis for ex situ conservation programmes.

Conservation genetics of snowy plovers (Charadrius alexandrinus) in the Western Hemisphere: Population genetic structure and delineation of subspecies

USGS Publications Warehouse

Funk, W.C.; Mullins, T.D.; Haig, S.M.

2007-01-01

We examined the genetic structure of snowy plovers (Charadrius alexandrinus) in North America, the Caribbean, and the west coast of South America to quantify variation within and among breeding areas and to test the validity of three previously recognized subspecies. Sequences (676 bp) from domains I and II of the mitochondrial control region were analyzed for 166 snowy plovers from 20 breeding areas. Variation was also examined at 10 microsatellite loci for 144 snowy plovers from 14 breeding areas. The mtDNA and microsatellite data provided strong evidence that the Puerto Rican breeding group is genetically divergent from sites in the continental U.S. (net sequence divergence = 0.38%; F ST for microsatellites = 0.190). Our data also revealed high levels of differentiation between sites from South America and North America (net sequence divergence = 0.81%; F ST for microsatellites = 0.253). In contrast, there was little genetic structure among breeding sites within the continental U.S. Our results suggest that snowy plovers in Florida should be considered part of C. a. nivosus (rather than part of C. a. tenuirostris, where they are currently placed), whereas snowy plovers from Puerto Rico should be considered part of C. a. tenuirostris. Snowy plovers in South America should remain a separate subspecies (C. a. occidentalis). Although U.S. Pacific and Gulf Coast breeding areas were not genetically distinct from other continental U.S. sites, demographic isolation, unique coastal habitats, and recent population declines suggest they warrant special concern. ?? 2007 Springer Science+Business Media, Inc.

Genetic Structure in a Small Pelagic Fish Coincides with a Marine Protected Area: Seascape Genetics in Patagonian Fjords

PubMed Central

Ferrada-Fuentes, Sandra; Galleguillos, Ricardo; Hernández, Cristián E.

2016-01-01

Marine environmental variables can play an important role in promoting population genetic differentiation in marine organisms. Although fjord ecosystems have attracted much attention due to the great oscillation of environmental variables that produce heterogeneous habitats, species inhabiting this kind of ecosystem have received less attention. In this study, we used Sprattus fuegensis, a small pelagic species that populates the inner waters of the continental shelf, channels and fjords of Chilean Patagonia and Argentina, as a model species to test whether environmental variables of fjords relate to population genetic structure. A total of 282 individuals were analyzed from Chilean Patagonia with eight microsatellite loci. Bayesian and non-Bayesian analyses were conducted to describe the genetic variability of S. fuegensis and whether it shows spatial genetic structure. Results showed two well-differentiated genetic clusters along the Chilean Patagonia distribution (i.e. inside the embayment area called TicToc, and the rest of the fjords), but no spatial isolation by distance (IBD) pattern was found with a Mantel test analysis. Temperature and nitrate were correlated to the expected heterozygosities and explained the allelic frequency variation of data in the redundancy analyses. These results suggest that the singular genetic differences found in S. fuegensis from inside TicToc Bay (East of the Corcovado Gulf) are the result of larvae retention bya combination of oceanographic mesoscale processes (i.e. the west wind drift current reaches the continental shelf exactly in this zone), and the local geographical configuration (i.e. embayment area, islands, archipelagos). We propose that these features generated an isolated area in the Patagonian fjords that promoted genetic differentiation by drift and a singular biodiversity, adding support to the existence of the largest marine protected area (MPA) of continental Chile, which is the Tic-Toc MPA. PMID:27505009

Genetic Structure of the Tree Peony (Paeonia rockii) and the Qinling Mountains as a Geographic Barrier Driving the Fragmentation of a Large Population

PubMed Central

Yuan, Jun–hui; Cheng, Fang–Yun; Zhou, Shi–Liang

2012-01-01

Background Tree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers. Methodology/Principal Findings Twenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm. Conclusions/Significance Our data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of this species and for improving the genetic basis for breeding its cultivars. PMID:22523566

GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.

PubMed

Curtis, Farren; Li, Xiayue; Rose, Timothy; Vázquez-Mayagoitia, Álvaro; Bhattacharya, Saswata; Ghiringhelli, Luca M; Marom, Noa

2018-04-10

We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.

Determinism and mass-media portrayals of genetics.

PubMed Central

Condit, C M; Ofulue, N; Sheedy, K M

1998-01-01

Scholars have expressed concern that the introduction of substantial coverage of "medical genetics" in the mass media during the past 2 decades represents an increase in biological determinism in public discourse. To test this contention, we analyzed the contents of a randomly selected, structured sample of American public newspapers (n=250) and magazines (n=722) published during 1919-95. Three coders, using three measures, all with intercoder reliability >85%, were employed. Results indicate that the introduction of the discourse of medical genetics is correlated with both a statistically significant decrease in the degree to which articles attribute human characteristics to genetic causes (P<.001) and a statistically significant increase in the differentiation of attributions to genetic and other causes among various conditions or outcomes (P<. 016). There has been no statistically significant change in the relative proportions of physical phenomena attributed to genetic causes, but there has been a statistically significant decrease in the number of articles assigning genetic causes to mental (P<.002) and behavioral (P<.000) characteristics. These results suggest that the current discourse of medical genetics is not accurately described as more biologically deterministic than its antecedents. PMID:9529342

Mobile Genetic Elements: In Silico, In Vitro, In Vivo

PubMed Central

Arkhipova, Irina R.; Rice, Phoebe A.

2016-01-01

Mobile genetic elements (MGEs), also called transposable elements (TEs), represent universal components of most genomes and are intimately involved in nearly all aspects of genome organization, function, and evolution. However, there is currently a gap between fast-paced TE discovery in silico, stimulated by exponential growth of comparative genomic studies, and a limited number of experimental models amenable to more traditional in vitro and in vivo studies of structural, mechanistic, and regulatory properties of diverse MGEs. Experimental and computational scientists came together to bridge this gap at a recent conference, “Mobile Genetic Elements: in silico, in vitro, in vivo,” held at the Marine Biological Laboratory (MBL) in Woods Hole, MA, USA. PMID:26822117

Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

PubMed

Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

2016-10-01

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard.

PubMed

Oliveira, Eliana Faria; Martinez, Pablo Ariel; São-Pedro, Vinícius Avelar; Gehara, Marcelo; Burbrink, Frank Thomas; Mesquita, Daniel Oliveira; Garda, Adrian Antonio; Colli, Guarino Rinaldi; Costa, Gabriel Correa

2018-03-01

Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

USDA-ARS?s Scientific Manuscript database

Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium...

Textbooks: Expectations vs. Reality: The DNA story

ERIC Educational Resources Information Center

Stansfield, William D.

2006-01-01

A history of the search for the structure of DNA, as revealed in the evolution of biochemistry and genetics textbooks, reveals that they are unacceptably tardy in presenting the current (or even the recent) state of knowledge. This problem places an extra burden on biology teachers to supplement these texts.

Dopamine and serotonin genetic risk scores predicting substance and nicotine use in Attention-Deficit/Hyperactivity Disorder

PubMed Central

Groenman, Annabeth P.; Greven, Corina U.; van Donkelaar, Marjolein M.J.; Schellekens, Arnt; van Hulzen, Kimm J.E.; Rommelse, Nanda; Hartman, Catharina A.; Hoekstra, Pieter J.; Luman, Marjolein; Franke, Barbara; Faraone, Stephen V.; Oosterlaan, Jaap; Buitelaar, Jan K.

2015-01-01

Individuals with attention-deficit/hyperactivity disorder (ADHD) are at increased risk of developing substance use disorders (SUDs) and nicotine dependence. The co-occurrence of ADHD and SUDs/nicotine dependence may in part be mediated by shared genetic liability. Several neurobiological pathways have been implicated in both ADHD and SUDs, including dopamine and serotonin pathways. We hypothesized that variations in dopamine and serotonin neurotransmission genes were involved in the genetic liability to develop SUDs/nicotine dependence in ADHD. The current study included participants with ADHD (n=280) who were originally part of the Dutch International Multicenter ADHD Genetics study. Participants were aged 5–15 years and attending outpatient clinics at enrollment in the study. Diagnoses of ADHD, SUDs, nicotine dependence, age of first nicotine and substance use, and alcohol use severity were based on semi-structured interviews and questionnaires. Genetic risk scores were created for both serotonergic and dopaminergic risk genes previously shown to be associated with ADHD and SUDs and/or nicotine dependence. The serotonin genetic risk score significantly predicted alcohol use severity. No significant serotonin*dopamine risk score or effect of stimulant medication was found. The current study adds to literature by providing insight into genetic underpinnings of the comorbidity of ADHD and SUDs. While the focus of the literature so far has been mostly on dopamine, our study suggests that serotonin may also play a role in the relationship between these disorders. PMID:25752199

Black and white and read all over: the past, present and future of giant panda genetics.

PubMed

Wei, Fuwen; Hu, Yibo; Zhu, Lifeng; Bruford, Michael W; Zhan, Xiangjiang; Zhang, Lei

2012-12-01

Few species attract much more attention from the public and scientists than the giant panda (Ailuropoda melanoleuca), a popular, enigmatic but highly endangered species. The application of molecular genetics to its biology and conservation has facilitated surprising insights into the biology of giant pandas as well as the effectiveness of conservation efforts during the past decades. Here, we review the history of genetic advances in this species, from phylogeny, demographical history, genetic variation, population structure, noninvasive population census and adaptive evolution to reveal to what extent the current status of the giant panda is a reflection of its evolutionary legacy, as opposed to the influence of anthropogenic factors that have negatively impacted this species. In addition, we summarize the conservation implications of these genetic findings applied for the management of this high-profile species. Finally, on the basis of these advances and predictable future changes in genetic technology, we discuss future research directions that seem promising for giant panda biology and conservation. © 2012 Blackwell Publishing Ltd.

[Genetic and neuroendocrine aspects in autism spectrum disorder].

PubMed

Oviedo, Norma; Manuel-Apolinar, Leticia; de la Chesnaye, Elsa; Guerra-Araiza, Christian

The autism spectrum disorder (ASD) was described in 1943 and is defined as a developmental disorder that affects social interaction and communication. It is usually identified in early stages of development from 18 months of age. Currently, autism is considered a neurological disorder with a spectrum covering cases of different degrees, which is associated with genetic factors, not genetic and environmental. Among the genetic factors, various syndromes have been described that are associated with this disorder. Also, the neurobiology of autism has been studied at the genetic, neurophysiological, neurochemical and neuropathological levels. Neuroimaging techniques have shown multiple structural abnormalities in these patients. There have also been changes in the serotonergic, GABAergic, catecholaminergic and cholinergic systems related to this disorder. This paper presents an update of the information presented in the genetic and neuroendocrine aspects of autism spectrum disorder. Copyright © 2014 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

The Genetics of Non-conventional Wine Yeasts: Current Knowledge and Future Challenges

PubMed Central

Masneuf-Pomarede, Isabelle; Bely, Marina; Marullo, Philippe; Albertin, Warren

2016-01-01

Saccharomyces cerevisiae is by far the most widely used yeast in oenology. However, during the last decade, several other yeasts species has been purposed for winemaking as they could positively impact wine quality. Some of these non-conventional yeasts (Torulaspora delbrueckii, Metschnikowia pulcherrima, Pichia kluyveri, Lachancea thermotolerans, etc.) are now proposed as starters culture for winemakers in mixed fermentation with S. cerevisiae, and several others are the subject of various studies (Hanseniaspora uvarum, Starmerella bacillaris, etc.). Along with their biotechnological use, the knowledge of these non-conventional yeasts greatly increased these last 10 years. The aim of this review is to describe the last updates and the current state-of-art of the genetics of non-conventional yeasts (including S. uvarum, T. delbrueckii, S. bacillaris, etc.). We describe how genomics and genetics tools provide new data into the population structure and biodiversity of non-conventional yeasts in winemaking environments. Future challenges will lie on the development of selection programs and/or genetic improvement of these non-conventional species. We discuss how genetics, genomics and the advances in next-generation sequencing will help the wine industry to develop the biotechnological use of non-conventional yeasts to improve the quality and differentiation of wines. PMID:26793188

Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases

PubMed Central

Goubert, C; Minard, G; Vieira, C; Boulesteix, M

2016-01-01

The Asian tiger mosquito Aedes albopictus is currently one of the most threatening invasive species in the world. Native to Southeast Asia, the species has spread throughout the world in the past 30 years and is now present in every continent but Antarctica. Because it was the main vector of recent Dengue and Chikungunya outbreaks, and because of its competency for numerous other viruses and pathogens such as the Zika virus, A. albopictus stands out as a model species for invasive diseases vector studies. A synthesis of the current knowledge about the genetic diversity of A. albopictus is needed, knowing the interplays between the vector, the pathogens, the environment and their epidemiological consequences. Such resources are also valuable for assessing the role of genetic diversity in the invasive success. We review here the large but sometimes dispersed literature about the population genetics of A. albopictus. We first debate about the experimental design of these studies and present an up-to-date assessment of the available molecular markers. We then summarize the main genetic characteristics of natural populations and synthesize the available data regarding the worldwide structuring of the vector. Finally, we pinpoint the gaps that remain to be addressed and suggest possible research directions. PMID:27273325

Phylogeography of Ophioblennius: the role of ocean currents and geography in reef fish evolution.

PubMed

Muss, A; Robertson, D R; Stepien, C A; Wirtz, P; Bowen, B W

2001-03-01

Many tropical reef fishes are divided into Atlantic and East Pacific taxa, placing similar species in two very different biogeographic regimes. The tropical Atlantic is a closed ocean basin with relatively stable currents, whereas the East Pacific is an open basin with unstable oceanic circulation. To assess how evolutionary processes are influenced by these differences in oceanography and geography, we analyze a 630-bp region of mitochondrial cytochrome b from 171 individuals in the blenniid genus Ophioblennius. Our results demonstrate deep genetic structuring in the Atlantic species, O. atlanticus, corresponding to recognized biogeographic provinces, with divergences of d = 5.2-12.7% among the Caribbean, Brazilian, St. Helena/Ascension Island, Gulf of Guinea, and Azores/Cape Verde regions. The Atlantic phylogeny is consistent with Pliocene dispersal from the western to eastern Atlantic, and the depth of these separations (along with prior morphological comparisons) may indicate previously unrecognized species. The eastern Pacific species, O. steindachneri, is characterized by markedly less structure than O. atlanticus, with shallow mitochondrial DNA lineages (dmax = 2.7%) and haplotype frequency shifts between locations in the Sea of Cortez, Pacific Panama, Clipperton Island, and the Galapagos Islands. No concordance between genetic structure and biogeographic provinces was found for O. steincdachneri. We attribute the phylogeographic pattern in O. atlanticus to dispersal during the reorganization of Atlantic circulation patterns that accompanied the shoaling of the Isthmus of Panama. The low degree of structure in the eastern Pacific is probably due to unstable circulation and linkage to the larger Pacific Ocean basin. The contrast in genetic signatures between Atlantic and eastern Pacific blennies demonstrates how differences in geology and oceanography have influenced evolutionary radiations within each region.

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

PubMed Central

Zhu, Yun; Fan, Ruzong; Xiong, Momiao

2017-01-01

Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data. To explore correlation information of genetic variants, effectively reduce data dimensions, and overcome critical barriers in advancing the development of novel statistical methods and computational algorithms for genetic pleiotropic analysis, we proposed a new statistic method referred to as a quadratically regularized functional CCA (QRFCCA) for association analysis which combines three approaches: (1) quadratically regularized matrix factorization, (2) functional data analysis and (3) canonical correlation analysis (CCA). Large-scale simulations show that the QRFCCA has a much higher power than that of the ten competing statistics while retaining the appropriate type 1 errors. To further evaluate performance, the QRFCCA and ten other statistics are applied to the whole genome sequencing dataset from the TwinsUK study. We identify a total of 79 genes with rare variants and 67 genes with common variants significantly associated with the 46 traits using QRFCCA. The results show that the QRFCCA substantially outperforms the ten other statistics. PMID:29040274

Assessing the Genetic Influence of Ancient Sociopolitical Structure: Micro-differentiation Patterns in the Population of Asturias (Northern Spain)

PubMed Central

Pardiñas, Antonio F.; Roca, Agustín; García-Vazquez, Eva; López, Belén

2012-01-01

The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as “micro-differentiation”. It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions. PMID:23209673

Bayesian Network Webserver: a comprehensive tool for biological network modeling.

PubMed

Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan

2013-11-01

The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.

The Genetic Basis of Peyronie Disease: A Review.

PubMed

Herati, Amin S; Pastuszak, Alexander W

2016-01-01

Peyronie disease (PD) is a progressive fibrotic disorder of the penile tunica albuginea that results in fibrotic penile plaques and can lead to penile deformity. Characterized by aberrant fibrosis resulting in part from the persistence of myofibroblasts and altered gene expression, the molecular factors underpinning PD and other related fibrotic diatheses are just being elucidated. A genetic link to PD was first identified three decades ago using pedigree analyses. However, the specific genetic factors that predispose patients to aberrant fibrosis remain unknown, and the relations between these fibrotic conditions and other heritable diseases, including malignancy, are uncharacterized. To review the current landscape linking molecular and genetic factors to aberrant fibrosis in PD and related fibrotic diatheses, including Dupuytren disease. Review and evaluation of the literature from 1970 to the present for genetic factors associated with PD were performed. Data describing the genetic factors associated with PD were obtained. We describe the known structural chromosomal abnormalities and single-nucleotide polymorphisms associated with fibrotic diatheses and discuss the spectrum of differential gene expression data comparing normal tissues with those derived from men with PD or Dupuytren disease. We discuss epigenetic mechanisms that might regulate gene expression and alter predisposition to fibrosis. Although the current understanding of the genetic factors associated with PD is limited, significant advances have been made during the past three decades. Further research is necessary to provide a more comprehensive understanding of the landscape of genetic factors responsible for the development of PD. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Genetic structure and demographic history of Colletotrichum gloeosporioides sensu lato and C. truncatum isolates from Trinidad and Mexico.

PubMed

Rampersad, Sephra N; Perez-Brito, Daisy; Torres-Calzada, Claudia; Tapia-Tussell, Raul; Carrington, Christine V F

2013-06-22

C. gloeosporioides sensu lato is one of the most economically important post-harvest diseases affecting papaya production worldwide. There is currently no information concerning the genetic structure or demographic history of this pathogen in any of the affected countries. Knowledge of molecular demographic parameters for different populations will improve our understanding of the biogeographic history as well as the evolutionary and adaptive potential of these pathogens. In this study, sequence data for ACT, GPDH, β-TUB and ITS gene regions were analyzed for C. gloeosporioides sensu lato and C. truncatum isolates infecting papaya in Trinidad and Mexico in order to determine the genetic structure and demographic history of these populations. The data indicated that Mexico is the ancestral C. gloeosporioides sensu lato population with asymmetrical migration to Trinidad. Mexico also had the larger effective population size but, both Mexico and Trinidad populations exhibited population expansion. Mexico also had greater nucleotide diversity and high levels of diversity for each gene. There was significant sub-division of the Trinidad and Mexico populations and low levels of genetic divergence among populations for three of the four gene regions; β-TUB was shown to be under positive selection. There were also dissimilar haplotype characteristics for both populations. Mutation may play a role in shaping the population structure of C. gloeosporioides sensu lato isolates from Trinidad and from Mexico, especially with respect to the ACT and GPDH gene regions. There was no evidence of gene flow between the C. truncatum populations and it is possible that the Mexico and Trinidad populations emerged independently of each other. The study revealed relevant information based on the genetic structure as well as the demographic history of two fungal pathogens infecting papaya, C. gloeosporioides sensu lato and C. truncatum, in Trinidad and Mexico. Understanding the genetic structure of pathogen populations will assist in determining the evolutionary potential of the pathogen and in identifying which evolutionary forces may have the greatest impact on durability of resistance. Intervention strategies that target these evolutionary forces would prove to be the most practical.

Genetic structure and demographic history of Colletotrichum gloeosporioides sensu lato and C. truncatum isolates from Trinidad and Mexico

PubMed Central

2013-01-01

Background C. gloeosporioides sensu lato is one of the most economically important post-harvest diseases affecting papaya production worldwide. There is currently no information concerning the genetic structure or demographic history of this pathogen in any of the affected countries. Knowledge of molecular demographic parameters for different populations will improve our understanding of the biogeographic history as well as the evolutionary and adaptive potential of these pathogens. In this study, sequence data for ACT, GPDH, β-TUB and ITS gene regions were analyzed for C. gloeosporioides sensu lato and C. truncatum isolates infecting papaya in Trinidad and Mexico in order to determine the genetic structure and demographic history of these populations. Results The data indicated that Mexico is the ancestral C. gloeosporioides sensu lato population with asymmetrical migration to Trinidad. Mexico also had the larger effective population size but, both Mexico and Trinidad populations exhibited population expansion. Mexico also had greater nucleotide diversity and high levels of diversity for each gene. There was significant sub-division of the Trinidad and Mexico populations and low levels of genetic divergence among populations for three of the four gene regions; β-TUB was shown to be under positive selection. There were also dissimilar haplotype characteristics for both populations. Mutation may play a role in shaping the population structure of C. gloeosporioides sensu lato isolates from Trinidad and from Mexico, especially with respect to the ACT and GPDH gene regions. There was no evidence of gene flow between the C. truncatum populations and it is possible that the Mexico and Trinidad populations emerged independently of each other. Conclusions The study revealed relevant information based on the genetic structure as well as the demographic history of two fungal pathogens infecting papaya, C. gloeosporioides sensu lato and C. truncatum, in Trinidad and Mexico. Understanding the genetic structure of pathogen populations will assist in determining the evolutionary potential of the pathogen and in identifying which evolutionary forces may have the greatest impact on durability of resistance. Intervention strategies that target these evolutionary forces would prove to be the most practical. PMID:23800297

Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

PubMed Central

Soler-Membrives, Anna; Linse, Katrin; Miller, Karen J.

2017-01-01

The evolutionary history of Antarctic organisms is becoming increasingly important to understand and manage population trajectories under rapid environmental change. The Antarctic sea spider Nymphon australe, with an apparently large population size compared with other sea spider species, is an ideal target to look for molecular signatures of past climatic events. We analysed mitochondrial DNA of specimens collected from the Antarctic continent and two Antarctic islands (AI) to infer past population processes and understand current genetic structure. Demographic history analyses suggest populations survived in refugia during the Last Glacial Maximum. The high genetic diversity found in the Antarctic Peninsula and East Antarctic (EA) seems related to multiple demographic contraction–expansion events associated with deep-sea refugia, while the low genetic diversity in the Weddell Sea points to a more recent expansion from a shelf refugium. We suggest the genetic structure of N. australe from AI reflects recent colonization from the continent. At a local level, EA populations reveal generally low genetic differentiation, geographically and bathymetrically, suggesting limited restrictions to dispersal. Results highlight regional differences in demographic histories and how these relate to the variation in intensity of glaciation–deglaciation events around Antarctica, critical for the study of local evolutionary processes. These are valuable data for understanding the remarkable success of Antarctic pycnogonids, and how environmental changes have shaped the evolution and diversification of Southern Ocean benthic biodiversity. PMID:29134072

Genetic signature of Last Glacial Maximum regional refugia in a circum-Antarctic sea spider

NASA Astrophysics Data System (ADS)

Soler-Membrives, Anna; Linse, Katrin; Miller, Karen J.; Arango, Claudia P.

2017-10-01

The evolutionary history of Antarctic organisms is becoming increasingly important to understand and manage population trajectories under rapid environmental change. The Antarctic sea spider Nymphon australe, with an apparently large population size compared with other sea spider species, is an ideal target to look for molecular signatures of past climatic events. We analysed mitochondrial DNA of specimens collected from the Antarctic continent and two Antarctic islands (AI) to infer past population processes and understand current genetic structure. Demographic history analyses suggest populations survived in refugia during the Last Glacial Maximum. The high genetic diversity found in the Antarctic Peninsula and East Antarctic (EA) seems related to multiple demographic contraction-expansion events associated with deep-sea refugia, while the low genetic diversity in the Weddell Sea points to a more recent expansion from a shelf refugium. We suggest the genetic structure of N. australe from AI reflects recent colonization from the continent. At a local level, EA populations reveal generally low genetic differentiation, geographically and bathymetrically, suggesting limited restrictions to dispersal. Results highlight regional differences in demographic histories and how these relate to the variation in intensity of glaciation-deglaciation events around Antarctica, critical for the study of local evolutionary processes. These are valuable data for understanding the remarkable success of Antarctic pycnogonids, and how environmental changes have shaped the evolution and diversification of Southern Ocean benthic biodiversity.

East-west genetic differentiation in Musk Ducks (Biziura lobata) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

USGS Publications Warehouse

Guay, P.-J.; Chesser, R.T.; Mulder, R.A.; Afton, A.D.; Paton, D.C.; McCracken, K.G.

2010-01-01

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (??ST = 0. 747), one nuclear intron (??ST = 0.193) and eight microsatellite loci (FST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews' (Austral Avian Record 2:83-107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other. ?? 2010 Springer Science+Business Media B.V.

FDA toxicity databases and real-time data entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arvidson, Kirk B.

Structure-searchable electronic databases are valuable new tools that are assisting the FDA in its mission to promptly and efficiently review incoming submissions for regulatory approval of new food additives and food contact substances. The Center for Food Safety and Applied Nutrition's Office of Food Additive Safety (CFSAN/OFAS), in collaboration with Leadscope, Inc., is consolidating genetic toxicity data submitted in food additive petitions from the 1960s to the present day. The Center for Drug Evaluation and Research, Office of Pharmaceutical Science's Informatics and Computational Safety Analysis Staff (CDER/OPS/ICSAS) is separately gathering similar information from their submissions. Presently, these data are distributedmore » in various locations such as paper files, microfiche, and non-standardized toxicology memoranda. The organization of the data into a consistent, searchable format will reduce paperwork, expedite the toxicology review process, and provide valuable information to industry that is currently available only to the FDA. Furthermore, by combining chemical structures with genetic toxicity information, biologically active moieties can be identified and used to develop quantitative structure-activity relationship (QSAR) modeling and testing guidelines. Additionally, chemicals devoid of toxicity data can be compared to known structures, allowing for improved safety review through the identification and analysis of structural analogs. Four database frameworks have been created: bacterial mutagenesis, in vitro chromosome aberration, in vitro mammalian mutagenesis, and in vivo micronucleus. Controlled vocabularies for these databases have been established. The four separate genetic toxicity databases are compiled into a single, structurally-searchable database for easy accessibility of the toxicity information. Beyond the genetic toxicity databases described here, additional databases for subchronic, chronic, and teratogenicity studies have been prepared.« less

Pleistocene glacial refugia across the Appalachian Mountains and coastal plain in the millipede genus Narceus: Evidence from population genetic, phylogeographic, and paleoclimatic data

PubMed Central

Walker, Matt J; Stockman, Amy K; Marek, Paul E; Bond, Jason E

2009-01-01

Background Species that are widespread throughout historically glaciated and currently non-glaciated areas provide excellent opportunities to investigate the role of Pleistocene climatic change on the distribution of North American biodiversity. Many studies indicate that northern animal populations exhibit low levels of genetic diversity over geographically widespread areas whereas southern populations exhibit relatively high levels. Recently, paleoclimatic data have been combined with niche-based distribution modeling to locate possible refugia during the Last Glacial Maximum. Using phylogeographic, population, and paleoclimatic data, we show that the distribution and mitochondrial data for the millipede genus Narceus are consistent with classical examples of Pleistocene refugia and subsequent post-glacial population expansion seen in other organismal groups. Results The phylogeographic structure of Narceus reveals a complex evolutionary history with signatures of multiple refugia in southeastern North America followed by two major northern expansions. Evidence for refugial populations were found in the southern Appalachian Mountains and in the coastal plain. The northern expansions appear to have radiated from two separate refugia, one from the Gulf Coastal Plain area and the other from the mid-Atlantic coastal region. Distributional models of Narceus during the Last Glacial Maximum show a dramatic reduction from the current distribution, with suitable ecological zones concentrated along the Gulf and Atlantic coastal plain. We found a strong correlation between these zones of ecological suitability inferred from our paleo-model with levels of genetic diversity derived from phylogenetic and population estimates of genetic structuring. Conclusion The signature of climatic change, during and after the Pleistocene, on the distribution of the millipede genus Narceus is evident in the genetic data presented. Niche-based historical distribution modeling strengthens the conclusions drawn from the genetic data and proves useful in identifying probable refugia. Such interdisciplinary biogeographic studies provide a comprehensive approach to understanding these processes that generate and maintain biodiversity as well as the framework necessary to explore questions regarding evolutionary diversification of taxa. PMID:19183468

Human neutral genetic variation and forensic STR data.

PubMed

Silva, Nuno M; Pereira, Luísa; Poloni, Estella S; Currat, Mathias

2012-01-01

The forensic genetics field is generating extensive population data on polymorphism of short tandem repeats (STR) markers in globally distributed samples. In this study we explored and quantified the informative power of these datasets to address issues related to human evolution and diversity, by using two online resources: an allele frequency dataset representing 141 populations summing up to almost 26 thousand individuals; a genotype dataset consisting of 42 populations and more than 11 thousand individuals. We show that the genetic relationships between populations based on forensic STRs are best explained by geography, as observed when analysing other worldwide datasets generated specifically to study human diversity. However, the global level of genetic differentiation between populations (as measured by a fixation index) is about half the value estimated with those other datasets, which contain a much higher number of markers but much less individuals. We suggest that the main factor explaining this difference is an ascertainment bias in forensics data resulting from the choice of markers for individual identification. We show that this choice results in average low variance of heterozygosity across world regions, and hence in low differentiation among populations. Thus, the forensic genetic markers currently produced for the purpose of individual assignment and identification allow the detection of the patterns of neutral genetic structure that characterize the human population but they do underestimate the levels of this genetic structure compared to the datasets of STRs (or other kinds of markers) generated specifically to study the diversity of human populations.

Geographic structure evidenced in the toxic dinoflagellate Alexandrium pacificum Litaker (A. catenella - group IV (Whedon & Kofoid) Balech) along Japanese and Chinese coastal waters.

PubMed

Genovesi, Benjamin; Berrebi, Patrick; Nagai, Satoshi; Reynaud, Nathalie; Wang, Jinhui; Masseret, Estelle

2015-09-15

The intra-specific diversity and genetic structure within the Alexandrium pacificum Litaker (A. catenella - Group IV) populations along the Temperate Asian coasts, were studied among individuals isolated from Japan to China. The UPGMA dendrogram and FCA revealed the existence of 3 clusters. Assignment analysis suggested the occurrence of gene flows between the Japanese Pacific coast (cluster-1) and the Chinese Zhejiang coast (cluster-2). Human transportations are suspected to explain the lack of genetic difference between several pairs of distant Japanese samples, hardly explained by a natural dispersal mechanism. The genetic isolation of the population established in the Sea of Japan (cluster-3) suggested the existence of a strong ecological and geographical barrier. Along the Pacific coasts, the South-North current allows limited exchanges between Chinese and Japanese populations. The relationships between Temperate Asian and Mediterranean individuals suggested different scenario of large-scale dispersal mechanisms. Copyright © 2015. Published by Elsevier Ltd.

Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia

PubMed Central

Misra, Raj Shekhar; Boonkorkaew, Patchareeya; Thanomchit, Kanokwan

2017-01-01

The corms and leaves of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agroforestry system. Although the plant is assumed to reproduce via panmixia, a comprehensive study on the genetic background across regions to enhance wider consumer palatability is still lacking. Here, ten informative microsatellites were analyzed in 29 populations across regions in India, Indonesia and Thailand to understand the genetic diversity, population structure and distribution to improve breeding and conservation programs. The genetic diversity was high among and within regions. Some populations exhibited excess heterozygosity and bottlenecking. Pairwise FST indicated very high genetic differentiation across regions (FST = 0.274), and the Asian population was unlikely to be panmictic. Phylogenetic tree construction grouped the populations according to country of origin with the exception of the Medan population from Indonesia. The current gene flow was apparent within the regions but was restricted among the regions. The present study revealed that Indonesia and Thailand populations could be alternative centers of the gene pool, together with India. Consequently, regional action should be incorporated in genetic conservation and breeding efforts to develop new varieties with global acceptance. PMID:28658282

Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge.

PubMed

Martins, Joana; Vasconcelos, Vitor

2015-11-13

Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

Population genetic testing for cancer susceptibility: founder mutations to genomes.

PubMed

Foulkes, William D; Knoppers, Bartha Maria; Turnbull, Clare

2016-01-01

The current standard model for identifying carriers of high-risk mutations in cancer-susceptibility genes (CSGs) generally involves a process that is not amenable to population-based testing: access to genetic tests is typically regulated by health-care providers on the basis of a labour-intensive assessment of an individual's personal and family history of cancer, with face-to-face genetic counselling performed before mutation testing. Several studies have shown that application of these selection criteria results in a substantial proportion of mutation carriers being missed. Population-based genetic testing has been proposed as an alternative approach to determining cancer susceptibility, and aims for a more-comprehensive detection of mutation carriers. Herein, we review the existing data on population-based genetic testing, and consider some of the barriers, pitfalls, and challenges related to the possible expansion of this approach. We consider mechanisms by which population-based genetic testing for cancer susceptibility could be delivered, and suggest how such genetic testing might be integrated into existing and emerging health-care structures. The existing models of genetic testing (including issues relating to informed consent) will very likely require considerable alteration if the potential benefits of population-based genetic testing are to be fully realized.

Genetically informed ecological niche models improve climate change predictions.

PubMed

Ikeda, Dana H; Max, Tamara L; Allan, Gerard J; Lau, Matthew K; Shuster, Stephen M; Whitham, Thomas G

2017-01-01

We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species' ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species' niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12-fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change. © 2016 John Wiley & Sons Ltd.

Corallite skeletal morphological variation in Hawaiian Porites lobata

NASA Astrophysics Data System (ADS)

Tisthammer, Kaho H.; Richmond, Robert H.

2018-06-01

Due to their high morphological plasticity and complex evolutionary history, the species boundaries of many reef-building corals are poorly understood. The skeletal structures of corals have traditionally been used for species identification, but these structures can be highly variable, and currently we lack knowledge regarding the extent of morphological variation within species. Porites species are notorious for their taxonomic difficulties, both morphologically and genetically, and currently there are several unresolved species complexes in the Pacific. Despite its ubiquitous presence and broad use in coral research, Porites lobata belongs to one such unresolved species complex. To understand the degree of intraspecific variation in skeletal morphology, 120 corallites from the Hawaiian P. lobata were examined. A subset of samples from two genetically differentiated populations from contrasting high- and low-stress environments in Maunalua Bay, Hawaii, were then quantitatively analyzed using multivariate morphometrics. Our observations revealed high intraspecific variation in corallite morphology, as well as significant morphological differences between the two populations of P. lobata. Additionally, significant correlation was found between the morphological and genetic distances calculated from approximately 18,000 loci generated from restriction site-associated DNA sequencing. The unique morphological characters observed from the genetically differentiated population under environmental stress suggest that these characters may have adaptive values, but how such traits relate to fitness and how much plasticity they can exhibit remain to be determined by future studies. Relatively simple morphometric analyses used in our study can be useful in clarifying the existing ambiguity in skeletal architecture, thus contributing to resolving species issues in corals.

Clinal variation at microsatellite loci reveals historical secondary intergradation between glacial races of Coregonus artedi (Teleostei: Coregoninae).

PubMed

Turgeon, J; Bernatchez, L

2001-11-11

Classical models of the spatial structure of population genetics rely on the assumption of migration-drift equilibrium, which is seldom met in natural populations having only recently colonized their current range (e.g., postglacial). Population structure then depicts historical events, and counfounding effects due to recent secondary contact between recently differentiated lineages can further counfound analyses of association between geographic and genetic distances. Mitochondrial polymorphisms have revealed the existence of two closely related lineages of the lake cisco, Coregonus artedi, whose significantly different but overlaping geographical distributions provided a weak signal of past range fragmentation blurred by putative subsequent extensive secondary contacts. In this study, we analyzed geographical patterns of genetic variation at seven microsatellite loci among 22 populations of lake cisco located along the axis of an area covered by proglacial lakes 12,000-8,000 years ago in North America. The results clearly confirmed the existence of two genetically distinct races characterized by different sets of microsatellite alleles whose frequencies varied clinally across some 3000 km. Equilibrium and nonequilibrium analyses of isolation by distance revealed historical signal of gene flow resulting from the nearly complete admixture of these races following neutral secondary contacts in their historical habitat and indicated that the colonization process occurred by a stepwise expansion of an eastern (Atlantic) race into a previously established Mississippian race. This historical signal of equilibrium contrasted with the current migration-drift disequilibrium within major extant watersheds and was apparently maintained by high effective population sizes and low migration regimes.

Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

PubMed Central

Jiménez, Rosa Alicia

2016-01-01

The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers. PMID:26788433

Biophysical Aspects of Spindle Evolution

NASA Astrophysics Data System (ADS)

Farhadifar, Reza; Baer, Charlie; Needleman, Daniel

2011-03-01

The continual propagation of genetic material from one generation to the next is one of the most basic characteristics of all organisms. In eukaryotes, DNA is segregated into the two daughter cells by a highly dynamic, self-organizing structure called the mitotic spindle. Mitotic spindles can show remarkable variability between tissues and organisms, but there is currently little understanding of the biophysical and evolutionary basis of this diversity. We are studying how spontaneous mutations modify cell division during nematode development. By comparing the mutational variation - the raw material of evolution - with the variation present in nature, we are investigating how the mitotic spindle is shaped over the course of evolution. This combination of quantitative genetics and cellular biophysics gives insight into how the structure and dynamics of the spindle is formed through selection, drift, and biophysical constraints.

Genetic differentiation and phylogeographical structure of the Brachionus calyciflorus complex in eastern China.

PubMed

Xiang, Xian-Ling; Xi, Yi-Long; Wen, Xin-Li; Zhang, Gen; Wang, Jin-Xia; Hu, Ke

2011-07-01

Spatio-temporal patterns and processes of genetic differentiation in passively dispersing zooplankton are drawing much attention from both ecologists and evolutionary biologists. Two opposite phylogeographical scenarios have already been demonstrated in rotifers, which consist of high levels of genetic differentiation among populations even on small geographical scales on the one hand and the traditionally known cosmopolitanism that is associated with high levels of gene flow and long-distance dispersal via diapausing stages on the other hand. Here, we analysed the population genetic structure and the phylogeography of the Brachionus calyciflorus species complex in eastern China. By screening a total of 318 individuals from ten locations along a 2320-km gradient and analysing samples from two growing seasons, we aimed at focusing on both small- and large-scale patterns. We identified eight cryptic species and verified species status of two of these by sexual reproduction tests. Samples in summer and winter yielded different cryptic species. The distribution patterns of these genetically distinct cryptic species were diverse across eastern China, from full cosmopolitanism to local endemism. The two most abundant cryptic species BcWIII and BcSW showed a pattern of strong genetic differentiation among populations and no significant isolation by distance. Long-distance colonization, secondary contact and recent range expansion are probably responsible for the indistinct pattern of isolation by distance. Our results suggest that geographical distance is more important than temporal segregation across seasons in explaining population differentiation and the occurrence of cryptic species. We explain the current phylogeographical structure in the B. calyciflorus species complex by a combination of recent population expansion, restricted gene flow, priority effects and long-distance colonization. © 2011 Blackwell Publishing Ltd.

Phylogeography of the Wheat Stem Sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae): Implications for Pest Management.

PubMed

Lesieur, Vincent; Martin, Jean-François; Weaver, David K; Hoelmer, Kim A; Smith, David R; Morrill, Wendell L; Kadiri, Nassera; Peairs, Frank B; Cockrell, Darren M; Randolph, Terri L; Waters, Debra K; Bon, Marie-Claude

2016-01-01

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), is a key pest of wheat in the northern Great Plains of North America, and damage resulting from this species has recently expanded southward. Current pest management practices are inadequate and uncertainty regarding geographic origin, as well as limited data on population structure and dynamics across North America impede progress towards more informed management. We examined the genetic divergence between samples collected in North America and northeastern Asia, the assumed native range of C. cinctus using two mitochondrial regions (COI and 16S). Subsequently, we characterized the structure of genetic diversity in the main wheat producing areas in North America using a combination of mtDNA marker and microsatellites in samples collected both in wheat fields and in grasses in wildlands. The strong genetic divergence observed between North American samples and Asian congeners, in particular the synonimized C. hyalinatus, did not support the hypothesis of a recent American colonization by C. cinctus. Furthermore, the relatively high genetic diversity both with mtDNA and microsatellite markers offered additional evidence in favor of the native American origin of this pest. The genetic diversity of North American populations is structured into three genetic clusters and these are highly correlated with geography. Regarding the recent southern outbreaks in North America, the results tend to exclude the hypothesis of recent movement of damaging wheat stem sawfly populations from the northern area. The shift in host plant use by local populations appears to be the most likely scenario. Finally, the significance of these findings is discussed in the context of pest management.

Phylogeography of the Wheat Stem Sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae): Implications for Pest Management

PubMed Central

Lesieur, Vincent; Martin, Jean-François; Weaver, David K.; Hoelmer, Kim A.; Smith, David R.; Morrill, Wendell L.; Kadiri, Nassera; Peairs, Frank B.; Cockrell, Darren M.; Randolph, Terri L.; Waters, Debra K.; Bon, Marie-Claude

2016-01-01

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), is a key pest of wheat in the northern Great Plains of North America, and damage resulting from this species has recently expanded southward. Current pest management practices are inadequate and uncertainty regarding geographic origin, as well as limited data on population structure and dynamics across North America impede progress towards more informed management. We examined the genetic divergence between samples collected in North America and northeastern Asia, the assumed native range of C. cinctus using two mitochondrial regions (COI and 16S). Subsequently, we characterized the structure of genetic diversity in the main wheat producing areas in North America using a combination of mtDNA marker and microsatellites in samples collected both in wheat fields and in grasses in wildlands. The strong genetic divergence observed between North American samples and Asian congeners, in particular the synonimized C. hyalinatus, did not support the hypothesis of a recent American colonization by C. cinctus. Furthermore, the relatively high genetic diversity both with mtDNA and microsatellite markers offered additional evidence in favor of the native American origin of this pest. The genetic diversity of North American populations is structured into three genetic clusters and these are highly correlated with geography. Regarding the recent southern outbreaks in North America, the results tend to exclude the hypothesis of recent movement of damaging wheat stem sawfly populations from the northern area. The shift in host plant use by local populations appears to be the most likely scenario. Finally, the significance of these findings is discussed in the context of pest management. PMID:27959958

Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland

PubMed Central

Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O’Grady, Martin; Mariani, Stefano; Phillimore, Albert

2014-01-01

Aim We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Location Ireland, Britain and continental Europe. Methods A total of 752 pike (Esox lucius) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Results Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Main conclusions Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two ‘waves’, the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species. PMID:25435649

Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland.

PubMed

Pedreschi, Debbi; Kelly-Quinn, Mary; Caffrey, Joe; O'Grady, Martin; Mariani, Stefano; Phillimore, Albert

2014-03-01

We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Ireland, Britain and continental Europe. A total of 752 pike ( Esox lucius ) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two 'waves', the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species.

Persistent genetic signatures of historic climatic events in an Antarctic octopus.

PubMed

Strugnell, J M; Watts, P C; Smith, P J; Allcock, A L

2012-06-01

Repeated cycles of glaciation have had major impacts on the distribution of genetic diversity of the Antarctic marine fauna. During glacial periods, ice cover limited the amount of benthic habitat on the continental shelf. Conversely, more habitat and possibly altered seaways were available during interglacials when the ice receded and the sea level was higher. We used microsatellites and partial sequences of the mitochondrial cytochrome oxidase 1 gene to examine genetic structure in the direct-developing, endemic Southern Ocean octopod Pareledone turqueti sampled from a broad range of areas that circumvent Antarctica. We find that, unusually for a species with poor dispersal potential, P. turqueti has a circumpolar distribution and is also found off the islands of South Georgia and Shag Rocks. The overriding pattern of spatial genetic structure can be explained by hydrographic (with ocean currents both facilitating and hindering gene flow) and bathymetric features. The Antarctic Peninsula region displays a complex population structure, consistent with its varied topographic and oceanographic influences. Genetic similarities between the Ross and Weddell Seas, however, are interpreted as a persistent historic genetic signature of connectivity during the hypothesized Pleistocene West Antarctic Ice Sheet collapses. A calibrated molecular clock indicates two major lineages within P. turqueti, a continental lineage and a sub-Antarctic lineage, that diverged in the mid-Pliocene with no subsequent gene flow. Both lineages survived subsequent major glacial cycles. Our data are indicative of potential refugia at Shag Rocks and South Georgia and also around the Antarctic continent within the Ross Sea, Weddell Sea and off Adélie Land. The mean age of mtDNA diversity within these main continental lineages coincides with Pleistocene glacial cycles. © 2012 Blackwell Publishing Ltd.

DNA-based approach to aging martens (Martes americana and M. caurina)

Treesearch

Jonathan N. Pauli; John P. Whiteman; Bruce G. Marcot; Terry M. McClean; Merav Ben-David

2011-01-01

Demographic structure is central to understanding the dynamics of animal populations. However, determining the age of free-ranging mammals is difficult, and currently impossible when sampling with noninvasive, genetic-based approaches. We present a method to estimate age class by combining measures of telomere lengths with other biologically meaningful covariates in a...

Ancient humans influenced the current spatial genetic structure of common walnut populations in Asia

Treesearch

Paola Pollegioni; Keith E. Woeste; Francesca Chiocchini; Stefano Del Lungo; Irene Olimpieri; Virginia Tortolano; Jo Clark; Gabriel E. Hemery; Sergio Mapelli; Maria Emilia Malvolti; Gyaneshwer Chaubey

2015-01-01

Common walnut (Juglans regia L) is an economically important species cultivated worldwide for its wood and nuts. It is generally accepted that J. regia survived and grew spontaneously in almost completely isolated stands in its Asian native range after the Last Glacial Maximum. Despite its natural geographic isolation, J....

Brachypodium distachyon as a Genetic Model System.

PubMed

Kellogg, Elizabeth A

2015-01-01

Brachypodium distachyon has emerged as a powerful model system for studying the genetics of flowering plants. Originally chosen for its phylogenetic proximity to the large-genome cereal crops wheat and barley, it is proving to be useful for more than simply providing markers for comparative mapping. Studies in B. distachyon have provided new insight into the structure and physiology of plant cell walls, the development and chemical composition of endosperm, and the genetic basis for cold tolerance. Recent work on auxin transport has uncovered mechanisms that apply to all angiosperms other than Arabidopsis. In addition to the areas in which it is currently used, B. distachyon is uniquely suited for studies of floral development, vein patterning, the controls of the perennial versus annual habit, and genome organization.

Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity

PubMed Central

Dendrou, Calliope A.; Cortes, Adrian; Shipman, Lydia; Evans, Hayley G.; Attfield, Kathrine E.; Jostins, Luke; Barber, Thomas; Kaur, Gurman; Kuttikkatte, Subita Balaram; Leach, Oliver A.; Desel, Christiane; Faergeman, Soren L.; Cheeseman, Jane; Neville, Matt J.; Sawcer, Stephen; Compston, Alastair; Johnson, Adam R.; Everett, Christine; Bell, John I.; Karpe, Fredrik; Ultsch, Mark; Eigenbrot, Charles; McVean, Gil; Fugger, Lars

2017-01-01

Thousands of genetic variants have been identified that contribute to the development of complex diseases, but determining how to fully elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders, subsequent molecular, cellular, in vivo and structural functional follow-up and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for multiple autoimmune disorders. PMID:27807284

Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation

PubMed Central

He, Shuilian; Wang, Yunsheng; Volis, Sergei; Li, Dezhu; Yi, Tingshuang

2012-01-01

Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and the other including northeastern China (NEC), Japan, Korea, MDRY, south China (SC) and southwestern China (SWC). Contrib analyses showed that southwestern China makes the greatest contribution to the total diversity and allelic richness, and is worthy of being given conservation priority. PMID:23202917

Historical and ecological determinants of genetic structure in arctic canids.

PubMed

Carmichael, L E; Krizan, J; Nagy, J A; Fuglei, E; Dumond, M; Johnson, D; Veitch, A; Berteaux, D; Strobeck, C

2007-08-01

Wolves (Canis lupus) and arctic foxes (Alopex lagopus) are the only canid species found throughout the mainland tundra and arctic islands of North America. Contrasting evolutionary histories, and the contemporary ecology of each species, have combined to produce their divergent population genetic characteristics. Arctic foxes are more variable than wolves, and both island and mainland fox populations possess similarly high microsatellite variation. These differences result from larger effective population sizes in arctic foxes, and the fact that, unlike wolves, foxes were not isolated in discrete refugia during the Pleistocene. Despite the large physical distances and distinct ecotypes represented, a single, panmictic population of arctic foxes was found which spans the Svalbard Archipelago and the North American range of the species. This pattern likely reflects both the absence of historical population bottlenecks and current, high levels of gene flow following frequent long-distance foraging movements. In contrast, genetic structure in wolves correlates strongly to transitions in habitat type, and is probably determined by natal habitat-biased dispersal. Nonrandom dispersal may be cued by relative levels of vegetation cover between tundra and forest habitats, but especially by wolf prey specialization on ungulate species of familiar type and behaviour (sedentary or migratory). Results presented here suggest that, through its influence on sea ice, vegetation, prey dynamics and distribution, continued arctic climate change may have effects as dramatic as those of the Pleistocene on the genetic structure of arctic canid species.

Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

PubMed

Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

2012-03-01

Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

Genetic structure of the Caribbean giant barrel sponge Xestospongia muta using the I3-M11 partition of COI

NASA Astrophysics Data System (ADS)

López-Legentil, S.; Pawlik, J. R.

2009-03-01

In recent years, reports of sponge bleaching, disease, and subsequent mortality have increased alarmingly. Population recovery may depend strongly on colonization capabilities of the affected species. The giant barrel sponge Xestospongia muta is a dominant reef constituent in the Caribbean. However, little is known about its population structure and gene flow. The 5'-end fragment of the mitochondrial gene cytochrome oxidase subunit I is often used to address these kinds of questions, but it presents very low intraspecific nucleotide variability in sponges. In this study, the usefulness of the I3-M11 partition of COI to determine the genetic structure of X. muta was tested for seven populations from Florida, the Bahamas and Belize. A total of 116 sequences of 544 bp were obtained for the I3-M11 partition corresponding to four haplotypes. In order to make a comparison with the 5'-end partition, 10 sequences per haplotype were analyzed for this fragment. The 40 resulting sequences were of 569 bp and corresponded to two haplotypes. The nucleotide diversity of the I3-M11 partition (π = 0.00386) was higher than that of the 5'-end partition (π = 0.00058), indicating better resolution at the intraspecific level. Sponges with the most divergent external morphologies (smooth vs. digitate surface) had different haplotypes, while those with the most common external morphology (rough surface) presented a mixture of haplotypes. Pairwise tests for genetic differentiation among geographic locations based on F ST values showed significant genetic divergence between most populations, but this genetic differentiation was not due to isolation by distance. While limited larval dispersal may have led to differentiation among some of the populations, the patterns of genetic structure appear to be most strongly related to patterns of ocean currents. Therefore, hydrological features may play a major role in sponge colonization and need to be considered in future plans for management and conservation of these important components of coral reef ecosystems.

Genetic and economic benefits of selection based on performance recording and genotyping in lower tiers of multi-tiered sheep breeding schemes.

PubMed

Santos, Bruno F S; van der Werf, Julius H J; Gibson, John P; Byrne, Timothy J; Amer, Peter R

2017-01-17

Performance recording and genotyping in the multiplier tier of multi-tiered sheep breeding schemes could potentially reduce the difference in the average genetic merit between nucleus and commercial flocks, and create additional economic benefits for the breeding structure. The genetic change in a multiple-trait breeding objective was predicted for various selection strategies that included performance recording, parentage testing and genomic selection. A deterministic simulation model was used to predict selection differentials and the flow of genetic superiority through the different tiers. Cumulative discounted economic benefits were calculated based on trait gains achieved in each of the tiers and considering the extra revenue and associated costs of applying recording, genotyping and selection practices in the multiplier tier of the breeding scheme. Performance recording combined with genomic or parentage information in the multiplier tier reduced the genetic lag between the nucleus and commercial flock by 2 to 3 years. The overall economic benefits of improved performance in the commercial tier offset the costs of recording the multiplier. However, it took more than 18 years before the cumulative net present value of benefits offset the costs at current test prices. Strategies in which recorded multiplier ewes were selected as replacements for the nucleus flock did modestly increase profitability when compared to a closed nucleus structure. Applying genomic selection is the most beneficial strategy if testing costs can be reduced or by genotyping only a proportion of the selection candidates. When the cost of genotyping was reduced, scenarios that combine performance recording with genomic selection were more profitable and reached breakeven point about 10 years earlier. Economic benefits can be generated in multiplier flocks by implementing performance recording in conjunction with either DNA pedigree recording or genomic technology. These recording practices reduce the long genetic lag between the nucleus and commercial flocks in multi-tiered breeding programs. Under current genotyping costs, the time to breakeven was found to be generally very long, although this varied between strategies. Strategies using either genomic selection or DNA pedigree verification were found to be economically viable provided the price paid for the tests is lower than current prices, in the long-term.

Recent Demographic History and Present Fine-Scale Structure in the Northwest Atlantic Leatherback (Dermochelys coriacea) Turtle Population

PubMed Central

Molfetti, Érica; Torres Vilaça, Sibelle; Georges, Jean-Yves; Plot, Virginie; Delcroix, Eric; Le Scao, Rozen; Lavergne, Anne; Barrioz, Sébastien; dos Santos, Fabrício Rodrigues; de Thoisy, Benoît

2013-01-01

The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic diversity and species history. PMID:23516429

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

PubMed Central

2014-01-01

Background The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe. Results Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD. Conclusions These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species. PMID:24581176

Evolution and connectivity in the world-wide migration system of the mallard: Inferences from mitochondrial DNA

PubMed Central

2011-01-01

Background Main waterfowl migration systems are well understood through ringing activities. However, in mallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere. Results Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (FST = 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero). Conclusions Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration. PMID:22093799

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Yellowstone bison genetics: let us move forward

USGS Publications Warehouse

Halbert, Natalie D.; Gogan, Peter J.P.; Hedrick, Philip W.; Wahl, Jacquelyn M.; Derr, James N.

2012-01-01

White and Wallen (2012) disagree with the conclusions and suggestions made in our recent assessment of population structure among Yellowstone National Park (YNP) bison based on 46 autosomal microsatellite loci in 661 animals (Halbert et al. 2012). First, they suggest that "the existing genetic substructure (that we observed) was artificially created." Specifically, they suggest that the substructure observed between the northern and central populations is the result of human activities, both historical and recent. In fact, the genetic composition of all known existing bison herds was created by, or has been influenced by, anthropogenic activities, although this obviously does not reduce the value of these herds for genetic conservation (Dratch and Gogan 2010). As perspective, many, if not most, species of conservation concern have been influenced by human actions and as a result currently exist as isolated populations. However, it is quite difficult to distinguish between genetic differences caused by human actions and important ancestral variation contained in separate populations without data from early time periods. Therefore, to not lose genetic variation that may be significant or indicative of important genetic variation, the generally acceptable management approach is to attempt to retain this variation based on the observed population genetic subdivision (Hedrick et al. 1986).

INTEGRATING GENETIC AND STRUCTURAL DATA ON HUMAN PROTEIN KINOME IN NETWORK-BASED MODELING OF KINASE SENSITIVITIES AND RESISTANCE TO TARGETED AND PERSONALIZED ANTICANCER DRUGS.

PubMed

Verkhivker, Gennady M

2016-01-01

The human protein kinome presents one of the largest protein families that orchestrate functional processes in complex cellular networks, and when perturbed, can cause various cancers. The abundance and diversity of genetic, structural, and biochemical data underlies the complexity of mechanisms by which targeted and personalized drugs can combat mutational profiles in protein kinases. Coupled with the evolution of system biology approaches, genomic and proteomic technologies are rapidly identifying and charactering novel resistance mechanisms with the goal to inform rationale design of personalized kinase drugs. Integration of experimental and computational approaches can help to bring these data into a unified conceptual framework and develop robust models for predicting the clinical drug resistance. In the current study, we employ a battery of synergistic computational approaches that integrate genetic, evolutionary, biochemical, and structural data to characterize the effect of cancer mutations in protein kinases. We provide a detailed structural classification and analysis of genetic signatures associated with oncogenic mutations. By integrating genetic and structural data, we employ network modeling to dissect mechanisms of kinase drug sensitivities to oncogenic EGFR mutations. Using biophysical simulations and analysis of protein structure networks, we show that conformational-specific drug binding of Lapatinib may elicit resistant mutations in the EGFR kinase that are linked with the ligand-mediated changes in the residue interaction networks and global network properties of key residues that are responsible for structural stability of specific functional states. A strong network dependency on high centrality residues in the conformation-specific Lapatinib-EGFR complex may explain vulnerability of drug binding to a broad spectrum of mutations and the emergence of drug resistance. Our study offers a systems-based perspective on drug design by unravelling complex relationships between robustness of targeted kinase genes and binding specificity of targeted kinase drugs. We discuss how these approaches can exploit advances in chemical biology and network science to develop novel strategies for rationally tailored and robust personalized drug therapies.

Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

PubMed

Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

2015-08-01

The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove invaluable in future studies linking the genetics of T. vaginalis with the clinical manifestation of trichomoniasis. Copyright © 2015 Elsevier B.V. All rights reserved.

A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera.

PubMed

Lal, Monal M; Southgate, Paul C; Jerry, Dean R; Bosserelle, Cyprien; Zenger, Kyall R

2016-01-01

Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.

Patterns of population structure and dispersal in the long-lived "redwood" of the coral reef, the giant barrel sponge ( Xestospongia muta)

NASA Astrophysics Data System (ADS)

Richards, Vincent P.; Bernard, Andrea M.; Feldheim, Kevin A.; Shivji, Mahmood S.

2016-09-01

Sponges are one of the dominant fauna on Florida and Caribbean coral reefs, with species diversity often exceeding that of scleractinian corals. Despite the key role of sponges as structural components, habitat providers, and nutrient recyclers in reef ecosystems, their dispersal dynamics are little understood. We used ten microsatellite markers to study the population structure and dispersal patterns of a prominent reef species, the giant barrel sponge ( Xestospongia muta), the long-lived "redwood" of the reef, throughout Florida and the Caribbean. F-statistics, exact tests of population differentiation, and Bayesian multi-locus genotype analyses revealed high levels of overall genetic partitioning ( F ST = 0.12, P = 0.001) and grouped 363 individuals collected from the Bahamas, Honduras, US Virgin Islands, Key Largo (Florida), and the remainder of the Florida reef tract into at minimum five genetic clusters ( K = 5). Exact tests, however, revealed further differentiation, grouping sponges sampled from five locations across the Florida reef tract (~250 km) into three populations, suggesting a total of six genetic populations across the eight locations sampled. Assignment tests showed dispersal over ecological timescales to be limited to relatively short distances, as the only migration detected among populations was within the Florida reef tract. Consequently, populations of this major coral reef benthic constituent appear largely self-recruiting. A combination of levels of genetic differentiation, genetic distance, and assignment tests support the important role of the Caribbean and Florida currents in shaping patterns of contemporary and historical gene flow in this widespread coral reef species.

NETWORK ASSISTED ANALYSIS TO REVEAL THE GENETIC BASIS OF AUTISM1

PubMed Central

Liu, Li; Lei, Jing; Roeder, Kathryn

2016-01-01

While studies show that autism is highly heritable, the nature of the genetic basis of this disorder remains illusive. Based on the idea that highly correlated genes are functionally interrelated and more likely to affect risk, we develop a novel statistical tool to find more potentially autism risk genes by combining the genetic association scores with gene co-expression in specific brain regions and periods of development. The gene dependence network is estimated using a novel partial neighborhood selection (PNS) algorithm, where node specific properties are incorporated into network estimation for improved statistical and computational efficiency. Then we adopt a hidden Markov random field (HMRF) model to combine the estimated network and the genetic association scores in a systematic manner. The proposed modeling framework can be naturally extended to incorporate additional structural information concerning the dependence between genes. Using currently available genetic association data from whole exome sequencing studies and brain gene expression levels, the proposed algorithm successfully identified 333 genes that plausibly affect autism risk. PMID:27134692

Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies.

PubMed

Bhaskar, Anand; Javanmard, Adel; Courtade, Thomas A; Tse, David

2017-03-15

Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either model-free algorithms, such as principal components analysis (PCA) and multidimensional scaling, or using explicit spatial probabilistic models of allele frequency evolution. We develop a general probabilistic model and an associated inference algorithm that unify the model-based and data-driven approaches to visualizing and inferring population structure. Our spatial inference algorithm can also be effectively applied to the problem of population stratification in genome-wide association studies (GWAS), where hidden population structure can create fictitious associations when population ancestry is correlated with both the genotype and the trait. Our algorithm Geographic Ancestry Positioning (GAP) relates local genetic distances between samples to their spatial distances, and can be used for visually discerning population structure as well as accurately inferring the spatial origin of individuals on a two-dimensional continuum. On both simulated and several real datasets from diverse human populations, GAP exhibits substantially lower error in reconstructing spatial ancestry coordinates compared to PCA. We also develop an association test that uses the ancestry coordinates inferred by GAP to accurately account for ancestry-induced correlations in GWAS. Based on simulations and analysis of a dataset of 10 metabolic traits measured in a Northern Finland cohort, which is known to exhibit significant population structure, we find that our method has superior power to current approaches. Our software is available at https://github.com/anand-bhaskar/gap . abhaskar@stanford.edu or ajavanma@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Advances in Autism

PubMed Central

Geschwind, Daniel H.

2013-01-01

Autism is a common childhood neurodevelopmental disorder with strong genetic liability. It is not a unitary entity but a clinical syndrome, with variable deficits in social behavior and language, restrictive interests, and repetitive behaviors. Recent advances in the genetics of autism emphasize its etiological heterogeneity, with each genetic susceptibility locus accounting for only a small fraction of cases or having a small effect. Therefore, it is not surprising that no unifying structural or neuropathological features have been conclusively identified. Given the heterogeneity of autism spectrum disorder (ASD), approaches based on studying heritable components of the disorder, or endophenotypes, such as language or social cognition, provide promising avenues for genetic and neurobiological investigations. Early intensive behavioral and cognitive interventions are efficacious in many cases, but autism does not remit in the majority of children. Therefore, development of targeted therapies based on pathophysiologically and etiologically defined subtypes of ASD remains an important and achievable goal of current research. PMID:19630577

Close genetic relationships in vast territories: autosomal and X chromosome Alu diversity in Yakuts from Siberia.

PubMed

Rocañín-Arjó, Ares; Rodríguez-Botigué, Laura; Esteban, Esther; Theves, Catherine; Evdokimova, Larissa E; Fedorova, Sardana A; Gibert, Morgane; Crubezy, Eric; Moral, Pedro

2013-01-01

Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations.

Autoimmunity in narcolepsy.

PubMed

Bonvalet, Melodie; Ollila, Hanna M; Ambati, Aditya; Mignot, Emmanuel

2017-11-01

Summarize the recent findings in narcolepsy focusing on the environmental and genetic risk factors in disease development. Both genetic and epidemiological evidence point towards an autoimmune mechanism in the destruction of orexin/hypocretin neurons. Recent studies suggest both humoral and cellular immune responses in the disease development. Narcolepsy is a severe sleep disorder, in which neurons producing orexin/hypocretin in the hypothalamus are destroyed. The core symptoms of narcolepsy are debilitating, extreme sleepiness, cataplexy, and abnormalities in the structure of sleep. Both genetic and epidemiological evidence point towards an autoimmune mechanism in the destruction of orexin/hypocretin neurons. Importantly, the highest environmental risk is seen with influenza-A infection and immunization. However, how the cells are destroyed is currently unknown. In this review we summarize the disease symptoms, and focus on the immunological findings in narcolepsy. We also discuss the environmental and genetic risk factors as well as propose a model for disease development.

Studies on the Pathophysiology and Genetic Basis of Migraine

PubMed Central

Gasparini, Claudia F; Sutherland, Heidi G.; Griffiths, Lyn R

2013-01-01

Migraine is a neurological disorder that affects the central nervous system causing painful attacks of headache. A genetic vulnerability and exposure to environmental triggers can influence the migraine phenotype. Migraine interferes in many facets of people’s daily life including employment commitments and their ability to look after their families resulting in a reduced quality of life. Identification of the biological processes that underlie this relatively common affliction has been difficult because migraine does not have any clearly identifiable pathology or structural lesion detectable by current medical technology. Theories to explain the symptoms of migraine have focused on the physiological mechanisms involved in the various phases of headache and include the vascular and neurogenic theories. In relation to migraine pathophysiology the trigeminovascular system and cortical spreading depression have also been implicated with supporting evidence from imaging studies and animal models. The objective of current research is to better understand the pathways and mechanisms involved in causing pain and headache to be able to target interventions. The genetic component of migraine has been teased apart using linkage studies and both candidate gene and genome-wide association studies, in family and case-control cohorts. Genomic regions that increase individual risk to migraine have been identified in neurological, vascular and hormonal pathways. This review discusses knowledge of the pathophysiology and genetic basis of migraine with the latest scientific evidence from genetic studies. PMID:24403849

Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge

PubMed Central

Martins, Joana; Vasconcelos, Vitor

2015-01-01

Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential. PMID:26580631

Ancient Divergence in the Trans-Oceanic Deep-Sea Shark Centroscymnus crepidater

PubMed Central

Cunha, Regina L.; Coscia, Ilaria; Madeira, Celine; Mariani, Stefano; Stefanni, Sergio; Castilho, Rita

2012-01-01

Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements. PMID:23145122

Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current.

PubMed

Kharbush, Jenan J; Ugalde, Juan A; Hogle, Shane L; Allen, Eric E; Aluwihare, Lihini I

2013-12-01

Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.

Trapped within the city: integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization.

PubMed

Lourenço, André; Álvarez, David; Wang, Ian J; Velo-Antón, Guillermo

2017-03-01

Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; N e ) and patch size on genetic diversity, population structure and contemporary N e . Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent N e declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary N e , while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted. © 2017 John Wiley & Sons Ltd.

Genetic studies of the Roma (Gypsies): a review

PubMed Central

Kalaydjieva, Luba; Gresham, David; Calafell, Francesc

2001-01-01

Background Data provided by the social sciences as well as genetic research suggest that the 8-10 million Roma (Gypsies) who live in Europe today are best described as a conglomerate of genetically isolated founder populations. The relationship between the traditional social structure observed by the Roma, where the Group is the primary unit, and the boundaries, demographic history and biological relatedness of the diverse founder populations appears complex and has not been addressed by population genetic studies. Results Recent medical genetic research has identified a number of novel, or previously known but rare conditions, caused by private founder mutations. A summary of the findings, provided in this review, should assist diagnosis and counselling in affected families, and promote future collaborative research. The available incomplete epidemiological data suggest a non-random distribution of disease-causing mutations among Romani groups. Conclusion Although far from systematic, the published information indicates that medical genetics has an important role to play in improving the health of this underprivileged and forgotten people of Europe. Reported carrier rates for some Mendelian disorders are in the range of 5 -15%, sufficient to justify newborn screening and early treatment, or community-based education and carrier testing programs for disorders where no therapy is currently available. To be most productive, future studies of the epidemiology of single gene disorders should take social organisation and cultural anthropology into consideration, thus allowing the targeting of public health programs and contributing to the understanding of population structure and demographic history of the Roma. PMID:11299048

Phylogeographic pattern suggests a general northeastward dispersal in the distribution of Machilus pauhoi in South China

PubMed Central

Zhu, Qin; Liao, Bo-Yong; Li, Pei; Li, Jun-Cheng; Deng, Xiao-Mei; Chen, Xiao-Yang

2017-01-01

Machilus pauhoi Kanehira is an important timber species in China. A provenance trial was recently set up to evaluate the growth performance of trees from different localities, with the aim of designing seed transfer guidelines. Here, we tested twelve nuclear microsatellite markers derived from other species of the Lauraceae family and investigated population genetic structure in M. pauhoi. Both the number of observed alleles per locus (Na) and the polymorphic information content (PIC) significantly decreased against the latitude, but showed an insignificant decrease against the longitude. Heterozygosity (Ho) and gene diversity (h) exhibited a weak correlation with geographic location. Private alleles were present in multiple populations, and a moderate level of population genetic differentiation was detected (Gst = 0.1691). The joint pattern of genetic diversity (Na, PIC, Ho, and h) suggests that general northeastward dispersal led to the current distribution of M. pauhoi. Significant but weak effects of isolation-by-distance (IBD) occurred, implicating the mountain ranges as the major barrier to gene flow. Both STRUCTURE and hierarchical clustering analyses showed three distinct groups of populations related to the physical connectivity among mountain ranges. A priority in designing genetic conservation should be given to the populations at the southwest side of the species’ distribution. This conservation strategy can also be combined with the pattern of adaptive genetic variation from the provenance trial for comprehensive genetic resource management of native M. pauhoi. PMID:28886133

Confluence of genes, environment, development, and behavior in a post Genome-Wide Association Study world.

PubMed

Vrieze, Scott I; Iacono, William G; McGue, Matt

2012-11-01

This article serves to outline a research paradigm to investigate main effects and interactions of genes, environment, and development on behavior and psychiatric illness. We provide a historical context for candidate gene studies and genome-wide association studies, including benefits, limitations, and expected payoffs. Using substance use and abuse as our driving example, we then turn to the importance of etiological psychological theory in guiding genetic, environmental, and developmental research, as well as the utility of refined phenotypic measures, such as endophenotypes, in the pursuit of etiological understanding and focused tests of genetic and environmental associations. Phenotypic measurement has received considerable attention in the history of psychology and is informed by psychometrics, whereas the environment remains relatively poorly measured and is often confounded with genetic effects (i.e., gene-environment correlation). Genetically informed designs, which are no longer limited to twin and adoption studies thanks to ever-cheaper genotyping, are required to understand environmental influences. Finally, we outline the vast amount of individual difference in structural genomic variation, most of which remains to be leveraged in genetic association tests. Although the genetic data can be massive and burdensome (tens of millions of variants per person), we argue that improved understanding of genomic structure and function will provide investigators with new tools to test specific a priori hypotheses derived from etiological psychological theory, much like current candidate gene research but with less confusion and more payoff than candidate gene research has to date.

Dissecting the phyloepidemiology of Trypanosoma cruzi I (TcI) in Brazil by the use of high resolution genetic markers.

PubMed

Roman, Fabiola; das Chagas Xavier, Samanta; Messenger, Louisa A; Pavan, Márcio G; Miles, Michael A; Jansen, Ana María; Yeo, Matthew

2018-05-01

Trypanosoma cruzi, the causal agent of Chagas disease, is monophyletic but genetically heterogeneous. It is currently represented by six genetic lineages (Discrete Typing Units, DTUs) designated TcI-TcVI. TcI is the most geographically widespread and genetically heterogeneous lineage, this as is evidenced by a wide range of genetic markers applied to isolates spanning a vast geographic range in Latin America. In total, 78 TcI isolated from hosts and vectors distributed in 5 different biomes of Brazil, were analyzed using 6 nuclear housekeeping genes, 25 microsatellite loci and one mitochondrial marker. Nuclear markers reveal substantial genetic diversity, significant gene flow between biomes, incongruence in phylogenies, and haplotypic analysis indicative of intra-DTU genetic exchange. Phylogenetic reconstructions based on mitochondrial and nuclear loci were incongruent, and consistent with introgression. Structure analysis of microsatellite data reveals that, amongst biomes, the Amazon is the most genetically diverse and experiences the lowest level of gene flow. Investigation of population structure based on the host species/genus, indicated that Didelphis marsupialis might play a role as the main disperser of TcI. The present work considers a large TcI sample from different hosts and vectors spanning multiple ecologically diverse biomes in Brazil. Importantly, we combine fast and slow evolving markers to contribute to the epizootiological understanding of TcI in five distinct Brazilian biomes. This constitutes the first instance in which MLST analysis was combined with the use of MLMT and maxicircle markers to evaluate the genetic diversity of TcI isolates in Brazil. Our results demonstrate the existence of substantial genetic diversity and the occurrence of introgression events. We provide evidence of genetic exchange in TcI isolates from Brazil and of the relative isolation of TcI in the Amazon biome. We observe the absence of strict associations with TcI genotypes to geographic areas and/or host species.

Dissecting the phyloepidemiology of Trypanosoma cruzi I (TcI) in Brazil by the use of high resolution genetic markers

PubMed Central

das Chagas Xavier, Samanta; Messenger, Louisa A.; Pavan, Márcio G.; Miles, Michael A.; Jansen, Ana María; Yeo, Matthew

2018-01-01

Background Trypanosoma cruzi, the causal agent of Chagas disease, is monophyletic but genetically heterogeneous. It is currently represented by six genetic lineages (Discrete Typing Units, DTUs) designated TcI-TcVI. TcI is the most geographically widespread and genetically heterogeneous lineage, this as is evidenced by a wide range of genetic markers applied to isolates spanning a vast geographic range in Latin America. Methodology/Principal findings In total, 78 TcI isolated from hosts and vectors distributed in 5 different biomes of Brazil, were analyzed using 6 nuclear housekeeping genes, 25 microsatellite loci and one mitochondrial marker. Nuclear markers reveal substantial genetic diversity, significant gene flow between biomes, incongruence in phylogenies, and haplotypic analysis indicative of intra-DTU genetic exchange. Phylogenetic reconstructions based on mitochondrial and nuclear loci were incongruent, and consistent with introgression. Structure analysis of microsatellite data reveals that, amongst biomes, the Amazon is the most genetically diverse and experiences the lowest level of gene flow. Investigation of population structure based on the host species/genus, indicated that Didelphis marsupialis might play a role as the main disperser of TcI. Conclusions/Significance The present work considers a large TcI sample from different hosts and vectors spanning multiple ecologically diverse biomes in Brazil. Importantly, we combine fast and slow evolving markers to contribute to the epizootiological understanding of TcI in five distinct Brazilian biomes. This constitutes the first instance in which MLST analysis was combined with the use of MLMT and maxicircle markers to evaluate the genetic diversity of TcI isolates in Brazil. Our results demonstrate the existence of substantial genetic diversity and the occurrence of introgression events. We provide evidence of genetic exchange in TcI isolates from Brazil and of the relative isolation of TcI in the Amazon biome. We observe the absence of strict associations with TcI genotypes to geographic areas and/or host species. PMID:29782493

Genetic studies of freshwater turtle and tortoises: a review of the past 70 years

USGS Publications Warehouse

FitzSimmons, Nancy N.; Hart, Kristen M.

2007-01-01

Powerful molecular techniques have been developed over many decades for resolving genetic relationships, population genetic structure, patterns of gene flow, mating systems, and the amount of genetic diversity in animals. Genetic studies of turtles were among the earliest and the rapid application of new genetic tools and analytical techniques is still apparent in the literature on turtles. At present, of the 198 freshwater turtles and tortoises that are listed as not extinct by the IUCN Red List, 69 species worldwide are listed as endangered or critically endangered, and an additional 56 species are listed as vulnerable. Of the ca. 300 species of the freshwater turtles and tortoises in the world, ca. 42% are considered to be facing a high risk extinction, and there is a need to focus intense conservation attention on these species. This includes a need to (i) assess our current state of knowledge regarding the application of genetics to studies of freshwater turtles and tortoises and (ii) determine future research directions. Here, we review all available published studies for the past 70 years that were written in English and used genetic markers (e.g. karyotypes, allozymes, DNA loci) to better understand the biology of freshwater turtles and tortoises. We review the types of studies conducted in relation to the species studied and quantify the countries where the studies were performed. We rack the changing use of different genetic markers through time and report on studies focused on aspects of molecular evolution within turtle genomes. We address the usefulness of particular genetic markers to answer phylogenetic questions and present data comparing population genetic structure and mating systems across species. We draw specific attention to whether authors have considered issues to turtle conservation in their research or provided new insights that have been translated into recommendations for conservation management.

Genetic diversity, structure and differentiation in cultivate walnut (Juglans regia L.)

Treesearch

M. Aradhya; K. Woeste; D. Velasco

2012-01-01

An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of walnut in Eurasia. Despite the narrow genetic...

Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation

USGS Publications Warehouse

Daniel P. Drinan,; Kalinowski, Steven T.; Vu, Ninh V.; Shepard, Bradley B.; Muhlfeld, Clint C.; Campbell, Matthew R.

2011-01-01

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei’s DS, populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention.

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection

PubMed Central

Guillamón, José M.; Barrio, Eladio

2017-01-01

The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties. PMID:28522998

Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

PubMed Central

Pérez-Alvarez, María José; Olavarría, Carlos; Moraga, Rodrigo; Baker, C. Scott; Hamner, Rebecca M.; Poulin, Elie

2015-01-01

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (FST = 0.15 and RST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies. PMID:25898340

Evaluating the role of Pleistocene refugia, rivers and environmental variation in the diversification of central African duikers (genera Cephalophus and Philantomba).

PubMed

Ntie, Stephan; Davis, Anne R; Hils, Katrin; Mickala, Patrick; Thomassen, Henri A; Morgan, Katy; Vanthomme, Hadrien; Gonder, Mary K; Anthony, Nicola M

2017-09-06

This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species (Cephalophus dorsalis, C. callipygus and Philantomba monticola). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci. Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola. The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation. Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species' capacity to adapt to environmental change.

Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America

PubMed Central

Liu, Jun-Jun; Sniezko, Richard; Murray, Michael; Wang, Ning; Chen, Hao; Zamany, Arezoo; Sturrock, Rona N.; Savin, Douglas; Kegley, Angelia

2016-01-01

Whitebark pine (WBP, Pinus albicaulis Engelm.) is an endangered conifer species due to heavy mortality from white pine blister rust (WPBR, caused by Cronartium ribicola) and mountain pine beetle (Dendroctonus ponderosae). Information about genetic diversity and population structure is of fundamental importance for its conservation and restoration. However, current knowledge on the genetic constitution and genomic variation is still limited for WBP. In this study, an integrated genomics approach was applied to characterize seed collections from WBP breeding programs in western North America. RNA-seq analysis was used for de novo assembly of the WBP needle transcriptome, which contains 97,447 protein-coding transcripts. Within the transcriptome, single nucleotide polymorphisms (SNPs) were discovered, and more than 22,000 of them were non-synonymous SNPs (ns-SNPs). Following the annotation of genes with ns-SNPs, 216 ns-SNPs within candidate genes with putative functions in disease resistance and plant defense were selected to design SNP arrays for high-throughput genotyping. Among these SNP loci, 71 were highly polymorphic, with sufficient variation to identify a unique genotype for each of the 371 individuals originating from British Columbia (Canada), Oregon and Washington (USA). A clear genetic differentiation was evident among seed families. Analyses of genetic spatial patterns revealed varying degrees of diversity and the existence of several genetic subgroups in the WBP breeding populations. Genetic components were associated with geographic variables and phenotypic rating of WPBR disease severity across landscapes, which may facilitate further identification of WBP genotypes and gene alleles contributing to local adaptation and quantitative resistance to WPBR. The WBP genomic resources developed here provide an invaluable tool for further studies and for exploitation and utilization of the genetic diversity preserved within this endangered conifer and other five-needle pines. PMID:27992468

CDPOP Users Manual

Treesearch

E. L. Landguth; B. K. Hand; J. M. Glassy; S. A. Cushman; M. Jacobi; T. J. Julian

2011-01-01

The goal of this user manual is to explain the technical aspects of the current release of the CDPOP program. CDPOP v1.0 is a major extension of the CDPOP program (Landguth and Cushman 2010). CDPOP is an individual-based program that simulates the influences of landscape structure on emergence of spatial patterns in population genetic data as functions of individual-...

Cassette structures associated with antibiotic resistance genes in Salmonella enterica isolated from processing plants, food animals, and retail meats

USDA-ARS?s Scientific Manuscript database

Slowing the spread of antibiotic resistance (AR) is one of the most urgent tasks currently facing the field of microbiology. Mobile genetic elements, like plasmids and integrons, allow AR genes to transfer horizontally, thus increasing the spread of AR genes. Determining which AR genes are found on ...

Self-digitization chip for single-cell genotyping of cancer-related mutations

PubMed Central

Monroe, Luke D.; Kreutz, Jason E.; Schneider, Thomas; Fujimoto, Bryant S.; Chiu, Daniel T.; Radich, Jerald P.; Paguirigan, Amy L.

2018-01-01

Cancer is a heterogeneous disease, and patient-level genetic assessments can guide therapy choice and impact prognosis. However, little is known about the impact of genetic variability within a tumor, intratumoral heterogeneity (ITH), on disease progression or outcome. Current approaches using bulk tumor specimens can suggest the presence of ITH, but only single-cell genetic methods have the resolution to describe the underlying clonal structures themselves. Current techniques tend to be labor and resource intensive and challenging to characterize with respect to sources of biological and technical variability. We have developed a platform using a microfluidic self-digitization chip to partition cells in stationary volumes for cell imaging and allele-specific PCR. Genotyping data from only confirmed single-cell volumes is obtained and subject to a variety of relevant quality control assessments such as allele dropout, false positive, and false negative rates. We demonstrate single-cell genotyping of the NPM1 type A mutation, an important prognostic indicator in acute myeloid leukemia, on single cells of the cell line OCI-AML3, describing a more complex zygosity distribution than would be predicted via bulk analysis. PMID:29718986

Self-digitization chip for single-cell genotyping of cancer-related mutations.

PubMed

Thompson, Alison M; Smith, Jordan L; Monroe, Luke D; Kreutz, Jason E; Schneider, Thomas; Fujimoto, Bryant S; Chiu, Daniel T; Radich, Jerald P; Paguirigan, Amy L

2018-01-01

Cancer is a heterogeneous disease, and patient-level genetic assessments can guide therapy choice and impact prognosis. However, little is known about the impact of genetic variability within a tumor, intratumoral heterogeneity (ITH), on disease progression or outcome. Current approaches using bulk tumor specimens can suggest the presence of ITH, but only single-cell genetic methods have the resolution to describe the underlying clonal structures themselves. Current techniques tend to be labor and resource intensive and challenging to characterize with respect to sources of biological and technical variability. We have developed a platform using a microfluidic self-digitization chip to partition cells in stationary volumes for cell imaging and allele-specific PCR. Genotyping data from only confirmed single-cell volumes is obtained and subject to a variety of relevant quality control assessments such as allele dropout, false positive, and false negative rates. We demonstrate single-cell genotyping of the NPM1 type A mutation, an important prognostic indicator in acute myeloid leukemia, on single cells of the cell line OCI-AML3, describing a more complex zygosity distribution than would be predicted via bulk analysis.

A weighted U statistic for association analyses considering genetic heterogeneity.

PubMed

Wei, Changshuai; Elston, Robert C; Lu, Qing

2016-07-20

Converging evidence suggests that common complex diseases with the same or similar clinical manifestations could have different underlying genetic etiologies. While current research interests have shifted toward uncovering rare variants and structural variations predisposing to human diseases, the impact of heterogeneity in genetic studies of complex diseases has been largely overlooked. Most of the existing statistical methods assume the disease under investigation has a homogeneous genetic effect and could, therefore, have low power if the disease undergoes heterogeneous pathophysiological and etiological processes. In this paper, we propose a heterogeneity-weighted U (HWU) method for association analyses considering genetic heterogeneity. HWU can be applied to various types of phenotypes (e.g., binary and continuous) and is computationally efficient for high-dimensional genetic data. Through simulations, we showed the advantage of HWU when the underlying genetic etiology of a disease was heterogeneous, as well as the robustness of HWU against different model assumptions (e.g., phenotype distributions). Using HWU, we conducted a genome-wide analysis of nicotine dependence from the Study of Addiction: Genetics and Environments dataset. The genome-wide analysis of nearly one million genetic markers took 7h, identifying heterogeneous effects of two new genes (i.e., CYP3A5 and IKBKB) on nicotine dependence. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Parents’ experiences of receiving their child’s genetic diagnosis: A qualitative study to inform clinical genetics practice

PubMed Central

Ashtiani, Setareh; Makela, Nancy; Carrion, Prescilla; Austin, Jehannine

2014-01-01

Purpose Little is currently known about how parents experience the medical genetics appointment at which their child receives a genetic diagnosis. Methods We conducted semi-structured in-person interviews with 13 parents of 10 index children to explore their experience in the medical genetics appointment in which they received their child’s genetic diagnosis. Guided by grounded theory, we used a constant comparative approach to data analysis, and the transcribed interviews were coded and sorted, and thematic categories identified. Results 61.5% of parents experienced the diagnosis session as negative, 23% felt the experience was positive, and 15.5% were ambivalent. Receiving emotional support, an outline of the follow-up plans, and messages of hope and perspective during the session seemed to positively influence parents’ experience, while feeling that their role was as a passive receiver of information and using difficult medical terminology negatively influenced parents’ overall experience. Parental preparedness for the information, and the parents’ emotional reaction to the diagnosis were also factors that influenced the parental experience. Few participants understood the role of the genetic counselor. Conclusion Our results provide in-depth insight into the parental experience of the pediatric medical genetics diagnosis session. We propose a mechanism through which parental experience shapes their perception of the medical genetics session. PMID:24706543

Benefits and Limitations of Prenatal Screening for Prader-Willi Syndrome

PubMed Central

Butler, Merlin G.

2016-01-01

This review the status of genetic laboratory testing in Prader-Willi syndrome (PWS) due to different genetic subtypes, most often a paternally derived 15q11-q13 deletion, with benefits and limitations related to prenatal screening. Medical literature was searched for prenatal screening and genetic laboratory testing methods in use or under development and discussed in relationship to PWS. Genetic testing includes six established laboratory diagnostic approaches for PWS with direct application to prenatal screening. Ultrasonographic, obstetric and cytogenetic reports were summarized in relationship to the cause of Prader-Willi syndrome and identification of specific genetic subtypes including maternal disomy 15. Advances in genetic technology were described for diagnosing PWS specifically DNA methylation and high-resolution chromosomal SNP microarrays as current tools for genetic screening and incorporating next generation DNA sequencing for noninvasive prenatal testing (NIPT) using cell-free fetal DNA. Positive experiences are reported with NIPT for detection of numerical chromosomal problems (aneuploidies) but not for structural problems (microdeletions). These reports will be discussed along with future directions for genetic screening of PWS. In summary, this review describes and discusses the status of established and ongoing genetic testing options for PWS applicable in prenatal screening including NIPT and future directions for early diagnosis in Prader-Willi syndrome. PMID:27537837

Benefits and limitations of prenatal screening for Prader-Willi syndrome.

PubMed

Butler, Merlin G

2017-01-01

This review summarizes the status of genetic laboratory testing in Prader-Willi syndrome (PWS) with different genetic subtypes, most often a paternally derived 15q11-q13 deletion and discusses benefits and limitations related to prenatal screening. Medical literature was searched for prenatal screening and genetic laboratory testing methods in use or under development and discussed in relationship to PWS. Genetic testing includes six established laboratory diagnostic approaches for PWS with direct application to prenatal screening. Ultrasonographic, obstetric and cytogenetic reports were summarized in relationship to the cause of PWS and identification of specific genetic subtypes including maternal disomy 15. Advances in genetic technology were described for diagnosing PWS specifically DNA methylation and high-resolution chromosomal SNP microarrays as current tools for genetic screening and incorporating next generation DNA sequencing for noninvasive prenatal testing (NIPT) using cell-free fetal DNA. Positive experiences are reported with NIPT for detection of numerical chromosomal problems (aneuploidies) but not for structural problems (microdeletions). These reports will be discussed along with future directions for genetic screening of PWS. In summary, this review describes and discusses the status of established and ongoing genetic testing options for PWS applicable in prenatal screening including NIPT and future directions for early diagnosis in PWS. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

Structural and functional organization of growing tips of Neurospora crassa Hyphae.

PubMed

Potapova, T V

2014-07-01

Data are presented on a variety of intracellular structures of the vegetative hyphae of the filamentous fungus Neurospora crassa and the involvement of these structures in the tip growth of the hyphae. Current ideas on the molecular and genetic mechanisms of tip growth and regulation of this process are considered. On the basis of comparison of data on behaviors of mitochondria and microtubules and data on the electrical heterogeneity of the hyphal apex, a hypothesis is proposed about a possible supervisory role of the longitudinal electric field in the structural and functional organization of growing tips of the N. crassa hyphae.

Molecular characterization and population structure study of cambuci: strategy for conservation and genetic improvement.

PubMed

Santos, D N; Nunes, C F; Setotaw, T A; Pio, R; Pasqual, M; Cançado, G M A

2016-12-19

Cambuci (Campomanesia phaea) belongs to the Myrtaceae family and is native to the Atlantic Forest of Brazil. It has ecological and social appeal but is exposed to problems associated with environmental degradation and expansion of agricultural activities in the region. Comprehensive studies on this species are rare, making its conservation and genetic improvement difficult. Thus, it is important to develop research activities to understand the current situation of the species as well as to make recommendations for its conservation and use. This study was performed to characterize the cambuci accessions found in the germplasm bank of Coordenadoria de Assistência Técnica Integral using inter-simple sequence repeat markers, with the goal of understanding the plant's population structure. The results showed the existence of some level of genetic diversity among the cambuci accessions that could be exploited for the genetic improvement of the species. Principal coordinate analysis and discriminant analysis clustered the 80 accessions into three groups, whereas Bayesian model-based clustering analysis clustered them into two groups. The formation of two cluster groups and the high membership coefficients within the groups pointed out the importance of further collection to cover more areas and more genetic variability within the species. The study also showed the lack of conservation activities; therefore, more attention from the appropriate organizations is needed to plan and implement natural and ex situ conservation activities.

Turtle groups or turtle soup: dispersal patterns of hawksbill turtles in the Caribbean.

PubMed

Blumenthal, J M; Abreu-Grobois, F A; Austin, T J; Broderick, A C; Bruford, M W; Coyne, M S; Ebanks-Petrie, G; Formia, A; Meylan, P A; Meylan, A B; Godley, B J

2009-12-01

Despite intense interest in conservation of marine turtles, spatial ecology during the oceanic juvenile phase remains relatively unknown. Here, we used mixed stock analysis and examination of oceanic drift to elucidate movements of hawksbill turtles (Eretmochelys imbricata) and address management implications within the Caribbean. Among samples collected from 92 neritic juvenile hawksbills in the Cayman Islands we detected 11 mtDNA control region haplotypes. To estimate contributions to the aggregation, we performed 'many-to-many' mixed stock analysis, incorporating published hawksbill genetic and population data. The Cayman Islands aggregation represents a diverse mixed stock: potentially contributing source rookeries spanned the Caribbean basin, delineating a scale of recruitment of 200-2500 km. As hawksbills undergo an extended phase of oceanic dispersal, ocean currents may drive patterns of genetic diversity observed on foraging aggregations. Therefore, using high-resolution Aviso ocean current data, we modelled movement of particles representing passively drifting oceanic juvenile hawksbills. Putative distribution patterns varied markedly by origin: particles from many rookeries were broadly distributed across the region, while others would appear to become entrained in local gyres. Overall, we detected a significant correlation between genetic profiles of foraging aggregations and patterns of particle distribution produced by a hatchling drift model (Mantel test, r = 0.77, P < 0.001; linear regression, r = 0.83, P < 0.001). Our results indicate that although there is a high degree of mixing across the Caribbean (a 'turtle soup'), current patterns play a substantial role in determining genetic structure of foraging aggregations (forming turtle groups). Thus, for marine turtles and other widely distributed marine species, integration of genetic and oceanographic data may enhance understanding of population connectivity and management requirements.

Biological variation in musculoskeletal injuries: current knowledge, future research and practical implications.

PubMed

Collins, Malcolm; September, Alison V; Posthumus, Michael

2015-12-01

Evidence from familial and genetic association studies have reported that DNA sequence variants play an important role, together with non-genetic factors, in the aetiology of both exercise-associated and occupational-associated acute and chronic musculoskeletal soft tissue injuries. The associated variants, which have been identified to date, may contribute to the interindividual variation in the structure and, by implication, mechanical properties of the collagen fibril and surrounding matrix within musculoskeletal soft tissues, as well as their response to mechanical loading and other stimuli. Future work should focus on the establishment of multidisciplinary international consortia for the identification of biologically relevant variants involved in modulating injury risk. These consortia will improve the limitations of the published hypothesis-driven genetic association studies, since they will allow resources to be pooled in recruiting large well-characterised cohorts required for whole-genome screening. Finally, clinicians and coaches need to be aware that many direct-to-consumer companies are currently marketing genetic tests directly to athletes without it being requested by an appropriately qualified healthcare professional, and without interpretation alongside other clinical indicators or lifestyle factors. These specific genetic tests are premature and are not necessarily required to evaluate susceptibility to musculoskeletal soft tissue injury. Current practice should rather consider susceptibility through known risk factors such as a positive family history of a specific injury, a history of other tendon and/or ligament injuries and participation in activities associated with the specific musculoskeletal injuries. Potential susceptible athletes may then be individually managed to reduce their risk profile. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

The Epigenetics of Adult (Somatic) Stem Cells

PubMed Central

Eilertsen, Kenneth J.; Floyd, Z. Elizabeth; Gimble, Jeffrey M.

2009-01-01

While genetic studies have provided a wealth of information about health and disease, there is a growing awareness that individual characteristics are also determined by factors other than genetic sequences. These “epigenetic” changes broadly encompass the influence of the environment on gene regulation and expression and in a more narrow sense, describe the mechanisms controlling DNA methylation, histone modification and genetic imprinting. In this review, we focus on the epigenetic mechanisms that regulate adult (somatic) stem cell differentiation, beginning with the metabolic pathways and factors regulating chromatin structure and DNA methylation and the molecular biological tools that are currently available to study these processes. The role of these epigenetic mechanisms in manipulating adult stem cells is followed by a discussion of the challenges and opportunities facing this emerging field. PMID:18540823

Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity.

PubMed

Dendrou, Calliope A; Cortes, Adrian; Shipman, Lydia; Evans, Hayley G; Attfield, Kathrine E; Jostins, Luke; Barber, Thomas; Kaur, Gurman; Kuttikkatte, Subita Balaram; Leach, Oliver A; Desel, Christiane; Faergeman, Soren L; Cheeseman, Jane; Neville, Matt J; Sawcer, Stephen; Compston, Alastair; Johnson, Adam R; Everett, Christine; Bell, John I; Karpe, Fredrik; Ultsch, Mark; Eigenbrot, Charles; McVean, Gil; Fugger, Lars

2016-11-02

Thousands of genetic variants have been identified, which contribute to the development of complex diseases, but determining how to elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders; subsequent molecular, cellular, in vivo, and structural functional follow-up; and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for certain common autoimmune disorders. Copyright © 2016, American Association for the Advancement of Science.

Saturation of recognition elements blocks evolution of new tRNA identities

PubMed Central

Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D.; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A.; Ribas de Pouplana, Lluís

2016-01-01

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. PMID:27386510

Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations.

PubMed

Wientjes, Yvonne C J; Bijma, Piter; Vandenplas, Jérémie; Calus, Mario P L

2017-10-01

Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. Copyright © 2017 by the Genetics Society of America.

IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific.

PubMed

Dudgeon, C L; Broderick, D; Ovenden, J R

2009-01-01

The Indo-West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum, is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: 'Least Concern' and 'Vulnerable'. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric F(ST) analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.

Between (Racial) Groups and a Hard Place: An Exploration of Social Science Approaches to Race and Genetics, 2000-2014.

PubMed

Byrd, W Carson; Best, Latrica E

2016-01-01

As the social sciences expand their involvement in genetic and genomic research, more information is needed to understand how theoretical concepts are applied to genetic data found in social surveys. Given the layers of complexity of studying race in relation to genetics and genomics, it is important to identify the varying approaches used to discuss and operationalize race and identity by social scientists. The present study explores how social scientists have used race, ethnicity, and ancestry in studies published in four social science journals from 2000 to 2014. We identify not only how race, ethnicity, and ancestry are classified and conceptualized in this growing area of research, but also how these concepts are incorporated into the methodology and presentation of results, all of which structure the discussion of race, identity, and inequality. This research indicates the slippage between concepts, classifications, and their use by social scientists in their genetics-related research. The current study can assist social scientists with clarifying their use and interpretations of race and ethnicity with the incorporation of genetic data, while limiting possible misinterpretations of the complexities of the connection between genetics and the social world.

History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae).

PubMed

Roberts, Trina E

2006-07-01

The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea-crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long-term processes rather than simply reflecting current conditions.

Headwater Capture Evidenced by Paleo-Rivers Reconstruction and Population Genetic Structure of the Armored Catfish (Pareiorhaphis garbei) in the Serra do Mar Mountains of Southeastern Brazil

PubMed Central

Lima, Sergio M. Q.; Berbel-Filho, Waldir M.; Araújo, Thais F. P.; Lazzarotto, Henrique; Tatarenkov, Andrey; Avise, John C.

2017-01-01

Paleo-drainage connections and headwater stream-captures are two main historical processes shaping the distribution of strictly freshwater fishes. Recently, bathymetric-based methods of paleo-drainage reconstruction have opened new possibilities to investigate how these processes have shaped the genetic structure of freshwater organisms. In this context, the present study used paleo-drainage reconstructions and single-locus cluster delimitation analyses to examine genetic structure on the whole distribution of Pareiorhaphis garbei, a ‘near threatened’ armored catfish from the Fluminense freshwater ecoregion in Southeastern Brazil. Sequences of two mitochondrial genes (cytochrome b and cytochrome c oxidase subunit 1) were obtained from five sampling sites in four coastal drainages: Macaé (KAE), São João (SJO), Guapi-Macacu [sub-basins Guapiaçu (GAC) and Guapimirim (GMI)], and Santo Aleixo (SAL). Pronounced genetic structure was found, involving 10 haplotypes for cytB and 6 for coi, with no haplotypes shared between localities. Coalescent-based delineation methods as well as distance-based methods revealed genetic clusters corresponding to each sample site. Paleo-drainage reconstructions showed two putative paleo-rivers: an eastern one connecting KAE and SJO; and a western one merging in the Guanabara Bay (GAC, GMI, and SAL). A disagreement was uncovered between the inferred past riverine connections and current population genetic structure. Although KAE and SJO belong to the same paleo-river, the latter is more closely related to specimens from the Guanabara paleo-river. This discordance between paleo-drainage connections and phylogenetic structure may indicate an ancient stream-capture event in headwaters of this region. Furthermore, all analyses showed high divergence between KAE and the other lineages, suggesting at least one cryptic species in the latter, and that the nominal species should be restricted to the Macaé river basin, its type locality. In this drainage, impacts such as the invasive species and habitat loss can be especially threatening for such species with a narrow range. Our results also suggest that freshwater fishes from headwaters in the Serra do Mar mountains might have different biogeographical patterns than those from the lowlands, indicating a complex and dynamic climatic and geomorphological history. PMID:29259623

Headwater Capture Evidenced by Paleo-Rivers Reconstruction and Population Genetic Structure of the Armored Catfish (Pareiorhaphis garbei) in the Serra do Mar Mountains of Southeastern Brazil.

PubMed

Lima, Sergio M Q; Berbel-Filho, Waldir M; Araújo, Thais F P; Lazzarotto, Henrique; Tatarenkov, Andrey; Avise, John C

2017-01-01

Paleo-drainage connections and headwater stream-captures are two main historical processes shaping the distribution of strictly freshwater fishes. Recently, bathymetric-based methods of paleo-drainage reconstruction have opened new possibilities to investigate how these processes have shaped the genetic structure of freshwater organisms. In this context, the present study used paleo-drainage reconstructions and single-locus cluster delimitation analyses to examine genetic structure on the whole distribution of Pareiorhaphis garbei , a 'near threatened' armored catfish from the Fluminense freshwater ecoregion in Southeastern Brazil. Sequences of two mitochondrial genes (cytochrome b and cytochrome c oxidase subunit 1) were obtained from five sampling sites in four coastal drainages: Macaé (KAE), São João (SJO), Guapi-Macacu [sub-basins Guapiaçu (GAC) and Guapimirim (GMI)], and Santo Aleixo (SAL). Pronounced genetic structure was found, involving 10 haplotypes for cytB and 6 for coi , with no haplotypes shared between localities. Coalescent-based delineation methods as well as distance-based methods revealed genetic clusters corresponding to each sample site. Paleo-drainage reconstructions showed two putative paleo-rivers: an eastern one connecting KAE and SJO; and a western one merging in the Guanabara Bay (GAC, GMI, and SAL). A disagreement was uncovered between the inferred past riverine connections and current population genetic structure. Although KAE and SJO belong to the same paleo-river, the latter is more closely related to specimens from the Guanabara paleo-river. This discordance between paleo-drainage connections and phylogenetic structure may indicate an ancient stream-capture event in headwaters of this region. Furthermore, all analyses showed high divergence between KAE and the other lineages, suggesting at least one cryptic species in the latter, and that the nominal species should be restricted to the Macaé river basin, its type locality. In this drainage, impacts such as the invasive species and habitat loss can be especially threatening for such species with a narrow range. Our results also suggest that freshwater fishes from headwaters in the Serra do Mar mountains might have different biogeographical patterns than those from the lowlands, indicating a complex and dynamic climatic and geomorphological history.

Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice

PubMed Central

Janecka, Magdalena; Marzi, Sarah J.; Parsons, Michael J.; Liu, Lin; Paya-Cano, Jose L.; Smith, Rebecca G.; Fernandes, Cathy; Schalkwyk, Leonard C.

2017-01-01

Although the search for quantitative trait loci for behaviour remains a considerable challenge, the complicated genetic architecture of quantitative traits is beginning to be understood. The current project utilised heterogeneous stock (HS) male mice (n = 580) to investigate the genetic basis for brain weights, activity, anxiety and cognitive phenotypes. We identified 126 single nucleotide polymorphisms (SNPs) in genes involved in regulation of neurotransmitter systems, nerve growth/death and gene expression, and subsequently investigated their associations with changes in behaviour and/or brain weights in our sample. We found significant associations between four SNP-phenotype pairs, after controlling for multiple testing. Specificity protein 2 (Sp2, rs3708840), tryptophan hydroxylase 1 (Tph1, rs262731280) and serotonin receptor 3A (Htr3a, rs50670893) were associated with activity/anxiety behaviours, and microtubule-associated protein 2 (Map2, rs13475902) was associated with cognitive performance. All these genes except for Tph1 were expressed in the brain above the array median, and remained significantly associated with relevant behaviours after controlling for the family structure. Additionally, we found evidence for a correlation between Htr3a expression and activity. We discuss our findings in the light of the advantages and limitations of currently available mouse genetic tools, suggesting further directions for association studies in rodents. PMID:28145470

Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus.

PubMed

Wang, W; Qiao, Y; Li, S; Pan, W; Yao, M

2017-06-01

Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

A double-edged sword: advantages and disadvantages to the current emphasis on biogenetic causes of child psychopathology.

PubMed

Burt, S Alexandra

2015-02-01

Research on child psychopathology is a largely biogenetic endeavor these days, at least according to current funding priorities at the National Institutes of Health in the US. This heavy focus on genetic contributions to child psychopathology has some real advantages. Available research has conclusively indicated that child and adolescent mental health problems are partially genetic in origin and, moreover, are related to neural structure and function (as an example, see Plomin et al.). Moreover, these genetic effects may be responsible for some previously reported 'environmental' effects, such that, what appear to be direct environmental risk factors may in fact reflect genetic/familial risks. As one example, Sengupta et al. (this issue) found that maternal smoking during pregnancy was in fact a marker of maternal and paternal psychopathology. Put another way, the association between ADHD and maternal smoking during pregnancy may index a genetic/familial risk for a more severe form of ADHD, rather than a direct effect of uterine exposure to cigarettes. A final, more subtle reason for the current trend towards biogenetic research is that it has the rarely-discussed but all-too-important 'allure of the unknown'. We have only just recently been able to directly explore the biological underpinnings of psychopathology; and as technology advances, so too will the insights gained (presumably). This offers both funding agencies and individual scientists the very real possibility of making a major new discovery - a siren's call for most of us. In sharp contrast, decades of research have explored putatively environmental contributions to child and adolescent psychopathology. New paradigm-shifting discoveries are thus likely to be fewer in number and farther between (if we continue using traditional study designs that omit joint consideration of biology, that is). In short, biogenetic research just feels more cutting edge at the moment. The clear merits of such work notwithstanding, there are a number of critical disadvantages to the current emphasis on genetics. These issues are presented below, not necessarily in order of importance. © 2015 Association for Child and Adolescent Mental Health.

The Anorexia Nervosa Genetics Initiative: Study description and sample characteristics of the Australian and New Zealand arm.

PubMed

Kirk, Katherine M; Martin, Felicity C; Mao, Amy; Parker, Richard; Maguire, Sarah; Thornton, Laura M; Zhu, Gu; McAloney, Kerrie; Freeman, Jeremy L; Hay, Phillipa; Madden, Sloane; Morgan, Christine; Russell, Janice; Sawyer, Susan M; Hughes, Elizabeth K; Fairweather-Schmidt, A Kate; Fursland, Anthea; McCormack, Julie; Wagg, Fiona; Jordan, Jennifer; Kennedy, Martin A; Ward, Warren; Wade, Tracey D; Bulik, Cynthia M; Martin, Nicholas G

2017-06-01

Anorexia nervosa is a severe psychiatric disorder with high mortality rates. While its aetiology is poorly understood, there is evidence of a significant genetic component. The Anorexia Nervosa Genetics Initiative is an international collaboration which aims to understand the genetic basis of the disorder. This paper describes the recruitment and characteristics of the Australasian Anorexia Nervosa Genetics Initiative sample, the largest sample of individuals with anorexia nervosa ever assembled across Australia and New Zealand. Participants completed an online questionnaire based on the Structured Clinical Interview Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) eating disorders section. Participants who met specified case criteria for lifetime anorexia nervosa were requested to provide a DNA sample for genetic analysis. Overall, the study recruited 3414 Australians and 543 New Zealanders meeting the lifetime anorexia nervosa case criteria by using a variety of conventional and social media recruitment methods. At the time of questionnaire completion, 28% had a body mass index ⩽ 18.5 kg/m 2 . Fasting and exercise were the most commonly employed methods of weight control, and were associated with the youngest reported ages of onset. At the time of the study, 32% of participants meeting lifetime anorexia nervosa case criteria were under the care of a medical practitioner; those with current body mass index < 18.5 kg/m 2 were more likely to be currently receiving medical care (56%) than those with current body mass index ⩾ 18.5 kg/m 2 (23%). Professional treatment for eating disorders was most likely to have been received from general practitioners (45% of study participants), dietitians (42%) and outpatient programmes (42%). This study was effective in assembling the largest community sample of people with lifetime anorexia nervosa in Australia and New Zealand to date. The proportion of people with anorexia nervosa currently receiving medical care, and the most common sources of treatment accessed, indicates the importance of training for general practitioners and dietitians in treating anorexia nervosa.

Ternary alloy material prediction using genetic algorithm and cluster expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Chong

2015-12-01

This thesis summarizes our study on the crystal structures prediction of Fe-V-Si system using genetic algorithm and cluster expansion. Our goal is to explore and look for new stable compounds. We started from the current ten known experimental phases, and calculated formation energies of those compounds using density functional theory (DFT) package, namely, VASP. The convex hull was generated based on the DFT calculations of the experimental known phases. Then we did random search on some metal rich (Fe and V) compositions and found that the lowest energy structures were body centered cube (bcc) underlying lattice, under which we didmore » our computational systematic searches using genetic algorithm and cluster expansion. Among hundreds of the searched compositions, thirteen were selected and DFT formation energies were obtained by VASP. The stability checking of those thirteen compounds was done in reference to the experimental convex hull. We found that the composition, 24-8-16, i.e., Fe 3VSi 2 is a new stable phase and it can be very inspiring to the future experiments.« less

Do (epi)genetics impact the brain in functional neurologic disorders?

PubMed

Frodl, T

2016-01-01

Advances in neuropsychiatric research are supposed to lead to significant improvements in understanding functional neurologic disorders and their diagnosis. However, epigenetic and genetic research on conversion disorders and somatoform disorders is only at its start. This review demonstrates the current state within this field and tries to bridge a gap from what is known on gene-stress interactions in other psychiatric disorders like depression. The etiology of conversion disorders is hypothesized to be multifactorial. These considerations also suggest that potential etiologic factors lead to alterations in brain function, either episodically or chronically, eventually leading to structural brain changes. In particular, the knowledge of how the environment influences brain structure and function, e.g., via epigenetic regulation, may be interesting for future research in functional neurologic disorders. Reviewing the literature results in evidence that childhood adversities play a role in the development of functional neurologic disorders, whereby at present no reports exist about the interactive effect between childhood adversity and genetic factors or about the impact of epigenetics. © 2016 Elsevier B.V. All rights reserved.

Geographical genetic structuring and phenotypic variation in the Vellozia hirsuta (Velloziaceae) ochlospecies complex.

PubMed

Barbosa, Ariane R; Fiorini, Cecília F; Silva-Pereira, Viviane; Mello-Silva, Renato; Borba, Eduardo L

2012-09-01

Vellozia hirsuta forms a complex presenting wide morphological and anatomical variation, resulting in five specific names and 14 morpho-anatomical patterns occurring in disjunct populations. We carried out a phylogeographical study to investigate the existence of correlation among the genetic and morphological patterns within this complex, and to determine whether it is composed of various species or should be treated as an ochlospecies, a species having widely polymorphic and weakly polytypic complex variation, with morphological characteristics varying independently. We carried out phylogeographical analyses using cpDNA rpl32F-trnL intergenic region. We found 20 haplotypes in 23 populations sampled. The populations are genetically structured (Φ(ST) = 0.818) into four phylogeographical groups demonstrating geographical structuring but with no correlation with morpho-anatomical patterns. Our analyses do not support recognizing any of the species now synonymized under Vellozia hirsuta. The northern populations were the most genetically differentiated and could be considered a distinct taxon, as they are also morphologically different. It is recommended that Vellozia hirsuta be considered a single enormously variable species. The patterns of variation within V. hirsuta probably are related to climatic changes that occurred during the Pleistocene Epoch in tropical Brazil when reductions in forest cover favored the expansion of V. hirsuta populations into extensive lowland areas. The expansion of forest cover at the end of the glaciations would have again restricted the occurrence of campos rupestres vegetation to high elevations, which constitute the current centers of diversity of this species.

A population on the rise: The origin of deepwater sculpin in Lake Ontario

USGS Publications Warehouse

Welsh, Amy B.; Scribner, Kim T.; Stott, Wendylee; Walsh, Maureen

2017-01-01

Deepwater sculpin, Myoxocephalus thompsonii, were thought to have been extirpated from Lake Ontario. However, in recent years, abundance has increased and recruitment has been documented. There are two hypotheses concerning the origin of the current Lake Ontario deepwater sculpin population. First, individuals from the upper Great Lakes may have recolonized Lake Ontario. Alternatively, the Lake Ontario population may have not been extirpated, and the remnant population has recovered naturally. To test these hypotheses, eight microsatellite loci were used to analyze samples from the current Lake Ontario population, museum specimens from the historic Lake Ontario population, and current upper Great Lakes populations. The genetic data suggest that historically throughout the Great Lakes, deepwater sculpin exhibited low levels of spatial genetic structure. Approximate Bayesian Computation analyses support the hypothesis that the current Lake Ontario population is more closely related to populations in the upper Great Lakes than to the historic Lake Ontario samples, indicating that the current Lake Ontario population likely resulted from recolonization from the Upper Great Lakes. The current Lake Ontario population has reduced allelic diversity relative to upper Great Lakes populations, indicating a possible founder effect. This study demonstrates the role life history variation can play in recolonization success. The pelagic larval phase of the deepwater sculpin allowed recolonization of Lake Ontario via passive larval drift.

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change

USGS Publications Warehouse

Sork, Victoria L.; Davis, Frank W.; Westfall, Robert; Flint, Alan L.; Ikegami, Makihiko; Wang, Hongfang; Grivet, Delphine

2010-01-01

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata N??e, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions. ?? 2010 Blackwell Publishing Ltd.

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change.

PubMed

Sork, Victoria L; Davis, Frank W; Westfall, Robert; Flint, Alan; Ikegami, Makihiko; Wang, Hongfang; Grivet, Delphine

2010-09-01

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions.

Restoration of genetic connectivity among Northern Rockies wolf populations.

PubMed

Hebblewhite, Mark; Musiani, Marco; Mills, L Scott

2010-10-01

Probably no conservation genetics issue is currently more controversial than the question of whether grey wolves (Canis lupus) in the Northern Rockies have recovered to genetically effective levels. Following the dispersal-based recolonization of Northwestern Montana from Canada, and reintroductions to Yellowstone and Central Idaho, wolves have vastly exceeded population recovery goals of 300 wolves distributed in at least 10 breeding pairs in each of Wyoming, Idaho and Montana. With >1700 wolves currently, efforts to delist wolves from endangered status have become mired in legal battles over the distinct population segment (DPS) clause of the Endangered Species Act (ESA), and whether subpopulations within the DPS were genetically isolated. An earlier study by vonHoldt et al. (2008) suggested Yellowstone National Park wolves were indeed isolated and was used against delisting in 2008. Since then, wolves were temporarily delisted, and a first controversial hunting season occurred in fall of 2009. Yet, concerns over the genetic recovery of wolves in the Northern Rockies remain, and upcoming District court rulings in the summer of 2010 will probably include consideration of gene flow between subpopulations. In this issue of Molecular Ecology, vonHoldt et al. (2010) conduct the largest analysis of gene flow and population structure of the Northern Rockies wolves to date. Using an impressive sampling design and novel analytic methods, vonHoldt et al. (2010) show substantial levels of gene flow between three identified subpopulations of wolves within the Northern Rockies, clarifying previous analyses and convincingly showing genetic recovery. © 2010 Blackwell Publishing Ltd.

Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

PubMed Central

Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

2014-01-01

Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

Surprisingly little population genetic structure in a fungus-associated beetle despite its exploitation of multiple hosts

PubMed Central

Wood, Corlett W; Donald, Hannah M; Formica, Vincent A; Brodie, Edmund D

2013-01-01

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure. PMID:23789061

Vicariance and dispersal across Baja California in disjunct marine fish populations.

PubMed

Bernardi, Giacomo; Findley, Lloyd; Rocha-Olivares, Axayacatl

2003-07-01

Population disjunctions, as a first step toward complete allopatry, present an interesting situation to study incipient speciation. The geological formation of the Baja California Peninsula currently divides 19 species of fish into disjunct populations that are found on its Pacific Coast and in the northern part of the Gulf of California (also called the Sea of Cortez), but are absent from the Cape (Cabo San Lucas) region. We studied the genetic makeup of disjunct populations for 12 of these 19 fish species. Phylogeographic patterns for the 12 species can be separated into two major classes: a first group (eight species) showed reciprocal monophyly and high genetic divergence between disjunct populations. A second group (four species) displayed what appeared to be panmictic populations. Population structure between Pacific Coast populations, across the Punta Eugenia biogeographic boundary, was also evaluated. While dispersal potential (inferred by pelagic larval duration) was a poor predictor of population structure between Gulf of California and Pacific populations, we found that population genetic subdivision along the Pacific Coast at Punta Eugenia was always positively correlated with differentiation between Pacific and Gulf of California populations. Vicariant events, ongoing gene flow, and ecological characteristics played essential roles in shaping the population structures observed in this study.

Developing approaches for linear mixed modeling in landscape genetics through landscape-directed dispersal simulations

USGS Publications Warehouse

Row, Jeffrey R.; Knick, Steven T.; Oyler-McCance, Sara J.; Lougheed, Stephen C.; Fedy, Bradley C.

2017-01-01

Dispersal can impact population dynamics and geographic variation, and thus, genetic approaches that can establish which landscape factors influence population connectivity have ecological and evolutionary importance. Mixed models that account for the error structure of pairwise datasets are increasingly used to compare models relating genetic differentiation to pairwise measures of landscape resistance. A model selection framework based on information criteria metrics or explained variance may help disentangle the ecological and landscape factors influencing genetic structure, yet there are currently no consensus for the best protocols. Here, we develop landscape-directed simulations and test a series of replicates that emulate independent empirical datasets of two species with different life history characteristics (greater sage-grouse; eastern foxsnake). We determined that in our simulated scenarios, AIC and BIC were the best model selection indices and that marginal R2 values were biased toward more complex models. The model coefficients for landscape variables generally reflected the underlying dispersal model with confidence intervals that did not overlap with zero across the entire model set. When we controlled for geographic distance, variables not in the underlying dispersal models (i.e., nontrue) typically overlapped zero. Our study helps establish methods for using linear mixed models to identify the features underlying patterns of dispersal across a variety of landscapes.

Comparative Population Genetic Structure of the Endangered Southern Brown Bandicoot, Isoodon obesulus, in Fragmented Landscapes of Southern Australia

PubMed Central

Li, You; Cooper, Steven J. B.; Lancaster, Melanie L.; Packer, Jasmin G.; Carthew, Susan M.

2016-01-01

Genetic connectivity is a key factor for maintaining the persistence of populations in fragmented landscapes. In highly modified landscapes such us peri-urban areas, organisms’ dispersal among fragmented habitat patches can be reduced due to the surrounding matrix, leading to subsequent decreased gene flow and increased potential extinction risk in isolated sub-populations. However, few studies have compared within species how dispersal/gene flow varies between regions and among different forms of matrix that might be encountered. In the current study, we investigated gene flow and dispersal in an endangered marsupial, the southern brown bandicoot (Isoodon obesulus) in a heavily modified peri-urban landscape in South Australia, Australia. We used 14 microsatellite markers to genotype 254 individuals which were sampled from 15 sites. Analyses revealed significant genetic structure. Our analyses also indicated that dispersal was mostly limited to neighbouring sites. Comparisons of these results with analyses of a different population of the same species revealed that gene flow/dispersal was more limited in this peri-urban landscape than in a pine plantation landscape approximately 400 km to the south-east. These findings increase our understanding of how the nature of fragmentation can lead to profound differences in levels of genetic connectivity among populations of the same species. PMID:27096952

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

PubMed Central

Wei, Su-Juan; Lu, Yong-Bin; Ye, Quan-Qing; Tang, Shao-Qing

2017-01-01

Camellia flavida is an endangered species of yellow camellia growing in limestone mountains in southwest China. The current classification of C. flavida into two varieties, var. flavida and var. patens, is controversial. We conducted a genetic analysis of C. flavida to determine its taxonomic structure. A total of 188 individual plants from 20 populations across the entire distribution range in southwest China were analyzed using two DNA fragments: a chloroplast DNA fragment from the small single copy region and a single-copy nuclear gene called phenylalanine ammonia-lyase (PAL). Sequences from both chloroplast and nuclear DNA were highly diverse; with high levels of genetic differentiation and restricted gene flow. This result can be attributed to the high habitat heterogeneity in limestone karst, which isolates C. flavida populations from each other. Our nuclear DNA results demonstrate that there are three differentiated groups within C. flavida: var. flavida 1, var. flavida 2, and var. patens. These genetic groupings are consistent with the morphological characteristics of the plants. We suggest that the samples included in this study constitute three taxa and the var. flavida 2 group is the genuine C. flavida. The three groups should be recognized as three management units for conservation concerns. PMID:28579991

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

PubMed Central

Miner, Brooks E.; Kerr, Benjamin

2011-01-01

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system. PMID:20943691

[Genetic characterization of different populations of Rhopilema esculentum based on the mitochondrial COI sequence.

PubMed

Li, Yu Long; Dong, Jing; Wang, Bin; Li, Yi Ping; Yu, Xu Guang; Fu, Jie; Wang, Wen Bo

2016-07-01

To investigate the genetic characterization and population genetic structure of Rhopilema esculentum, we sequenced the mtDNA COI gene (624 bp) in 56 individuals collected from Liaodong Bay and the Ganghwado Island in the estuarine waters of the Han River. In addition, the homologous sequences of other 15 individuals which were sampled from the Bohai and Yellow seas and Sea of Japan were analyzed. A total of 28 polymorphic nucleotide sites were detected among the 71 individuals, which defined 32 haplotypes. Haplotype diversity levels were high (0.91±0.06-0.94±0.01) in R. esculentum populations, whereas those of nucleotide diversity were moderate to low [(0.60±0.34)%-(0.68±0.40)%]. Compared with several other giant jellyfish species, the variation level of R. esculentum was high. Phylogeographic analysis of the COI region revealed two lineages. The pairwise F ST comparison and hierarchical molecular variance analysis (AMOVA) showed that significant population structure existed throughout the range of R. esculentum. The results of this study indicated that the life-cycle characteristics, together with possible anthropogenic introduction such as stock enhancement and the prevailing ocean currents in this region, were proposed as the main factors that determined the genetic patterns of R. esculentum.

Genetic structure among continental and island populations of gyrfalcons.

PubMed

Johnson, Jeff A; Burnham, Kurt K; Burnham, William A; Mindell, David P

2007-08-01

Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub-Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (F(ST)). With the microsatellite results, significant population structure (F(ST), principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1-16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial-age refugium to their current circumpolar distribution. Additional sampling of gyrfalcons from Fennoscandia and Russia throughout Siberia is necessary to test putative gene flow between Norway and Alaska and Canada as suggested by this study.

Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA.

PubMed

E, Guang-Xin; Zhao, Yong-Ju; Chen, Li-Peng; Ma, Yue-Hui; Chu, Ming-Xing; Li, Xiang-Long; Hong, Qiong-Hua; Li, Lan-Hui; Guo, Ji-Jun; Zhu, Lan; Han, Yan-Guo; Gao, Hui-Jiang; Zhang, Jia-Hua; Jiang, Huai-Zhi; Jiang, Cao-De; Wang, Gao-Fu; Ren, Hang-Xing; Jin, Mei-Lan; Sun, Yuan-Zhi; Zhou, Peng; Huang, Yong-Fu

2018-05-01

The objective of this study was to assess the genetic diversity and population structure of goats in the Yangtze River region using microsatellite and mtDNA to better understand the current status of those goat genetic diversity and the effects of natural landscape in fashion of domestic animal genetic diversity. The genetic variability of 16 goat populations in the littoral zone of the Yangtze River was estimated using 21 autosomal microsatellites, which revealed high diversity and genetic population clustering with a dispersed geographical distribution. A phylogenetic analysis of the mitochondrial D-loop region (482 bp) was conducted in 494 goats from the Yangtze River region. In total, 117 SNPs were reconstructed, and 173 haplotypes were identified, 94.5% of which belonged to lineages A and B. Lineages C, D, and G had lower frequencies (5.2%), and lineage F haplotypes were undetected. Several high-frequency haplotypes were shared by different ecogeographically distributed populations, and the close phylogenetic relationships among certain low-frequency haplotypes indicated the historical exchange of genetic material among these populations. In particular, the lineage G haplotype suggests that some west Asian goat genetic material may have been transferred to China via Muslim migration.

Extreme mitochondrial variation in the Atlantic gall crab Opecarcinus hypostegus (Decapoda: Cryptochiridae) reveals adaptive genetic divergence over Agaricia coral hosts

PubMed Central

van Tienderen, Kaj M.; van der Meij, Sancia E. T.

2017-01-01

The effectiveness of migration in marine species exhibiting a pelagic larval stage is determined by various factors, such as ocean currents, pelagic larval stage duration and active habitat selection. Direct measurement of larval movements is difficult and, consequently, factors determining the gene flow patterns remain poorly understood for many species. Patterns of gene flow play a key role in maintaining genetic homogeneity in a species by dampening the effects of local adaptation. Coral-dwelling gall crabs (Cryptochiridae) are obligate symbionts of stony corals (Scleractinia). Preliminary data showed high genetic diversity on the COI gene for 19 Opecarcinus hypostegus specimens collected off Curaçao. In this study, an additional 176 specimens were sequenced and used to characterize the population structure along the leeward side of Curaçao. Extremely high COI genetic variation was observed, with 146 polymorphic sites and 187 unique haplotypes. To determine the cause of this high genetic diversity, various gene flow scenarios (geographical distance along the coast, genetic partitioning over depth, and genetic differentiation by coral host) were examined. Adaptive genetic divergence across Agariciidae host species is suggested to be the main cause for the observed high intra-specific variance, hypothesised as early signs of speciation in O. hypostegus. PMID:28079106

Population Genetics of Jaguars (Panthera onca) in the Brazilian Pantanal: Molecular Evidence for Demographic Connectivity on a Regional Scale.

PubMed

Valdez, Fernanda Pedone; Haag, Taiana; Azevedo, Fernando C C; Silveira, Leandro; Cavalcanti, Sandra M C; Salzano, Francisco M; Eizirik, Eduardo

2015-01-01

Habitat loss and fragmentation are important threats to carnivores worldwide, and can be especially intense for large predators. Jaguars have already been extirpated from over half of their original area of distribution, and few regions still maintain large populations. For these, detailed understanding is crucial for setting appropriate recovery targets in impacted areas. The Pantanal is among the best examples of a region with a large jaguar population in a healthy environment. Here, we analyzed 12 microsatellite loci to characterize genetic diversity and population structure of 52 jaguars sampled in 4 localities of the southern Pantanal, and compared them with prior studies of heavily fragmented populations of the Atlantic Forest. Although we observed some internal structure among the Pantanal localities, our results indicated that this area comprises a single population with high genetic variability. Moreover, our comparative analyses supported the hypothesis that the strong population structure observed in the Atlantic Forest derives from recent, anthropogenic fragmentation. We also observed significant but low levels of genetic differentiation between the Pantanal and Atlantic Forest populations, indicating recent connectivity between jaguars occurring in these biomes. Evidence for admixture between the Pantanal and a population on the western boundary of the Atlantic Forest corroborates the transitional nature of the latter area, where the jaguar population has already been extirpated. Our results can be used to understand jaguar population dynamics in a region that is less disturbed than the Atlantic forest, and to support the design of conservation strategies that maintain and restore natural connectivity among currently isolated areas. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection

PubMed Central

Llewellyn, Martin S.; Miles, Michael A.; Carrasco, Hernan J.; Lewis, Michael D.; Yeo, Matthew; Vargas, Jorge; Torrico, Faustino; Diosque, Patricio; Valente, Vera; Valente, Sebastiao A.; Gaunt, Michael W.

2009-01-01

Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs) reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is “hidden” at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed. PMID:19412340

Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories.

PubMed

Fruet, Pedro F; Secchi, Eduardo R; Di Tullio, Juliana C; Simões-Lopes, Paulo César; Daura-Jorge, Fábio; Costa, Ana P B; Vermeulen, Els; Flores, Paulo A C; Genoves, Rodrigo Cezar; Laporta, Paula; Beheregaray, Luciano B; Möller, Luciana M

2017-11-01

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal ( n  = 127) and offshore ( n  = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites F ST  = 0.385, p  < .001; mtDNA F ST  =  0.183, p  < .001; Φ ST  = 0.385, p  < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential "contact zones", we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.

The ups and downs of coral reef fishes: the genetic characteristics of a formerly severely overfished but currently recovering Nassau grouper fish spawning aggregation

NASA Astrophysics Data System (ADS)

Bernard, A. M.; Feldheim, K. A.; Nemeth, R.; Kadison, E.; Blondeau, J.; Semmens, B. X.; Shivji, M. S.

2016-03-01

The Nassau grouper ( Epinephelus striatus) has sustained large declines across its distribution, including extirpation of many of its fish spawning aggregations (FSAs). Within US Virgin Islands (USVI) waters, Nassau grouper FSAs were overfished until their disappearance in the 1970s and 1980s. In the early 2000s, however, Nassau grouper were found gathering at Grammanik Bank, USVI, a mesophotic coral reef adjacent to one of the extinct aggregation sites, and regulatory protective measures were implemented to protect this fledgling FSA. The population genetic dynamics of this rapid FSA deterioration followed by protection-facilitated, incipient recovery are unknown. We addressed two objectives: (1) we explored which factors (i.e., local vs. external recruitment) might be key in shaping the USVI FSA recovery; and (2) we examined the consequences of severe past overfishing on this FSA's current genetic status. We genotyped individuals (15 microsatellites) from the USVI FSA comprising three successive spawning years (2008-2010), as well as individuals from a much larger, presumably less impacted, Nassau grouper FSA in the Cayman Islands, to assess their comparative population dynamics. No population structure was detected between the USVI and Cayman FSAs ( F ST = -0.0004); however, a temporally waning, genetic bottleneck signal was detected in the USVI FSA. Parentage analysis failed to identify any parent-offspring matches between USVI FSA adults and nearby juveniles, and relatedness analysis showed low levels of genetic relatedness among USVI FSA individuals. Genetic diversity across USVI FSA temporal collections was relatively high, and no marked differences were found between the USVI and Cayman FSAs. These collective results suggest that external recruitment is an important driver of the USVI FSA recovery. Furthermore, despite an apparent genetic bottleneck, the genetic diversity of USVI Nassau grouper has not been severely compromised. Our findings also provide a baseline for future genetic monitoring of the nascent USVI aggregation.

Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

PubMed

Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

2012-04-22

Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw.

PubMed

Gomes Viana, João Paulo; Bohrer Monteiro Siqueira, Marcos Vinícius; Araujo, Fabiano Lucas; Grando, Carolina; Sanae Sujii, Patricia; Silvestre, Ellida de Aguiar; Novello, Mariana; Pinheiro, José Baldin; Cavallari, Marcelo Mattos; Brancalion, Pedro H S; Rodrigues, Ricardo Ribeiro; Pereira de Souza, Anete; Catchen, Julian; Zucchi, Maria I

2018-01-01

The primary focus of tropical forest restoration has been the recovery of forest structure and tree taxonomic diversity, with limited attention given to genetic conservation. Populations reintroduced through restoration plantings may have low genetic diversity and be genetically structured due to founder effects and genetic drift, which limit the potential of restoration to recover ecologically resilient plant communities. Here, we studied the genetic diversity, genetic structure and differentiation using single nucleotide polymorphisms (SNP) markers between restored and natural populations of the native tree Casearia sylvestris in the Atlantic Forest of Brazil. We sampled leaves from approximately 24 adult individuals in each of the study sites: two restoration plantations (27 and 62 years old) and two forest remnants. We prepared and sequenced a genotyping-by-sequencing library, SNP markers were identified de novo using Stacks pipeline, and genetic parameters and structure analyses were then estimated for populations. The sequencing step was successful for 80 sampled individuals. Neutral genetic diversity was similar among restored and natural populations (AR = 1.72 ± 0.005; HO = 0.135 ± 0.005; HE = 0.167 ± 0.005; FIS = 0.16 ± 0.022), which were not genetically structured by population subdivision. In spite of this absence of genetic structure by population we found genetic structure within populations but even so there is not spatial genetic structure in any population studied. Less than 1% of the neutral alleles were exclusive to a population. In general, contrary to our expectations, restoration plantations were then effective for conserving tree genetic diversity in human-modified tropical landscapes. Furthermore, we demonstrate that genotyping-by-sequencing can be a useful tool in restoration genetics.

A comparative framework to infer landscape effects on population genetic structure: Are habitat suitability models effective in explaining gene flow?

Treesearch

Maria C. Mateo-Sanchez; Niko Balkenhol; Samuel Cushman; Trinidad Perez; Ana Dominguez; Santiago Saura

2015-01-01

Most current methods to assess connectivity begin with landscape resistance maps. The prevailing resistance models are commonly based on expert opinion and, more recently, on a direct transformation of habitat suitability. However, habitat associations are not necessarily accurate indicators of dispersal, and thus may fail as a surrogate of resistance to...

Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

PubMed

Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L

2012-08-20

Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process.

Methods for the Study of Gonadal Development.

PubMed

Piprek, Rafal P

2016-01-01

Current knowledge on gonadal development and sex determination is the product of many decades of research involving a variety of scientific methods from different biological disciplines such as histology, genetics, biochemistry, and molecular biology. The earliest embryological investigations, followed by the invention of microscopy and staining methods, were based on histological examinations. The most robust development of histological staining techniques occurred in the second half of the nineteenth century and resulted in structural descriptions of gonadogenesis. These first studies on gonadal development were conducted on domesticated animals; however, currently the mouse is the most extensively studied species. The next key point in the study of gonadogenesis was the advancement of methods allowing for the in vitro culture of fetal gonads. For instance, this led to the description of the origin of cell lines forming the gonads. Protein detection using antibodies and immunolabeling methods and the use of reporter genes were also invaluable for developmental studies, enabling the visualization of the formation of gonadal structure. Recently, genetic and molecular biology techniques, especially gene expression analysis, have revolutionized studies on gonadogenesis and have provided insight into the molecular mechanisms that govern this process. The successive invention of new methods is reflected in the progress of research on gonadal development.

NACSN, note 67--Application for revision of Articles 36 and 37, Lithodemic units of the North American stratigraphic code

USGS Publications Warehouse

Easton, Robert M.; Edwards, Lucy E.; Orndorff, Randall C.; Duguet, Manuel; Ferrusquia-Villafranca, Ismael

2015-01-01

Currently the North American Stratigraphic Code, (NACSN 2005, Article 37) sets restrictions on the use of the term “complex” for lithodemic units. With exceptions for “volcanic complex” and “structural complex,” a complex must consist of more than one genetic class of rock (i.e., sedimentary, igneous or metamorphic). Thus, the use of the term “complex” to describe masses of intrusive rocks is not allowed. Asimilar restriction is also included in a recent British Geological Survey proposal for using lithodemic units to classify igneous rocks (Gillespie et al. 2008).Currently the North American Stratigraphic Code, (NACSN 2005, Article 37) sets restrictions on the use of the term “complex” for lithodemic units. With exceptions for “volcanic complex” and “structural complex,” a complex must consist of more than one genetic class of rock (i.e., sedimentary, igneous or metamorphic). Thus, the use of the term “complex” to describe masses of intrusive rocks is not allowed. Asimilar restriction is also included in a recent British Geological Survey proposal for using lithodemic units to classify igneous rocks (Gillespie et al. 2008).

Assortative mating and fragmentation within dog breeds.

PubMed

Björnerfeldt, Susanne; Hailer, Frank; Nord, Maria; Vilà, Carles

2008-01-28

There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds.

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae).

PubMed

da Silva, Marjorie; Noll, Fernando Barbosa; E Castro, Adriana C Morales-Corrêa

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks.

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae)

PubMed Central

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks. PMID:29538451

Assortative mating and fragmentation within dog breeds

PubMed Central

2008-01-01

Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have historically created dog breeds are still ongoing, and create further subdivision within current dog breeds. PMID:18226210

Genetic connectivity in scleractinian corals across the Northern Gulf of Mexico: oil/gas platforms, and relationship to the Flower Garden Banks.

PubMed

Sammarco, Paul W; Brazeau, Daniel A; Sinclair, James

2012-01-01

The 3,000 oil/gas structures currently deployed in the northern Gulf of Mexico (GOM) provide hard substratum for marine organisms in a region where such has been rare since the Holocene. The major exception to this are the Flower Garden Banks (FGB). Corals are known to have colonized oil/gas platforms around the FGB, facilitating biogeographic expansion. We ask the question, what are the patterns of genetic affinity in these coral populations. We sampled coral tissue from populations of two species occurring on oil and gas platforms: Madracis decactis (hermatype) and Tubastraea coccinea (invasive ahermatype). We sampled 28 platforms along four transects from 20 km offshore to the continental shelf edge off 1) Matagorda Island, TX; 2) Lake Sabine, TX; 3) Terrebonne Bay, LA; and 4) Mobile, AL. The entire population of M. decactis was sampled between depths of 5 m and 37 m. T. coccinea populations were sub-sampled. Genetic variation was assessed using the PCR-based Amplified Fragment Length Polymorphisms (AFLPs). Data were analyzed via AFLPOP and STRUCTURE. Genetic connectivity among M. decactis platform populations was highest near the FGB and decreased to the east. Connectivity increased again in the eastern sector, indicating isolation between the populations from different sides of the Mississippi River (Transects 3 and 4). A point-drop in genetic affinity (relatedness) at the shelf edge south of Terrebonne Bay, LA indicated a population differing from all others in the northern GOM. Genetic affinities among T. coccinea were highest in the west and decreased to the east. Very low genetic affinities off Mobile, AL indicated a dramatic difference between those populations and those west of the Mississippi River, apparently a formidable barrier to larval dispersal.

Genetic Connectivity in Scleractinian Corals across the Northern Gulf of Mexico: Oil/Gas Platforms, and Relationship to the Flower Garden Banks

PubMed Central

Sammarco, Paul W.; Brazeau, Daniel A.; Sinclair, James

2012-01-01

The 3,000 oil/gas structures currently deployed in the northern Gulf of Mexico (GOM) provide hard substratum for marine organisms in a region where such has been rare since the Holocene. The major exception to this are the Flower Garden Banks (FGB). Corals are known to have colonized oil/gas platforms around the FGB, facilitating biogeographic expansion. We ask the question, what are the patterns of genetic affinity in these coral populations. We sampled coral tissue from populations of two species occurring on oil and gas platforms: Madracis decactis (hermatype) and Tubastraea coccinea (invasive ahermatype). We sampled 28 platforms along four transects from 20 km offshore to the continental shelf edge off 1) Matagorda Island, TX; 2) Lake Sabine, TX; 3) Terrebonne Bay, LA; and 4) Mobile, AL. The entire population of M. decactis was sampled between depths of 5 m and 37 m. T. coccinea populations were sub-sampled. Genetic variation was assessed using the PCR-based Amplified Fragment Length Polymorphisms (AFLPs). Data were analyzed via AFLPOP and STRUCTURE. Genetic connectivity among M. decactis platform populations was highest near the FGB and decreased to the east. Connectivity increased again in the eastern sector, indicating isolation between the populations from different sides of the Mississippi River (Transects 3 and 4). A point-drop in genetic affinity (relatedness) at the shelf edge south of Terrebonne Bay, LA indicated a population differing from all others in the northern GOM. Genetic affinities among T. coccinea were highest in the west and decreased to the east. Very low genetic affinities off Mobile, AL indicated a dramatic difference between those populations and those west of the Mississippi River, apparently a formidable barrier to larval dispersal. PMID:22558066

Population genetics studies of the walrus (Odobenus rosmarus): A summary and interpretation of results and research needs

USGS Publications Warehouse

Scribner, Kim T.; Hills, Susan; Fain, Steven R.; Cronin, Matthew A.; Dizon, Andrew E.; Chivers, Susan J.; Perrin, William F.

1997-01-01

A summary of population genetics data is presented for the walrus (Odobenus rosmarus). Current information on the ecology and behavior of the species is highlighted to aid in the interpretation of genetics results and to suggest future areas of research. Walruses are discontinuously distributed across the Arctic and are currently subdivided into six regional populations on the basis of historical distribution and morphology. Few population genetics studies have been conducted on the walrus. Only three of the six trigonal populations have been surveyed with biochemical or molecular techniques. Analysis of mitochondrial DNA (mtDNA) variation among walruses from the northern Pacific (Chukchi Sea) and western Atlantic (Greenland) regions revealed 13 haplotypes; 6 were found only in Pacific walruses while 7 were unique to the Atlantic subspecies. Estimates of sequence divergence between Atlantic and Pacific haplotypes were 1.0%-1.6%. No evidence of microgeographic structuring within the northern Pacific or western Atlantic regional populations was found on the basis of mtDNA haplotype frequency distributions or multilocus minisatellite band sharing. Minisatellite analysis of adult-juvenile and adult-adult pairs suggests that assemblages of walruses on individual ice floes are made up at least in part by groups of related individuals from more than one generation. Furthermore, high mtDNA haplotype diversities and low minisatellite band-sharing values suggest that both the northern Pacific and western Atlantic walruses have retained a high degree of genetic variability.

Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus

PubMed Central

Slavov, Gancho; Allison, Gordon; Bosch, Maurice

2013-01-01

Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field. PMID:23847628

Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India.

PubMed

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; Navya, R; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-10-29

Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST) of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.

Ecology Driving Genetic Variation: A Comparative Phylogeography of Jungle Cat (Felis chaus) and Leopard Cat (Prionailurus bengalensis) in India

PubMed Central

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; R, Navya; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-01-01

Background Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. Methodology/Principal Findings We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Conclusions/Significance Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention. PMID:21060831

Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

PubMed

Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

2016-03-01

Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species.

Strong population genetic structure and contrasting demographic histories for the small-spotted catshark (Scyliorhinus canicula) in the Mediterranean Sea

PubMed Central

Kousteni, V; Kasapidis, P; Kotoulas, G; Megalofonou, P

2015-01-01

Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed. PMID:25469687

Enhancing cellulose utilization for fuels and chemicals by genetic modification of plant cell wall architecture.

PubMed

Vermerris, Wilfred; Abril, Alejandra

2015-04-01

Cellulose from plant biomass can serve as a sustainable feedstock for fuels, chemicals and polymers that are currently produced from petroleum. In order to enhance economic feasibility, the efficiency of cell wall deconstruction needs to be enhanced. With the use of genetic and biotechnological approaches cell wall composition can be modified in such a way that interactions between the major cell wall polymers—cellulose, hemicellulosic polysaccharides and lignin—are altered. Some of the resulting plants are compromised in their growth and development, but this may be caused in part by the plant's overcompensation for metabolic perturbances. In other cases novel structures have been introduced in the cell wall without negative effects. The first field studies with engineered bioenergy crops look promising, while detailed structural analyses of cellulose synthase offer new opportunities to modify cellulose itself. Copyright © 2014 Elsevier Ltd. All rights reserved.

Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks.

PubMed

Mullen, Lindy B; Arthur Woods, H; Schwartz, Michael K; Sepulveda, Adam J; Lowe, Winsor H

2010-03-01

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks; and (ii) testing for genetic isolation by distance along stream corridors vs. overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. amova identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in-stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.

Temporal genetic changes in Plasmodium vivax apical membrane antigen 1 over 19 years of transmission in southern Mexico.

PubMed

Flores-Alanis, Alejandro; González-Cerón, Lilia; Santillán, Frida; Ximenez, Cecilia; Sandoval, Marco A; Cerritos, René

2017-05-02

Mexico advanced to the pre-elimination phase in 2009 due to a significant reduction in malaria cases, and since 2000, Plasmodium vivax is the only species transmitted. During the last two decades, malaria transmission has been mostly local and isolated to a few regions. It is important to gain further insights into the impact of control measures on the parasite population structure. Hence, the aim of the current study was to determine detailed changes in P. vivax genetic diversity and population structure based on analysing the gene that encodes the apical membrane antigen 1 (pvama1). This analysis covered from control to pre-elimination (1993-2011) in a hypo-endemic region in southern Mexico. The 213 pvama1 I-II sequences presently analysed were grouped into six periods of three years each. They showed low genetic diversity, with 15 haplotypes resolved. Among the DNA sequences, there was a gradual decrease in genetic diversity, the number of mixed genotype infections and the intensity of positive selection, in agreement with the parallel decline in malaria cases. At the same time, linkage disequilibrium (R 2 ) increased. The three-dimensional haplotype network revealed that pvama1 I-II haplotypes were separated by 1-11 mutational steps, and between one another by 0-3 unsampled haplotypes. In the temporal network, seven haplotypes were detected in at least two of the six-time layers, and only four distinct haplotypes were evidenced in the pre-elimination phase. Structure analysis indicated that three subpopulations fluctuated over time. Only 8.5% of the samples had mixed ancestry. In the pre-elimination phase, subpopulation P1 was drastically reduced, and the admixture was absent. The results suggest that P. vivax in southern Mexico evolved based on local adaptation into three "pseudoclonal" subpopulations that diversified at the regional level and persisted over time, although with varying frequency. Control measures and climate events influenced the number of malaria cases and the genetic structure. The sharp decrease in parasite diversity and other related genetic parameters during the pre-elimination phase suggests that malaria elimination is possible in the near future. These results are useful for epidemiological surveillance.

Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor)

PubMed Central

Peucker, Amanda J.; Valautham, Sureen K.; Styan, Craig A.; Dann, Peter

2015-01-01

Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. PMID:25833231

Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed.

PubMed

Wang, Rong; Compton, Stephen G; Shi, Yi-Su; Chen, Xiao-Yong

2012-09-01

Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations.

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

USDA-ARS?s Scientific Manuscript database

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identi...

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

PubMed

Hoban, Sean; Kelley, Joanna L; Lotterhos, Katie E; Antolin, Michael F; Bradburd, Gideon; Lowry, David B; Poss, Mary L; Reed, Laura K; Storfer, Andrew; Whitlock, Michael C

2016-10-01

Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.

Genetic risk for violent behavior and environmental exposure to disadvantage and violent crime: the case for gene-environment interaction.

PubMed

Barnes, J C; Jacobs, Bruce A

2013-01-01

Despite mounds of evidence to suggest that neighborhood structural factors predict violent behavior, almost no attention has been given to how these influences work synergistically (i.e., interact) with an individual's genetic propensity toward violent behavior. Indeed, two streams of research have, heretofore, flowed independently of one another. On one hand, criminologists have underscored the importance of neighborhood context in the etiology of violence. On the other hand, behavioral geneticists have argued that individual-level genetic propensities are important for understanding violence. The current study seeks to integrate these two compatible frameworks by exploring gene-environment interactions (GxE). Two GxEs were examined and supported by the data (i.e., the National Longitudinal Study of Adolescent Health). Using a scale of genetic risk based on three dopamine genes, the analysis revealed that genetic risk had a greater influence on violent behavior when the individual was also exposed to neighborhood disadvantage or when the individual was exposed to higher violent crime rates. The relevance of these findings for criminological theorizing was considered.

Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments.

PubMed

Hauquier, Freija; Leliaert, Frederik; Rigaux, Annelien; Derycke, Sofie; Vanreusel, Ann

2017-05-30

Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera Sabatieria and Desmodora using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200-500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations. Sequence analyses resulted in the delimitation of four divergent species lineages in Sabatieria, two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in Desmodora, one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling Sabatieria species, which are generally less prone to resuspension and passive dispersal in the water column than surface Desmodora species. Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with different habitat preferences (surface versus deeper sediment layers).

A Qualitative Study of Anticipated Decision Making around Type 2 Diabetes Genetic Testing: The Role of Scientifically Concordant and Discordant Expectations

PubMed Central

Carmichael, Alicia G.; Hulswit, Bailey B.; Moe, Emily J.; Jayaratne, Toby Epstein; Yashar, Beverly M.

2016-01-01

Type 2 diabetes mellitus (T2DM) genetic testing is undergoing clinical trials to measure the efficacy of genetic counseling for behavior-based risk reduction. The expectations patients bring to the testing process may play an important role in individual outcomes. We conducted a qualitative exploration of anticipated decision-making and expectations around T2DM genetic testing. Semi-structured interviews were completed with Mexican Americans (n = 34), non-Hispanic Black Americans (n = 39), and non-Hispanic White Americans (n = 39) at risk for T2DM. Transcripts were analyzed for themes. Most participants would accept T2DM genetic testing in order to motivate risk-reducing behaviors or apprise family members of their risk. Participants who would decline testing wished to avoid emotional distress or believed the test would not reveal new risk information. Non-Hispanic Whites and those with college education declined genetic testing more often than other groups. Those without college education were more likely to have testing expectations that were discordant with current science, such as conflating genetic testing with common ‘blood tests.’ Understanding expectations and decision-making factors around T2DM genetic testing will better prepare healthcare professionals to counsel their patients. This may lead to a higher efficacy of T2DM genetic testing and counseling. PMID:27465809

Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor.

PubMed

Jorde, Per Erik; Søvik, Guldborg; Westgaard, Jon-Ivar; Albretsen, Jon; André, Carl; Hvingel, Carsten; Johansen, Torild; Sandvik, Anne Dagrun; Kingsley, Michael; Jørstad, Knut Eirik

2015-04-01

The large-scale population genetic structure of northern shrimp, Pandalus borealis, was investigated over the species' range in the North Atlantic, identifying multiple genetically distinct groups. Genetic divergence among sample localities varied among 10 microsatellite loci (range: FST = -0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P < 0.0001). In contrast, little or no genetic differences were observed among temporal replicates from the same localities (FST = 0.0004; P = 0.33). Spatial genetic patterns were compared to geographic distances, patterns of larval drift obtained through oceanographic modelling, and temperature differences, within a multiple linear regression framework. The best-fit model included all three factors and explained approximately 29% of all spatial genetic divergence. However, geographic distance and larval drift alone had only minor effects (2.5-4.7%) on large-scale genetic differentiation patterns, whereas bottom temperature differences explained most (26%). Larval drift was found to promote genetic homogeneity in parts of the study area with strong currents, but appeared ineffective across large temperature gradients. These findings highlight the breakdown of gene flow in a species with a long pelagic larval phase (up to 3 months) and indicate a role for local adaptation to temperature conditions in promoting evolutionary diversification and speciation in the marine environment. © 2015 John Wiley & Sons Ltd.

A Qualitative Study of Anticipated Decision Making around Type 2 Diabetes Genetic Testing: the Role of Scientifically Concordant and Discordant Expectations.

PubMed

Carmichael, Alicia G; Hulswit, Bailey B; Moe, Emily J; Jayaratne, Toby Epstein; Yashar, Beverly M

2017-06-01

Type 2 diabetes mellitus (T2DM) genetic testing is undergoing clinical trials to measure the efficacy of genetic counseling for behavior-based risk reduction. The expectations patients bring to the testing process may play an important role in individual outcomes. We conducted a qualitative exploration of anticipated decision-making and expectations around T2DM genetic testing. Semi-structured interviews were completed with Mexican Americans (n = 34), non-Hispanic Black Americans (n = 39), and non-Hispanic White Americans (n = 39) at risk for T2DM. Transcripts were analyzed for themes. Most participants would accept T2DM genetic testing in order to motivate risk-reducing behaviors or apprise family members of their risk. Participants who would decline testing wished to avoid emotional distress or believed the test would not reveal new risk information. Non-Hispanic Whites and those with college education declined genetic testing more often than other groups. Those without college education were more likely to have testing expectations that were discordant with current science, such as conflating genetic testing with common 'blood tests.' Understanding expectations and decision-making factors around T2DM genetic testing will better prepare healthcare professionals to counsel their patients. This may lead to a higher efficacy of T2DM genetic testing and counseling.

Genetic diversity and structure in two species of Leavenworthia with self-incompatible and self-compatible populations

PubMed Central

Koelling, V A; Hamrick, J L; Mauricio, R

2011-01-01

Self-fertilization is a common mating system in plants and is known to reduce genetic diversity, increase genetic structure and potentially put populations at greater risk of extinction. In this study, we measured the genetic diversity and structure of two cedar glade endemic species, Leavenworthia alabamica and L. crassa. These species have self-incompatible (SI) and self-compatible (SC) populations and are therefore ideal for understanding how the mating system affects genetic diversity and structure. We found that L. alabamica and L. crassa had high species-level genetic diversity (He=0.229 and 0.183, respectively) and high genetic structure among their populations (FST=0.45 and 0.36, respectively), but that mean genetic diversity was significantly lower in SC compared with SI populations (SC vs SI, He for L. alabamica was 0.065 vs 0.206 and for L. crassa was 0.084 vs 0.189). We also found significant genetic structure using maximum-likelihood clustering methods. These data indicate that the loss of SI leads to the loss of genetic diversity within populations. In addition, we examined genetic distance relationships between SI and SC populations to analyze possible population history and origins of self-compatibility. We find there may have been multiple origins of self-compatibility in L. alabamica and L. crassa. However, further work is required to test this hypothesis. Finally, given their high genetic structure and that individual populations harbor unique alleles, conservation strategies seeking to maximize species-level genetic diversity for these or similar species should protect multiple populations. PMID:20485327

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

PubMed Central

Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh; Petersen, Desiree C.; Wittekindt, Nicola E.; Miller, Jason; Walenz, Brian; Knight, James; Qi, Ji; Zhao, Fangqing; Wang, Qingyu; Bedoya-Reina, Oscar C.; Katiyar, Neerja; Tomsho, Lynn P.; Kasson, Lindsay McClellan; Hardie, Rae-Anne; Woodbridge, Paula; Tindall, Elizabeth A.; Bertelsen, Mads Frost; Dixon, Dale; Pyecroft, Stephen; Helgen, Kristofer M.; Lesk, Arthur M.; Pringle, Thomas H.; Patterson, Nick; Zhang, Yu; Kreiss, Alexandre; Woods, Gregory M.; Jones, Menna E.; Schuster, Stephan C.

2011-01-01

The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations. PMID:21709235

Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: Implications for conservation

USGS Publications Warehouse

Drinan, D.P.; Kalinowski, S.T.; Vu, N.V.; Shepard, B.B.; Muhlfeld, C.C.; Campbell, M.R.

2011-01-01

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei's DS, populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention. ?? 2011 Springer Science+Business Media B.V.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae).

PubMed

Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M; Marcet, Paula L

2013-12-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. Copyright © 2013. Published by Elsevier B.V.

Eco-geographical differentiation among Colombian populations of the Chagas disease vector Triatoma dimidiata (Hemiptera: Reduviidae)

PubMed Central

Gómez-Palacio, Andrés; Triana, Omar; Jaramillo-O, Nicolás; Dotson, Ellen M.; Marcet, Paula L.

2016-01-01

Triatoma dimidiata is currently the main vector of Chagas disease in Mexico, most Central American countries and several zones of Ecuador and Colombia. Although this species has been the subject of several recent phylogeographic studies, the relationship among different populations within the species remains unclear. To elucidate the population genetic structure of T. dimidiata in Colombia, we analyzed individuals from distinct geographical locations using the cytochrome c oxidase subunit 1 gene and 7 microsatellite loci. A clear genetic differentiation was observed among specimens from three Colombian eco-geographical regions: Inter Andean Valleys, Caribbean Plains and Sierra Nevada de Santa Marta mountain (SNSM). Additionally, evidence of genetic subdivision was found within the Caribbean Plains region as well as moderate gene flow between the populations from the Caribbean Plains and SNSM regions. The genetic differentiation found among Colombian populations correlates, albeit weakly, with an isolation-by-distance model (IBD). The genetic heterogeneity among Colombian populations correlates with the eco-epidemiological and morphological traits observed in this species across regions within the country. Such genetic and epidemiological diversity should be taken into consideration for the development of vector control strategies and entomological surveillance. PMID:24035810

Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus).

PubMed

Chuluunbat, B; Charruau, P; Silbermayr, K; Khorloojav, T; Burger, P A

2014-08-01

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro-ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization. © 2014 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

The structure of genetic diversity in eelgrass (Zostera marina L.) along the North Pacific and Bering Sea coasts of Alaska

USGS Publications Warehouse

Talbot, Sandra L.; Sage, Kevin; Rearick, Jolene; Fowler, Megan C.; Muñiz-Salazar, Raquel; Baibak, Bethany; Wyllie-Echeverria, Sandy; Cabello-Pasini, Alehandro; Ward, David H.

2016-01-01

Eelgrass (Zostera marina) populations occupying coastal waters of Alaska are separated by a peninsula and island archipelago into two Large Marine Ecosystems (LMEs). From populations in both LMEs, we characterize genetic diversity, population structure, and polarity in gene flow using nuclear microsatellite fragment and chloroplast and nuclear sequence data. An inverse relationship between genetic diversity and latitude was observed (heterozygosity: R2 = 0.738, P < 0.001; allelic richness: R2 = 0.327, P = 0.047), as was significant genetic partitioning across most sampling sites (θ = 0.302, P < 0.0001). Variance in allele frequency was significantly partitioned by region only in cases when a population geographically in the Gulf of Alaska LME (Kinzarof Lagoon) was instead included with populations in the Eastern Bering Sea LME (θp = 0.128–0.172; P < 0.003), suggesting gene flow between the two LMEs in this region. Gene flow among locales was rarely symmetrical, with notable exceptions generally following net coastal ocean current direction. Genetic data failed to support recent proposals that multiple Zostera species (i.e. Z. japonica and Z. angustifolia) are codistributed with Z. marina in Alaska. Comparative analyses also failed to support the hypothesis that eelgrass populations in the North Atlantic derived from eelgrass retained in northeastern Pacific Last Glacial Maximum refugia. These data suggest northeastern Pacific populations are derived from populations expanding northward from temperate populations following climate amelioration at the terminus of the last Pleistocene glaciation.

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information.

PubMed

Knowlton, Michelle N; Li, Tongbin; Ren, Yongliang; Bill, Brent R; Ellis, Lynda Bm; Ekker, Stephen C

2008-01-07

The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies. The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced. MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.

The Structure of Genetic Diversity in Eelgrass (Zostera marina L.) along the North Pacific and Bering Sea Coasts of Alaska

PubMed Central

Talbot, Sandra L.; Sage, George K; Rearick, Jolene R.; Fowler, Meg C.; Muñiz-Salazar, Raquel; Baibak, Bethany; Wyllie-Echeverria, Sandy; Cabello-Pasini, Alejandro; Ward, David H.

2016-01-01

Eelgrass (Zostera marina) populations occupying coastal waters of Alaska are separated by a peninsula and island archipelago into two Large Marine Ecosystems (LMEs). From populations in both LMEs, we characterize genetic diversity, population structure, and polarity in gene flow using nuclear microsatellite fragment and chloroplast and nuclear sequence data. An inverse relationship between genetic diversity and latitude was observed (heterozygosity: R2 = 0.738, P < 0.001; allelic richness: R2 = 0.327, P = 0.047), as was significant genetic partitioning across most sampling sites (θ = 0.302, P < 0.0001). Variance in allele frequency was significantly partitioned by region only in cases when a population geographically in the Gulf of Alaska LME (Kinzarof Lagoon) was instead included with populations in the Eastern Bering Sea LME (θp = 0.128–0.172; P < 0.003), suggesting gene flow between the two LMEs in this region. Gene flow among locales was rarely symmetrical, with notable exceptions generally following net coastal ocean current direction. Genetic data failed to support recent proposals that multiple Zostera species (i.e. Z. japonica and Z. angustifolia) are codistributed with Z. marina in Alaska. Comparative analyses also failed to support the hypothesis that eelgrass populations in the North Atlantic derived from eelgrass retained in northeastern Pacific Last Glacial Maximum refugia. These data suggest northeastern Pacific populations are derived from populations expanding northward from temperate populations following climate amelioration at the terminus of the last Pleistocene glaciation. PMID:27104836

The Structure of Genetic Diversity in Eelgrass (Zostera marina L.) along the North Pacific and Bering Sea Coasts of Alaska.

PubMed

Talbot, Sandra L; Sage, George K; Rearick, Jolene R; Fowler, Meg C; Muñiz-Salazar, Raquel; Baibak, Bethany; Wyllie-Echeverria, Sandy; Cabello-Pasini, Alejandro; Ward, David H

2016-01-01

Eelgrass (Zostera marina) populations occupying coastal waters of Alaska are separated by a peninsula and island archipelago into two Large Marine Ecosystems (LMEs). From populations in both LMEs, we characterize genetic diversity, population structure, and polarity in gene flow using nuclear microsatellite fragment and chloroplast and nuclear sequence data. An inverse relationship between genetic diversity and latitude was observed (heterozygosity: R2 = 0.738, P < 0.001; allelic richness: R2 = 0.327, P = 0.047), as was significant genetic partitioning across most sampling sites (θ = 0.302, P < 0.0001). Variance in allele frequency was significantly partitioned by region only in cases when a population geographically in the Gulf of Alaska LME (Kinzarof Lagoon) was instead included with populations in the Eastern Bering Sea LME (θp = 0.128-0.172; P < 0.003), suggesting gene flow between the two LMEs in this region. Gene flow among locales was rarely symmetrical, with notable exceptions generally following net coastal ocean current direction. Genetic data failed to support recent proposals that multiple Zostera species (i.e. Z. japonica and Z. angustifolia) are codistributed with Z. marina in Alaska. Comparative analyses also failed to support the hypothesis that eelgrass populations in the North Atlantic derived from eelgrass retained in northeastern Pacific Last Glacial Maximum refugia. These data suggest northeastern Pacific populations are derived from populations expanding northward from temperate populations following climate amelioration at the terminus of the last Pleistocene glaciation.

Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis

PubMed Central

2010-01-01

Background The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. Ctenomys australis (the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales. Results Our results show that dispersal in C. australis is not restricted at regional spatial scales (~ 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females. Conclusions Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females. PMID:20109219

Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor

PubMed Central

Naydenov, Krassimir; Senneville, Sauphie; Beaulieu, Jean; Tremblay, Francine; Bousquet, Jean

2007-01-01

Background At the last glacial maximum, Fennoscandia was covered by an ice sheet while the tundra occupied most of the rest of northern Eurasia. More or less disjunct refugial populations of plants were dispersed in southern Europe, often trapped between mountain ranges and seas. Genetic and paleobotanical evidences indicate that these populations have contributed much to Holocene recolonization of more northern latitudes. Less supportive evidence has been found for the existence of glacial populations located closer to the ice margin. Scots pine (Pinus sylvestris L.) is a nordic conifer with a wide natural range covering much of Eurasia. Fractures in its extant genetic structure might be indicative of glacial vicariance and how different refugia contributed to the current distribution at the continental level. The population structure of Scots pine was investigated on much of its Eurasian natural range using maternally inherited mitochondrial DNA polymorphisms. Results A novel polymorphic region of the Scots pine mitochondrial genome has been identified, the intron 1 of nad7, with three variants caused by insertions-deletions. From 986 trees distributed among 54 populations, four distinct multi-locus mitochondrial haplotypes (mitotypes) were detected based on the three nad7 intron 1 haplotypes and two previously reported size variants for nad1 intron B/C. Population differentiation was high (GST = 0.657) and the distribution of the mitotypes was geographically highly structured, suggesting at least four genetically distinct ancestral lineages. A cosmopolitan lineage was widely distributed in much of Europe throughout eastern Asia. A previously reported lineage limited to the Iberian Peninsula was confirmed. A new geographically restricted lineage was found confined to Asia Minor. A new lineage was restricted to more northern latitudes in northeastern Europe and the Baltic region. Conclusion The contribution of the various ancestral lineages to the current distribution of Scots pine was asymmetric and extant endemism reflected the presence of large geographic barriers to migration. The results suggest a complex biogeographical history with glacial refugia shared with temperate plant species in southern European Peninsulas and Asia Minor, and a genetically distinct glacial population located more North. These results confirm recent observations for cold tolerant species about the possible existence of refugial populations at mid-northern latitudes contributing significantly to the recolonization of northern Europe. Thus, Eurasian populations of nordic plant species might not be as genetically homogenous as assumed by simply considering them as offsets of glacial populations located in southern peninsulas. As such, they might have evolved distinctive genetic adaptations during glacial vicariance, worth evaluating and considering for conservation. PMID:18034901

Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications

PubMed Central

2014-01-01

Background Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Results Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). Conclusions According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B. papayae forms in Southern Thailand and West Malaysia. Both forms can be treated as a single target pest for the SIT program in an area-wide sense. Additionally, the result of species identification based on molecular data and morphological character are not congruent. The use of independent, multiple approaches in the characterization of the target population may ensure the effectiveness and feasibility of SIT-based control in the target area. PMID:24929425

Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications.

PubMed

Aketarawong, Nidchaya; Isasawin, Siriwan; Thanaphum, Sujinda

2014-06-14

Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B. papayae forms in Southern Thailand and West Malaysia. Both forms can be treated as a single target pest for the SIT program in an area-wide sense. Additionally, the result of species identification based on molecular data and morphological character are not congruent. The use of independent, multiple approaches in the characterization of the target population may ensure the effectiveness and feasibility of SIT-based control in the target area.

"The Google of Healthcare": enabling the privatization of genetic bio/databanking.

PubMed

Spector-Bagdady, Kayte

2016-07-01

23andMe is back on the market as the first direct-to-consumer genetic testing company that "includes reports that meet Food and Drug Administration (FDA) standards…." But, whereas its front-end product is selling individual genetic tests online, its back-end business model is amassing one of the largest privately owned genetic databases in the world. What is the effect, however, of the private control of bio/databases on genetic epidemiology and public health research? The recent federal government notices of proposed rulemaking for: (1) revisions to regulations governing human subjects research and (2) whether certain direct-to-consumer genetic tests should require premarket FDA review, were reviewed and related to the 23andMe product, business model, and consumer agreements. FDA regulatory action so far has focused on the return of consumer test reports but it should also consider the broader misuse of data and information not otherwise protected by human subjects research regulations. As the federal government revises its decades-old human subjects research structure, the Executive Office of the President (EOP) should consider a cohesive approach to regulating private genetic bio/databanks. This strategy should allow the FDA and other agencies to play a role in expanding current regulatory coverage. Copyright © 2016 Elsevier Inc. All rights reserved.

Call types of Bigg's killer whales (Orcinus orca) in western Alaska: Using vocal dialects to assess population structure

NASA Astrophysics Data System (ADS)

Sharpe, Deborah Lynn

Apex predators are important indicators of ecosystem health, but little is known about the population structure of Bigg's killer whales ( Orcinus orca; i.e. 'transient' ecotype) in western Alaska. Currently, all Bigg's killer whales in western Alaska are ascribed to a single broad stock for management under the US Marine Mammal Protection Act. However, recent nuclear microsatellite and mitochondrial DNA analyses indicate that this stock is likely comprised of genetically distinct sub-populations. In accordance with what is known about killer whale vocal dialects in other locations, I sought to evaluate Bigg's killer whale population structure by examining the spatial distribution of group-specific call types in western Alaska. Digital audio recordings were collected from 33 encounters with Bigg's killer whales throughout the Aleutian and Pribilof Islands in the summers of 2001-2007 and 2009-2010. Recorded calls were perceptually classified into discrete types and then quantitatively described using 12 structural and time-frequency measures. Resulting call categories were objectively validated using a random forest approach. A total of 36 call types and subtypes were identified across the entire study area, and regional patterns of call type usage revealed three distinct dialects, each of which corresponding to proposed genetic delineations. I suggest that at least three acoustically and genetically distinct subpopulations are present in western Alaska, and put forth an initial catalog for this area describing the regional vocal repertoires of Bigg's killer whale call types.

Environmental isolation explains Iberian genetic diversity in the highly homozygous model grass Brachypodium distachyon.

PubMed

Marques, Isabel; Shiposha, Valeriia; López-Alvarez, Diana; Manzaneda, Antonio J; Hernandez, Pilar; Olonova, Marina; Catalán, Pilar

2017-06-15

Brachypodium distachyon (Poaceae), an annual Mediterranean Aluminum (Al)-sensitive grass, is currently being used as a model species to provide new information on cereals and biofuel crops. The plant has a short life cycle and one of the smallest genomes in the grasses being well suited to experimental manipulation. Its genome has been fully sequenced and several genomic resources are being developed to elucidate key traits and gene functions. A reliable germplasm collection that reflects the natural diversity of this species is therefore needed for all these genomic resources. However, despite being a model plant, we still know very little about its genetic diversity. As a first step to overcome this gap, we used nuclear Simple Sequence Repeats (nSSR) to study the patterns of genetic diversity and population structure of B. distachyon in 14 populations sampled across the Iberian Peninsula (Spain), one of its best known areas. We found very low levels of genetic diversity, allelic number and heterozygosity in B. distachyon, congruent with a highly selfing system. Our results indicate the existence of at least three genetic clusters providing additional evidence for the existence of a significant genetic structure in the Iberian Peninsula and supporting this geographical area as an important genetic reservoir. Several hotspots of genetic diversity were detected and populations growing on basic soils were significantly more diverse than those growing in acidic soils. A partial Mantel test confirmed a statistically significant Isolation-By-Distance (IBD) among all studied populations, as well as a statistically significant Isolation-By-Environment (IBE) revealing the presence of environmental-driven isolation as one explanation for the genetic patterns found in the Iberian Peninsula. The finding of higher genetic diversity in eastern Iberian populations occurring in basic soils suggests that these populations can be better adapted than those occurring in western areas of the Iberian Peninsula where the soils are more acidic and accumulate toxic Al ions. This suggests that the western Iberian acidic soils might prevent the establishment of Al-sensitive B. distachyon populations, potentially causing the existence of more genetically depauperated individuals.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

PubMed

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics

PubMed Central

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Background Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. Results We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Conclusions Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant. PMID:27711241

The current state of genetic counseling and newborn screening: an interview with Megan Tucker

PubMed Central

Tucker, Megan

2017-01-01

Megan Tucker talks to Francesca Lake, Managing Editor: A certified genetic counselor for over 10 years, Megan is currently the director of the Indiana State University Genetic Counseling Graduate Program and the Genetic Counseling Clinic at Union Hospital (Terre Haute, IN, USA). She began her career split between the Center for Prenatal Diagnosis and the Medical Genetics and Neurodevelopmental Center at St Vincent Hospital (Indianapolis, IN, USA). During this time she was instrumental in both the development of the statewide Perinatal Loss Evaluation Program and a hospital protocol to ensure collection of cord blood to allow time to effectively genetically evaluate babies. Her current clinical focus is in cancer and psychiatric genetic counseling. PMID:28883988

Genetic Variation and Structure in Contrasting Geographic Distributions: Widespread Versus Restricted Black-Tailed Prairie Dogs (Subgenus Cynomys).

PubMed

Castellanos-Morales, Gabriela; Ortega, Jorge; Castillo-Gámez, Reyna A; Sackett, Loren C; Eguiarte, Luis E

2015-01-01

Species of restricted distribution are considered more vulnerable to extinction because of low levels of genetic variation relative to widespread taxa. Species of the subgenus Cynomys are an excellent system to compare genetic variation and degree of genetic structure in contrasting geographic distributions. We assessed levels of genetic variation, genetic structure, and genetic differentiation in widespread Cynomys ludovicianus and restricted C. mexicanus using 1997bp from the cytochrome b and control region (n = 223 C. ludovicianus; 77 C. mexicanus), and 10 nuclear microsatellite loci (n = 207 and 78, respectively). Genetic variation for both species was high, and genetic structure in the widespread species was higher than in the restricted species. C. mexicanus showed values of genetic variation, genetic structure, and genetic differentiation similar to C. ludovicianus at smaller geographic scales. Results suggest the presence of at least 2 historical refuges for C. ludovicianus and that the Sierra Madre Occidental represents a barrier to gene flow. Chihuahua and New Mexico possess high levels of genetic diversity and should be protected, while Sonora should be treated as an independent management unit. For C. mexicanus, connectivity among colonies is very important and habitat fragmentation and habitat loss should be mitigated to maintain gene flow. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia.

PubMed

Dequigiovanni, Gabriel; Ramos, Santiago Linorio Ferreyra; Alves-Pereira, Alessandro; Fabri, Eliane Gomes; Picanço-Rodrigues, Doriane; Clement, Charles Roland; Gepts, Paul; Veasey, Elizabeth Ann

2018-01-01

Annatto (Bixa orellana L.) is a tropical American crop, commercially valuable due to its application in the food and cosmetics industries as a natural dye. The wild ancestor of cultivated annatto is B. orellana var. urucurana. Although never cultivated, this variety occurs in open forests and anthropogenic landscapes, and is always associated with riparian environments. In this study, we evaluated the genetic diversity and structure of B. orellana var. urucurana populations in Brazilian Amazonia using 16 microsatellite loci. We used Ecological Niche Modeling (ENM) to characterize the potential geographical range of this variety in northern South America. We analyzed 170 samples from 10 municipalities in the states of Rondônia, Pará and Roraima. A total of 194 alleles was observed, with an average of 12.1 alleles per locus. Higher levels of expected (HE) than observed (HO) heterozygosities were found for all populations. Bayesian analysis, Neighbor-Joining dendrograms and PCAs suggest the existence of three strongly structured groups of populations. A strong and positive correlation between genetic and geographic distances was found, suggesting that genetic differentiation might be caused by geographic isolation. From species distribution modelling, we detected that South Rondônia, Madre di Dios River basin, Llanos de Mojos, Llanos de Orinoco and eastern Ecuador are highly suitable areas for wild annatto to occur, providing additional targets for future exploration and conservation. Climatic adaptation analyses revealed strong differentiation among populations, suggesting that precipitation plays a key role in wild annatto's current and potential distribution patterns.

Genetic variation and factors affecting the genetic structure of the lichenicolous fungus Heterocephalacria bachmannii (Filobasidiales, Basidiomycota)

PubMed Central

Laakso, Into; Stenroos, Soili

2017-01-01

Heterocephalacria bachmannii is a lichenicolous fungus that takes as hosts numerous lichen species of the genus Cladonia. In the present study we analyze whether the geographical distance, the host species or the host secondary metabolites determine the genetic structure of this parasite. To address the question, populations mainly from the Southern Europe, Southern Finland and the Azores were sampled. The specimens were collected from 20 different host species representing ten chemotypes. Three loci, ITS rDNA, LSU rDNA and mtSSU, were sequenced. The genetic structure was assessed by AMOVA, redundance analyses and Bayesian clustering methods. The results indicated that the host species and the host secondary metabolites are the most influential factors over the genetic structure of this lichenicolous fungus. In addition, the genetic structure of H. bachmannii was compared with that of one of its hosts, Cladonia rangiformis. The population structure of parasite and host were discordant. The contents in phenolic compounds and fatty acids of C. rangiformis were quantified in order to test whether it had some influence on the genetic structure of the species. But no correlation was found with the genetic clusters of H. bachmannii. PMID:29253026

Structured parenting of toddlers at high versus low genetic risk: two pathways to child problems.

PubMed

Leve, Leslie D; Harold, Gordon T; Ge, Xiaojia; Neiderhiser, Jenae M; Shaw, Daniel; Scaramella, Laura V; Reiss, David

2009-11-01

Little is known about how parenting might offset genetic risk to prevent the onset of child problems during toddlerhood. We used a prospective adoption design to separate genetic and environmental influences and test whether associations between structured parenting and toddler behavior problems were conditioned by genetic risk for psychopathology. The sample included 290 linked sets of adoptive families and birth mothers and 95 linked birth fathers. Genetic risk was assessed via birth mother and birth father psychopathology (anxiety, depression, antisociality, and drug use). Structured parenting was assessed via microsocial coding of adoptive mothers' behavior during a cleanup task. Toddler behavior problems were assessed with the Child Behavior Checklist. Controlling for temperamental risk at 9 months, there was an interaction between birth mother psychopathology and adoptive mothers' parenting on toddler behavior problems at 18 months. The interaction indicated two pathways to child problems: structured parenting was beneficial for toddlers at high genetic risk but was related to behavior problems for toddlers at low genetic risk. This crossover interaction pattern was replicated with birth father psychopathology as the index of genetic risk. The effects of structured parenting on toddler behavior problems varied as a function of genetic risk. Children at genetic risk might benefit from parenting interventions during toddlerhood that enhance structured parenting.

Population Genetics of Boise Basin Bull Trout (Salvelinus confluentus)

Treesearch

A.R. Whiteley; P. Spruell; F.W. Allendorf

2003-01-01

We analyzed the population genetic structure of bull trout (Salvelinus confluentus) in the Boise River Basin, Idaho. We determined the influence of contemporary (including anthropogenic) and historic factors on genetic structure, taking into accountexisting data on bull trout habitat patches in this basin. We tested three models of the organization of genetic structure...

Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons.

PubMed

Curto, M; Puppo, P; Kratschmer, S; Meimberg, H

2017-08-22

Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572-575, 2005; Saunders and Gibson, J Ecol 93: 649-652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168-173, 2004; Silvertown et al., J Ecol 93: 653-657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different effect: hybridization might always be related to colonization within the archipelago as well, making initial genetic diversity to be high to begin with. Thus the emergence of new islands promotes multiple colonization events, contributing to the establishment of hybrid swarms that may enhance adaptive ability and radiation events. With time, population sizes grow and niches start to fill. Consequently, gene-flow is not as effective at maintaining the species syngameon, which allows genetic differentiation and reproductive isolation to be established between species. This process contributes to an even further decrease in gene-flow between species.

Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses

PubMed Central

2014-01-01

Background Wild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia. Results Our data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea. Conclusions Our results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia. PMID:25034725

Genetic and Environmental Influences on Smoking Behavior across Adolescence and Young Adulthood in the Virginia Twin Study of Adolescent Behavioral Development and the Transitions to Substance Abuse Follow-Up

PubMed Central

Do, Elizabeth K.; Prom-Wormley, Elizabeth C.; Eaves, Lindon J.; Silberg, Judy L.; Miles, Donna R.; Maes, Hermine H.

2016-01-01

Little is known regarding the underlying relationship between smoking initiation and current quantity smoked during adolescence into young adulthood. It is possible that the influences of genetic and environmental factors on this relationship vary across sex and age. To investigate this further, the current study applied a common causal contingency model to data from a Virginia-based twin study to determine: (1) if the same genetic and environmental factors are contributing to smoking initiation and current quantity smoked; (2) whether the magnitude of genetic and environmental factor contributions are the same across adolescence and young adulthood; and (3) if qualitative and quantitative differences in the sources of variance between males and females exist. Study results found no qualitative or quantitative sex differences in the relationship between smoking initiation and current quantity smoked, though relative contributions of genetic and environmental factors changed across adolescence and young adulthood. More specifically, smoking initiation and current quantity smoked remain separate constructs until young adulthood, when liabilities are correlated. Smoking initiation is explained by genetic, shared, and unique environmental factors in early adolescence and by genetic and unique environmental factors in young adulthood; while current quantity smoked is explained by shared environmental and unique environmental factors until young adulthood, when genetic and unique environmental factors play a larger role. PMID:25662421

Genetic and Environmental Influences on Smoking Behavior across Adolescence and Young Adulthood in the Virginia Twin Study of Adolescent Behavioral Development and the Transitions to Substance Abuse Follow-Up.

PubMed

Do, Elizabeth K; Prom-Wormley, Elizabeth C; Eaves, Lindon J; Silberg, Judy L; Miles, Donna R; Maes, Hermine H

2015-02-01

Little is known regarding the underlying relationship between smoking initiation and current quantity smoked during adolescence into young adulthood. It is possible that the influences of genetic and environmental factors on this relationship vary across sex and age. To investigate this further, the current study applied a common causal contingency model to data from a Virginia-based twin study to determine: (1) if the same genetic and environmental factors are contributing to smoking initiation and current quantity smoked; (2) whether the magnitude of genetic and environmental factor contributions are the same across adolescence and young adulthood; and (3) if qualitative and quantitative differences in the sources of variance between males and females exist. Study results found no qualitative or quantitative sex differences in the relationship between smoking initiation and current quantity smoked, though relative contributions of genetic and environmental factors changed across adolescence and young adulthood. More specifically, smoking initiation and current quantity smoked remain separate constructs until young adulthood, when liabilities are correlated. Smoking initiation is explained by genetic, shared, and unique environmental factors in early adolescence and by genetic and unique environmental factors in young adulthood; while current quantity smoked is explained by shared environmental and unique environmental factors until young adulthood, when genetic and unique environmental factors play a larger role.

Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

PubMed

Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

2017-10-01

Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.

Genetic considerations on the introduction of farmed fish in marine protected areas: The case of study of white seabream restocking in the Gulf of Castellammare (Southern Tyrrhenian Sea)

NASA Astrophysics Data System (ADS)

González-Wangüemert, Mercedes; Fernández, Tomás Vega; Pérez-Ruzafa, Angel; Giacalone, Maximiliano; D'Anna, Giovanni; Badalamenti, Fabio

2012-02-01

Human exploitation has drastically reduced the abundance and distribution of several marine fish and invertebrate populations through overfishing and habitat destruction. Restocking can potentially mitigate these impacts and help to reconstitute depleted stocks but genetic repercussions must be considered. In the present study, the degree of genetic similarity between white seabream (Diplodus sargus Linnaeus 1758) individuals reared for restocking purposes and the receiving population in the Gulf of Castellammare fishery reserve (Sicily, Italy) was assessed using microsatellites. We also inferred the spatial pattern of the genetic structure of D. sargus and connectivity along Sicilian coasts. The farmed population showed significant heterozygosity deficiency in 6 loci and an important reduction in the number of alleles, which could indicate an incipient inbreeding. Both the farmed population and the target one for restocking (Castellammare fishery reserve), showed high and significant values of genetic differentiation due to different allele frequencies, number of privative alleles and total number of alleles. These findings indicate a low degree of genetic similarity between both populations, therefore this restocking initiative is not advisable. The genetic connectivity pattern, highly consistent with oceanographic currents, identified two distinct metapopulations of white seabream around Sicily. Thus it is recommended to utilize broods from the same metapopulation for restocking purposes to provide a better genetic match to the wild populations.

Genetic Status and Timing of a Weevil Introduction to Santa Cruz Island, Galápagos

PubMed Central

2014-01-01

Successful invasive species can overcome or circumvent the potential genetic loss caused by an introduction bottleneck through a rapid population expansion and admixture from multiple introductions. We explore the genetic makeup and the timing of a species introduction to Santa Cruz Island in the Galápagos archipelago. We investigate the presence of processes that can maintain genetic diversity in populations of the broad-nosed weevil Galapaganus howdenae howdenae. Analyses of combined genotypes for 8 microsatellite loci showed evidence of past population size reductions through moment and likelihood-based estimators. No evidence of admixture through multiple introductions was found, but substantial current population sizes (N0 298, 95% credible limits 50–2300), genetic diversity comparable with long-established endemics (Mean number of alleles = 3.875), and lack of genetic structure across the introduced range (F ST = 0.01359) could suggest that foundations are in place for populations to rapidly recover any loss of genetic variability. The time estimates for the introduction into Santa Cruz support an accidental transfer during the colonization period (1832–1959) predating the spurt in human population growth. Our evaluation of the genetic status of G. h. howdenae suggests potential for population growth in addition to our field observations of a concurrent expansion in range and feeding preferences towards protected areas and endemic host plants. PMID:24399746

Can genetics help psychometrics? Improving dimensionality assessment through genetic factor modeling.

PubMed

Franić, Sanja; Dolan, Conor V; Borsboom, Denny; Hudziak, James J; van Beijsterveldt, Catherina E M; Boomsma, Dorret I

2013-09-01

In the present article, we discuss the role that quantitative genetic methodology may play in assessing and understanding the dimensionality of psychological (psychometric) instruments. Specifically, we study the relationship between the observed covariance structures, on the one hand, and the underlying genetic and environmental influences giving rise to such structures, on the other. We note that this relationship may be such that it hampers obtaining a clear estimate of dimensionality using standard tools for dimensionality assessment alone. One situation in which dimensionality assessment may be impeded is that in which genetic and environmental influences, of which the observed covariance structure is a function, differ from each other in structure and dimensionality. We demonstrate that in such situations settling dimensionality issues may be problematic, and propose using quantitative genetic modeling to uncover the (possibly different) dimensionalities of the underlying genetic and environmental structures. We illustrate using simulations and an empirical example on childhood internalizing problems.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast.

PubMed

Britto, Fábio B; Schmidt, Anders J; Carvalho, Adriana M F; Vasconcelos, Carolina C M P; Farias, Antonia M; Bentzen, Paul; Diniz, Fábio M

2018-01-01

The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of F ST (= 0.019; P < 0.001). F ST and Jost's D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs ( P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition ( P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation ( F CT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus . Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PubMed Central

Schmidt, Anders J.; Carvalho, Adriana M.F.; Vasconcelos, Carolina C.M.P.; Farias, Antonia M.; Bentzen, Paul

2018-01-01

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs. PMID:29736340

Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases

PubMed Central

Haan, Claude; Behrmann, Iris; Haan, Serge

2010-01-01

Abstract Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets. PMID:20132407

Extreme Glacial Legacies: A Synthesis of the Antarctic Springtail Phylogeographic Record

PubMed Central

McGaughran, Angela; Stevens, Mark I.; Hogg, Ian D.; Carapelli, Antonio

2011-01-01

We review current phylogeographic knowledge from across the Antarctic terrestrial landscape with a focus on springtail taxa. We describe consistent patterns of high genetic diversity and structure among populations which have persisted in glacial refugia across Antarctica over both short (<2 Mya) and long (>10 Mya) timescales. Despite a general concordance of results among species, we explain why location is important in determining population genetic patterns within bioregions. We complete our review by drawing attention to the main limitations in the field of Antarctic phylogeography, namely that the scope of geographic focus is often lacking within studies, and that large gaps remain in our phylogeographic knowledge for most terrestrial groups. PMID:26467614

Aminoacyl-tRNA synthetases database Y2K

PubMed Central

Szymanski, Maciej; Barciszewski, Jan

2000-01-01

The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloroplasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html PMID:10592262

Aminoacyl-tRNA synthetases database Y2K.

PubMed

Szymanski, M; Barciszewski, J

2000-01-01

The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloro-plasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html

Breeding-assisted genomics.

PubMed

Poland, Jesse

2015-04-01

The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genomic resources and genetic diversity of captive lesser kudu (Tragelaphus imberbis).

PubMed

Bock, Friederike; Gallus, Susanne; Janke, Axel; Hailer, Frank; Steck, Beatrice L; Kumar, Vikas; Nilsson, Maria A

2014-01-01

The lesser kudu (Tragelaphus imberbis) is a spiral-horned antelope native to northeastern Africa. Individuals kept in zoological gardens are suspected to be highly inbred due to few founder individuals and a small breeding stock. A morphological study suggested two distinct subspecies of the lesser kudu. However, subspecies designation and population structure in zoological gardens has not been analyzed using molecular markers. We analyzed one mitochondrial marker and two nuclear intron loci (total: 2,239 nucleotides) in 52 lesser kudu individuals. Of these, 48 individuals were bred in captivity and sampled from seven different zoos. The four remaining individuals were recently captured in Somalia and are currently held in the Maktoum zoo. Maternally inherited mitochondrial sequences indicate substantial amounts of genetic variation in the zoo populations, while the biparentally inherited intron sequences are, as expected, less variable. The analyzed individuals show 10 mitochondrial haplotypes with a maximal distance of 10 mutational steps. No prominent subspecies structure is detectable in this study. For further studies of the lesser kudu population genetics, we present microsatellite markers from a low-coverage genome survey using 454 sequencing technology. © 2014 Wiley Periodicals, Inc.

Geomorphology Influencing the Diversification of Fish in Small-Order Rivers of Neighboring Basins.

PubMed

Morais-Silva, João P; Oliveira, Alessandra V de; Fabrin, Thomaz M C; Diamante, Nathália Alves; Prioli, Sônia M A P; Frota, Augusto; Graça, Weferson J da; Prioli, Alberto J

2018-03-13

The current analysis investigates whether the uplift of the Serra da Esperança and the Ponta Grossa Arch in the Serra Geral resulted in ichthyofaunistic changes in adjacent basins. For this, we describe the phylogeographic structure among populations of Trichomycterus collected in hydrographic basins in southern Brazil by using partial nucleotide sequences of the mitochondrial gene Cytochrome C Oxidase subunit I. Analyses revealed that the nomenclature Trichomycterus davisi fails to contain the whole genetic diversity range found in the collected specimens and indicates at least six genetic lineages in Trichomycterus. Diagnostic morphological characteristics not associated to T. davisi could be identified in some specimens from the Iguaçu Piquiri haplogroup, indicating the occurrence of species Trichomycterus stawiarski. The lack of morphological differences among the other clades clearly suggests a cryptic species case. Molecular analyses revealed at least five new species besides T. davisi in the hydrographic basins and support the interpretation that genetic structure in T. davisi species complex is explained by tectonic events intrinsic to the areas of influence of Serra da Esperança and the Ponta Grossa Arch which occurred around 1.7 My.

Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity

PubMed Central

Athanasiadis, Georgios; Cheng, Jade Y.; Vilhjálmsson, Bjarni J.; Jørgensen, Frank G.; Als, Thomas D.; Le Hellard, Stephanie; Espeseth, Thomas; Sullivan, Patrick F.; Hultman, Christina M.; Kjærgaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas

2016-01-01

Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country. Denmark presented genomic affinity with primarily neighboring countries with overall resemblance of decreasing weight from Britain, Sweden, Norway, Germany, and France. A Polish admixture signal was detected in Zealand and Funen, and our date estimates coincided with historical evidence of Wend settlements in the south of Denmark. We also observed considerably diverse demographic histories among Scandinavian countries, with Denmark having the smallest current effective population size compared to Norway and Sweden. Finally, we found that polygenic prediction of self-reported adolescent height in the population was remarkably accurate (R2 = 0.639 ± 0.015). The high homogeneity of the Danish population could render population structure a lesser concern for the upcoming large-scale gene-mapping studies in the country. PMID:27535931

Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodríguez Guilbe, María M.; Protein Research and Development Center, University of Puerto Rico; Alfaro Malavé, Elisa C.

The genetically encoded fluorescent calcium-indicator protein GCaMP2 was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution and the structure was solved by molecular replacement. Fluorescent proteins and their engineered variants have played an important role in the study of biology. The genetically encoded calcium-indicator protein GCaMP2 comprises a circularly permuted fluorescent protein coupled to the calcium-binding protein calmodulin and a calmodulin target peptide, M13, derived from the intracellular calmodulin target myosin light-chain kinase and has been used to image calcium transients in vivo. To aid rational efforts to engineer improved variants of GCaMP2, thismore » protein was crystallized in the calcium-saturated form. X-ray diffraction data were collected to 2.0 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 126.1, b = 47.1, c = 68.8 Å, β = 100.5° and one GCaMP2 molecule in the asymmetric unit. The structure was phased by molecular replacement and refinement is currently under way.« less

The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.

PubMed

Shaw, Robyn E; Banks, Sam C; Peakall, Rod

2018-01-01

For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure. © 2017 John Wiley & Sons Ltd.

Can mathematics explain the evolution of human language?

PubMed

Witzany, Guenther

2011-09-01

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer science-based formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language.

Between destiny and disease: genetics and molecular pathways of human central nervous system aging.

PubMed

Glorioso, Christin; Sibille, Etienne

2011-02-01

Aging of the human brain is associated with "normal" functional, structural, and molecular changes that underlie alterations in cognition, memory, mood and motor function, amongst other processes. Normal aging also imposes a robust constraint on the onset of many neurological diseases, ranging from late onset neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's diseases (PD), to early onset psychiatric disorders, such as bipolar disorder (BPD) and schizophrenia (SCZ). The molecular mechanisms and genetic underpinnings of age-related changes in the brain are understudied, and, while they share some overlap with peripheral mechanisms of aging, many are unique to the largely non-mitotic brain. Hence, understanding mechanisms of brain aging and identifying associated modulators may have profound consequences for the prevention and treatment of age-related impairments and diseases. Here we review current knowledge on age-related functional and structural changes, their molecular and genetic underpinnings, and discuss how these pathways may contribute to the vulnerability to develop age-related neurological diseases. We highlight recent findings from human post-mortem brain microarray studies, which we hypothesize, point to a potential genetically controlled transcriptional program underlying molecular changes and age-gating of neurological diseases. Finally, we discuss the implications of this model for understanding basic mechanisms of brain aging and for the future investigation of therapeutic approaches. Copyright © 2010 Elsevier Ltd. All rights reserved.

Application of network methods for understanding evolutionary dynamics in discrete habitats.

PubMed

Greenbaum, Gili; Fefferman, Nina H

2017-06-01

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene-flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population-genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene-flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. © 2017 John Wiley & Sons Ltd.

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico.

PubMed

Domínguez-Contreras, José F; Munguia-Vega, Adrian; Ceballos-Vázquez, Bertha P; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J; Culver, Melanie; Reyes-Bonilla, Hector

2018-01-01

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides . These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

PubMed Central

Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

2014-01-01

Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

Polymorphic microsatellite markers for the endangered fish, the slender shiner Pseudopungtungia tenuicorpa and cross-species amplification across five related species.

PubMed

Kim, K S; Moon, S J; Han, S H; Kim, K Y; Bang, I C

2016-09-02

The slender shiner Pseudopungtungia tenuicorpa (Cypriniformes; Cyprinidae; Gobioninae) is an endangered freshwater fish species endemic to Korea. The current strategies for its conservation involve the study of population genetic characters and identification of management units. These strategies require suitable molecular markers to study genetic diversity and genetic structure. Here, we developed nine polymorphic microsatellite markers for P. tenuicorpa for the first time by applying an enrichment method from a size-selected genomic library. The developed microsatellite markers produced a total of 101 alleles (average 11.2). The observed and expected heterozygosities averaged 0.805 and 0.835, respectively. Among the nine identified markers, five markers showed successful amplification across five related Korean Gobioninae species. Thus, the microsatellite markers developed in this study will be useful to establish conservation strategies for both P. tenuicorpa and other related species.

Computational intelligence in bioinformatics: SNP/haplotype data in genetic association study for common diseases.

PubMed

Kelemen, Arpad; Vasilakos, Athanasios V; Liang, Yulan

2009-09-01

Comprehensive evaluation of common genetic variations through association of single-nucleotide polymorphism (SNP) structure with common complex disease in the genome-wide scale is currently a hot area in human genome research due to the recent development of the Human Genome Project and HapMap Project. Computational science, which includes computational intelligence (CI), has recently become the third method of scientific enquiry besides theory and experimentation. There have been fast growing interests in developing and applying CI in disease mapping using SNP and haplotype data. Some of the recent studies have demonstrated the promise and importance of CI for common complex diseases in genomic association study using SNP/haplotype data, especially for tackling challenges, such as gene-gene and gene-environment interactions, and the notorious "curse of dimensionality" problem. This review provides coverage of recent developments of CI approaches for complex diseases in genetic association study with SNP/haplotype data.

The Genetics of Osteosarcoma

PubMed Central

Martin, Jeff W.; Squire, Jeremy A.; Zielenska, Maria

2012-01-01

Osteosarcoma is a primary bone malignancy with a particularly high incidence rate in children and adolescents relative to other age groups. The etiology of this often aggressive cancer is currently unknown, because complicated structural and numeric genomic rearrangements in cancer cells preclude understanding of tumour development. In addition, few consistent genetic changes that may indicate effective molecular therapeutic targets have been reported. However, high-resolution techniques continue to improve knowledge of distinct areas of the genome that are more commonly associated with osteosarcomas. Copy number gains at chromosomes 1p, 1q, 6p, 8q, and 17p as well as copy number losses at chromosomes 3q, 6q, 9, 10, 13, 17p, and 18q have been detected by numerous groups, but definitive oncogenes or tumour suppressor genes remain elusive with respect to many loci. In this paper, we examine studies of the genetics of osteosarcoma to comprehensively describe the heterogeneity and complexity of this cancer. PMID:22685381

Defining a new candidate gene for amelogenesis imperfecta: from molecular genetics to biochemistry.

PubMed

Urzúa, Blanca; Ortega-Pinto, Ana; Morales-Bozo, Irene; Rojas-Alcayaga, Gonzalo; Cifuentes, Víctor

2011-02-01

Amelogenesis imperfecta is a group of genetic conditions that affect the structure and clinical appearance of tooth enamel. The types (hypoplastic, hypocalcified, and hypomature) are correlated with defects in different stages of the process of enamel synthesis. Autosomal dominant, recessive, and X-linked types have been previously described. These disorders are considered clinically and genetically heterogeneous in etiology, involving a variety of genes, such as AMELX, ENAM, DLX3, FAM83H, MMP-20, KLK4, and WDR72. The mutations identified within these causal genes explain less than half of all cases of amelogenesis imperfecta. Most of the candidate and causal genes currently identified encode proteins involved in enamel synthesis. We think it is necessary to refocus the search for candidate genes using biochemical processes. This review provides theoretical evidence that the human SLC4A4 gene (sodium bicarbonate cotransporter) may be a new candidate gene.

Admixture into and within sub-Saharan Africa.

PubMed

Busby, George Bj; Band, Gavin; Si Le, Quang; Jallow, Muminatou; Bougama, Edith; Mangano, Valentina D; Amenga-Etego, Lucas N; Enimil, Anthony; Apinjoh, Tobias; Ndila, Carolyne M; Manjurano, Alphaxard; Nyirongo, Vysaul; Doumba, Ogobara; Rockett, Kirk A; Kwiatkowski, Dominic P; Spencer, Chris Ca

2016-06-21

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Evaluation of the contribution of D9S1120 to anthropological studies in Native American populations.

PubMed

Aguilar-Velázquez, J A; Martínez-Sevilla, V Manuel; Sosa-Macías, M; González-Martin, A; Muñoz-Valle, J F; Rangel-Villalobos, H

2017-12-01

The D9S1120 locus exhibits a population-specific allele of 9 repeats (9RA) in all Native American and two Siberian populations currently studied, but it is absent in other worldwide populations. Although this feature has been used in anthropological genetic studies, its impact on the evaluation of the structure and genetic relations among Native American populations has been scarcely assessed. Consequently, the aim of this study was to evaluate the anthropological impact of D9S1120 when it was added to STR population datasets in Mexican Native American groups. We analyzed D9S1120 by PCR and capillary electrophoresis (CE) in 1117 unrelated individuals from 13 native groups from the north and west of Mexico. Additional worldwide populations previously studied with D9S1120 and/or 15 autosomal STRs (Identifier kit) were included for interpopulation analyses. We report statistical results of forensic importance for D9S1120. On average, the modal alleles were the Native American-specific allele 9RA (0.3254) and 16 (0.3362). Genetic distances between Native American and worldwide populations were estimated. When D9S1120 was included in the 15 STR population dataset, we observed improvements for admixture estimation in Mestizo populations and for representing congruent genetic relationships in dendrograms. Analysis of molecular variance (AMOVA) based on D9S1120 confirms that most of the genetic variability in the Mexican population is attributable to their Native American backgrounds, and allows the detection of significant intercontinental differentiation attributed to the exclusive presence of 9RA in America. Our findings demonstrate the contribution of D9S1120 to a better understanding of the genetic relationships and structure among Mexican Native groups. Copyright © 2017 Elsevier GmbH. All rights reserved.

Host association drives genetic divergence in the bed bug, Cimex lectularius.

PubMed

Booth, Warren; Balvín, Ondřej; Vargo, Edward L; Vilímová, Jitka; Schal, Coby

2015-03-01

Genetic differentiation may exist among sympatric populations of a species due to long-term associations with alternative hosts (i.e. host-associated differentiation). While host-associated differentiation has been documented in several phytophagus insects, there are far fewer cases known in animal parasites. The bed bug, Cimex lectularius, a wingless insect, represents a potential model organism for elucidating the processes involved in host-associated differentiation in animal parasites with relatively limited mobility. In conjunction with the expansion of modern humans from Africa into Eurasia, it has been speculated that bed bugs extended their host range from bats to humans in their shared cave domiciles throughout Eurasia. C. lectularius that associate with humans have a cosmopolitan distribution, whereas those associated with bats occur across Europe, often in human-built structures. We assessed genetic structure and gene flow within and among populations collected in association with each host using mtDNA, microsatellite loci and knock-down resistance gene variants. Both nuclear and mitochondrial data support a lack of significant contemporary gene flow between host-specific populations. Within locations human-associated bed bug populations exhibit limited genetic diversity and elevated levels of inbreeding, likely due to human-mediated movement, infrequent additional introduction events per infestation, and pest control. In contrast, populations within bat roosts exhibit higher genetic diversity and lower levels of relatedness, suggesting populations are stable with temporal fluctuations due to host dispersal and bug mortality. In concert with previously published evidence of morphological and behavioural differentiation, the genetic data presented here suggest C. lectularius is currently undergoing lineage divergence through host association. © 2015 John Wiley & Sons Ltd.

Alpine Crossroads or Origin of Genetic Diversity? Comparative Phylogeography of Two Sympatric Microgastropod Species

PubMed Central

Weigand, Alexander M.; Pfenninger, Markus; Jochum, Adrienne; Klussmann-Kolb, Annette

2012-01-01

The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa – Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae) – by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant ‘hot-spot’ for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general. PMID:22606334

Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests

PubMed Central

Duminil, J; Daïnou, K; Kaviriri, D K; Gillet, P; Loo, J; Doucet, J-L; Hardy, O J

2016-01-01

Owing to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low-quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide indirect evidence of the potential impacts of logging. Here, we analysed patterns of genetic diversity, mating system and gene flow in three Central African populations of the self-compatible legume timber species Erythrophleum suaveolens with contrasting densities (0.11, 0.68 and 1.72 adults per ha). The comparison of inbreeding levels among cohorts suggests that selfing is detrimental as inbred individuals are eliminated between seedling and adult stages. Levels of genetic diversity, selfing rates (∼16%) and patterns of spatial genetic structure (Sp ∼0.006) were similar in all three populations. However, the extent of gene dispersal differed markedly among populations: the average distance of pollen dispersal increased with decreasing density (from 200 m in the high-density population to 1000 m in the low-density one). Overall, our results suggest that the reproductive biology and genetic diversity of the species are not affected by current logging practices. However, further investigations need to be conducted in low-density populations to evaluate (1) whether pollen limitation may reduce seed production and (2) the regeneration potential of the species. PMID:26696137

A Population Genetic Signal of Polygenic Adaptation

PubMed Central

Berg, Jeremy J.; Coop, Graham

2014-01-01

Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed knowledge about the specific loci underlying polygenic traits has begun to emerge from genome-wide association studies (GWAS). Here we combine this knowledge from GWAS with robust population genetic modeling to identify traits that may have been influenced by local adaptation. We exploit the fact that GWAS provide an estimate of the additive effect size of many loci to estimate the mean additive genetic value for a given phenotype across many populations as simple weighted sums of allele frequencies. We use a general model of neutral genetic value drift for an arbitrary number of populations with an arbitrary relatedness structure. Based on this model, we develop methods for detecting unusually strong correlations between genetic values and specific environmental variables, as well as a generalization of comparisons to test for over-dispersion of genetic values among populations. Finally we lay out a framework to identify the individual populations or groups of populations that contribute to the signal of overdispersion. These tests have considerably greater power than their single locus equivalents due to the fact that they look for positive covariance between like effect alleles, and also significantly outperform methods that do not account for population structure. We apply our tests to the Human Genome Diversity Panel (HGDP) dataset using GWAS data for height, skin pigmentation, type 2 diabetes, body mass index, and two inflammatory bowel disease datasets. This analysis uncovers a number of putative signals of local adaptation, and we discuss the biological interpretation and caveats of these results. PMID:25102153

Contrasting Genetic Structure and Diversity of Galaxias maculatus (Jenyns, 1848) Along the Chilean Coast: Stock Identification for Fishery Management.

PubMed

González-Wevar, Claudio; Salinas, Pilar; Hüne, Mathias; Segovia, Nicolás; Vargas-Chacoff, Luis; Oda, Esteban; Poulin, Elie

2015-01-01

Galaxias maculatus (Pisces: Galaxiidae) commonly known as "puye" has a disjunct distribution along the Southern Hemisphere including landlocked and migratory populations at latitudes over 30°S in South America, Australia, Tasmania, and New Zealand. Chilean artisanal fishery of G. maculatus has become less important as a resource due to multiple factors including overexploitation, pollution, introduction of predators, and competitors. At the same time, the current conservation status of the species in Chile is still uncertain. Here, we used mtDNA control region sequences (925bp) to investigate main patterns of genetic diversity and structure in populations from 2 biogeographic areas along the Chilean coast. Extremely high levels of genetic diversity characterize the species, suggesting a low amount of influence of the last glacial cycle over its demography compared with other studies in freshwater and marine South American fishes. However, we recognized contrasting genetic patterns between the Intermediate Area (between 30°S and 42°S) and the Magellanic Province (between 42°S and 56°S). On the one hand, over a narrow geographical range (<200 km) each Intermediate Area estuarine population constitutes a different genetic unit. On the other hand, the Magellanic populations of the species exhibited low levels of differentiation in an area extending for more than 500 km. Such differences may be a consequence of different coastal configurations, oceanographic regimes, and Quaternary glacial histories. Finally, our results support the existence of different stock units for G. maculatus and this information should be integrated in future management strategies and aquaculture programs for this species. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ancient geographical gaps and paleo-climate shape the phylogeography of an endemic bird in the sky islands of southern India.

PubMed

Robin, V V; Sinha, Anindya; Ramakrishnan, Uma

2010-10-13

Sky islands, formed by the highest reaches of mountain tracts physically isolated from one another, represent one of the biodiversity-rich regions of the world. Comparative studies of geographically isolated populations on such islands can provide valuable insights into the biogeography and evolution of species on these islands. The Western Ghats mountains of southern India form a sky island system, where the relationship between the island structure and the evolution of its species remains virtually unknown despite a few population genetic studies. We investigated how ancient geographic gaps and glacial cycles have partitioned genetic variation in modern populations of a threatened endemic bird, the White-bellied Shortwing Brachypteryx major, across the montane Shola forests on these islands and also inferred its evolutionary history. We used bayesian and maximum likelihood-based phylogenetic and population-genetic analyses on data from three mitochondrial markers and one nuclear marker (totally 2594 bp) obtained from 33 White-bellied Shortwing individuals across five islands. Genetic differentiation between populations of the species correlated with the locations of deep valleys in the Western Ghats but not with geographical distance between these populations. All populations revealed demographic histories consistent with population founding and expansion during the Last Glacial Maximum. Given the level of genetic differentiation north and south of the Palghat Gap, we suggest that these populations be considered two different taxonomic species. Our results show that the physiography and paleo-climate of this region historically resulted in multiple glacial refugia that may have subsequently driven the evolutionary history and current population structure of this bird. The first avian genetic study from this biodiversity hotspot, our results provide insights into processes that may have impacted the speciation and evolution of the endemic fauna of this region.

Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data

PubMed Central

Vergara, Rodrigo; Gitzendanner, Matthew A; Soltis, Douglas E; Soltis, Pamela S

2014-01-01

The effect of glaciation on the levels and patterns of genetic variation has been well studied in the Northern Hemisphere. However, although glaciation has undoubtedly shaped the genetic structure of plants in the Southern Hemisphere, fewer studies have characterized the effect, and almost none of them using microsatellites. Particularly, complex patterns of genetic structure might be expected in areas such as the Andes, where both latitudinal and altitudinal glacial advance and retreat have molded modern plant communities. We therefore studied the population genetics of three closely related, hybridizing species of Nothofagus (N. obliqua, N. alpina, and N. glauca, all of subgenus Lophozonia; Nothofagaceae) from Chile. To estimate population genetic parameters and infer the influence of the last ice age on the spatial and genetic distribution of these species, we examined and analyzed genetic variability at seven polymorphic microsatellite DNA loci in 640 individuals from 40 populations covering most of the ranges of these species in Chile. Populations showed no significant inbreeding and exhibited relatively high levels of genetic diversity (HE = 0.502–0.662) and slight, but significant, genetic structure (RST = 8.7–16.0%). However, in N. obliqua, the small amount of genetic structure was spatially organized into three well-defined latitudinal groups. Our data may also suggest some introgression of N. alpina genes into N. obliqua in the northern populations. These results allowed us to reconstruct the influence of the last ice age on the genetic structure of these species, suggesting several centers of genetic diversity for N. obliqua and N. alpina, in agreement with the multiple refugia hypothesis. PMID:25360279

Why do different oceanic archipelagos harbour contrasting levels of species diversity? The macaronesian endemic genus Pericallis (Asteraceae) provides insight into explaining the 'Azores diversity Enigma'.

PubMed

Jones, K E; Pérez-Espona, S; Reyes-Betancort, J A; Pattinson, D; Caujapé-Castells, J; Hiscock, S J; Carine, M A

2016-10-08

Oceanic archipelagos typically harbour extensive radiations of flowering plants and a high proportion of endemics, many of which are restricted to a single island (Single Island Endemics; SIEs). The Azores represents an anomaly as overall levels of endemism are low; there are few SIEs and few documented cases of intra-archipelago radiations. The distinctiveness of the flora was first recognized by Darwin and has been referred to as the 'Azores Diversity Enigma' (ADE). Diversity patterns in the Macaronesian endemic genus Pericallis (Asteraceae) exemplify the ADE. In this study we used morphometric, Amplified Length Polymorphisms, and bioclimatic data for herbaceous Pericallis lineages endemic to the Azores and the Canaries, to test two key hypotheses proposed to explain the ADE: i) that it is a taxonomic artefact or Linnean shortfall, ie. the under description of taxa in the Azores or the over-splitting of taxa in the Canaries and (ii) that it reflects the greater ecological homogeneity of the Azores, which results in limited opportunity for ecological diversification compared to the Canaries. In both the Azores and the Canaries, morphological patterns were generally consistent with current taxonomic classifications. However, the AFLP data showed no genetic differentiation between the two currently recognized Azorean subspecies that are ecologically differentiated. Instead, genetic diversity in the Azores was structured geographically across the archipelago. In contrast, in the Canaries genetic differentiation was mostly consistent with morphology and current taxonomic treatments. Both Azorean and Canarian lineages exhibited ecological differentiation between currently recognized taxa. Neither a Linnean shortfall nor the perceived ecological homogeneity of the Azores fully explained the ADE-like pattern observed in Pericallis. Whilst variation in genetic data and morphological data in the Canaries were largely congruent, this was not the case in the Azores, where genetic patterns reflected inter-island geographical isolation, and morphology reflected intra-island bioclimatic variation. The combined effects of differences in (i) the extent of geographical isolation, (ii) population sizes and (iii) geographical occupancy of bioclimatic niche space, coupled with the morphological plasticity of Pericallis, may all have contributed to generating the contrasting patterns observed in the archipelagos.

Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

NASA Astrophysics Data System (ADS)

Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

2014-03-01

Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p < 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.