High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China

PubMed Central

Du, Xi-Hui; Zhao, Qi; Xu, Jianping; Yang, Zhu L.

2016-01-01

As highly prized, popular mushrooms, morels are widely distributed in the northern hemisphere, with China as a modern centre of speciation and diversity. Overharvesting of morels has caused concern over how to effectively preserve their biological and genetic diversity. However, little is known about their population biology and life cycle. In this study, we selected two sympatric phylogenetic species, Mel-13 (124 collections from 11 geographical locations) and Morchella eohespera (156 collections from 14 geographical locations), using fragments of 4 DNA sequences, to analyse their genetic structure. Our results indicated significant differentiation among geographic locations in both species, whereas no obvious correlation between genetic and geographic distance was identified in either species. M. eohespera exhibited a predominantly clonal population structure with limited recombination detected in only 1 of the 14 geographic locations. In contrast, relatively frequent recombination was identified in 6 of the 11 geographic locations of Mel-13. Our analysis indicated that the sympatric species Mel-13 and M. eohespera might have divergent evolutionary patterns, with the former showing signatures of recent population expansion and the latter being relatively stable. Interestingly, we found no heterozygosity but strong evidence for genealogical incongruence, indicating a high level of inbreeding and hybridisation among morel species. PMID:26928176

Direct and indirect effects of biological factors on extinction risk in fossil bivalves

PubMed Central

Harnik, Paul G.

2011-01-01

Biological factors, such as abundance and body size, may contribute directly to extinction risk and indirectly through their influence on other biological characteristics, such as geographic range size. Paleontological data can be used to explicitly test many of these hypothesized relationships, and general patterns revealed through analysis of the fossil record can help refine predictive models of extinction risk developed for extant species. Here, I use structural equation modeling to tease apart the contributions of three canonical predictors of extinction—abundance, body size, and geographic range size—to the duration of bivalve species in the early Cenozoic marine fossil record of the eastern United States. I find that geographic range size has a strong direct effect on extinction risk and that an apparent direct effect of abundance can be explained entirely by its covariation with geographic range. The influence of geographic range on extinction risk is manifest across three ecologically disparate bivalve clades. Body size also has strong direct effects on extinction risk but operates in opposing directions in different clades, and thus, it seems to be decoupled from extinction risk in bivalves as a whole. Although abundance does not directly predict extinction risk, I reveal weak indirect effects of both abundance and body size through their positive influence on geographic range size. Multivariate models that account for the pervasive covariation between biological factors and extinction are necessary for assessing causality in evolutionary processes and making informed predictions in applied conservation efforts. PMID:21808004

Direct and indirect effects of biological factors on extinction risk in fossil bivalves.

PubMed

Harnik, Paul G

2011-08-16

Biological factors, such as abundance and body size, may contribute directly to extinction risk and indirectly through their influence on other biological characteristics, such as geographic range size. Paleontological data can be used to explicitly test many of these hypothesized relationships, and general patterns revealed through analysis of the fossil record can help refine predictive models of extinction risk developed for extant species. Here, I use structural equation modeling to tease apart the contributions of three canonical predictors of extinction--abundance, body size, and geographic range size--to the duration of bivalve species in the early Cenozoic marine fossil record of the eastern United States. I find that geographic range size has a strong direct effect on extinction risk and that an apparent direct effect of abundance can be explained entirely by its covariation with geographic range. The influence of geographic range on extinction risk is manifest across three ecologically disparate bivalve clades. Body size also has strong direct effects on extinction risk but operates in opposing directions in different clades, and thus, it seems to be decoupled from extinction risk in bivalves as a whole. Although abundance does not directly predict extinction risk, I reveal weak indirect effects of both abundance and body size through their positive influence on geographic range size. Multivariate models that account for the pervasive covariation between biological factors and extinction are necessary for assessing causality in evolutionary processes and making informed predictions in applied conservation efforts.

Genetic structure of colline and montane populations of an endangered plant species

PubMed Central

Maurice, Tiphaine; Matthies, Diethart; Muller, Serge; Colling, Guy

2016-01-01

Due to land-use intensification, lowland and colline populations of many plants of nutrient-poor grasslands have been strongly fragmented in the last decades, with potentially negative consequences for their genetic diversity and persistence. Populations in mountains might represent a genetic reservoir for grassland plants, because they have been less affected by land-use changes. We studied the genetic structure and diversity of colline and montane Vosges populations of the threatened perennial plant Arnica montana in western central Europe using AFLP markers. Our results indicate that in contrast to our expectation even strongly fragmented colline populations of A. montana have conserved a considerable amount of genetic diversity. However, mean seed mass increased with the proportion of polymorphic loci, suggesting inbreeding effects in low diversity populations. At a similar small geographical scale, there was a clear IBD pattern for the montane Vosges but not for the colline populations. However, there was a strong IBD-pattern for the colline populations at a large geographical scale suggesting that this pattern is a legacy of historical gene flow, as most of the colline populations are today strongly isolated from each other. Genetic differentiation between colline and montane Vosges populations was strong. Moreover, results of a genome scan study indicated differences in loci under selection, suggesting that plants from montane Vosges populations might be maladapted to conditions at colline sites. Our results suggest caution in using material from montane populations of rare plants for the reinforcement of small genetically depauperate lowland populations. PMID:27519913

Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient

PubMed Central

Wu, Zhigang; Yu, Dan; Wang, Zhong; Li, Xing; Xu, Xinwei

2015-01-01

Understanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift. PMID:26494202

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.

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

PubMed

Filker, Sabine; Sommaruga, Ruben; Vila, Irma; Stoeck, Thorsten

2016-05-01

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures. © 2016 John Wiley & Sons Ltd.

United States forest disturbance trends observed with landsat time series

Treesearch

Jeffrey G. Masek; Samuel N. Goward; Robert E. Kennedy; Warren B. Cohen; Gretchen G. Moisen; Karen Schleweiss; Chengquan Huang

2013-01-01

Disturbance events strongly affect the composition, structure, and function of forest ecosystems; however, existing US land management inventories were not designed to monitor disturbance. To begin addressing this gap, the North American Forest Dynamics (NAFD) project has examined a geographic sample of 50 Landsat satellite image time series to assess trends in forest...

Geographic approaches to biodiversity conservation: implications of scale and error to landscape planning

Treesearch

Curtis H. Flather; Kenneth R. Wilson; Susan A. Shriner

2009-01-01

Conservation science is concerned with understanding why distribution and abundance patterns of species vary in time and space. Although these patterns have strong signatures tied to the availability of energy and nutrients, variation in climate, physiographic heterogeneity, and differences in the structural complexity of natural vegetation, it is becoming more...

Distance Education and Spatial Citizenship in Africa--Challenges and Prospects

ERIC Educational Resources Information Center

Kanwischer, Detlef; Quennet, Fabienne

2012-01-01

The relevance of GIS for sustainable development in Africa is undisputed. One web 2.0 application which plays a particularly strong role within local governance structures in Africa is PGIS (Participatory Geographical Information System). In fact, Spatial Citizenship education is the basis for the empowerment of the indigenous capacity for using…

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

Insights into the historical construction of species-rich Mesoamerican seasonally dry tropical forests: the diversification of Bursera (Burseraceae, Sapindales).

PubMed

De-Nova, J Arturo; Medina, Rosalinda; Montero, Juan Carlos; Weeks, Andrea; Rosell, Julieta A; Olson, Mark E; Eguiarte, Luis E; Magallón, Susana

2012-01-01

• Mesoamerican arid biomes epitomize neotropical rich and complex biodiversity. To document some of the macroevolutionary processes underlying the vast species richness of Mesoamerican seasonally dry tropical forests (SDTFs), and to evaluate specific predictions about the age, geographical structure and niche conservatism of SDTF-centered woody plant lineages, the diversification of Bursera is reconstructed. • Using a nearly complete Bursera species-level phylogeny from nuclear and plastid genomic markers, we estimate divergence times, test for phylogenetic and temporal diversification heterogeneity, test for geographical structure, and reconstruct habitat shifts. • Bursera became differentiated in the earliest Eocene, but diversified during independent early Miocene consecutive radiations that took place in SDTFs. The late Miocene average age of Bursera species, the presence of phylogenetic geographical structure, and its strong conservatism to SDTFs conform to expectations derived from South American SDTF-centered lineages. • The diversification of Bursera suggests that Mesoamerican SDTF richness derives from high speciation from the Miocene onwards uncoupled from habitat shifts, during a period of enhanced aridity resulting mainly from global cooling and regional rain shadows. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

PubMed

Alexander, Alana; Steel, Debbie; Hoekzema, Kendra; Mesnick, Sarah L; Engelhaupt, Daniel; Kerr, Iain; Payne, Roger; Baker, C Scott

2016-06-01

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394-bp mtDNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (π = 0.430%) reflecting an expansion event <80 000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male-mediated gene flow. A hierarchical amova showed that regions were important for explaining mtDNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mtDNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization. © 2016 John Wiley & Sons Ltd.

Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient

PubMed Central

Ferrera, Isabel; Sarmento, Hugo; Priscu, John C.; Chiuchiolo, Amy; González, José M.; Grossart, Hans-Peter

2017-01-01

Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient). PMID:28275369

Self-fertilization, long-distance flash invasion and biogeography shape the population structure of Pseudosuccinea columella at the worldwide scale.

PubMed

Lounnas, M; Correa, A C; Vázquez, A A; Dia, A; Escobar, J S; Nicot, A; Arenas, J; Ayaqui, R; Dubois, M P; Gimenez, T; Gutiérrez, A; González-Ramírez, C; Noya, O; Prepelitchi, L; Uribe, N; Wisnivesky-Colli, C; Yong, M; David, P; Loker, E S; Jarne, P; Pointier, J P; Hurtrez-Boussès, S

2017-02-01

Population genetic studies are efficient for inferring the invasion history based on a comparison of native and invasive populations, especially when conducted at species scale. An expected outcome in invasive populations is variability loss, and this is especially true in self-fertilizing species. We here focus on the self-fertilizing Pseudosuccinea columella, an invasive hermaphroditic freshwater snail that has greatly expanded its geographic distribution and that acts as intermediate host of Fasciola hepatica, the causative agent of human and veterinary fasciolosis. We evaluated the distribution of genetic diversity at the largest geographic scale analysed to date in this species by surveying 80 populations collected during 16 years from 14 countries, using eight nuclear microsatellites and two mitochondrial genes. As expected, populations from North America, the putative origin area, were strongly structured by selfing and history and harboured much more genetic variability than invasive populations. We found high selfing rates (when it was possible to infer it), none-to-low genetic variability and strong population structure in most invasive populations. Strikingly, we found a unique genotype/haplotype in populations from eight invaded regions sampled all over the world. Moreover, snail populations resistant to infection by the parasite are genetically distinct from susceptible populations. Our results are compatible with repeated introductions in South America and flash worldwide invasion by this unique genotype/haplotype. Our study illustrates the population genetic consequences of biological invasion in a highly selfing species at very large geographic scale. We discuss how such a large-scale flash invasion may affect the spread of fasciolosis. © 2016 John Wiley & Sons Ltd.

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow.

PubMed

Whittaker, Kerry A; Rynearson, Tatiana A

2017-03-07

The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations ( F ST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a , a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time.

Pitfalls of the Geographic Population Structure (GPS) Approach Applied to Human Genetic History: A Case Study of Ashkenazi Jews

PubMed Central

Flegontov, Pavel; Kassian, Alexei; Thomas, Mark G.; Fedchenko, Valentina; Changmai, Piya; Starostin, George

2016-01-01

In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016. Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132–1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata. PMID:27389685

Genus age, provincial area and the taxonomic structure of marine faunas.

PubMed

Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

2010-11-22

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.

Genus age, provincial area and the taxonomic structure of marine faunas

PubMed Central

Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

2010-01-01

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

Genome-wide analysis of Epstein-Barr virus identifies variants and genes associated with gastric carcinoma and population structure.

PubMed

Yao, Youyuan; Xu, Miao; Liang, Liming; Zhang, Haojiong; Xu, Ruihua; Feng, Qisheng; Feng, Lin; Luo, Bing; Zeng, Yi-Xin

2017-10-01

Epstein-Barr virus is a ubiquitous virus and is associated with several human malignances, including the significant subset of gastric carcinoma, Epstein-Barr virus-associated gastric carcinoma. Some Epstein-Barr virus-associated diseases are uniquely prevalent in populations with different geographic origins. However, the features of the disease and geographically associated Epstein-Barr virus genetic variation as well as the roles that the variation plays in carcinogenesis and evolution remain unclear. Therefore, in this study, we sequenced 95 geographically distinct Epstein-Barr virus isolates from Epstein-Barr virus-associated gastric carcinoma biopsies and saliva of healthy donors to detect variants and genes associated with gastric carcinoma and population structure from a genome-wide spectrum. We demonstrated that Epstein-Barr virus revealed the population structure between North China and South China. In addition, we observed population stratification between Epstein-Barr virus strains from gastric carcinoma and healthy controls, indicating that certain Epstein-Barr virus subtypes are associated with different gastric carcinoma risks. We identified that the BRLF1, BBRF3, and BBLF2/BBLF3 genes had significant associations with gastric carcinoma. LMP1 and BNLF2a genes were strongly geographically associated genes in Epstein-Barr virus. Our study provides insights into the genetic basis of oncogenic Epstein-Barr virus for gastric carcinoma, and the genetic variants associated with gastric carcinoma can serve as biomarkers for oncogenic Epstein-Barr virus.

Seismic damage to structures in the M s6.5 Ludian earthquake

NASA Astrophysics Data System (ADS)

Chen, Hao; Xie, Quancai; Dai, Boyang; Zhang, Haoyu; Chen, Hongfu

2016-03-01

On 3 August 2014, the Ludian earthquake struck northwest Yunnan Province with a surface wave magnitude of 6.5. This moderate earthquake unexpectedly caused high fatalities and great economic loss. Four strong motion stations were located in the areas with intensity V, VI, VII and IX, near the epicentre. The characteristics of the ground motion are discussed herein, including 1) ground motion was strong at a period of less than 1.4 s, which covered the natural vibration period of a large number of structures; and 2) the release energy was concentrated geographically. Based on materials collected during emergency building inspections, the damage patterns of adobe, masonry, timber frame and reinforced concrete (RC) frame structures in areas with different intensities are summarised. Earthquake damage matrices of local buildings are also given for fragility evaluation and earthquake damage prediction. It is found that the collapse ratios of RC frame and confined masonry structures based on the new design code are significantly lower than non-seismic buildings. However, the RC frame structures still failed to achieve the `strong column, weak beam' design target. Traditional timber frame structures with a light infill wall showed good aseismic performance.

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.

The Regional Structure of Technical Innovation

NASA Astrophysics Data System (ADS)

O'Neale, Dion

2014-03-01

There is strong evidence that the productivity per capita of cities and regions increases with population. One likely explanation for this phenomenon is that densely populated regions bring together otherwise unlikely combinations of individuals and organisations with diverse, specialised capabilities, leading to increased innovation and productivity. We have used the REGPAT patent database to construct a bipartite network of geographic regions and the patent classes for which those regions display a revealed comparative advantage. By analysing this network, we can infer relationships between different types of patent classes - and hence the structure of (patentable) technology. The network also provides a novel perspective for studying the combinations of technical capabilities in different geographic regions. We investigate measures such as the diversity and ubiquity of innovations within regions and find that diversity (resp. ubiquity) is positively (resp. negatively) correlated with population. We also find evidence of a nested structure for technical innovation. That is, specialised innovations tend to occur only when other more general innovations are already present.

Evolutionary characterization of the West Nile Virus complete genome.

PubMed

Gray, R R; Veras, N M C; Santos, L A; Salemi, M

2010-07-01

The spatial dynamics of the West Nile Virus epidemic in North America are largely unknown. Previous studies that investigated the evolutionary history of the virus used sequence data from the structural genes (prM and E); however, these regions may lack phylogenetic information and obscure true evolutionary relationships. This study systematically evaluated the evolutionary patterns in the eleven genes of the WNV genome in order to determine which region(s) were most phylogenetically informative. We found that while the E region lacks resolution and can potentially result in misleading conclusions, the full NS3 or NS5 regions have strong phylogenetic signal. Furthermore, we show that geographic structure of WNV infection within the US is more pronounced than previously reported in studies that used the structural genes. We conclude that future evolutionary studies should focus on NS3 and NS5 in order to maximize the available sequences while retaining maximal interpretative power to infer temporal and geographic trends among WNV strains. Copyright 2010 Elsevier Inc. All rights reserved.

Population genetic structure in migratory sandhill cranes and the role of Pleistocene glaciations.

PubMed

Jones, Kenneth L; Krapu, Gary L; Brandt, David A; Ashley, Mary V

2005-08-01

Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present-day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolation-by-distance model. Male-mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic-nesting subspecies G. c. canadensis to the nonArctic subspecies G. c. tabida. Analogous to other Arctic-nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.

Nursery practices with exotic conifers in Patagonia, Argentina, and some reasons to afforest the region with these species

Treesearch

Maria Gabriela Buamscha

2002-01-01

The southern portion of Argentina is called Patagonia, and is located between 37° and 55° south latitude. Across this region, there is a strong topographic and environmental gradient. Precipitation decreases from the western mountains towards the east and temperatures from north to south. These geographic gradients impose different structural patterns of soils and...

Broad-scale latitudinal variation in female reproductive success contributes to the maintenance of a geographic range boundary in bagworms (Lepidoptera: Psychidae).

PubMed

Rhainds, Marc; Fagan, William F

2010-11-30

Geographic range limits and the factors structuring them are of great interest to biologists, in part because of concerns about how global change may shift range boundaries. However, scientists lack strong mechanistic understanding of the factors that set geographic range limits in empirical systems, especially in animals. Across dozens of populations spread over six degrees of latitude in the American Midwest, female mating success of the evergreen bagworm Thyridopteryx ephemeraeformis (Lepidoptera: Psychidae) declines from ∼100% to ∼0% near the edge of the species range. When coupled with additional latitudinal declines in fecundity and in egg and pupal survivorship, a spatial gradient of bagworm reproductive success emerges. This gradient is associated with a progressive decline in local abundance and an increased risk of local population extinction, up to a latitudinal threshold where extremely low female fitness meshes spatially with the species' geographic range boundary. The reduction in fitness of female bagworms near the geographic range limit, which concords with the abundant centre hypothesis from biogeography, provides a concrete, empirical example of how an Allee effect (increased pre-reproductive mortality of females in sparsely populated areas) may interact with other demographic factors to induce a geographic range limit.

Chromosomal Inversions, Natural Selection and Adaptation in the Malaria Vector Anopheles funestus

PubMed Central

Ayala, Diego; Fontaine, Michael C.; Cohuet, Anna; Fontenille, Didier; Vitalis, Renaud; Simard, Frédéric

2011-01-01

Chromosomal polymorphisms, such as inversions, are presumably involved in the rapid adaptation of populations to local environmental conditions. Reduced recombination between alternative arrangements in heterozygotes may protect sets of locally adapted genes, promoting ecological divergence and potentially leading to reproductive isolation and speciation. Through a comparative analysis of chromosomal inversions and microsatellite marker polymorphisms, we hereby present biological evidence that strengthens this view in the mosquito Anopheles funestus s.s, one of the most important and widespread malaria vectors in Africa. Specimens were collected across a wide range of geographical, ecological, and climatic conditions in Cameroon. We observed a sharp contrast between population structure measured at neutral microsatellite markers and at chromosomal inversions. Microsatellite data detected only a weak signal for population structuring among geographical zones (FST < 0.013, P < 0.01). By contrast, strong differentiation among ecological zones was revealed by chromosomal inversions (FST > 0.190, P < 0.01). Using standardized estimates of FST, we show that inversions behave at odds with neutral expectations strongly suggesting a role of environmental selection in shaping their distribution. We further demonstrate through canonical correspondence analysis that heterogeneity in eco-geographical variables measured at specimen sampling sites explained 89% of chromosomal variance in A. funestus. These results are in agreement with a role of chromosomal inversions in ecotypic adaptation in this species. We argue that this widespread mosquito represents an interesting model system for the study of chromosomal speciation mechanisms and should provide ample opportunity for comparative studies on the evolution of reproductive isolation and speciation in major human malaria vectors. PMID:20837604

The Geographic Distribution of Saccharomyces cerevisiae Isolates within three Italian Neighboring Winemaking Regions Reveals Strong Differences in Yeast Abundance, Genetic Diversity and Industrial Strain Dissemination

PubMed Central

Viel, Alessia; Legras, Jean-Luc; Nadai, Chiara; Carlot, Milena; Lombardi, Angiolella; Crespan, Manna; Migliaro, Daniele; Giacomini, Alessio; Corich, Viviana

2017-01-01

In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota. PMID:28883812

United States Forest Disturbance Trends Observed Using Landsat Time Series

NASA Technical Reports Server (NTRS)

Masek, Jeffrey G.; Goward, Samuel N.; Kennedy, Robert E.; Cohen, Warren B.; Moisen, Gretchen G.; Schleeweis, Karen; Huang, Chengquan

2013-01-01

Disturbance events strongly affect the composition, structure, and function of forest ecosystems; however, existing U.S. land management inventories were not designed to monitor disturbance. To begin addressing this gap, the North American Forest Dynamics (NAFD) project has examined a geographic sample of 50 Landsat satellite image time series to assess trends in forest disturbance across the conterminous United States for 1985-2005. The geographic sample design used a probability-based scheme to encompass major forest types and maximize geographic dispersion. For each sample location disturbance was identified in the Landsat series using the Vegetation Change Tracker (VCT) algorithm. The NAFD analysis indicates that, on average, 2.77 Mha/yr of forests were disturbed annually, representing 1.09%/yr of US forestland. These satellite-based national disturbance rates estimates tend to be lower than those derived from land management inventories, reflecting both methodological and definitional differences. In particular the VCT approach used with a biennial time step has limited sensitivity to low-intensity disturbances. Unlike prior satellite studies, our biennial forest disturbance rates vary by nearly a factor of two between high and low years. High western US disturbance rates were associated with active fire years and insect activity, while variability in the east is more strongly related to harvest rates in managed forests. We note that generating a geographic sample based on representing forest type and variability may be problematic since the spatial pattern of disturbance does not necessarily correlate with forest type. We also find that the prevalence of diffuse, non-stand clearing disturbance in US forests makes the application of a biennial geographic sample problematic. Future satellite-based studies of disturbance at regional and national scales should focus on wall-to-wall analyses with annual time step for improved accuracy.

Phylogeographic distribution of very virulent infectious bursal disease virus isolates in the Iberian Peninsula.

PubMed

Cortey, Martí; Bertran, Kateri; Toskano, Jennifer; Majó, Natàlia; Dolz, Roser

2012-01-01

Viral population dynamics of very virulent infectious bursal disease virus (vvIBDV) field strains isolated in the Iberian Peninsula since the first outbreak in the 1990s have been analysed. Low levels of genetic variability and a global purification selection pattern were reported in 480 base pairs of the hypervariable region of the VP2 gene, indicating a lack of a selection-driven immune escape in the evolutive pathway of the virus. The viral population structure of vvIBDV strains in the Iberian Peninsula showed a strong relationship between geography and phylogeny, with two main groups observed. A global comparison among vvIBDV strains also showed an association with sequences from the same country. The low variability, the strong purifying selection and the geographical pattern observed point to a picture where the virus evolves slowly, occupying the same geographical niche for a long time. The scenario depicted fits well with the biological features of the virus: being able to remain viable for long periods of time due to a strong environmental resistance, and as an immunosuppressive agent, capable per se of annihilating temporally the immune system of the host.

A Spatial Framework for Understanding Population Structure and Admixture.

PubMed

Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M

2016-01-01

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

Pitfalls of the Geographic Population Structure (GPS) Approach Applied to Human Genetic History: A Case Study of Ashkenazi Jews.

PubMed

Flegontov, Pavel; Kassian, Alexei; Thomas, Mark G; Fedchenko, Valentina; Changmai, Piya; Starostin, George

2016-08-16

In a recent interdisciplinary study, Das et al. have attempted to trace the homeland of Ashkenazi Jews and of their historical language, Yiddish (Das et al. 2016 Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz. Genome Biol Evol. 8:1132-1149). Das et al. applied the geographic population structure (GPS) method to autosomal genotyping data and inferred geographic coordinates of populations supposedly ancestral to Ashkenazi Jews, placing them in Eastern Turkey. They argued that this unexpected genetic result goes against the widely accepted notion of Ashkenazi origin in the Levant, and speculated that Yiddish was originally a Slavic language strongly influenced by Iranian and Turkic languages, and later remodeled completely under Germanic influence. In our view, there are major conceptual problems with both the genetic and linguistic parts of the work. We argue that GPS is a provenancing tool suited to inferring the geographic region where a modern and recently unadmixed genome is most likely to arise, but is hardly suitable for admixed populations and for tracing ancestry up to 1,000 years before present, as its authors have previously claimed. Moreover, all methods of historical linguistics concur that Yiddish is a Germanic language, with no reliable evidence for Slavic, Iranian, or Turkic substrata. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Spatial Framework for Understanding Population Structure and Admixture

PubMed Central

Bradburd, Gideon S.; Ralph, Peter L.; Coop, Graham M.

2016-01-01

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps,” which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix. PMID:26771578

Lack of genetic structure in the jellyfish Pelagia noctiluca (Cnidaria: Scyphozoa: Semaeostomeae) across European seas.

PubMed

Stopar, Katja; Ramsak, Andreja; Trontelj, Peter; Malej, Alenka

2010-10-01

The genetic structure of the holopelagic scyphozoan Pelagia noctiluca was inferred based on the study of 144 adult medusae. The areas of study were five geographic regions in two European seas (Eastern Atlantic and Mediterranean Sea). A 655-bp sequence of mitochondrial cytochrome c oxidase subunit I (COI), and a 645-bp sequence of two nuclear internal transcribed spacers (ITS1 and ITS2) were analyzed. The protein coding COI gene showed a higher level of divergence than the combined nuclear ITS fragment (haplotype diversity 0.962 vs. 0.723, nucleotide diversity 1.16% vs. 0.31%). Phylogeographic analysis on COI gene revealed two clades, the larger consisting of specimens from all sampling sites, and the smaller mostly formed of specimens from the Mediterranean Sea. Haplotype diversity was very high throughout the sampled area, and within sample diversity was higher than diversity among geographical regions. No strongly supported genetically or geographically distinct groups of P. noctiluca were found. The results - long distance dispersal, insignificant F(ST) values, lack of isolation by distance - pointed toward an admixture among Mediterranean and East Atlantic populations. Copyright 2010 Elsevier Inc. All rights reserved.

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

USGS Publications Warehouse

Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

2004-01-01

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Environmental Complexity and Biodiversity: The Multi-Layered Evolutionary History of a Log-Dwelling Velvet Worm in Montane Temperate Australia

PubMed Central

Garrick, Ryan C.; Gardner, Michael G.; Tait, Noel N.; Briscoe, David A.; Rowell, David M.; Sunnucks, Paul

2013-01-01

Phylogeographic studies provide a framework for understanding the importance of intrinsic versus extrinsic factors in shaping patterns of biodiversity through identifying past and present microevolutionary processes that contributed to lineage divergence. Here we investigate population structure and diversity of the Onychophoran (velvet worm) Euperipatoides rowelli in southeastern Australian montane forests that were not subject to Pleistocene glaciations, and thus likely retained more forest cover than systems under glaciation. Over a ~100 km transect of structurally-connected forest, we found marked nuclear and mitochondrial (mt) DNA genetic structuring, with spatially-localised groups. Patterns from mtDNA and nuclear data broadly corresponded with previously defined geographic regions, consistent with repeated isolation in refuges during Pleistocene climatic cycling. Nevertheless, some E. rowelli genetic contact zones were displaced relative to hypothesized influential landscape structures, implying more recent processes overlying impacts of past environmental history. Major impacts at different timescales were seen in the phylogenetic relationships among mtDNA sequences, which matched geographic relationships and nuclear data only at recent timescales, indicating historical gene flow and/or incomplete lineage sorting. Five major E. rowelli phylogeographic groups were identified, showing substantial but incomplete reproductive isolation despite continuous habitat. Regional distinctiveness, in the face of lineages abutting within forest habitat, could indicate pre- and/or postzygotic gene flow limitation. A potentially functional phenotypic character, colour pattern variation, reflected the geographic patterns in the molecular data. Spatial-genetic patterns broadly match those in previously-studied, co-occurring low-mobility organisms, despite a variety of life histories. We suggest that for E. rowelli, the complex topography and history of the region has led to interplay among limited dispersal ability, historical responses to environmental change, local adaptation, and some resistance to free admixture at geographic secondary contact, leading to strong genetic structuring at fine spatial scale. PMID:24358365

The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.

PubMed

Taboada, B; Isa, P; Gutiérrez-Escolano, A L; Del Ángel, R M; Ludert, J E; Vázquez, N; Tapia-Palacios, M A; Chávez, P; Garrido, E; Espinosa, A C; Eguiarte, L E; López, S; Souza, V; Arias, C F

2018-06-01

The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare. IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status. Copyright © 2018 American Society for Microbiology.

Latitudinal environmental niches and riverine barriers shaped the phylogeography of the Central Chilean endemic Dioscorea humilis (Dioscoreaceae).

PubMed

Viruel, Juan; Catalán, Pilar; Segarra-Moragues, José Gabriel

2014-01-01

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary.

Latitudinal Environmental Niches and Riverine Barriers Shaped the Phylogeography of the Central Chilean Endemic Dioscorea humilis (Dioscoreaceae)

PubMed Central

Viruel, Juan; Catalán, Pilar; Segarra-Moragues, José Gabriel

2014-01-01

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary. PMID:25295517

Restricted gene flow at the micro- and macro-geographical scale in marble trout based on mtDNA and microsatellite polymorphism.

PubMed

Pujolar, José M; Lucarda, Alvise N; Simonato, Mauro; Patarnello, Tomaso

2011-04-14

The genetic structure of the marble trout Salmo trutta marmoratus, an endemic salmonid of northern Italy and the Balkan peninsula, was explored at the macro- and micro-scale level using a combination of mitochondrial DNA (mtDNA) and microsatellite data. Sequence variation in the mitochondrial control region showed the presence of nonindigenous haplotypes indicative of introgression from brown trout into marble trout. This was confirmed using microsatellite markers, which showed a higher introgression at nuclear level. Microsatellite loci revealed a strong genetic differentiation across the geographical range of marble trout, which suggests restricted gene flow both at the micro-geographic (within rivers) and macro-geographic (among river systems) scale. A pattern of Isolation-by-Distance was found, in which genetic samples were correlated with hydrographic distances. A general West-to-East partition of the microsatellite polymorphism was observed, which was supported by the geographic distribution of mitochondrial haplotypes. While introgression at both mitochondrial and nuclear level is unlikely to result from natural migration and might be the consequence of current restocking practices, the pattern of genetic substructuring found at microsatellites has been likely shaped by historical colonization patterns determined by the geological evolution of the hydrographic networks.

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.

Genetic Analysis of Phytophthora nicotianae Populations from Different Hosts Using Microsatellite Markers.

PubMed

Biasi, Antonio; Martin, Frank N; Cacciola, Santa O; di San Lio, Gaetano Magnano; Grünwald, Niklaus J; Schena, Leonardo

2016-09-01

In all, 231 isolates of Phytophthora nicotianae representing 14 populations from different host genera, including agricultural crops (Citrus, Nicotiana, and Lycopersicon), potted ornamental species in nurseries (Lavandula, Convolvulus, Myrtus, Correa, and Ruta), and other plant genera were characterized using simple-sequence repeat markers. In total, 99 multilocus genotypes (MLG) were identified, revealing a strong association between genetic grouping and host of recovery, with most MLG being associated with a single host genus. Significant differences in the structure of populations were revealed but clonality prevailed in all populations. Isolates from Citrus were found to be genetically related regardless of their geographic origin and were characterized by high genetic uniformity and high inbreeding coefficients. Higher variability was observed for other populations and a significant geographical structuring was determined for isolates from Nicotiana. Detected differences were related to the propagation and cultivation systems of different crops. Isolates obtained from Citrus spp. are more likely to be distributed worldwide with infected plant material whereas Nicotiana and Lycopersicon spp. are propagated by seed, which would not contribute to the spread of the pathogen and result in a greater chance for geographic isolation of lineages. With regard to ornamental species in nurseries, the high genetic variation is likely the result of the admixture of diverse pathogen genotypes through the trade of infected plant material from various geographic origins, the presence of several hosts in the same nursery, and genetic recombination through sexual reproduction of this heterothallic species.

Benthic Algal Community Structures and Their Response to Geographic Distance and Environmental Variables in the Qinghai-Tibetan Lakes With Different Salinity

PubMed Central

Yang, Jian; Jiang, Hongchen; Liu, Wen; Wang, Beichen

2018-01-01

Uncovering the limiting factors for benthic algal distributions in lakes is of great importance to understanding of their role in global carbon cycling. However, limited is known about the benthic algal community distribution and how they are influenced by geographic distance and environmental variables in alpine lakes. Here, we investigated the benthic algal community compositions in the surface sediments of six lakes on the Qinghai-Tibetan Plateau (QTP), China (salinity ranging from 0.8 to 365.6 g/L; pairwise geographic distance among the studied lakes ranging 8–514 km) employing an integrated approach including Illumina-Miseq sequencing and environmental geochemistry. The results showed that the algal communities of the studied samples were mainly composed of orders of Bacillariales, Ceramiales, Naviculales, Oscillatoriales, Spirulinales, Synechococcales, and Vaucheriales. The benthic algal community compositions in these QTP lakes were significantly (p < 0.05) correlated with many environmental (e.g., dissolved inorganic and organic carbon, illumination intensity, total nitrogen and phosphorus, turbidity and water temperature) and spatial factors, and salinity did not show significant influence on the benthic algal community structures in the studied lakes. Furthermore, geographic distance showed strong, significant correlation (r = 0.578, p < 0.001) with the benthic algal community compositions among the studied lakes, suggesting that spatial factors may play important roles in influencing the benthic algal distribution. These results expand our current knowledge on the influencing factors for the distributions of benthic alga in alpine lakes. PMID:29636745

Molecular Evidence of Demographic Expansion of the Chagas Disease Vector Triatoma dimidiata (Hemiptera, Reduviidae, Triatominae) in Colombia

PubMed Central

Gómez-Palacio, Andrés; Triana, Omar

2014-01-01

Background Triatoma dimidiata is one of the most significant vectors of Chagas disease in Central America and Colombia, and, as in most species, its pattern of genetic variation within and among populations is strongly affected by its phylogeographic history. A putative origin from Central America has been proposed for Colombian populations, and high genetic differentiation among three biographically different population groups has recently been evidenced. Analyses based on putatively neutral markers provide data from which past events, such as population expansions and colonization, can be inferred. We analyzed the genealogies of the nicotinamide adenine dinucleotide dehydrogenase 4 (ND4) and the cytochrome oxidase subunit 1-mitochondrial genes, as well as partial nuclear ITS-2 DNA sequences obtained across most of the eco-geographical range in Colombia, to assess the population structure and demographic factors that may explain the geographical distribution of T. dimidiata in this country. Results The population structure results support a significant association between genetic divergence and the eco-geographical location of population groups, suggesting that clear signals of demographic expansion can explain the geographical distribution of haplotypes of population groups. Additionally, empirical date estimation of the event suggests that the population's expansion can be placed after the emergence of the Panama Isthmus, and that it was possibly followed by a population fragmentation process, perhaps resulting from local adaptation accomplished by orographic factors such as geographical isolation. Conclusion Inferences about the historical population processes in Colombian T. dimidiata populations are generally in accordance with population expansions that may have been accomplished by two important biotic and orographic events such as the Great American Interchange and the uplift of the eastern range of the Andes mountains in central Colombia. PMID:24625572

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

Environmental and Spatial Influences on Biogeography and Community Structure of Benthic Diatoms

NASA Astrophysics Data System (ADS)

Plante, C.; Hill-Spanik, K.; Lowry, J.

2016-02-01

Several theoretical and practical reasons suggest that benthic microalgae could be useful bioindicators. For instance, an ideal indicator species or community would be associated with a given habitat due to local physical conditions or biotic interactions (i.e., `environmental filtering'), not due to dispersal limitation. Due to their small size, immense abundances, and reliance on passive dispersal, the popular notion about micro-organisms is that `Everything is everywhere, but, the environment selects' (Baas-Becking 1934). Although much recent research concerning planktonic bacteria and dispersal limitation has been conducted, very little in this regard is known about microeukaryotes, especially benthic microbes. The purpose of our study was to identify and compare spatial and environmental influences on benthic diatom community structure and biogeography. In summer 2015, sediment was sampled at various spatial scales from four barrier island beaches in South Carolina, USA, and high-throughput (Ion Torrent) DNA sequencing was used to characterize diatom assemblages. ANOSIM and principal coordinates analysis revealed that communities were statistically distinct on the four islands. Community dissimilarity was compared to both spatial distance and environmental differences to determine potential influences of these variables on community structure. We found that geographic distance had the strongest correlation with community similarity, with and without one anomalous location, while differences in temperature (air, water, and sediment), nutrients, organic matter, and turbidity also had significant but weaker relationships with community structure. Surprisingly, air temperature, which changes on very short time scales, appeared to be the environmental factor most strongly related to diatom species composition, potentially implicating some unmeasured variable (e.g., cloud cover). However, we also found that temperature and geographic distance were strongly correlated. Future research will expand the spatial scope of this preliminary study and employ techniques (partial Mantel tests) to control for co-variation among variables.

Explaining geographic gradients in winter selection of landscapes by boreal caribou with implications under global changes in Eastern Canada.

PubMed

Beguin, Julien; McIntire, Eliot J B; Fortin, Daniel; Cumming, Steven G; Raulier, Frédéric; Racine, Pierre; Dussault, Claude

2013-01-01

Many animal species exhibit broad-scale latitudinal or longitudinal gradients in their response to biotic and abiotic components of their habitat. Although knowing the underlying mechanism of these patterns can be critical to the development of sound measures for the preservation or recovery of endangered species, few studies have yet identified which processes drive the existence of geographical gradients in habitat selection. Using extensive spatial data of broad latitudinal and longitudinal extent, we tested three hypotheses that could explain the presence of geographical gradients in landscape selection of the endangered boreal woodland caribou (Rangifer tarandus caribou) during winter in Eastern Canadian boreal forests: 1) climate-driven selection, which postulates that geographic gradients are surrogates for climatic gradients; 2) road-driven selection, which proposes that boreal caribou adjust their selection for certain habitat classes as a function of proximity to roads; and 3) an additive effect of both roads and climate. Our data strongly supported road-driven selection over climate influences. Thus, direct human alteration of landscapes drives boreal caribou distribution and should likely remain so until the climate changes sufficiently from present conditions. Boreal caribou avoided logged areas two-fold more strongly than burnt areas. Limiting the spread of road networks and accounting for the uneven impact of logging compared to wildfire should therefore be integral parts of any habitat management plan and conservation measures within the range of the endangered boreal caribou. The use of hierarchical spatial models allowed us to explore the distribution of spatially-structured errors in our models, which in turn provided valuable insights for generating alternative hypotheses about processes responsible for boreal caribou distribution.

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

The problem and promise of scale dependency in community phylogenetics.

PubMed

Swenson, Nathan G; Enquist, Brian J; Pither, Jason; Thompson, Jill; Zimmerman, Jess K

2006-10-01

The problem of scale dependency is widespread in investigations of ecological communities. Null model investigations of community assembly exemplify the challenges involved because they typically include subjectively defined "regional species pools." The burgeoning field of community phylogenetics appears poised to face similar challenges. Our objective is to quantify the scope of the problem of scale dependency by comparing the phylogenetic structure of assemblages across contrasting geographic and taxonomic scales. We conduct phylogenetic analyses on communities within three tropical forests, and perform a sensitivity analysis with respect to two scaleable inputs: taxonomy and species pool size. We show that (1) estimates of phylogenetic overdispersion within local assemblages depend strongly on the taxonomic makeup of the local assemblage and (2) comparing the phylogenetic structure of a local assemblage to a species pool drawn from increasingly larger geographic scales results in an increased signal of phylogenetic clustering. We argue that, rather than posing a problem, "scale sensitivities" are likely to reveal general patterns of diversity that could help identify critical scales at which local or regional influences gain primacy for the structuring of communities. In this way, community phylogenetics promises to fill an important gap in community ecology and biogeography research.

Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet.

PubMed

Hirano, Ryoko; Naito, Ken; Fukunaga, Kenji; Watanabe, Kazuo N; Ohsawa, Ryo; Kawase, Makoto

2011-06-01

Although the origin and domestication process of foxtail millet (Setaria italica subsp. italica (L.) P. Beauv.) has been studied by several groups, the issue is still ambiguous. It is essential to resolve this issue by studying a large number of accessions with sufficient markers covering the entire genome. Genetic structures were analyzed by transposon display (TD) using 425 accessions of foxtail millet and 12 of the wild ancestor green foxtail (Setaria italica subsp. viridis (L.) P. Beauv.). We used three recently active transposons (TSI-1, TSI-7, and TSI-10) as genome-wide markers and succeeded in demonstrating geographical structures of the foxtail millet. A neighbor-joining dendrogram based on TD grouped the foxtail millet accessions into eight major clusters, each of which consisted of accessions collected from adjacent geographical areas. Eleven out of 12 green foxtail accessions were grouped separately from the clusters of foxtail millet. These results indicated strong regional differentiations and a long history of cultivation in each region. Furthermore, we discuss the relationship between foxtail millet and green foxtail and suggest a monophyletic origin of foxtail millet domestication.

Molecular Zoogeography of Freshwater Fishes in the Southeastern United States

PubMed Central

Bermingham, Eldredge; Avise, John C.

1986-01-01

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were used to reconstruct evolutionary relationships of conspecific populations in four species of freshwater fish—Amia calva, Lepomis punctatus, L. gulosus, and L. microlophus. A suite of 14-17 endonucleases was employed to assay mtDNAs from 305 specimens collected from 14 river drainages extending from South Carolina to Louisiana. Extensive mtDNA polymorphism was observed within each assayed species. In both phenograms and Wagner parsimony networks, mtDNA clones that were closely related genetically were usually geographically contiguous. Within each species, major mtDNA phylogenetic breaks also distinguished populations from separate geographic regions, demonstrating that dispersal and gene flow have not been sufficient to override geographic influences on population subdivision.—Importantly, there were strong patterns of congruence across species in the geographic placements of the mtDNA phylogenetic breaks. Three major boundary regions were characterized by concentrations of phylogenetic discontinuities, and these zones agree well with previously described zoogeographic boundaries identified by a different kind of data base—distributional limits of species—suggesting that a common set of historical factors may account for both phenomena. Repeated episodes of eustatic sea level change along a relatively static continental morphology are the likely causes of several patterns of drainage isolation and coalescence, and these are discussed in relation to the genetic data.—Overall, results exemplify the positive role that intraspecific genetic analyses may play in historical zoogeographic reconstruction. They also point out the potential inadequacies of any interpretations of population genetic structure that fail to consider the influences of history in shaping that structure. PMID:17246340

Health, Information, and Migration: Geographic Mobility of Union Army Veterans, 1860–1880

PubMed Central

Lee, Chulhee

2009-01-01

This article explores how injuries, sickness, and the geographic mobility of Union Army veterans while in service affected their postservice migrations. Wartime wounds and illnesses significantly diminished the geographic mobility of veterans after the war. Geographic moves while carrying out military missions had strong positive effects on their postservice geographic mobility. Geographic moves while in service also influenced the choice of destination among the migrants. I discuss some implications of the results for the elements of self-selection in migration, the roles of different types of information in migration decisions, and the overall impact of the Civil War on geographic mobility. PMID:20234796

Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939).

PubMed

Zardus, John D; Etter, Ron J; Chase, Michael R; Rex, Michael A; Boyle, Elizabeth E

2006-03-01

The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high (h = 0.73) with pronounced population structure (Phi(ST) = 0.877) and highly significant geographic associations (P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

Strong population structure in the marine sponge Crambe crambe (Poecilosclerida) as revealed by microsatellite markers.

PubMed

Duran, S; Pascual, M; Estoup, A; Turon, X

2004-03-01

Different categories of molecular markers have been used so far to study the population structure of sponges. However, these markers often did not have the resolution power to address precisely questions on structuring processes, especially at the intrapopulational level. In this study we show that microsatellites fulfil these expectations, allowing a fine description of population structure at different geographical scales in the marine sponge Crambe crambe. Specimens were collected in 11 locations, representing most of the Atlanto-Mediterranean range of the species, and were analysed at six loci. As expected for a sessile invertebrate with lecitotrophic larvae, high levels of between-population structure were found (FST = 0.18) and a significant isolation-by-distance pattern was observed. A strong genetic structure was also found within sampled sites (FIS = 0.21) that may be explained by several factors including inbreeding, selfing and the Wahlund effect. In spite of a sampling design planned to avoid the sampling of clones, genotypically identical individuals for the six loci were found in some locations. The significance of these potential clones is discussed and their effect on the observed pattern of population structure assessed. Patterns of allelic distribution within populations suggest the possibility of a recent colonization of the Atlantic range from the Mediterranean Sea.

DOG1 expression is predicted by the seed-maturation environment and contributes to geographical variation in germination in Arabidopsis thaliana.

PubMed

Chiang, George C K; Bartsch, Melanie; Barua, Deepak; Nakabayashi, Kazumi; Debieu, Marilyne; Kronholm, Ilkka; Koornneef, Maarten; Soppe, Wim J J; Donohue, Kathleen; De Meaux, Juliette

2011-08-01

Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in A. thaliana. Here, we report interaccession variation in DOG1 expression and document that DOG1 expression is associated with seed-maturation temperature effects on germination; DOG1 expression increased when seeds were matured at low temperature, and this increased expression was associated with increased dormancy of those seeds. Variation in DOG1 expression suggests a geographical structure such that southern accessions, which are more dormant, tend to initiate DOG1 expression earlier during seed maturation and achieved higher expression levels at the end of silique development than did northern accessions. Although elimination of the synthesis of phytohormone abscisic acid (ABA) results in the elimination of maternal temperature effects on dormancy, DOG1 expression predicted dormancy better than expression of genes involved in ABA metabolism. © 2011 Blackwell Publishing Ltd.

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

The Relative Importance of Spatial and Local Environmental Factors in Determining Beetle Assemblages in the Inner Mongolia Grassland.

PubMed

Yu, Xiao-Dong; Lü, Liang; Wang, Feng-Yan; Luo, Tian-Hong; Zou, Si-Si; Wang, Cheng-Bin; Song, Ting-Ting; Zhou, Hong-Zhang

2016-01-01

The aim of this paper is to increase understanding of the relative importance of the input of geographic and local environmental factors on richness and composition of epigaeic steppe beetles (Coleoptera: Carabidae and Tenebrionidae) along a geographic (longitudinal/precipitation) gradient in the Inner Mongolia grassland. Specifically, we evaluate the associations of environmental variables representing climate and environmental heterogeneity with beetle assemblages. Beetles were sampled using pitfall traps at 25 sites scattered across the full geographic extent of the study biome in 2011-2012. We used variance partitioning techniques and multi-model selection based on the Akaike information criterion to assess the relative importance of the spatial and environmental variables on beetle assemblages. Species richness and abundance showed unimodal patterns along the geographic gradient. Together with space, climate variables associated with precipitation, water-energy balance and harshness of climate had strong explanatory power in richness pattern. Abundance pattern showed strongest association with variation in temperature and environmental heterogeneity. Climatic factors associated with temperature and precipitation variables and the interaction between climate with space were able to explain a substantial amount of variation in community structure. In addition, the turnover of species increased significantly as geographic distances increased. We confirmed that spatial and local environmental factors worked together to shape epigaeic beetle communities along the geographic gradient in the Inner Mongolia grassland. Moreover, the climate features, especially precipitation, water-energy balance and temperature, and the interaction between climate with space and environmental heterogeneity appeared to play important roles on controlling richness and abundance, and species compositions of epigaeic beetles.

Genes mirror geography in Daphnia magna.

PubMed

Fields, Peter D; Reisser, Céline; Dukić, Marinela; Haag, Christoph R; Ebert, Dieter

2015-09-01

Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next-generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the crustacean Daphnia magna suggested that, despite strong genetic differentiation among populations at a local scale, the species shows only moderate genetic structure across its European range, with a spatially patchy occurrence of individual lineages. We apply RAD sequencing to a sample of D. magna collected across a wide swath of the species' Eurasian range and analyse the data using principle component analysis (PCA) of genetic variation and Procrustes analytical approaches, to quantify spatial genetic structure. We find remarkable consistency between the first two PCA axes and the geographic coordinates of individual sampling points, suggesting that, on a continent-wide scale, genetic differentiation is driven to a large extent by geographic distance. The observed pattern is consistent with unimpeded (i.e. no barriers, landscape or otherwise) migration at large spatial scales, despite the fragmented and patchy nature of favourable habitats at local scales. With high-resolution genetic data similar patterns may be uncovered for other species with wide geographic distributions, allowing an increased understanding of how genetic drift and selection have shaped their evolutionary history. © 2015 John Wiley & Sons Ltd.

Biodiversity of Costa Rican salamanders: Implications of high levels of genetic differentiation and phylogeographic structure for species formation

PubMed Central

García-París, Mario; Good, David A.; Parra-Olea, Gabriela; Wake, David B.

2000-01-01

Although salamanders are characteristic amphibians in Holarctic temperate habitats, in tropical regions they have diversified evolutionarily only in tropical America. An adaptive radiation centered in Middle America occurred late in the history of a single clade, the supergenus Bolitoglossa (Plethodontidae), and large numbers of species now occur in diverse habitats. Sublineages within this clade decrease in number from the northern to southern parts of Middle America, and in Costa Rica, there are but three. Despite this phylogenetic constraint, Costa Rica has many species; the number of salamander species on one local elevational transect in the Cordillera de Talamanca may be the largest for any such transect in the world. Extraordinary variation in sequences of the mitochondrial gene cytochrome b within a clade of the genus Bolitoglossa in Costa Rica reveals strong phylogeographic structure within a single species, Bolitoglossa pesrubra. Allozymic variation in 19 proteins reveals a pattern largely concordant with the mitochondrial DNA phylogeography. More species exist than are currently recognized. Diversification occurs in restricted geographic areas and involves sharp geographic and elevational differentiation and zonation. In their degree of genetic differentiation at a local scale, these species of the deep tropics exceed the known variation of extratropical salamanders, which also differ in being less restricted in elevational range. Salamanders display “tropicality” in that although speciose, they are usually local in distribution and rare. They display strong ecological and physiological differentiation that may contribute importantly to morphological divergence and species formation. PMID:10677512

Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata.

PubMed

Polato, Nicholas R; Concepcion, Gregory T; Toonen, Robert J; Baums, Iliana B

2010-11-01

There is an ongoing debate on the scale of pelagic larval dispersal in promoting connectivity among populations of shallow, benthic marine organisms. The linearly arranged Hawaiian Islands are uniquely suited to study scales of population connectivity and have been used extensively as a natural laboratory in terrestrial systems. Here, we focus on Hawaiian populations of the lobe coral Porites lobata, an ecosystem engineer of shallow reefs throughout the Pacific. Patterns of recent gene flow and population structure in P. lobata samples (n = 318) from two regions, the Hawaiian Islands (n = 10 sites) and from their nearest neighbour Johnston Atoll, were analysed with nine microsatellite loci. Despite its massive growth form, ∼ 6% of the samples from both regions were the product of asexual reproduction via fragmentation. Cluster analysis and measures of genetic differentiation indicated that P. lobata from the Hawaiian Islands are strongly isolated from those on Johnston Atoll (F(ST)  = 0.311; P < 0.001), with the descendants of recent migrants (n = 6) being clearly identifiable. Within the Hawaiian Islands, P. lobata conforms to a pattern of isolation by distance. Here, over 37% (P = 0.001) of the variation in genetic distance was explained by geographical distance. This pattern indicates that while the majority of ongoing gene flow in Hawaiian P. lobata occurs among geographically proximate reefs, inter-island distances are insufficient to generate strong population structure across the archipelago. © 2010 Blackwell Publishing Ltd.

Functional acclimation across microgeographic scales in Dodonaea viscosa

PubMed Central

Baruch, Zdravko; Jones, Alice R; Hill, Kathryn E; McInerney, Francesca A; Blyth, Colette; Caddy-Retalic, Stefan; Christmas, Matthew J; Gellie, Nicholas J C; Lowe, Andrew J; Martin-Fores, Irene; Nielson, Kristine E

2018-01-01

Abstract Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait–environment associations, and it is imperative for studies that make trait–environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait–trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope δ13C and δ15N ratios, and Narea, whereas the offspring ordination was less structured. Parent trait–trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.

D Geomarketing Segmentation: a Higher Spatial Dimension Planning Perspective

NASA Astrophysics Data System (ADS)

Suhaibah, A.; Uznir, U.; Rahman, A. A.; Anton, F.; Mioc, D.

2016-09-01

Geomarketing is a discipline which uses geographic information in the process of planning and implementation of marketing activities. It can be used in any aspect of the marketing such as price, promotion or geo targeting. The analysis of geomarketing data use a huge data pool such as location residential areas, topography, it also analyzes demographic information such as age, genre, annual income and lifestyle. This information can help users to develop successful promotional campaigns in order to achieve marketing goals. One of the common activities in geomarketing is market segmentation. The segmentation clusters the data into several groups based on its geographic criteria. To refine the search operation during analysis, we proposed an approach to cluster the data using a clustering algorithm. However, with the huge data pool, overlap among clusters may happen and leads to inefficient analysis. Moreover, geomarketing is usually active in urban areas and requires clusters to be organized in a three-dimensional (3D) way (i.e. multi-level shop lots, residential apartments). This is a constraint with the current Geographic Information System (GIS) framework. To avoid this issue, we proposed a combination of market segmentation based on geographic criteria and clustering algorithm for 3D geomarketing data management. The proposed approach is capable in minimizing the overlap region during market segmentation. In this paper, geomarketing in urban area is used as a case study. Based on the case study, several locations of customers and stores in 3D are used in the test. The experiments demonstrated in this paper substantiated that the proposed approach is capable of minimizing overlapping segmentation and reducing repetitive data entries. The structure is also tested for retrieving the spatial records from the database. For marketing purposes, certain radius of point is used to analyzing marketing targets. Based on the presented tests in this paper, we strongly believe that the structure is capable in handling and managing huge pool of geomarketing data. For future outlook, this paper also discusses the possibilities of expanding the structure.

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

PubMed Central

Zimmerman, Naupaka B.; Vitousek, Peter M.

2012-01-01

We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities. PMID:22837398

Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds.

PubMed

Chen, Rubing; Holmes, Edward C

2009-01-05

Revealing the factors that shape the genetic structure of avian influenza viruses (AIVs) in wild bird populations is essential to understanding their evolution. However, the relationship between epidemiological dynamics and patterns of genetic diversity in AIV is not well understood, especially at the continental scale. To address this question, we undertook a phylogeographic analysis of complete genome sequences of AIV sampled from wild birds in North America. In particular, we asked whether host species, geographic location or sampling time played the major role in shaping patterns of viral genetic diversity. Strikingly, our analysis revealed no strong species effect, yet a significant viral clustering by time and place of sampling, as well as the circulation of multiple viral lineages in single locations. These results suggest that AIVs can readily infect many of the bird species that share breeding/feeding areas.

Geographic variation and acoustic structure of the underwater vocalization of harbor seal (Phoca vitulina) in Norway, Sweden and Scotland.

PubMed

Bjørgesaeter, Anders; Ugland, Karl Inne; Bjørge, Arne

2004-10-01

The male harbor seal (Phoca vitulina) produces broadband nonharmonic vocalizations underwater during the breeding season. In total, 120 vocalizations from six colonies were analyzed to provide a description of the acoustic structure and for the presence of geographic variation. The complex harbor seal vocalizations may be described by how the frequency bandwidth varies over time. An algorithm that identifies the boundaries between noise and signal from digital spectrograms was developed in order to extract a frequency bandwidth contour. The contours were used as inputs for multivariate analysis. The vocalizations' sound types (e.g., pulsed sound, whistle, and broadband nonharmonic sound) were determined by comparing the vocalizations' spectrographic representations with sound waves produced by known sound sources. Comparison between colonies revealed differences in the frequency contours, as well as some geographical variation in use of sound types. The vocal differences may reflect a limited exchange of individuals between the six colonies due to long distances and strong site fidelity. Geographically different vocal repertoires have potential for identifying discrete breeding colonies of harbor seals, but more information is needed on the nature and extent of early movements of young, the degree of learning, and the stability of the vocal repertoire. A characteristic feature of many vocalizations in this study was the presence of tonal-like introductory phrases that fit into the categories pulsed sound and whistles. The functions of these phrases are unknown but may be important in distance perception and localization of the sound source. The potential behavioral consequences of the observed variability may be indicative of adaptations to different environmental properties influencing determination of distance and direction and plausible different male mating tactics.

Mesoscale Variability in SUCCESS Data

NASA Technical Reports Server (NTRS)

Eckermann, Stephen D.

1998-01-01

Analysis of meteorological, chemical, and microphysical data from the airborne SUCCESS mission is reported. Careful analysis of the complex DC-8 flight pattern of May 2, 1996 reveals 19 linear or nearly linear flight segments within six main geographical areas, which we have analyzed. Significant mountain wave activity is revealed in the data from the MMS and MTP instruments on the DC-8, which resembles previous observations of mountain wave structures near Boulder, CO. Strong mountain-wave-induced upwelling downwind of the Rockies is noted. Turbulence is also noted in regions of the mountain wave consistent with overturning near the tropopause. Zonal winds recorded on the ER-2 are shown to consistent with mountain wave breaking at or near critical levels in the stratosphere, consistent with the strong turbulence reported by the pilot during the ER-2 flight. Those observations have been supported with spectral analyses and modeling studies. "Postcasts" of mountain wave activity on May 2, 1996, using the Naval Research Laboratory Mountain Wave Forecast Model (NRL/MWFM) predicts both strong mountain wave activity near the tropopause (as measured by the DC-8) and strong mountain-wave-induced turbulence in the stratosphere (as encountered by the ER-2). Two-dimensional simulations of fluid flow over topography reveal similar isentropic structures to observations.

Abstract Profiles of Structural Stability Point to Universal Tendencies, Family-Specific Factors, and Ancient Connections between Languages

PubMed Central

Dediu, Dan; Levinson, Stephen C.

2012-01-01

Language is the best example of a cultural evolutionary system, able to retain a phylogenetic signal over many thousands of years. The temporal stability (conservatism) of basic vocabulary is relatively well understood, but the stability of the structural properties of language (phonology, morphology, syntax) is still unclear. Here we report an extensive Bayesian phylogenetic investigation of the structural stability of numerous features across many language families and we introduce a novel method for analyzing the relationships between the “stability profiles” of language families. We found that there is a strong universal component across language families, suggesting the existence of universal linguistic, cognitive and genetic constraints. Against this background, however, each language family has a distinct stability profile, and these profiles cluster by geographic area and likely deep genealogical relationships. These stability profiles seem to show, for example, the ancient historical relationships between the Siberian and American language families, presumed to be separated by at least 12,000 years, and possible connections between the Eurasian families. We also found preliminary support for the punctuated evolution of structural features of language across families, types of features and geographic areas. Thus, such higher-level properties of language seen as an evolutionary system might allow the investigation of ancient connections between languages and shed light on the peopling of the world. PMID:23028843

Abstract profiles of structural stability point to universal tendencies, family-specific factors, and ancient connections between languages.

PubMed

Dediu, Dan; Levinson, Stephen C

2012-01-01

Language is the best example of a cultural evolutionary system, able to retain a phylogenetic signal over many thousands of years. The temporal stability (conservatism) of basic vocabulary is relatively well understood, but the stability of the structural properties of language (phonology, morphology, syntax) is still unclear. Here we report an extensive Bayesian phylogenetic investigation of the structural stability of numerous features across many language families and we introduce a novel method for analyzing the relationships between the "stability profiles" of language families. We found that there is a strong universal component across language families, suggesting the existence of universal linguistic, cognitive and genetic constraints. Against this background, however, each language family has a distinct stability profile, and these profiles cluster by geographic area and likely deep genealogical relationships. These stability profiles seem to show, for example, the ancient historical relationships between the Siberian and American language families, presumed to be separated by at least 12,000 years, and possible connections between the Eurasian families. We also found preliminary support for the punctuated evolution of structural features of language across families, types of features and geographic areas. Thus, such higher-level properties of language seen as an evolutionary system might allow the investigation of ancient connections between languages and shed light on the peopling of the world.

Insular Celtic population structure and genomic footprints of migration

PubMed Central

Hellenthal, Garrett

2018-01-01

Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits. PMID:29370172

Origin, genetic diversity, and population structure of Chinese domestic sheep.

PubMed

Chen, Shan-Yuan; Duan, Zi-Yuan; Sha, Tao; Xiangyu, Jinggong; Wu, Shi-Fang; Zhang, Ya-Ping

2006-07-19

To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.

General method to unravel ancient population structures through surnames, final validation on Italian data.

PubMed

Boattini, Alessio; Lisa, Antonella; Fiorani, Ornella; Zei, Gianna; Pettener, Davide; Manni, Franz

2012-06-01

We analyze the geographic location of 77,451 different Italian surnames (17,579,891 individuals) obtained from the lists of telephone subscribers of the year 1993. By using a specific neural network analysis (Self-Organizing Maps, SOMs), we automatically identify the geographic origin of 49,117 different surnames. To validate the methodology, we compare the results to a study, previously conducted, on the same database, with accurate supervised methods. By comparing the results, we find an overlap of 97%, meaning that the SOMs methodology is highly reliable and well traces back the geographic origin of surnames at the time of their introduction (Late Middle Ages/Renaissance in Italy). SOMs results enables one to distinguish monophyletic surnames from polyphyletic ones, that is surnames having had a single geographic and historic origin from those that started to be in use, with an identical spelling, in different locations (respectively, 76.06% and 21.05% of the total). As we are interested in geographic origins, polyphyletic surnames are excluded from further analyses. By comparing the present location of each monophyletic surname to its inferred geographic origin in late Middle Ages/Renaissance, we measure the extent of the migrations having occurred in Italy since that time. We find that the percentage of individuals presently living in the very area where their surname started to be in use centuries ago is extremely variable (ranging from 22.77% to 77.86% according to the province), thus meaning that self-assessed regional identities seldom correspond to the "autochthony" they imply. For example the upper part of the Thyrennian coast (Northern Latium, Tuscany) has a strong identity but few "autochthonous" inhabitants (∼28%) having been a passageway from the North to the South of Italy.

mvMapper: statistical and geographical data exploration and visualization of multivariate analysis of population structure

USDA-ARS?s Scientific Manuscript database

Characterizing population genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata is not always easily integrated into t...

Nuclear microsatellites reveal contrasting patterns of genetic structure between western and southeastern European populations of the common ash (Fraxinus excelsior L.).

PubMed

Heuertz, Myriam; Hausman, Jean-François; Hardy, Olivier J; Vendramin, Giovanni G; Frascaria-Lacoste, Nathalie; Vekemans, Xavier

2004-05-01

To determine extant patterns of population genetic structure in common ash and gain insight into postglacial recolonization processes, we applied multilocus-based Bayesian approaches to data from 36 European populations genotyped at five nuclear microsatellite loci. We identified two contrasting patterns in terms of population genetic structure: (1) a large area from the British Isles to Lithuania throughout central Europe constituted effectively a single deme, whereas (2) strong genetic differentiation occurred over short distances in Sweden and southeastern Europe. Concomitant geographical variation was observed in estimates of allelic richness and genetic diversity, which were lowest in populations from southeastern Europe, that is, in regions close to putative ice age refuges, but high in western and central Europe, that is, in more recently recolonized areas. We suggest that in southeastern Europe, restricted postglacial gene flow caused by a rapid expansion of refuge populations in a mountainous topography is responsible for the observed strong genetic structure. In contrast, admixture of previously differentiated gene pools and high gene flow at the onset of postglacial recolonization of western and central Europe would have homogenized the genetic structure and raised the levels of genetic diversity above values in the refuges.

Social Network Analysis and Qualitative Interviews for Assessing Geographic Characteristics of Tourism Business Networks.

PubMed

Kelman, Ilan; Luthe, Tobias; Wyss, Romano; Tørnblad, Silje H; Evers, Yvette; Curran, Marina Martin; Williams, Richard J; Berlow, Eric L

2016-01-01

This study integrates quantitative social network analysis (SNA) and qualitative interviews for understanding tourism business links in isolated communities through analysing spatial characteristics. Two case studies are used, the Surselva-Gotthard region in the Swiss Alps and Longyearbyen in the Arctic archipelago of Svalbard, to test the spatial characteristics of physical proximity, isolation, and smallness for understanding tourism business links. In the larger Surselva-Gotthard region, we found a strong relationship between geographic separation of the three communities on compartmentalization of the collaboration network. A small set of businesses played a central role in steering collaborative decisions for this community, while a group of structurally 'peripheral' actors were less influential. By contrast, the business community in Svalbard showed compartmentalization that was independent of geographic distance between actors. Within towns of similar size and governance scale, Svalbard is more compartmentalized, and those compartments are not driven by geographic separation of the collaboration clusters. This compartmentalization in Svalbard was reflected in a lower density of formal business collaboration ties compared to the communities of the Alps. We infer that the difference is due to Svalbard having higher cultural diversity and population turnover than the Alps communities. We propose that integrating quantitative network analysis from simple surveys with qualitative interviews targeted from the network results is an efficient general approach to identify regionally specific constraints and opportunities for effective governance.

Geographic variations of ecosystem service intensity in Fuzhou City, China.

PubMed

Hu, Xisheng; Hong, Wei; Qiu, Rongzu; Hong, Tao; Chen, Can; Wu, Chengzhen

2015-04-15

Ecosystem services are strongly influenced by the landscape configuration of natural and human systems. So they are heterogeneous across landscapes. However lack of the knowledge of spatial variations of ecosystem services constrains the effective management and conservation of ecosystems. We presented a spatially explicit and quantitative assessment of the geographic variations in ecosystem services for the Fuzhou City in 2009 using exploratory spatial data analysis (ESDA) and semivariance analysis. Results confirmed a significant and positive spatial autocorrelation, and revealed several hot-spots and cold-spots for the spatial distribution of ecosystem service intensity (ESI) in the study area. Also the trend surface analysis indicated that the level of ESI tended to be reduced gradually from north to south and from west to east, with a trough in the urban central area, which was quite in accordance with land-use structure. A more precise cluster map was then developed using the range of lag distance, deriving from semivariance analysis, as neighborhood size instead of default value in the software of ESRI ArcGIS 10.0, and geographical clusters where population growth and land-use pressure varied significantly and positively with ESI across the city were also created by geographically weighted regression (GWR). This study has good policy implications applicable to prioritize areas for conservation or construction, and design ecological corridor to improve ecosystem service delivery to benefiting areas. Copyright © 2015 Elsevier B.V. All rights reserved.

Social Network Analysis and Qualitative Interviews for Assessing Geographic Characteristics of Tourism Business Networks

PubMed Central

Luthe, Tobias; Wyss, Romano; Tørnblad, Silje H.; Evers, Yvette; Curran, Marina Martin; Williams, Richard J.; Berlow, Eric L.

2016-01-01

This study integrates quantitative social network analysis (SNA) and qualitative interviews for understanding tourism business links in isolated communities through analysing spatial characteristics. Two case studies are used, the Surselva-Gotthard region in the Swiss Alps and Longyearbyen in the Arctic archipelago of Svalbard, to test the spatial characteristics of physical proximity, isolation, and smallness for understanding tourism business links. In the larger Surselva-Gotthard region, we found a strong relationship between geographic separation of the three communities on compartmentalization of the collaboration network. A small set of businesses played a central role in steering collaborative decisions for this community, while a group of structurally ‘peripheral’ actors were less influential. By contrast, the business community in Svalbard showed compartmentalization that was independent of geographic distance between actors. Within towns of similar size and governance scale, Svalbard is more compartmentalized, and those compartments are not driven by geographic separation of the collaboration clusters. This compartmentalization in Svalbard was reflected in a lower density of formal business collaboration ties compared to the communities of the Alps. We infer that the difference is due to Svalbard having higher cultural diversity and population turnover than the Alps communities. We propose that integrating quantitative network analysis from simple surveys with qualitative interviews targeted from the network results is an efficient general approach to identify regionally specific constraints and opportunities for effective governance. PMID:27258007

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.

Unravelling the structure of species extinction risk for predictive conservation science.

PubMed

Lee, Tien Ming; Jetz, Walter

2011-05-07

Extinction risk varies across species and space owing to the combined and interactive effects of ecology/life history and geography. For predictive conservation science to be effective, large datasets and integrative models that quantify the relative importance of potential factors and separate rapidly changing from relatively static threat drivers are urgently required. Here, we integrate and map in space the relative and joint effects of key correlates of The International Union for Conservation of Nature-assessed extinction risk for 8700 living birds. Extinction risk varies significantly with species' broad-scale environmental niche, geographical range size, and life-history and ecological traits such as body size, developmental mode, primary diet and foraging height. Even at this broad scale, simple quantifications of past human encroachment across species' ranges emerge as key in predicting extinction risk, supporting the use of land-cover change projections for estimating future threat in an integrative setting. A final joint model explains much of the interspecific variation in extinction risk and provides a remarkably strong prediction of its observed global geography. Our approach unravels the species-level structure underlying geographical gradients in extinction risk and offers a means of disentangling static from changing components of current and future threat. This reconciliation of intrinsic and extrinsic, and of past and future extinction risk factors may offer a critical step towards a more continuous, forward-looking assessment of species' threat status based on geographically explicit environmental change projections, potentially advancing global predictive conservation science.

Host and geographic structure of endophytic and endolichenic fungi at a continental scale.

PubMed

U'Ren, Jana M; Lutzoni, François; Miadlikowska, Jolanta; Laetsch, Alexander D; Arnold, A Elizabeth

2012-05-01

Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities. Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of five North American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska). Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, reflecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences reflected climate factors more strongly than geographic distance alone. Our study provides a first evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition reflect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specificity, metabolic capability, and comparative genomics.

Genetic Structure of First Nation Communities in the Pacific Northwest.

PubMed

Hughes, Cris E; Rogers, Mary P; Owings, Amanda C; Petzelt, Barbara; Mitchell, Joycelynn; Harry, Harold; Williams, Theresa; Goldberg, Dena; Labuda, Damian; Smith, David Glenn; Cybulski, Jerome S; Malhi, Ripan S

2016-10-01

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal, and autosomal DNA variants, we aimed to more closely address the relationships of geography and language with present genetic diversity among the regional PNW Native American populations. Patterns of genetic diversity exhibited by the three genetic systems were consistent with our hypotheses: genetic variation was more strongly explained by geographic proximity than by linguistic structure. Our findings were corroborated through a variety on analytic approaches, with the unrooted trees for the three genetic systems consistently separating inland from coastal PNW populations. Furthermore, analyses of molecular variance support the trends exhibited by the unrooted trees, with geographic partitioning of PNW populations (F CT = 19.43%, p = 0.010 ± 0.009) accounting for over twice as much of the observed genetic variation as linguistic partitioning of the same populations (F CT = 9.15%, p = 0.193 ± 0.013). These findings demonstrate a consensus with previous PNW population studies examining the relationships of genome-wide variation, mitochondrial haplogroup frequencies, and skeletal morphology with geography and language.

A Semantic Approach for Geospatial Information Extraction from Unstructured Documents

NASA Astrophysics Data System (ADS)

Sallaberry, Christian; Gaio, Mauro; Lesbegueries, Julien; Loustau, Pierre

Local cultural heritage document collections are characterized by their content, which is strongly attached to a territory and its land history (i.e., geographical references). Our contribution aims at making the content retrieval process more efficient whenever a query includes geographic criteria. We propose a core model for a formal representation of geographic information. It takes into account characteristics of different modes of expression, such as written language, captures of drawings, maps, photographs, etc. We have developed a prototype that fully implements geographic information extraction (IE) and geographic information retrieval (IR) processes. All PIV prototype processing resources are designed as Web Services. We propose a geographic IE process based on semantic treatment as a supplement to classical IE approaches. We implement geographic IR by using intersection computing algorithms that seek out any intersection between formal geocoded representations of geographic information in a user query and similar representations in document collection indexes.

Salmonella Strains Isolated from Galápagos Iguanas Show Spatial Structuring of Serovar and Genomic Diversity

PubMed Central

Lankau, Emily W.; Cruz Bedon, Lenin; Mackie, Roderick I.

2012-01-01

It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome. PMID:22615968

Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian Ocean.

PubMed

Huyghe, Filip; Kochzius, Marc

2018-01-01

In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci. Analysis included estimation of genetic diversity and population differentiation. A haplotype network was inferred using mtDNA. Nuclear markers were used in Bayesian clustering and a principal component analysis. Both markers confirmed strong genetic differentiation between WIO and Eastern Indian Ocean (EIO) populations, and a shallower population structure among Malagasy and East African mainland populations. Limited gene flow across the Mozambique Channel may be explained by its complex oceanography, which could cause local retention of larvae, limiting dispersal between Madagascar and the East African coast. Two other potential current-mediated barriers to larval dispersal suggested in the WIO, the split of the SEC at approximately 10° S and the convergence of the Somali Current with the East African Coast Current at approximately 3° S, were not found to form a barrier to gene flow in this species.

Sea surface currents and geographic isolation shape the genetic population structure of a coral reef fish in the Indian Ocean

PubMed Central

Kochzius, Marc

2018-01-01

In this contribution, we determine the genetic population structure in the Skunk Clownfish (Amphiprion akallopsisos) across the Indian Ocean, and on a smaller geographic scale in the Western Indian Ocean (WIO). Highly restricted gene flow was discovered between populations on either side of the Indian Ocean using the control region as a mitochondrial marker (mtDNA). We verify this conclusion using 13 microsatellite markers and infer fine scale genetic structuring within the WIO. In total 387 samples from 21 sites were analysed using mtDNA and 13 microsatellite loci. Analysis included estimation of genetic diversity and population differentiation. A haplotype network was inferred using mtDNA. Nuclear markers were used in Bayesian clustering and a principal component analysis. Both markers confirmed strong genetic differentiation between WIO and Eastern Indian Ocean (EIO) populations, and a shallower population structure among Malagasy and East African mainland populations. Limited gene flow across the Mozambique Channel may be explained by its complex oceanography, which could cause local retention of larvae, limiting dispersal between Madagascar and the East African coast. Two other potential current-mediated barriers to larval dispersal suggested in the WIO, the split of the SEC at approximately 10° S and the convergence of the Somali Current with the East African Coast Current at approximately 3° S, were not found to form a barrier to gene flow in this species. PMID:29522547

Continental synchronicity of human influenza virus epidemics despite climatic variation.

PubMed

Geoghegan, Jemma L; Saavedra, Aldo F; Duchêne, Sebastián; Sullivan, Sheena; Barr, Ian; Holmes, Edward C

2018-01-01

The factors that determine the pattern and rate of spread of influenza virus at a continental-scale are uncertain. Although recent work suggests that influenza epidemics in the United States exhibit a strong geographical correlation, the spatiotemporal dynamics of influenza in Australia, a country and continent of approximately similar size and climate complexity but with a far smaller population, are not known. Using a unique combination of large-scale laboratory-confirmed influenza surveillance comprising >450,000 entries and genomic sequence data we determined the local-level spatial diffusion of this important human pathogen nationwide in Australia. We used laboratory-confirmed influenza data to characterize the spread of influenza virus across Australia during 2007-2016. The onset of established epidemics varied across seasons, with highly synchronized epidemics coinciding with the emergence of antigenically distinct viruses, particularly during the 2009 A/H1N1 pandemic. The onset of epidemics was largely synchronized between the most populous cities, even those separated by distances of >3000 km and those that experience vastly diverse climates. In addition, by analyzing global phylogeographic patterns we show that the synchronized dissemination of influenza across Australian cities involved multiple introductions from the global influenza population, coupled with strong domestic connectivity, rather than through the distinct radial patterns of geographic dispersal that are driven by work-flow transmission as observed in the United States. In addition, by comparing the spatial structure of influenza A and B, we found that these viruses tended to occupy different geographic regions, and peak in different seasons, perhaps indicative of moderate cross-protective immunity or viral interference effects. The highly synchronized outbreaks of influenza virus at a continental-scale revealed here highlight the importance of coordinated public health responses in the event of the emergence of a novel, human-to-human transmissible, virus.

Spatial Autocorrelation Can Generate Stronger Correlations between Range Size and Climatic Niches Than the Biological Signal - A Demonstration Using Bird and Mammal Range Maps.

PubMed

Boucher-Lalonde, Véronique; Currie, David J

2016-01-01

Species' geographic ranges could primarily be physiological tolerances drawn in space. Alternatively, geographic ranges could be only broadly constrained by physiological climatic tolerances: there could generally be much more proximate constraints on species' ranges (dispersal limitation, biotic interactions, etc.) such that species often occupy a small and unpredictable subset of tolerable climates. In the literature, species' climatic tolerances are typically estimated from the set of conditions observed within their geographic range. Using this method, studies have concluded that broader climatic niches permit larger ranges. Similarly, other studies have investigated the biological causes of incomplete range filling. But, when climatic constraints are measured directly from species' ranges, are correlations between species' range size and climate necessarily consistent with a causal link? We evaluated the extent to which variation in range size among 3277 bird and 1659 mammal species occurring in the Americas is statistically related to characteristics of species' realized climatic niches. We then compared how these relationships differed from the ones expected in the absence of a causal link. We used a null model that randomizes the predictor variables (climate), while retaining their broad spatial autocorrelation structure, thereby removing any causal relationship between range size and climate. We found that, although range size is strongly positively related to climatic niche breadth, range filling and, to a lesser extent, niche position in nature, the observed relationships are not always stronger than expected from spatial autocorrelation alone. Thus, we conclude that equally strong relationships between range size and climate would result from any processes causing ranges to be highly spatially autocorrelated.

Spatial Autocorrelation Can Generate Stronger Correlations between Range Size and Climatic Niches Than the Biological Signal — A Demonstration Using Bird and Mammal Range Maps

PubMed Central

Boucher-Lalonde, Véronique; Currie, David J.

2016-01-01

Species’ geographic ranges could primarily be physiological tolerances drawn in space. Alternatively, geographic ranges could be only broadly constrained by physiological climatic tolerances: there could generally be much more proximate constraints on species’ ranges (dispersal limitation, biotic interactions, etc.) such that species often occupy a small and unpredictable subset of tolerable climates. In the literature, species’ climatic tolerances are typically estimated from the set of conditions observed within their geographic range. Using this method, studies have concluded that broader climatic niches permit larger ranges. Similarly, other studies have investigated the biological causes of incomplete range filling. But, when climatic constraints are measured directly from species’ ranges, are correlations between species’ range size and climate necessarily consistent with a causal link? We evaluated the extent to which variation in range size among 3277 bird and 1659 mammal species occurring in the Americas is statistically related to characteristics of species’ realized climatic niches. We then compared how these relationships differed from the ones expected in the absence of a causal link. We used a null model that randomizes the predictor variables (climate), while retaining their broad spatial autocorrelation structure, thereby removing any causal relationship between range size and climate. We found that, although range size is strongly positively related to climatic niche breadth, range filling and, to a lesser extent, niche position in nature, the observed relationships are not always stronger than expected from spatial autocorrelation alone. Thus, we conclude that equally strong relationships between range size and climate would result from any processes causing ranges to be highly spatially autocorrelated. PMID:27855201

Applications of geographic information systems (GIS) for highway traffic noise analysis : case studies of select transportation agencies

DOT National Transportation Integrated Search

2012-11-30

Noise from highway traffic can be pervasive in areas near roadways. How and to what extent noise travels is strongly influenced by geospatial features such as terrain and elevation. Thus geographic information systems (GIS), which enable users to mor...

Urban-Rural Differentials: A Spatial Analysis of Alabama Students’ Recent Alcohol Use and Marijuana Use

PubMed Central

Lo, Celia C.; Weber, Joe; Cheng, Tyrone C.

2013-01-01

Background and Objectives This study of Alabama public school students sought urban-rural differences in social and spatial mechanisms connecting structural factors to recent use of alcohol and marijuana. Methods Its dataset comprised a state-sponsored 2002 need-assessment survey of Alabama students; Alabama education department data; U. S. Census data; and alcohol-outlet locations listed by Alabama’s Alcoholic Beverage Control Board. It measured structural-disadvantage factors (population disadvantages, community instability, alcohol-outlet density), social-organization factors (protective role of community, protective role of school), and recent-use factors. Using Geographic Information Systems (GIS), it generated maps of school catchment areas (SCAs)—the units of analysis for the study—that outline spatial patterns (across areas deemed urban or rural) of students’ recent use of alcohol and marijuana. Results In the final sample of 370 SCAs, significant urban-versus-rural differences were observed for certain structural factors and in how these factors were associated with substance use. These differences aside, spatial analysis weighing the SCAs’ particular geographic characteristics suggested location’s importance, showing that a school playing a strong protective role significantly reduced not just its own students’ recent substance use, but that of students in neighboring SCAs as well. Conclusions and Scientific Significance The findings show students’ recent use of alcohol and marijuana are associated with characteristics of the environment. PMID:23617858

77 FR 35711 - Strong Cities, Strong Communities National Resource Network Pilot Program Advance Notice and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-14

... economic need, strong local leadership and collaboration, potential for economic growth, geographic... $1 million that they will use to administer an ``X-prize style'' competition, whereby they will... founding mandate in the 1965 Department of Housing and Urban Development Act to ``Exercise leadership at...

Marine turtle mitogenome phylogenetics and evolution.

PubMed

Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H; Thomas P Gilbert, M; Morin, Phillip A

2012-10-01

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. Published by Elsevier Inc.

Evaluating the Significance of Paleophylogeographic Species Distribution Models in Reconstructing Quaternary Range-Shifts of Nearctic Chelonians

PubMed Central

Flecks, Morris; Ahmadzadeh, Faraham; Dambach, Johannes; Engler, Jan O.; Habel, Jan Christian; Hartmann, Timo; Hörnes, David; Ihlow, Flora; Schidelko, Kathrin; Stiels, Darius; Polly, P. David

2013-01-01

The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5–10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future. PMID:24130664

Spatiotemporal modelling and mapping of the bubonic plague epidemic in India.

PubMed

Yu, Hwa-Lung; Christakos, George

2006-03-17

This work studies the spatiotemporal evolution of bubonic plague in India during 1896-1906 using stochastic concepts and geographical information science techniques. In the past, most investigations focused on selected cities to conduct different kinds of studies, such as the ecology of rats. No detailed maps existed incorporating the space-time dependence structure and uncertainty sources of the epidemic system and providing a composite space-time picture of the disease propagation characteristics. Informative spatiotemporal maps were generated that represented mortality rates and geographical spread of the disease, and epidemic indicator plots were derived that offered meaningful characterizations of the spatiotemporal disease distribution. The bubonic plague in India exhibited strong seasonal and geographical features. During its entire duration, the plague continued to invade new geographical areas, while it followed a re-emergence pattern at many localities; its rate changed significantly during each year and the mortality distribution exhibited space-time heterogeneous patterns; prevalence usually occurred in the autumn and spring, whereas the plague stopped moving towards new locations during the summers. Modern stochastic modelling and geographical information science provide powerful means to study the spatiotemporal distribution of the bubonic plague epidemic under conditions of uncertainty and multi-sourced databases; to account for various forms of interdisciplinary knowledge; and to generate informative space-time maps of mortality rates and propagation patterns. To the best of our knowledge, this kind of plague maps and plots become available for the first time, thus providing novel perspectives concerning the distribution and space-time propagation of the deadly epidemic. Furthermore, systematic maps and indicator plots make possible the comparison of the spatial-temporal propagation patterns of different diseases.

Spatiotemporal modelling and mapping of the bubonic plague epidemic in India

PubMed Central

Yu, Hwa-Lung; Christakos, George

2006-01-01

Background This work studies the spatiotemporal evolution of bubonic plague in India during 1896–1906 using stochastic concepts and geographical information science techniques. In the past, most investigations focused on selected cities to conduct different kinds of studies, such as the ecology of rats. No detailed maps existed incorporating the space-time dependence structure and uncertainty sources of the epidemic system and providing a composite space-time picture of the disease propagation characteristics. Results Informative spatiotemporal maps were generated that represented mortality rates and geographical spread of the disease, and epidemic indicator plots were derived that offered meaningful characterizations of the spatiotemporal disease distribution. The bubonic plague in India exhibited strong seasonal and geographical features. During its entire duration, the plague continued to invade new geographical areas, while it followed a re-emergence pattern at many localities; its rate changed significantly during each year and the mortality distribution exhibited space-time heterogeneous patterns; prevalence usually occurred in the autumn and spring, whereas the plague stopped moving towards new locations during the summers. Conclusion Modern stochastic modelling and geographical information science provide powerful means to study the spatiotemporal distribution of the bubonic plague epidemic under conditions of uncertainty and multi-sourced databases; to account for various forms of interdisciplinary knowledge; and to generate informative space-time maps of mortality rates and propagation patterns. To the best of our knowledge, this kind of plague maps and plots become available for the first time, thus providing novel perspectives concerning the distribution and space-time propagation of the deadly epidemic. Furthermore, systematic maps and indicator plots make possible the comparison of the spatial-temporal propagation patterns of different diseases. PMID:16545128

Range size heritability and diversification patterns in the liverwort genus Radula.

PubMed

Patiño, Jairo; Wang, Jian; Renner, Matt A M; Gradstein, S Robbert; Laenen, Benjamin; Devos, Nicolas; Shaw, A Jonathan; Vanderpoorten, Alain

2017-01-01

Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively. The congruence between the divergence time of these lineages and continental split suggests that plate tectonics could have played a major role in their present distribution, suggesting that a strong imprint of vicariance can still be found in extant distribution patterns in these highly mobile organisms. Amentuloradula, Volutoradula and Metaradula species did not appear to exhibit losses of dispersal capacities in terms of dispersal life-history traits, but evidence for significant phylogenetic signal in macroecological niche traits suggests that niche conservatism accounts for their restricted geographic ranges. Despite their greatly restricted distribution to Australasia and Neotropics respectively, Amentuloradula and Volutoradula did not exhibit significantly lower diversification rates than more widespread lineages, in contrast with the hypothesis that the probability of speciation increases with range size by promoting geographic isolation and increasing the rate at which novel habitats are encountered. We suggest that stochastic long-distance dispersal events may balance allele frequencies across large spatial scales, leading to low genetic structure among geographically distant areas or even continents, ultimately decreasing the diversification rates in highly mobile, widespread lineages. Copyright © 2016 Elsevier Inc. All rights reserved.

Mitochondrial DNA variation in natural populations of endangered Indian feather-back fish, Chitala chitala.

PubMed

Mandal, Anup; Mohindra, Vindhya; Singh, Rajeev Kumar; Punia, Peyush; Singh, Ajay Kumar; Lal, Kuldeep Kumar

2012-02-01

Genetic variation at mitochondrial cytochrome b (cyt b) and D-loop region reveals the evidence of population sub-structuring in Indian populations of highly endangered primitive feather-back fish Chitala chitala. Samples collected through commercial catches from eight riverine populations from different geographical locations of India were analyzed for cyt b region (307 bp) and D-loop region (636-716 bp). The sequences of the both the mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The patterns of genetic diversity, haplotypes networks clearly indicated two distinct mitochondrial lineages and mismatch distribution strongly suggest a historical influence on the genetic structure of C. chitala populations. The baseline information on genetic variation and the evidence of population sub-structuring generated from this study would be useful for planning effective strategies for conservation and rehabilitation of this highly endangered species.

Communication networks of men facing a diagnosis of prostate cancer.

PubMed

Brown, Dot; Oetzel, John; Henderson, Alison

2016-11-01

This study seeks to identify the factors that shape the communication networks of men who face a potential diagnosis of prostate cancer, and how these factors relate to their disclosure about their changing health status. Men facing a potential diagnosis of prostate cancer are in a challenging situation; the support benefits of disclosing their changing health status to others in their communication networks is set against a backdrop of the potential stigma and uncertainty of the diagnosis. All men on a prostate biopsy waiting list were eligible for inclusion in an exploratory and interpretive study. Semi-structured interviews with 40 men explored their network structures and disclosure of health information. Thematic analysis highlighted the factors which contributed to their network structures and their disclosure about their health status. Four network factors shaped men's perspectives about disclosing their health status: (1) tie strength, comprising both strong and weak ties; (2) knowledgeable others, with a focus on medical professionals in the family; (3) homophily, which included other individuals with a similar medical condition; and (4) geographical proximity, with a preference for face-to-face communication. Communication networks influence men's disclosure of their health status and in particular weak ties with medical knowledge have an important role. Men who use the potential for support in their networks may experience improved psychosocial outcomes. Using these four network factors-tie strength, knowledgeable others, homophily or geographical proximity-to forecast men's willingness to disclose helps identify men who lack potential support and so are at risk of poor psychosocial health. Those with few strong ties or knowledgeable others in their networks may be in the at-risk cohort. The support provided in communication networks complements formal medical care from nurses and other health professionals, and encouraging patients to use their communication networks improves the psychosocial health of the men themselves, their partners and their families. © 2016 John Wiley & Sons Ltd.

Fecal Microbiomes of Non-Human Primates in Western Uganda Reveal Species-Specific Communities Largely Resistant to Habitat Perturbation

PubMed Central

McCORD, ALEIA I.; CHAPMAN, COLIN A.; WENY, GEOFFREY; TUMUKUNDE, ALEX; HYEROBA, DAVID; KLOTZ, KELLY; KOBLINGS, AVERY S.; MBORA, DAVID N.M.; CREGGER, MELISSA; WHITE, BRYAN A.; LEIGH, STEVEN R.; GOLDBERG, TONY L.

2014-01-01

Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate “microbiomes” remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance. PMID:24285224

Currency co-movement and network correlation structure of foreign exchange market

NASA Astrophysics Data System (ADS)

Mai, Yong; Chen, Huan; Zou, Jun-Zhong; Li, Sai-Ping

2018-02-01

We study the correlations of exchange rate volatility in the global foreign exchange(FX) market based on complex network graphs. Correlation matrices (CM) and the theoretical information flow method (Infomap) are employed to analyze the modular structure of the global foreign exchange network. The analysis demonstrates that there exist currency modules in the network, which is consistent with the geographical nature of currencies. The European and the East Asian currency modules in the FX network are most significant. We introduce a measure of the impact of individual currency based on its partial correlations with other currencies. We further incorporate an impact elimination method to filter out the impact of core nodes and construct subnetworks after the removal of these core nodes. The result reveals that (i) the US Dollar has prominent global influence on the FX market while the Euro has great impact on European currencies; (ii) the East Asian currency module is more strongly correlated than the European currency module. The strong correlation is a result of the strong co-movement of currencies in the region. The co-movement of currencies is further used to study the formation of international monetary bloc and the result is in good agreement with the consideration based on international trade.

Web-based objective structured clinical examination with remote standardized patients and Skype: resident experience.

PubMed

Langenau, Erik; Kachur, Elizabeth; Horber, Dot

2014-07-01

Using Skype and remote standardized patients (RSPs), investigators sought to evaluate user acceptance of a web-based objective structured clinical examination (OSCE) among resident physicians. After participating in four web-based clinical encounters addressing pain with RSPs, 59 residents from different training programs, disciplines and geographic locations completed a 52-item questionnaire regarding their experience with Skype and RSPs. Open-ended responses were solicited as well. The majority of participants (97%) agreed or strongly agreed the web-based format was convenient and a practical learning exercise, and 90% agreed or strongly agreed the format was effective in teaching communication skills. Although 93% agreed or strongly agreed they could communicate easily with RSPs using Skype, 80% preferred traditional face-to-face clinical encounters, and 58% reported technical difficulties during the encounters. Open-ended written responses supported survey results. Findings from this study expose challenges with technology and human factors, but positive experiences support the continued investigation of web-based OSCEs as a synchronous e-learning initiative for teaching and assessing doctor-patient communication. Such educational programs are valuable but unlikely to replace face-to-face encounters with patients. This web-based OSCE program provides physician learners with additional opportunity to improve doctor-patient communication. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Variation in sclerophylly among Iberian populations of Quercus coccifera L. is associated with genetic differentiation across contrasting environments.

PubMed

Rubio de Casas, R; Vargas, P; Pérez-Corona, E; Cano, E; Manrique, E; García-Verdugo, C; Balaguer, L

2009-05-01

Evergreen oaks are an emblematic element of the Mediterranean vegetation and have a leaf phenotype that seems to have remained unchanged since the Miocene. We hypothesise that variation of the sclerophyll phenotype among Iberian populations of Quercus coccifera is partly due to an ulterior process of ecotypic differentiation. We analysed the genetic structure of nine Iberian populations using ISSR fingerprints, and their leaf phenotypes using mean and intracanopy plasticity values of eight morphological (leaf angle, area, spinescence, lobation and specific area) and biochemical traits (VAZ pool, chlorophyll and beta-carotene content). Climate and soil were also characterised at the population sites. Significant genetic and phenotypic differences were found among populations and between NE Iberia and the rest of the populations of the peninsula. Mean phenotypes showed a strong and independent correlation with both genetic and geographic distances. Northeastern plants were smaller, less plastic, with smaller, spinier and thicker leaves, a phenotype consistent with the stressful conditions that prevailed in the steppe environments of the refugia within this geographic area during glaciations. These genetic, phenotypic, geographic and environmental patterns are consistent with previously reported palaeoecological and common evidence. Such consistency leads us to conclude that there has been a Quaternary divergence within the sclerophyllous syndrome that was at least partially driven by ecological factors.

Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

PubMed Central

Silva, Gonçalo; Lima, Fernando P.; Martel, Paulo; Castilho, Rita

2014-01-01

Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy. PMID:25143035

Biogeographical and evolutionary importance of the European high mountain systems

PubMed Central

Schmitt, Thomas

2009-01-01

Europe is characterised by several high mountain systems dominating major parts of its area, and these structures have strongly influenced the evolution of taxa. For species now restricted to these high mountain systems, characteristic biogeographical patterns of differentiation exist. (i) Many local endemics are found in most of the European high mountain systems especially in the Alps and the more geographically peripheral regions of Europe. Populations isolated in these peripheral mountain ranges often have strongly differentiated endemic genetic lineages, which survived and evolved in the vicinity of these mountain areas over long time periods. (ii) Populations of taxa with wide distributions in the Alps often have two or more genetic lineages, which in some cases even have the status of cryptic species. In many cases, these lineages are the results of several centres of glacial survival in the perialpine areas. Similar patterns also apply to the other geographically extended European high mountain systems, especially the Pyrenees and Carpathians. (iii) Populations from adjoining high mountain systems often show similar genetic lineages, a phenomenon best explained by postglacial retreat to these mountains from one single differentiation centre between them. (iv) The populations of a number of species show gradients of genetic diversity from a genetically richer East to a poorer West. This might indicate better glacial survival conditions for this biogeographical group of species in the more eastern parts of Europe. PMID:19480666

Tracking modern human population history from linguistic and cranial phenotype

PubMed Central

Reyes-Centeno, Hugo; Harvati, Katerina; Jäger, Gerhard

2016-01-01

Languages and genes arguably follow parallel evolutionary trajectories, descending from a common source and subsequently differentiating. However, although common ancestry is established within language families, it remains controversial whether language preserves a deep historical signal. To address this question, we evaluate the association between linguistic and geographic distances across 265 language families, as well as between linguistic, geographic, and cranial distances among eleven populations from Africa, Asia, and Australia. We take advantage of differential population history signals reflected by human cranial anatomy, where temporal bone shape reliably tracks deep population history and neutral genetic changes, while facial shape is more strongly associated with recent environmental effects. We show that linguistic distances are strongly geographically patterned, even within widely dispersed groups. However, they are correlated predominantly with facial, rather than temporal bone, morphology, suggesting that variation in vocabulary likely tracks relatively recent events and possibly population contact. PMID:27833101

The local environment determines the assembly of root endophytic fungi at a continental scale.

PubMed

Glynou, Kyriaki; Ali, Tahir; Buch, Ann-Katrin; Haghi Kia, Sevda; Ploch, Sebastian; Xia, Xiaojuan; Çelik, Ali; Thines, Marco; Maciá-Vicente, Jose G

2016-09-01

Root endophytic fungi are found in a great variety of plants and ecosystems, but the ecological drivers of their biogeographic distribution are poorly understood. Here, we investigate the occurrence of root endophytes in the non-mycorrhizal plant genus Microthlaspi, and the effect of environmental factors and geographic distance in structuring their communities at a continental scale. We sampled 52 plant populations across the northern Mediterranean and central Europe and used a cultivation approach to study their endophytic communities. Cultivation of roots yielded 2601 isolates, which were grouped into 296 operational taxonomic units (OTUs) by internal transcribed spacer sequencing of 1998 representative colonies. Climatic and spatial factors were the best descriptors of the structure of endophytic communities, outweighing soil characteristics, host genotype and geographical distance. OTU richness was negatively affected by precipitation, and the composition of communities followed latitudinal gradients of precipitation and temperature. Only six widespread OTUs belonging to the orders Pleosporales, Hypocreales and Helotiales represented about 50% of all isolates. Assessments of their individual distribution revealed particular ecological preferences or a cosmopolitan occurrence. Our findings support a strong influence of the local environment in determining root endophytic communities, and show a different niche occupancy by individual endophytes. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Climatic and geographic predictors of life history variation in Eastern Massasauga (Sistrurus catenatus): A range-wide synthesis.

PubMed

Hileman, Eric T; King, Richard B; Adamski, John M; Anton, Thomas G; Bailey, Robyn L; Baker, Sarah J; Bieser, Nickolas D; Bell, Thomas A; Bissell, Kristin M; Bradke, Danielle R; Campa, Henry; Casper, Gary S; Cedar, Karen; Cross, Matthew D; DeGregorio, Brett A; Dreslik, Michael J; Faust, Lisa J; Harvey, Daniel S; Hay, Robert W; Jellen, Benjamin C; Johnson, Brent D; Johnson, Glenn; Kiel, Brooke D; Kingsbury, Bruce A; Kowalski, Matthew J; Lee, Yu Man; Lentini, Andrew M; Marshall, John C; Mauger, David; Moore, Jennifer A; Paloski, Rori A; Phillips, Christopher A; Pratt, Paul D; Preney, Thomas; Prior, Kent A; Promaine, Andrew; Redmer, Michael; Reinert, Howard K; Rouse, Jeremy D; Shoemaker, Kevin T; Sutton, Scott; VanDeWalle, Terry J; Weatherhead, Patrick J; Wynn, Doug; Yagi, Anne

2017-01-01

Elucidating how life history traits vary geographically is important to understanding variation in population dynamics. Because many aspects of ectotherm life history are climate-dependent, geographic variation in climate is expected to have a large impact on population dynamics through effects on annual survival, body size, growth rate, age at first reproduction, size-fecundity relationship, and reproductive frequency. The Eastern Massasauga (Sistrurus catenatus) is a small, imperiled North American rattlesnake with a distribution centered on the Great Lakes region, where lake effects strongly influence local conditions. To address Eastern Massasauga life history data gaps, we compiled data from 47 study sites representing 38 counties across the range. We used multimodel inference and general linear models with geographic coordinates and annual climate normals as explanatory variables to clarify patterns of variation in life history traits. We found strong evidence for geographic variation in six of nine life history variables. Adult female snout-vent length and neonate mass increased with increasing mean annual precipitation. Litter size decreased with increasing mean temperature, and the size-fecundity relationship and growth prior to first hibernation both increased with increasing latitude. The proportion of gravid females also increased with increasing latitude, but this relationship may be the result of geographically varying detection bias. Our results provide insights into ectotherm life history variation and fill critical data gaps, which will inform Eastern Massasauga conservation efforts by improving biological realism for models of population viability and climate change.

Climatic and geographic predictors of life history variation in Eastern Massasauga (Sistrurus catenatus): A range-wide synthesis

PubMed Central

King, Richard B.; Adamski, John M.; Anton, Thomas G.; Bailey, Robyn L.; Baker, Sarah J.; Bieser, Nickolas D.; Bell, Thomas A.; Bissell, Kristin M.; Bradke, Danielle R.; Campa, Henry; Casper, Gary S.; Cedar, Karen; Cross, Matthew D.; DeGregorio, Brett A.; Dreslik, Michael J.; Faust, Lisa J.; Harvey, Daniel S.; Hay, Robert W.; Jellen, Benjamin C.; Johnson, Brent D.; Johnson, Glenn; Kiel, Brooke D.; Kingsbury, Bruce A.; Kowalski, Matthew J.; Lee, Yu Man; Lentini, Andrew M.; Marshall, John C.; Mauger, David; Moore, Jennifer A.; Paloski, Rori A.; Phillips, Christopher A.; Pratt, Paul D.; Preney, Thomas; Prior, Kent A.; Promaine, Andrew; Redmer, Michael; Reinert, Howard K.; Rouse, Jeremy D.; Shoemaker, Kevin T.; Sutton, Scott; VanDeWalle, Terry J.; Weatherhead, Patrick J.; Wynn, Doug; Yagi, Anne

2017-01-01

Elucidating how life history traits vary geographically is important to understanding variation in population dynamics. Because many aspects of ectotherm life history are climate-dependent, geographic variation in climate is expected to have a large impact on population dynamics through effects on annual survival, body size, growth rate, age at first reproduction, size–fecundity relationship, and reproductive frequency. The Eastern Massasauga (Sistrurus catenatus) is a small, imperiled North American rattlesnake with a distribution centered on the Great Lakes region, where lake effects strongly influence local conditions. To address Eastern Massasauga life history data gaps, we compiled data from 47 study sites representing 38 counties across the range. We used multimodel inference and general linear models with geographic coordinates and annual climate normals as explanatory variables to clarify patterns of variation in life history traits. We found strong evidence for geographic variation in six of nine life history variables. Adult female snout-vent length and neonate mass increased with increasing mean annual precipitation. Litter size decreased with increasing mean temperature, and the size–fecundity relationship and growth prior to first hibernation both increased with increasing latitude. The proportion of gravid females also increased with increasing latitude, but this relationship may be the result of geographically varying detection bias. Our results provide insights into ectotherm life history variation and fill critical data gaps, which will inform Eastern Massasauga conservation efforts by improving biological realism for models of population viability and climate change. PMID:28196149

The Effects of Geographic Isolation and Social Support on the Health of Wisconsin Women.

PubMed

Tittman, Sarah M; Harteau, Christy; Beyer, Kirsten M M

2016-04-01

Rural residents are less likely to receive preventive health screening, more likely to be uninsured, and more likely to report fair to poor health than urban residents. Social disconnectedness and perceived isolation are known to be negative predictors of self-rated physical health; however, the direct effects of geographic isolation and social support on overall health have not been well elucidated. A cross-sectional survey of women (n = 113) participating in Wisconsin Rural Women's initiative programming was conducted, which included measures of geographic isolation, an assessment of overall health, and social support using the validated Interpersonal Support Evaluation List with 3 subscales, including belonging support, tangible support, and appraisal support. Geographic isolation was shown to be a negative predictor of belonging support (P = .0064) and tangible support (P = .0349); however, geographic isolation was not a statistically significant predictor of appraisal support. A strong and direct relationship was observed between social support and self-perceived health status among this population of Wisconsin women, and hospital access based on geographic proximity was positively correlated (P = .028) with overall health status. The direct relationship between social support and overall health demonstrated here stresses the importance of developing and maintaining strong social support networks, which can be improved through rural support groups that have the unique ability to assist rural residents in fostering social support systems, advocating stress management techniques, and achieving a greater sense of well-being.

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

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins.

PubMed

Eriksson, Anders; Manica, Andrea

2012-08-28

Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar

PubMed Central

Bletz, Molly C.; Archer, Holly; Harris, Reid N.; McKenzie, Valerie J.; Rabemananjara, Falitiana C. E.; Rakotoarison, Andolalao; Vences, Miguel

2017-01-01

Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae) was enriched on terrestrial frogs. The presence of shared bacterial OTUs across geographic regions for selected host genera suggests the presence of core microbial communities which in Madagascar, might be driven more strongly by a species’ preference for specific microhabitats than by the physical, physiological or biochemical properties of their skin. These results corroborate that both host and environmental factors are driving community assembly of amphibian cutaneous microbial communities, and provide an improved foundation for elucidating their role in disease resistance. PMID:28861051

Remote sensing and geographically based information systems

NASA Technical Reports Server (NTRS)

Cicone, R. C.

1977-01-01

A structure is proposed for a geographically-oriented computer-based information system applicable to the analysis of remote sensing digital data. The structure, intended to answer a wide variety of user needs, would permit multiple views of the data, provide independent management of data security, quality and integrity, and rely on automatic data filing. Problems in geographically-oriented data systems, including those related to line encoding and cell encoding, are considered.

Intense sub-kilometer-scale boundary layer rolls observed in hurricane fran

PubMed

Wurman; Winslow

1998-04-24

High-resolution observations obtained with the Doppler On Wheels (DOW) mobile weather radar near the point of landfall of hurricane Fran (1996) revealed the existence of intense, sub-kilometer-scale, boundary layer rolls that strongly modulated the near-surface wind speed. It is proposed that these structures are one cause of geographically varying surface damage patterns that have been observed after some landfalling hurricanes and that they cause much of the observed gustiness, bringing high-velocity air from aloft to the lowest observable levels. High-resolution DOW radar observations are contrasted with lower-resolution observations obtained with an operational weather radar, which underestimated peak low-level wind speeds.

Regional and local species richness in an insular environment: Serpentine plants in California

USGS Publications Warehouse

Harrison, S.; Safford, H.D.; Grace, J.B.; Viers, J.H.; Davies, K.F.

2006-01-01

We asked how the richness of the specialized (endemic) flora of serpentine rock outcrops in California varies at both the regional and local scales. Our study had two goals: first, to test whether endemic richness is affected by spatial habitat structure (e.g., regional serpentine area, local serpentine outcrop area, regional and local measures of outcrop isolation), and second, to conduct this test in the context of a broader assessment of environmental influences (e.g., climate, soils, vegetation, disturbance) and historical influences (e.g., geologic age, geographic province) on local and regional species richness. We measured endemic and total richness and environmental variables in 109 serpentine sites (1000-m2 paired plots) in 78 serpentine-containing regions of the state. We used structural equation modeling (SEM) to simultaneously relate regional richness to regionalscale predictors, and local richness to both local-scale and regional-scale predictors. Our model for serpentine endemics explained 66% of the variation in local endemic richness based on local environment (vegetation, soils, rock cover) and on regional endemic richness. It explained 73% of the variation in regional endemic richness based on regional environment (climate and productivity), historical factors (geologic age and geographic province), and spatial structure (regional total area of serpentine, the only significant spatial variable in our analysis). We did not find a strong influence of spatial structure on species richness. However, we were able to distinguish local vs. regional influences on species richness to a novel extent, despite the existence of correlations between local and regional conditions. ?? 2006 by the Ecological Society of America.

Temporal Patterns and Environmental Correlates of Macroinvertebrate Communities in Temporary Streams.

PubMed

Botwe, Paul K; Barmuta, Leon A; Magierowski, Regina; McEvoy, Paul; Goonan, Peter; Carver, Scott

2015-01-01

Temporary streams are characterised by short periods of seasonal or annual stream flow after which streams contract into waterholes or pools of varying hydrological connectivity and permanence. Although these streams are widespread globally, temporal variability of their ecology is understudied, and understanding the processes that structure community composition in these systems is vital for predicting and managing the consequences of anthropogenic impacts. We used multivariate and univariate approaches to investigate temporal variability in macroinvertebrate compositional data from 13 years of sampling across multiple sites from autumn and spring, in South Australia, the driest state in the driest inhabited continent in the world. We examined the potential of land-use, geographic and environmental variables to predict the temporal variability in macroinvertebrate assemblages, and also identified indicator taxa, that is, those highly correlated with the most significantly associated physical variables. Temporal trajectories of macroinvertebrate communities varied within site in both seasons and across years. A combination of land-use, geographic and environmental variables accounted for 24% of the variation in community structure in autumn and 27% in spring. In autumn, community composition among sites were more closely clustered together relative to spring suggesting that communities were more similar in autumn than in spring. In both seasons, community structure was most strongly correlated with conductivity and latitude, and community structure was more associated with cover by agriculture than urban land-use. Maintaining temporary streams will require improved catchment management aimed at sustaining seasonal flows and critical refuge habitats, while also limiting the damaging effects from increased agriculture and urban developments.

Temporal Patterns and Environmental Correlates of Macroinvertebrate Communities in Temporary Streams

PubMed Central

Botwe, Paul K.; Barmuta, Leon A.; Magierowski, Regina; McEvoy, Paul; Goonan, Peter; Carver, Scott

2015-01-01

Temporary streams are characterised by short periods of seasonal or annual stream flow after which streams contract into waterholes or pools of varying hydrological connectivity and permanence. Although these streams are widespread globally, temporal variability of their ecology is understudied, and understanding the processes that structure community composition in these systems is vital for predicting and managing the consequences of anthropogenic impacts. We used multivariate and univariate approaches to investigate temporal variability in macroinvertebrate compositional data from 13 years of sampling across multiple sites from autumn and spring, in South Australia, the driest state in the driest inhabited continent in the world. We examined the potential of land-use, geographic and environmental variables to predict the temporal variability in macroinvertebrate assemblages, and also identified indicator taxa, that is, those highly correlated with the most significantly associated physical variables. Temporal trajectories of macroinvertebrate communities varied within site in both seasons and across years. A combination of land-use, geographic and environmental variables accounted for 24% of the variation in community structure in autumn and 27% in spring. In autumn, community composition among sites were more closely clustered together relative to spring suggesting that communities were more similar in autumn than in spring. In both seasons, community structure was most strongly correlated with conductivity and latitude, and community structure was more associated with cover by agriculture than urban land-use. Maintaining temporary streams will require improved catchment management aimed at sustaining seasonal flows and critical refuge habitats, while also limiting the damaging effects from increased agriculture and urban developments. PMID:26556711

A statistical study of the low-altitude ionospheric magnetic fields over the north pole of Venus

NASA Astrophysics Data System (ADS)

Zhang, T. L.; Baumjohann, W.; Russell, C. T.; Villarreal, M. N.; Luhmann, J. G.; Teh, W. L.

2015-08-01

Examination of Venus Express (VEX) low-altitude ionospheric magnetic field measurements during solar minimum has revealed the presence of strong magnetic fields at low altitudes over the north pole of Venus. A total of 77 events with strong magnetic fields as VEX crossed the northern polar region were identified between July 2008 and October 2009. These events all have strong horizontal fields, slowly varying with position. Using the superposed epoch method, we find that the averaged peak field is about 45 nT, which is well above the average ambient ionospheric field of 20 nT, with a full width at half maximum duration of 32 s, equivalent to a width of about 300 km. Considering the field orientation preference and spacecraft trajectory geometry, we conclude that these strong fields are found over the northern hemisphere with an occurrence frequency of more than 33% during solar minimum. They do not show a preference for any particular interplanetary magnetic field (IMF) orientation. However, they are found over the geographic pole more often when the interplanetary field is in the Venus orbital plane than when it is perpendicular to the orbital plane of Venus. The structures were found most frequently in the -E hemisphere, determined from the IMF orientation. The enhanced magnetic field is mainly quasi perpendicular to solar wind flow direction, and it is suggested that these structures form in the low-altitude collisional ionosphere where the diffusion and convection times are long.

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes.

PubMed

Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

2014-05-01

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco - the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity.

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes

PubMed Central

Leys, Marie; Petit, Eric J; El-Bahloul, Yasmina; Liso, Camille; Fournet, Sylvain; Arnaud, Jean-François

2014-01-01

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity. PMID:24963380

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population.

PubMed

Hoffman, J I; Kowalski, G J; Klimova, A; Eberhart-Phillips, L J; Staniland, I J; Baylis, A M M

2016-07-01

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

PubMed Central

Hoffman, J. I.; Kowalski, G. J.; Klimova, A.; Staniland, I. J.; Baylis, A. M. M.

2016-01-01

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations. PMID:27493782

The effect of geographical indices on left ventricular structure in healthy Han Chinese population

NASA Astrophysics Data System (ADS)

Cen, Minyi; Ge, Miao; Liu, Yonglin; Wang, Congxia; Yang, Shaofang

2017-02-01

The left ventricular posterior wall thickness (LVPWT) and interventricular septum thickness (IVST) are generally regarded as the functional parts of the left ventricular (LV) structure. This paper aims to examine the effects of geographical indices on healthy Han adults' LV structural indices and to offer a scientific basis for developing a unified standard for the reference values of adults' LV structural indices in China. Fifteen terrain, climate, and soil indices were examined as geographical explanatory variables. Statistical analysis was performed using correlation analysis. Moreover, a back propagation neural network (BPNN) and a support vector regression (SVR) were applied to developing models to predict the values of two indices. After the prediction models were built, distribution maps were produced. The results show that LV structural indices are characteristically associated with latitude, longitude, altitude, average temperature, average wind velocity, topsoil sand fraction, topsoil silt fraction, topsoil organic carbon, and topsoil sodicity. The model test analyses show the BPNN model possesses better simulative and predictive ability in comparison with the SVR model. The distribution maps of the LV structural indices show that, in China, the values are higher in the west and lower in the east. These results demonstrate that the reference values of the adults' LV structural indices will be different affected by different geographical environment. The reference values of LV structural indices in one region can be calculated by setting up a BPNN, which showed better applicability in this study. The distribution of the reference values of the LV structural indices can be seen clearly on the geographical distribution map.

The effect of geographical indices on left ventricular structure in healthy Han Chinese population.

PubMed

Cen, Minyi; Ge, Miao; Liu, Yonglin; Wang, Congxia; Yang, Shaofang

2017-02-01

The left ventricular posterior wall thickness (LVPWT) and interventricular septum thickness (IVST) are generally regarded as the functional parts of the left ventricular (LV) structure. This paper aims to examine the effects of geographical indices on healthy Han adults' LV structural indices and to offer a scientific basis for developing a unified standard for the reference values of adults' LV structural indices in China. Fifteen terrain, climate, and soil indices were examined as geographical explanatory variables. Statistical analysis was performed using correlation analysis. Moreover, a back propagation neural network (BPNN) and a support vector regression (SVR) were applied to developing models to predict the values of two indices. After the prediction models were built, distribution maps were produced. The results show that LV structural indices are characteristically associated with latitude, longitude, altitude, average temperature, average wind velocity, topsoil sand fraction, topsoil silt fraction, topsoil organic carbon, and topsoil sodicity. The model test analyses show the BPNN model possesses better simulative and predictive ability in comparison with the SVR model. The distribution maps of the LV structural indices show that, in China, the values are higher in the west and lower in the east. These results demonstrate that the reference values of the adults' LV structural indices will be different affected by different geographical environment. The reference values of LV structural indices in one region can be calculated by setting up a BPNN, which showed better applicability in this study. The distribution of the reference values of the LV structural indices can be seen clearly on the geographical distribution map.

Does Walkability Contribute to Geographic Variation in Psychosocial Distress? A Spatial Analysis of 91,142 Members of the 45 and Up Study in Sydney, Australia

PubMed Central

Morgan, Geoffrey G.; Jalaludin, Bin B.; Bauman, Adrian E.

2018-01-01

Walkability describes the capacity of the built environment to promote walking, and has been proposed as a potential focus for community-level mental health planning. We evaluated this possibility by examining the contribution of area-level walkability to variation in psychosocial distress in a population cohort at spatial scales comparable to those used for regional planning in Sydney, Australia. Data on psychosocial distress were analysed for 91,142 respondents to the 45 and Up Study baseline survey between January 2006 and April 2009. We fit conditional auto regression models at the postal area level to obtain smoothed “disease maps” for psychosocial distress, and assess its association with area-level walkability after adjusting for individual- and area-level factors. Prevalence of psychosocial distress was 7.8%; similar for low (7.9%), low-medium (7.9%), medium-high (8.0%), and high (7.4%) walkability areas; and decreased with reducing postal area socioeconomic disadvantage: 12.2% (most), 9.3%, 7.5%, 5.9%, and 4.7% (least). Unadjusted disease maps indicated strong geographic clustering of psychosocial distress with 99.0% of excess prevalence due to unobserved and spatially structured factors, which was reduced to 55.3% in fully adjusted maps. Spatial and unstructured variance decreased by 97.3% and 39.8% after adjusting for individual-level factors, and another 2.3% and 4.2% with the inclusions of area-level factors. Excess prevalence of psychosocial distress in postal areas was attenuated in adjusted models but remained spatially structured. Postal area prevalence of high psychosocial distress is geographically clustered in Sydney, but is unrelated to postal area walkability. Area-level socioeconomic disadvantage makes a small contribution to this spatial structure; however, community-level mental health planning will likely deliver greatest benefits by focusing on individual-level contributors to disease burden and inequality associated with psychosocial distress. PMID:29415461

Does Walkability Contribute to Geographic Variation in Psychosocial Distress? A Spatial Analysis of 91,142 Members of the 45 and Up Study in Sydney, Australia.

PubMed

Mayne, Darren J; Morgan, Geoffrey G; Jalaludin, Bin B; Bauman, Adrian E

2018-02-06

Walkability describes the capacity of the built environment to promote walking, and has been proposed as a potential focus for community-level mental health planning. We evaluated this possibility by examining the contribution of area-level walkability to variation in psychosocial distress in a population cohort at spatial scales comparable to those used for regional planning in Sydney, Australia. Data on psychosocial distress were analysed for 91,142 respondents to the 45 and Up Study baseline survey between January 2006 and April 2009. We fit conditional auto regression models at the postal area level to obtain smoothed "disease maps" for psychosocial distress, and assess its association with area-level walkability after adjusting for individual- and area-level factors. Prevalence of psychosocial distress was 7.8%; similar for low (7.9%), low-medium (7.9%), medium-high (8.0%), and high (7.4%) walkability areas; and decreased with reducing postal area socioeconomic disadvantage: 12.2% (most), 9.3%, 7.5%, 5.9%, and 4.7% (least). Unadjusted disease maps indicated strong geographic clustering of psychosocial distress with 99.0% of excess prevalence due to unobserved and spatially structured factors, which was reduced to 55.3% in fully adjusted maps. Spatial and unstructured variance decreased by 97.3% and 39.8% after adjusting for individual-level factors, and another 2.3% and 4.2% with the inclusions of area-level factors. Excess prevalence of psychosocial distress in postal areas was attenuated in adjusted models but remained spatially structured. Postal area prevalence of high psychosocial distress is geographically clustered in Sydney, but is unrelated to postal area walkability. Area-level socioeconomic disadvantage makes a small contribution to this spatial structure; however, community-level mental health planning will likely deliver greatest benefits by focusing on individual-level contributors to disease burden and inequality associated with psychosocial distress.

Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range

PubMed Central

Muñoz, Joaquín; Amat, Francisco; Green, Andy J.; Figuerola, Jordi

2013-01-01

Since Darwin’s time, waterbirds have been considered an important vector for the dispersal of continental aquatic invertebrates. Bird movements have facilitated the worldwide invasion of the American brine shrimp Artemia franciscana, transporting cysts (diapausing eggs), and favouring rapid range expansions from introduction sites. Here we address the impact of bird migratory flyways on the population genetic structure and phylogeography of A. franciscana in its native range in the Americas. We examined sequence variation for two mitochondrial gene fragments (COI and 16S for a subset of the data) in a large set of population samples representing the entire native range of A. franciscana. Furthermore, we performed Mantel tests and redundancy analyses (RDA) to test the role of flyways, geography and human introductions on the phylogeography and population genetic structure at a continental scale. A. franciscana mitochondrial DNA was very diverse, with two main clades, largely corresponding to Pacific and Atlantic populations, mirroring American bird flyways. There was a high degree of regional endemism, with populations subdivided into at least 12 divergent, geographically restricted and largely allopatric mitochondrial lineages, and high levels of population structure (ΦST of 0.92), indicating low ongoing gene flow. We found evidence of human-mediated introductions in nine out of 39 populations analysed. Once these populations were removed, Mantel tests revealed a strong association between genetic variation and geographic distance (i.e., isolation-by-distance pattern). RDA showed that shared bird flyways explained around 20% of the variance in genetic distance between populations and this was highly significant, once geographic distance was controlled for. The variance explained increased to 30% when the factor human introduction was included in the model. Our findings suggest that bird-mediated transport of brine shrimp propagules does not result in substantial ongoing gene flow; instead, it had a significant historical role on the current species phylogeography, facilitating the colonisation of new aquatic environments as they become available along their main migratory flyways. PMID:24255814

Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system, Lake Mývatn, Iceland.

PubMed

Millet, Antoine; Kristjánsson, Bjarni K; Einarsson, Arni; Räsänen, Katja

2013-09-01

Eco-evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments - favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow.

Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system, Lake Mývatn, Iceland

PubMed Central

Millet, Antoine; Kristjánsson, Bjarni K; Einarsson, Árni; Räsänen, Katja

2013-01-01

Eco-evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments – favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow. PMID:24223263

Mesoscale Variability in SUCCESS Data

NASA Technical Reports Server (NTRS)

Eckermann, Stephen D.; Stewart, Richard W. (Technical Monitor)

1998-01-01

Analysis of meteorological, chemical and microphysical data from the airborne SUCCESS (SUbsonic aircraft Contrail and Cloud Effects Special Study) mission is reported. Careful analysis of the complex DC-8 flight pattern of May 2, 1996 reveals 19 linear flight segments within six main geographical areas, which we have analyzed. Significant mountain wave activity is revealed in the data from the MMS (Meteorology Measurement System) and MTP (Microwave Temperature Profiler) instruments on the DC-8, which resembles previous observations of mountain wave structures near Boulder, Colorado. Strong mountain-wave-induced upwelling downwind of the Rockies is noted. Turbulence is also noted in regions of the mountain wave consistent with overturning near the tropopause. Zonal winds recorded on the ER-2 are shown to be consistent with mountain wave breaking at or near critical levels in the stratosphere, consistent with the strong turbulence reported by the pilot during the ER-2 flight. These observations have been supported with spectral analyses and modeling studies. 'Postcasts' of mountain wave activity on May 2, 1996 using the Naval Research Laboratory Mountain Wave Forecast Model predicts both strong mountain wave activity near the tropopause and strong mountain-wave-induced turbulence in the stratosphere.

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.

Farmers without borders—genetic structuring in century old barley (Hordeum vulgare)

PubMed Central

Forsberg, N E G; Russell, J; Macaulay, M; Leino, M W; Hagenblad, J

2015-01-01

The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. FST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes. PMID:25227257

Farmers without borders-genetic structuring in century old barley (Hordeum vulgare).

PubMed

Forsberg, N E G; Russell, J; Macaulay, M; Leino, M W; Hagenblad, J

2015-02-01

The geographic distribution of genetic diversity can reveal the evolutionary history of a species. For crop plants, phylogeographic patterns also indicate how seed has been exchanged and spread in agrarian communities. Such patterns are, however, easily blurred by the intense seed trade, plant improvement and even genebank conservation during the twentieth century, and discerning fine-scale phylogeographic patterns is thus particularly challenging. Using historical crop specimens, these problems are circumvented and we show here how high-throughput genotyping of historical nineteenth century crop specimens can reveal detailed geographic population structure. Thirty-one historical and nine extant accessions of North European landrace barley (Hordeum vulgare L.), in total 231 individuals, were genotyped on a 384 single nucleotide polymorphism assay. The historical material shows constant high levels of within-accession diversity, whereas the extant accessions show more varying levels of diversity and a higher degree of total genotype sharing. Structure, discriminant analysis of principal components and principal component analysis cluster the accessions in latitudinal groups across country borders in Finland, Norway and Sweden. FST statistics indicate strong differentiation between accessions from southern Fennoscandia and accessions from central or northern Fennoscandia, and less differentiation between central and northern accessions. These findings are discussed in the context of contrasting historical records on intense within-country south to north seed movement. Our results suggest that although seeds were traded long distances, long-term cultivation has instead been of locally available, possibly better adapted, genotypes.

The roles of geography and founder effects in promoting host-associated differentiation in the generalist bogus yucca moth Prodoxus decipiens.

PubMed

Darwell, C T; Fox, K A; Althoff, D M

2014-12-01

There is ample evidence that host shifts in plant-feeding insects have been instrumental in generating the enormous diversity of insects. Changes in host use can cause host-associated differentiation (HAD) among populations that may lead to reproductive isolation and eventual speciation. The importance of geography in facilitating this process remains controversial. We examined the geographic context of HAD in the wide-ranging generalist yucca moth Prodoxus decipiens. Previous work demonstrated HAD among sympatric moth populations feeding on two different Yucca species occurring on the barrier islands of North Carolina, USA. We assessed the genetic structure of P. decipiens across its entire geographic and host range to determine whether HAD is widespread in this generalist herbivore. Population genetic analyses of microsatellite and mtDNA sequence data across the entire range showed genetic structuring with respect to host use and geography. In particular, genetic differentiation was relatively strong between mainland populations and those on the barrier islands of North Carolina. Finer scale analyses, however, among sympatric populations using different host plant species only showed significant clustering based on host use for populations on the barrier islands. Mainland populations did not form population clusters based on host plant use. Reduced genetic diversity in the barrier island populations, especially on the derived host, suggests that founder effects may have been instrumental in facilitating HAD. In general, results suggest that the interplay of local adaptation, geography and demography can determine the tempo of HAD. We argue that future studies should include comprehensive surveys across a wide range of environmental and geographic conditions to elucidate the contribution of various processes to HAD. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Differences in wing morphometrics of Lymantria dispar (Lepidoptera: Erebidae) between populations that vary in female flight capability

Treesearch

Juan Shi; Fang Chen; Melody A. Keena

2015-01-01

All male gypsy moths, Lymantria dispar L., are capable of strong directed flight, but flight in females varies, increasing from west to east geographically across Eurasia. To better understand how the wings differ between female flight capable and flightless strains, a wing morphometric analysis of 821 gypsy moths from eight geographic strains (three...

Global late Quaternary megafauna extinctions linked to humans, not climate change.

PubMed

Sandom, Christopher; Faurby, Søren; Sandel, Brody; Svenning, Jens-Christian

2014-07-22

The late Quaternary megafauna extinction was a severe global-scale event. Two factors, climate change and modern humans, have received broad support as the primary drivers, but their absolute and relative importance remains controversial. To date, focus has been on the extinction chronology of individual or small groups of species, specific geographical regions or macroscale studies at very coarse geographical and taxonomic resolution, limiting the possibility of adequately testing the proposed hypotheses. We present, to our knowledge, the first global analysis of this extinction based on comprehensive country-level data on the geographical distribution of all large mammal species (more than or equal to 10 kg) that have gone globally or continentally extinct between the beginning of the Last Interglacial at 132,000 years BP and the late Holocene 1000 years BP, testing the relative roles played by glacial-interglacial climate change and humans. We show that the severity of extinction is strongly tied to hominin palaeobiogeography, with at most a weak, Eurasia-specific link to climate change. This first species-level macroscale analysis at relatively high geographical resolution provides strong support for modern humans as the primary driver of the worldwide megafauna losses during the late Quaternary.

Measuring Geographic Migration Patterns Using Matrículas Consulares.

PubMed

Caballero, Maria Esther; Cadena, Brian C; Kovak, Brian K

2018-05-14

In this article, we show how to use administrative data from the Matrícula Consular de Alta Seguridad (MCAS) identification card program to measure the joint distribution of sending and receiving locations for migrants from Mexico to the United States. Whereas other data sources cover only a small fraction of source or destination locations or include only very coarse geographic information, the MCAS data provide complete geographic coverage of both countries, detailed information on migrants' sources and destinations, and a very large sample size. We first confirm the quality and representativeness of the MCAS data by comparing them with well-known household surveys in Mexico and the United States, finding strong agreement on the migrant location distributions available across data sets. We then document substantial differences in the mix of destinations for migrants from different places within the same source state, demonstrating the importance of detailed substate geographical information. We conclude with an example of how these detailed data can be used to study the effects of destination-specific conditions on migration patterns. We find that an Arizona law reducing employment opportunities for unauthorized migrants decreased emigration from and increased return migration to Mexican source regions with strong initial ties to Arizona.

Global late Quaternary megafauna extinctions linked to humans, not climate change

PubMed Central

Sandom, Christopher; Faurby, Søren; Sandel, Brody; Svenning, Jens-Christian

2014-01-01

The late Quaternary megafauna extinction was a severe global-scale event. Two factors, climate change and modern humans, have received broad support as the primary drivers, but their absolute and relative importance remains controversial. To date, focus has been on the extinction chronology of individual or small groups of species, specific geographical regions or macroscale studies at very coarse geographical and taxonomic resolution, limiting the possibility of adequately testing the proposed hypotheses. We present, to our knowledge, the first global analysis of this extinction based on comprehensive country-level data on the geographical distribution of all large mammal species (more than or equal to 10 kg) that have gone globally or continentally extinct between the beginning of the Last Interglacial at 132 000 years BP and the late Holocene 1000 years BP, testing the relative roles played by glacial–interglacial climate change and humans. We show that the severity of extinction is strongly tied to hominin palaeobiogeography, with at most a weak, Eurasia-specific link to climate change. This first species-level macroscale analysis at relatively high geographical resolution provides strong support for modern humans as the primary driver of the worldwide megafauna losses during the late Quaternary. PMID:24898370

Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

PubMed Central

Staley, Christopher

2016-01-01

ABSTRACT Recent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P < 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P < 0.001), where freshwater sands had significantly higher abundances of taxa within the Actinobacteria, Betaproteobacteria, and Verrucomicrobia than marine environments. In contrast, marine sands harbored greater abundances of Gammaproteobacteria and Planctomycetes, and those from Florida had more Deltaproteobacteria and Firmicutes. Marine beaches had significantly different phylogenetic community structures (P ≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P < 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment. IMPORTANCE This study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives. PMID:26921429

Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide.

PubMed

Kissling, W Daniel; Eiserhardt, Wolf L; Baker, William J; Borchsenius, Finn; Couvreur, Thomas L P; Balslev, Henrik; Svenning, Jens-Christian

2012-05-08

Despite long-standing interest in the origin and maintenance of species diversity, little is known about historical drivers of species assemblage structure at large spatiotemporal scales. Here, we use global species distribution data, a dated genus-level phylogeny, and paleo-reconstructions of biomes and climate to examine Cenozoic imprints on the phylogenetic structure of regional species assemblages of palms (Arecaceae), a species-rich plant family characteristic of tropical ecosystems. We find a strong imprint on phylogenetic clustering due to geographic isolation and in situ diversification, especially in the Neotropics and on islands with spectacular palm radiations (e.g., Madagascar, Hawaii, and Cuba). Phylogenetic overdispersion on mainlands and islands corresponds to biotic interchange areas. Differences in the degree of phylogenetic clustering among biogeographic realms are related to differential losses of tropical rainforests during the Cenozoic, but not to the cumulative area of tropical rainforest over geological time. A largely random phylogenetic assemblage structure in Africa coincides with severe losses of rainforest area, especially after the Miocene. More recent events also appear to be influential: phylogenetic clustering increases with increasing intensity of Quaternary glacial-interglacial climatic oscillations in South America and, to a lesser extent, Africa, indicating that specific clades perform better in climatically unstable regions. Our results suggest that continental isolation (in combination with limited long-distance dispersal) and changing climate and habitat loss throughout the Cenozoic have had strong impacts on the phylogenetic structure of regional species assemblages in the tropics.

Phylogenetic information in polymorphic L1 and Alu insertions from East Asians and Native American populations.

PubMed

Mateus Pereira, L H; Socorro, A; Fernandez, I; Masleh, M; Vidal, D; Bianchi, N O; Bonatto, S L; Salzano, F M; Herrera, R J

2005-09-01

This study attempts to ascertain genetic affinities between Native American and East Asian populations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was demonstrated, with clear discrimination from African and European groups. Most of the variation was assigned to differences occurring within groups, but the interpopulation variation found for South Amerindians was recognizably higher in comparison to the other sampled groups of populations. Our data suggest that bottleneck events followed by strong influence of genetic drift in the process of the peopling of the Americas may have been determinant factors in delineating the genetic background of present-day South Amerindians. Since no clear subgroups were detected within Native Americans and East Asians, there is no indication of multiple waves in the early colonization of the New World. (c) 2005 Wiley-Liss, Inc.

Geographic distance affects dispersal of the patchy distributed greater long-tailed hamster (Tscherskia triton).

PubMed

Xue, Huiliang; Zhong, Min; Xu, Jinhui; Xu, Laixiang

2014-01-01

Dispersal is a fundamental process in ecology influencing the genetic structure and the viability of populations. Understanding how variable factors influence the dispersal of the population is becoming an important question in animal ecology. To date, geographic distance and geographic barriers are often considered as main factors impacting dispersal, but their effects are variable depending on different conditions. In general, geographic barriers affect more significantly than geographic distance on dispersal. In rapidly expanding populations, however, geographic barriers have less effect on dispersal than geographic distance. The effects of both geographic distance and geographic barriers in low-density populations with patchy distributions are poorly understood. By using a panel of 10 microsatellite loci we investigated the genetic structure of three patchy-distributed populations of the Greater long-tailed hamster (Tscherskia triton) from Raoyang, Guan and Shunyi counties of the North China Plain. The results showed that (i) high genetic diversity and differentiation exist in three geographic populations with patchy distributions; (ii) gene flow occurs among these three populations with physical barriers of Beijing city and Hutuo River, which potentially restricted the dispersal of the animal; (iii) the gene flow is negatively correlated with the geographic distance, while the genetic distance shows the positive correlation. Our results suggest that the effect of the physical barriers is conditional-dependent, including barrier capacity or individual potentially dispersal ability. Geographic distance also acts as an important factor affecting dispersal for the patchy distributed geographic populations. So, gene flow is effective, even at relatively long distances, in balancing the effect of geographic barrier in this study.

Personality and place.

PubMed

Gelade, Garry A

2013-02-01

This paper examines the distribution of national personality dimensions in geographical space. The relationship between geographical location and aggregate personality in a wide range of nations is quantified using spatial autocorrelation, and it is found that the personalities of nations that are geographical neighbours are more similar than those that are far apart. The five factors of both the Revised NEO Personality Inventory (NEO-PI-R) and the Big Five Inventory (BFI), all show a significant degree of spatial organization. The personality factors most strongly associated with geographical location are NEO-PI-R extraversion and BFI conscientiousness; both vary with position around the globe about as much as the physical climate. These findings support previous research suggesting associations between aggregate personality and geography, and imply that the sources of variation in national personality are themselves geographically organized. © 2012 The British Psychological Society.

Sex-biased dispersal and volcanic activities shaped phylogeographic patterns of extant Orangutans (genus: Pongo).

PubMed

Nater, Alexander; Nietlisbach, Pirmin; Arora, Natasha; van Schaik, Carel P; van Noordwijk, Maria A; Willems, Erik P; Singleton, Ian; Wich, Serge A; Goossens, Benoit; Warren, Kristin S; Verschoor, Ernst J; Perwitasari-Farajallah, Dyah; Pamungkas, Joko; Krützen, Michael

2011-08-01

The Southeast Asian Sunda archipelago harbors a rich biodiversity with a substantial proportion of endemic species. The evolutionary history of these species has been drastically influenced by environmental forces, such as fluctuating sea levels, climatic changes, and severe volcanic activities. Orangutans (genus: Pongo), the only Asian great apes, are well suited to study the relative impact of these forces due to their well-documented behavioral ecology, strict habitat requirements, and exceptionally slow life history. We investigated the phylogeographic patterns and evolutionary history of orangutans in the light of the complex geological and climatic history of the Sunda archipelago. Our study is based on the most extensive genetic sampling to date, covering the entire range of extant orangutan populations. Using data from three mitochondrial DNA (mtDNA) genes from 112 wild orangutans, we show that Sumatran orangutans, Pongo abelii, are paraphyletic with respect to Bornean orangutans (P. pygmaeus), the only other currently recognized species within this genus. The deepest split in the mtDNA phylogeny of orangutans occurs across the Toba caldera in northern Sumatra and, not as expected, between both islands. Until the recent past, the Toba region has experienced extensive volcanic activity, which has shaped the current phylogeographic patterns. Like their Bornean counterparts, Sumatran orangutans exhibit a strong, yet previously undocumented structuring into four geographical clusters. However, with 3.50 Ma, the Sumatran haplotypes have a much older coalescence than their Bornean counterparts (178 kya). In sharp contrast to the mtDNA data, 18 Y-chromosomal polymorphisms show a much more recent coalescence within Sumatra compared with Borneo. Moreover, the deep geographic structure evident in mtDNA is not reflected in the male population history, strongly suggesting male-biased dispersal. We conclude that volcanic activities have played an important role in the evolutionary history of orangutans and potentially of many other forest-dwelling Sundaland species. Furthermore, we demonstrate that a strong sex bias in dispersal can lead to conflicting patterns in uniparentally inherited markers even at a genus-wide scale, highlighting the need for a combined usage of maternally and paternally inherited marker systems in phylogenetic studies.

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.

PubMed

Di Giallonardo, Francesca; Geoghegan, Jemma L; Docherty, Douglas E; McLean, Robert G; Zody, Michael C; Qu, James; Yang, Xiao; Birren, Bruce W; Malboeuf, Christine M; Newman, Ruchi M; Ip, Hon S; Holmes, Edward C

2016-01-15

The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers. How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

COMPARISON OF GEOGRAPHIC CLASSIFICATION SCHEMES FOR MID-ATLANTIC STREAM FISH ASSEMBLAGES

EPA Science Inventory

Understanding the influence of geographic factors in structuring fish assemblages is crucial to developing a comprehensive assessment of stream conditions. We compared the classification strengths (CS) of geographic groups (ecoregions and catchments), stream order, and groups bas...

Geographical Variation in Community Divergence: Insights from Tropical Forest Monodominance by Ectomycorrhizal Trees.

PubMed

Fukami, Tadashi; Nakajima, Mifuyu; Fortunel, Claire; Fine, Paul V A; Baraloto, Christopher; Russo, Sabrina E; Peay, Kabir G

2017-08-01

Convergence occurs in both species traits and community structure, but how convergence at the two scales influences each other remains unclear. To address this question, we focus on tropical forest monodominance, in which a single, often ectomycorrhizal (EM) tree species occasionally dominates forest stands within a landscape otherwise characterized by diverse communities of arbuscular mycorrhizal (AM) trees. Such monodominance is a striking potential example of community divergence resulting in alternative stable states. However, it is observed only in some tropical regions. A diverse suite of AM and EM trees locally codominate forest stands elsewhere. We develop a hypothesis to explain this geographical difference using a simulation model of plant community assembly. Simulation results suggest that in a region with a few EM species (e.g., South America), EM trees experience strong selection for convergent traits that match the abiotic conditions of the environment. Consequently, EM species successfully compete against other species to form monodominant stands via positive plant-soil feedbacks. By contrast, in a region with many EM species (e.g., Southeast Asia), species maintain divergent traits because of complex plant-soil feedbacks, with no species having traits that enable monodominance. An analysis of plant trait data from Borneo and Peruvian Amazon was inconclusive. Overall, this work highlights the utility of geographical comparison in understanding the relationship between trait convergence and community convergence.

Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices

PubMed Central

Pellissier, Loïc; Oppliger, Anne; Hirzel, Alexandre H.; Savova-Bianchi, Dessislava; Mbayo, Guilain; Mascher, Fabio; Kellenberger, Stefan

2016-01-01

Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km2 along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities. PMID:26826229

Risk perception and public acceptance toward a highly protested Waste-to-Energy facility.

PubMed

Ren, Xiangyu; Che, Yue; Yang, Kai; Tao, Yun

2016-02-01

The application of Waste-to-Energy treatment in Municipal Solid Waste faces strong protest by local communities, especially in cities with high population densities. This study introduces insight into the public awareness, acceptance and risk perception toward Waste-to-Energy through a structured questionnaire survey around a Waste-to-Energy facility in Shanghai, China. The Dichotomous-Choice contingent valuation method was applied to study the willingness to accept of residents as an indicator of risk perception and tolerance. The factors influencing risk perception and the protest response choice were analyzed. The geographical distributions of the acceptance of Waste-to-Energy facility and protest response were explored using geographical information systems. The findings of the research indicated an encouraging vision of promoting Waste-to-Energy, considering its benefits of renewable energy and the conservation of land. A high percentage of protest willingness to accept (50.94%) was highlighted with the effect of income, opinion about Waste-to-Energy, gender and perceived impact. The fuzzy classification among people with different opinions on compensation (valid 0, positive or protest willingness to accept) revealed the existing yet rejected demand of compensation among protesters. Geographical distribution in the public attitude can also be observed. Finally significant statistical relation between knowledge and risk perception indicates the need of risk communication, as well as involving public into whole management process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Lack of congruence between morphometric evolution and genetic differentiation suggests a recent dispersal and local habitat adaptation of the Madeiran lizard Lacerta dugesii

PubMed Central

Brehm, António; Khadem, Mahnaz; Jesus, José; Andrade, Paula; Vicente, Luis

2001-01-01

Genetic differentiation among nine populations of the endemic lizard Lacerta dugesii Milne-Edwards 1829 (Lacertidae) from four groups of islands constituting the Archipelago of Madeira, was investigated by protein electrophoresis at 23 enzyme loci. Among twenty polymorphic loci, the total genetic diversity was due primarily to intra-population variation. The allele and genotypic frequencies among populations showed some heterogeneity, allowing the species to present a structuring pattern compatible with their geographical clustering. Some evidence suggests that selection acting on some loci in different ecological conditions may be responsible for the clustering of the populations studied. There was no apparent isolation effect expected under an "island" model of population divergence, and no correlation was found between genetic and geographic distances among populations. Morphological variation of the proposed three L. dugesii subspecies is not congruent with the allozyme analysis. This most probably suggests a rapid colonization of the islands followed by a strong effect of selection operating over the morphological characters used to define the subspecies. PMID:11742635

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae)

PubMed Central

Zhang, Yong-Hua; Wang, Ian J.; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-01-01

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors. PMID:27137438

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).

PubMed

Zhang, Yong-Hua; Wang, Ian J; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-05-03

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels - phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important - climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.

Immigrants Equilibrate Local Labor Markets: Evidence from the Great Recession*

PubMed Central

Cadena, Brian C.; Kovak, Brian K.

2016-01-01

This paper demonstrates that low-skilled Mexican-born immigrants’ location choices in the U.S. respond strongly to changes in local labor demand, and that this geographic elasticity helps equalize spatial differences in labor market outcomes for low-skilled native workers, who are much less responsive. We leverage the substantial geographic variation in employment losses that occurred during Great Recession, and our results confirm the standard finding that high-skilled populations are quite geographically responsive to employment opportunities while low-skilled populations are much less so. However, low-skilled immigrants, especially those from Mexico, respond even more strongly than high-skilled native-born workers. Moreover, we show that natives living in metro areas with a substantial Mexican-born population are insulated from the effects of local labor demand shocks compared to those in places with few Mexicans. The reallocation of the Mexican-born workforce reduced the incidence of local demand shocks on low-skilled natives’ employment outcomes by more than 50 percent. PMID:27551329

Enhancing robustness and immunization in geographical networks

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

Huang Liang; Department of Physics, Lanzhou University, Lanzhou 730000; Yang Kongqing

2007-03-15

We find that different geographical structures of networks lead to varied percolation thresholds, although these networks may have similar abstract topological structures. Thus, strategies for enhancing robustness and immunization of a geographical network are proposed. Using the generating function formalism, we obtain an explicit form of the percolation threshold q{sub c} for networks containing arbitrary order cycles. For three-cycles, the dependence of q{sub c} on the clustering coefficients is ascertained. The analysis substantiates the validity of the strategies with analytical evidence.

Spatial and temporal determinants of genetic structure in Gentianella bohemica

PubMed Central

Königer, Julia; Rebernig, Carolin A; Brabec, Jiří; Kiehl, Kathrin; Greimler, Josef

2012-01-01

The biennial plant Gentianella bohemica is a subendemic of the Bohemian Massif, where it occurs in seminatural grasslands. It has become rare in recent decades as a result of profound changes in land use. Using amplified fragment length polymorphisms (AFLP) fingerprint data, we investigated the genetic structure within and among populations of G. bohemica in Bavaria, the Czech Republic, and the Austrian border region. The aim of our study was (1) to analyze the genetic structure among populations and to discuss these findings in the context of present and historical patterns of connectivity and isolation of populations, (2) to analyze genetic structure among consecutive generations (cohorts of two consecutive years), and (3) to investigate relationships between intrapopulational diversity and effective population size (Ne) as well as plant traits. (1) The German populations were strongly isolated from each other (pairwise FST= 0.29–0.60) and from all other populations (FST= 0.24–0.49). We found a pattern of near panmixis among the latter (FST= 0.15–0.35) with geographical distance explaining only 8% of the genetic variance. These results were congruent with a principal coordinate analysis (PCoA) and analysis using STRUCTURE to identify genetically coherent groups. These findings are in line with the strong physical barrier and historical constraints, resulting in separation of the German populations from the others. (2) We found pronounced genetic differences between consecutive cohorts of the German populations (pairwise FST= 0.23 and 0.31), which can be explained by local population history (land use, disturbance). (3) Genetic diversity within populations (Shannon index, HSh) was significantly correlated with Ne (RS= 0.733) and reflected a loss of diversity due to several demographic bottlenecks. Overall, we found that the genetic structure in G. bohemica is strongly influenced by historical periods of high connectivity and isolation as well as by marked demographic fluctuations in declining populations. PMID:22822440

Internationalization as a Challenge for Geographical Education in Poland: Experience of a New Postgraduate Study "Cultural Industries in the Development Policies of Cities and Regions"

ERIC Educational Resources Information Center

Churski, Pawel; Motek, Pawel; Stryjakiewicz, Tadeusz; Cybal-Michalska, Agnieszka

2017-01-01

For many years internationalization has not been a strong point of geographical education in post-socialist countries, including Poland. Therefore, all attempts at intensifying it are a real challenge and good practices deserve dissemination. This paper seeks to present the organizational and programme assumptions of a new field of postgraduate…

Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula.

PubMed

Gómez, Africa; Montero-Pau, Javier; Lunt, David H; Serra, Manuel; Campillo, Sergi

2007-08-01

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long-distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration-drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these species, Brachionus manjavacas, in the Iberian Peninsula, where it often co-occurs with the morphologically similar species B. plicatilis sensu stricto. We obtained sequences from 233 individuals from diapausing eggs and clonal cultures from 16 lakes in the Iberian Peninsula, and a Tunisian lake. Two strongly supported deep mitochondrial DNA clades were found (A and B). Phylogenetic and nested clade analysis showed that clade A has a strong phylogeographical structure, with a strong similarity of phylogeographical patterns between B. manjavacas clade A and B. plicatilis s.s. These include (i) signatures of allopatric fragmentation between central and southern populations, and (ii) range expansions in the Iberian Peninsula, both likely to have occurred during the Pleistocene. We find evidence for a glacial refugium in the Guadiana basin. Clades A and B co-occurred in several of these lakes because of range expansion and secondary contact between both clades. The co-occurrence between B. plicatilis s.s. and B. manjavacas is not recent, and both species might have experienced similar environmental challenges during the Pleistocene. The strong correlation of genetic and geographical distance found suggests that historical events can lead to such correlation, mirroring the effects of 'isolation by distance' in equilibrium populations.

Exploring the Y Chromosomal Ancestry of Modern Panamanians.

PubMed

Grugni, Viola; Battaglia, Vincenza; Perego, Ugo Alessandro; Raveane, Alessandro; Lancioni, Hovirag; Olivieri, Anna; Ferretti, Luca; Woodward, Scott R; Pascale, Juan Miguel; Cooke, Richard; Myres, Natalie; Motta, Jorge; Torroni, Antonio; Achilli, Alessandro; Semino, Ornella

2015-01-01

Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama's population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.

Continental synchronicity of human influenza virus epidemics despite climactic variation

PubMed Central

Sullivan, Sheena; Barr, Ian

2018-01-01

The factors that determine the pattern and rate of spread of influenza virus at a continental-scale are uncertain. Although recent work suggests that influenza epidemics in the United States exhibit a strong geographical correlation, the spatiotemporal dynamics of influenza in Australia, a country and continent of approximately similar size and climate complexity but with a far smaller population, are not known. Using a unique combination of large-scale laboratory-confirmed influenza surveillance comprising >450,000 entries and genomic sequence data we determined the local-level spatial diffusion of this important human pathogen nationwide in Australia. We used laboratory-confirmed influenza data to characterize the spread of influenza virus across Australia during 2007–2016. The onset of established epidemics varied across seasons, with highly synchronized epidemics coinciding with the emergence of antigenically distinct viruses, particularly during the 2009 A/H1N1 pandemic. The onset of epidemics was largely synchronized between the most populous cities, even those separated by distances of >3000 km and those that experience vastly diverse climates. In addition, by analyzing global phylogeographic patterns we show that the synchronized dissemination of influenza across Australian cities involved multiple introductions from the global influenza population, coupled with strong domestic connectivity, rather than through the distinct radial patterns of geographic dispersal that are driven by work-flow transmission as observed in the United States. In addition, by comparing the spatial structure of influenza A and B, we found that these viruses tended to occupy different geographic regions, and peak in different seasons, perhaps indicative of moderate cross-protective immunity or viral interference effects. The highly synchronized outbreaks of influenza virus at a continental-scale revealed here highlight the importance of coordinated public health responses in the event of the emergence of a novel, human-to-human transmissible, virus. PMID:29324895

Exploring the Y Chromosomal Ancestry of Modern Panamanians

PubMed Central

Grugni, Viola; Battaglia, Vincenza; Perego, Ugo Alessandro; Raveane, Alessandro; Lancioni, Hovirag; Olivieri, Anna; Ferretti, Luca; Woodward, Scott R.; Pascale, Juan Miguel; Cooke, Richard; Myres, Natalie; Motta, Jorge; Torroni, Antonio; Achilli, Alessandro; Semino, Ornella

2015-01-01

Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations. PMID:26636572

Structure and application of an interface program between a geographic-information system and a ground-water flow model

USGS Publications Warehouse

Van Metre, P.C.

1990-01-01

A computer-program interface between a geographic-information system and a groundwater flow model links two unrelated software systems for use in developing the flow models. The interface program allows the modeler to compile and manage geographic components of a groundwater model within the geographic information system. A significant savings of time and effort is realized in developing, calibrating, and displaying the groundwater flow model. Four major guidelines were followed in developing the interface program: (1) no changes to the groundwater flow model code were to be made; (2) a data structure was to be designed within the geographic information system that follows the same basic data structure as the groundwater flow model; (3) the interface program was to be flexible enough to support all basic data options available within the model; and (4) the interface program was to be as efficient as possible in terms of computer time used and online-storage space needed. Because some programs in the interface are written in control-program language, the interface will run only on a computer with the PRIMOS operating system. (USGS)

High-resolution probing of inner core structure with seismic interferometry

NASA Astrophysics Data System (ADS)

Huang, Hsin-Hua; Lin, Fan-Chi; Tsai, Victor C.; Koper, Keith D.

2015-12-01

Increasing complexity of Earth's inner core has been revealed in recent decades as the global distribution of seismic stations has improved. The uneven distribution of earthquakes, however, still causes a biased geographical sampling of the inner core. Recent developments in seismic interferometry, which allow for the retrieval of core-sensitive body waves propagating between two receivers, can significantly improve ray path coverage of the inner core. In this study, we apply such earthquake coda interferometry to 1846 USArray stations deployed across the U.S. from 2004 through 2013. Clear inner core phases PKIKP2 and PKIIKP2 are observed across the entire array. Spatial analysis of the differential travel time residuals between the two phases reveals significant short-wavelength variation and implies the existence of strong structural variability in the deep Earth. A linear N-S trending anomaly across the middle of the U.S. may reflect an asymmetric quasi-hemispherical structure deep within the inner core with boundaries of 99°W and 88°E.

Comparison of population genetic patterns in two widespread freshwater mussels with contrasting life histories in western North America.

PubMed

Mock, K E; Brim Box, J C; Chong, J P; Furnish, J; Howard, J K

2013-12-01

We investigate population genetic structuring in Margaritifera falcata, a freshwater mussel native to western North America, across the majority of its geographical range. We find shallow rangewide genetic structure, strong population-level structuring and very low population diversity in this species, using both mitochondrial sequence and nuclear microsatellite data. We contrast these patterns with previous findings in another freshwater mussel species group (Anodonta californiensis/A. nuttalliana) occupying the same continental region and many of the same watersheds. We conclude that differences are likely caused by contrasting life history attributes between genera, particularly host fish requirements and hermaphroditism. Further, we demonstrate the occurrence of a 'hotspot' for genetic diversity in both groups of mussels, occurring in the vicinity of the lower Columbia River drainage. We suggest that stream hierarchy may be responsible for this pattern and may produce similar patterns in other widespread freshwater species. © 2013 John Wiley & Sons Ltd.

Australia's regional innovation systems: inter-industry interaction in innovative activities in three Australian territories

PubMed Central

Schütz, Marlies H.

2017-01-01

ABSTRACT Regional specifics reveal in differences in economic activity and structure, the institutional, socio-economic and cultural environment and not least in the capability of regions to create new knowledge and to generate innovations. Focusing on the regional level, this paper for three Australian territories (New South Wales, Victoria and Queensland) explores patterns of innovative activities in their private business sectors. Furthermore, these patterns are compared to specifics of each region's economic structure. We make use of input–output-based innovation flow networks, which are directed and weighted instead of binary. The value added of the proposed analysis is that we are able to trace a variety of different aspects related to the structure of innovative activities for each territory. It gets evident that mostly innovative activities in each territory are not strong in ‘niche’ branches but in fields of intense economic activity, signalising the high path-dependency of innovative activities in a specific geographical environment. PMID:29097849

Australia's regional innovation systems: inter-industry interaction in innovative activities in three Australian territories.

PubMed

Schütz, Marlies H

2017-07-03

Regional specifics reveal in differences in economic activity and structure, the institutional, socio-economic and cultural environment and not least in the capability of regions to create new knowledge and to generate innovations. Focusing on the regional level, this paper for three Australian territories (New South Wales, Victoria and Queensland) explores patterns of innovative activities in their private business sectors. Furthermore, these patterns are compared to specifics of each region's economic structure. We make use of input-output-based innovation flow networks, which are directed and weighted instead of binary. The value added of the proposed analysis is that we are able to trace a variety of different aspects related to the structure of innovative activities for each territory. It gets evident that mostly innovative activities in each territory are not strong in 'niche' branches but in fields of intense economic activity, signalising the high path-dependency of innovative activities in a specific geographical environment.

A search for stability gradients in North American breeding bird communities

USGS Publications Warehouse

Noon, B.R.; Dawson, D.K.; Kelly, J.P.

1985-01-01

To search for the existence of stability gradients in North American breeding land bird communities we operationally defined stability (after Jarvinen 1979) as year-to-year persistence in species composition and distribution of species abundances. From the census data for 174 study plots we derived nine indices that estimate the annual variability of species composition, the species abundance distribution, diversity, and breeding density. The resulting matrix of study plot by stability indices was used to estimate the correlation structure of the stability indices. The correlation matrix was, in turn, subjected to a principal components analysis to derive synthetic gradients of variation. We then searched for patterns of variation in these stability gradients associated with either geographic location or habitat type. Three independent principal component axes reproduced most of the variation in the initial data and were interpreted as gradients of variation in species turnover, diversity, and breeding abundance. Thus, the annual stability of community structure apparently responds independently to species and abundance variation. Despite the clarity of the derived gradients, few patterns emerged when the plots were ordinated by either habitat or geographic location. In general, grasslands showed greater annual variation in diversity than forested habitats, and, for some habitats, northern communities were less stable than more southern communities. However, few of these patterns were very strong, and we interpret them cautiously.

Geographic and socioeconomic variation in the onset of decline of coronary heart disease mortality in white women.

PubMed Central

Wing, S; Barnett, E; Casper, M; Tyroler, H A

1992-01-01

BACKGROUND. Regional, metropolitan, and socioeconomic factors related to the onset of decline of coronary heart disease (CHD) mortality among White women are reported. Such studies are important for planning population-level interventions. METHODS. Mortality data for 1962 to 1978 were used, to estimate the year of onset of decline. Ecological analyses of socioeconomic data from the US census were used to emphasize structural and organizational aspects of changes in disease, rather than as a substitute for an individual-level design. RESULTS. Onset of decline of CHD mortality among White women was estimated to have occurred by 1962 in 53% of 507 state economic areas (SEAs), ranging from 79% in the Northeast to 39% in the South. Metropolitan areas experienced earlier onset of decline than did nonmetropolitan areas. Average income, education, and occupational levels were highest in early onset areas and declined across onset categories. CONCLUSIONS. The results provide additional evidence for previously observed geographic and social patterns of CHD decline. Emphasis on structural economic factors determining the shape of the CHD epidemic curve does not detract from the medical importance of risk factors, but underscores the importance of community development to public health improvements. The results are consistent with the idea that the course of the CHD epidemic in the United States has been strongly influenced by socioeconomic development. PMID:1739148

Biogeography of Drosophila (Diptera: Drosophilidae) in East and Southeast Asia

PubMed Central

Robert Liu, Fu-Guo; Tsaur, Shun-Chern; Huang, Hsiao-Ting

2015-01-01

The causes of high biological diversity in biodiversity hotspots have long been a major subject of study in conservation biology. To investigate this matter, we conducted a phylogeographic study of five Drosophila (Diptera: Drosophilidae) species from East and Southeast Asia: Drosophila albomicans Duda, D. formosana Duda, D. immigrans Sturtevant, D. melanogaster Meigen, and D. simulans Sturtevant. We collected 185 samples from 28 localities in eight countries. From each collected individual, we sequenced the autosomal extra sex comb gene (esc) and seven mitochondrial genes, including nicotinamide adenine dinucleotide hydrate-reductase dehydrogenase subunit 4 (ND4), ND4L, tRNA-His, tRNA-Pro, tRNA-Thr, partial ND5, and partial ND6. Phylogenetic analyses using maximum- likelihood and Bayesian methods revealed interesting population structure and identified the existence of two distinct D. formosana lineages (Southeast Asian and Taiwanese populations). Genetic differentiation among groups of D. immigrans suggests the possibility of endemic speciation in Taiwan. In contrast, D. melanogaster remained one extensively large population throughout East and Southeast Asia, including nearby islets. A molecular clock was used to estimate divergence times, which were compared with past geographical events to infer evolutionary scenarios. Our findings suggest that interglacial periods may have caused population isolation, thus enhancing population differentiation more strongly for some of the Drosophila species. The population structure of each Drosophila species in East and Southeast Asia has been influenced by past geographic events. PMID:26078303

Synoptic-scale Rossby waves and the geographic distribution of lateral transport routes between the tropics and the extratropics in the lower stratosphere

NASA Astrophysics Data System (ADS)

Horinouchi, Takeshi; Sassi, Fabrizio; Boville, Byron A.

2000-11-01

Atmospheric transport between the tropics and the extratropics, in the lowest part of the stratosphere during Northern Hemisphere winter, is investigated. The role of synoptic-scale disturbances that propagate laterally into the tropics is examined using the middle atmosphere version of the National Center for Atmospheric Research Community Climate Model Version 3 general circulation model. In the lower stratosphere, synoptic-scale Rossby waves propagate vigorously from the northern (i.e., winter) extratropics through two ``westerly ducts,'' where the westerly zonal mean winds near the equator are favorable to Rossby wave propagation. The waves break in the westerly ducts and modify the mean potential vorticity (PV) structure to connect subtropical and equatorial regions of sharp PV gradients. Frequent wave breaking and the wave -induced PV structure create distinct routes where transport occurs vigorously between the tropics and the northern extratropics. Interhemispheric transport also occurs through regions associated with the westerly ducts. In the Southern (summer) Hemisphere lower stratosphere, synoptic-scale disturbances propagate mainly as ``tongues'' of PV elongated from extratropical disturbances. The transport between the tropics and the southern extratropics has a strong geographic preference but is dominated by the monsoon circulation, as was shown for the upper troposphere by Chen [1995]. PV tongues and other transient anomalies are of secondary importance.

Identifying Local Hotspots of Pediatric Chronic Diseases Using Emergency Department Surveillance

PubMed Central

Lee, David C.; Yi, Stella S.; Fong, Hiu-Fai; Athens, Jessica K.; Ravenell, Joseph E.; Sevick, Mary Ann; Wall, Stephen P.; Elbel, Brian

2016-01-01

Objective To use novel geographic methods and large-scale claims data to identify the local distribution of pediatric chronic diseases in New York City. Methods Using a 2009 all-payer emergency claims database, we identified the proportion of unique children aged 0 to 17 with diagnosis codes for specific medical and psychiatric conditions. As a proof of concept, we compared these prevalence estimates to traditional health surveys and registry data using the most geographically granular data available. In addition, we used home addresses to map local variation in pediatric disease burden. Results We identified 549,547 New York City children who visited an emergency department at least once in 2009. Though our sample included more publicly insured and uninsured children, we found moderate to strong correlations of prevalence estimates when compared to health surveys and registry data at pre-specified geographic levels. Strongest correlations were found for asthma and mental health conditions by county among younger children (0.88, p=0.05 and 0.99, p<0.01, respectively). Moderate correlations by neighborhood were identified for obesity and cancer (0.53 and 0.54, p<0.01). Among adolescents, correlations by health districts were strong for obesity (0.95, p=0.05), and depression estimates had a non-significant, but strong negative correlation with suicide attempts (−0.88, p=0.12). Using SaTScan, we also identified local hotspots of pediatric chronic disease. Conclusions For conditions easily identified in claims data, emergency department surveillance may help estimate pediatric chronic disease prevalence with higher geographic resolution. More studies are needed to investigate limitations of these methods and assess reliability of local disease estimates. What’s New This study demonstrated how emergency department surveillance may improve estimates of pediatric disease prevalence with higher geographic resolution. We identified 29% of New York City children with a single year of data and identified local hotspots of pediatric chronic diseases. PMID:28385326

Climate change alters stability and species potential interactions in a large marine ecosystem.

PubMed

Griffith, Gary P; Strutton, Peter G; Semmens, Jayson M

2018-01-01

We have little empirical evidence of how large-scale overlaps between large numbers of marine species may have altered in response to human impacts. Here, we synthesized all available distribution data (>1 million records) since 1992 for 61 species of the East Australian marine ecosystem, a global hot spot of ocean warming and continuing fisheries exploitation. Using a novel approach, we constructed networks of the annual changes in geographical overlaps between species. Using indices of changes in species overlap, we quantified changes in the ecosystem stability, species robustness, species sensitivity and structural keystone species. We then compared the species overlap indices with environmental and fisheries data to identify potential factors leading to the changes in distributional overlaps between species. We found that the structure of the ecosystem has changed with a decrease in asymmetrical geographical overlaps between species. This suggests that the ecosystem has become less stable and potentially more susceptible to environmental perturbations. Most species have shown a decrease in overlaps with other species. The greatest decrease in species overlap robustness and sensitivity to the loss of other species has occurred in the pelagic community. Some demersal species have become more robust and less sensitive. Pelagic structural keystone species, predominately the tunas and billfish, have been replaced by demersal fish species. The changes in species overlap were strongly correlated with regional oceanographic changes, in particular increasing ocean warming and the southward transport of warmer and saltier water with the East Australian Current, but less correlated with fisheries catch. Our study illustrates how large-scale multispecies distribution changes can help identify structural changes in marine ecosystems associated with climate change. © 2017 John Wiley & Sons Ltd.

Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

PubMed Central

Rosetti, Natalia; Remis, Maria Isabel

2012-01-01

Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss associated with recent anthropogenic fragmentation of the D. elongatus studied range. PMID:22859953

Shallow phylogeographic structuring of Vimba vimba across Europe suggests two distinct refugia during the last glaciation.

PubMed

Hänfling, B; Dümpelmann, C; Bogutskaya, N G; Brandl, R; Brändle, M

2009-12-01

Genetic variation and geographical structuring of vimba Vimba vimba were analysed across 26 sites (80 individuals) by means of mtDNA sequences (cyt b gene, mitochondrial control region) to localize hypothesized glacial refugia and to reconstruct postglacial recoloniation routes. Although genetic diversity among sequenced individuals was low, a combined analysis of the two sequenced fragments revealed a western (central and northern Europe: Danube, Elbe and lakes of Sweden) and an eastern clade (eastern Europe: Dnieper-South Bug, Don, Neman). Furthermore, a number of divergent ancestral haplotypes distributed around the Black and Caspian Seas became apparent. Mismatch analyses supported a sudden expansion model for the populations of the western clade between 50 and 10 000 bp. Overall, the study provides strong evidence for a northward and westward expansion of V. vimba from two refugial regions located in the Danubian drainage and the northern Pontic regions respectively.

Vertex centralities in input-output networks reveal the structure of modern economies

NASA Astrophysics Data System (ADS)

Blöchl, Florian; Theis, Fabian J.; Vega-Redondo, Fernando; Fisher, Eric O.'N.

2011-04-01

Input-output tables describe the flows of goods and services between the sectors of an economy. These tables can be interpreted as weighted directed networks. At the usual level of aggregation, they contain nodes with strong self-loops and are almost completely connected. We derive two measures of node centrality that are well suited for such networks. Both are based on random walks and have interpretations as the propagation of supply shocks through the economy. Random walk centrality reveals the vertices most immediately affected by a shock. Counting betweenness identifies the nodes where a shock lingers longest. The two measures differ in how they treat self-loops. We apply both to data from a wide set of countries and uncover salient characteristics of the structures of these national economies. We further validate our indices by clustering according to sectors’ centralities. This analysis reveals geographical proximity and similar developmental status.

Seismic anisotropy in the lowermost mantle near the Perm Anomaly

NASA Astrophysics Data System (ADS)

Long, Maureen D.; Lynner, Colton

2015-09-01

The lower mantle is dominated by two large structures with anomalously low shear wave velocities, known as Large Low-Shear Velocity Provinces (LLSVPs). Several studies have documented evidence for strong seismic anisotropy at the base of the mantle near the edges of the African LLSVP. Recent work has identified a smaller structure with similar low-shear wave velocities beneath Eurasia, dubbed the Perm Anomaly. Here we probe lowermost mantle anisotropy near the Perm Anomaly using the differential splitting of SKS and SKKS phases measured at stations in Europe. We find evidence for lowermost mantle anisotropy in the vicinity of the Perm Anomaly, with geographic trends hinting at lateral variations in anisotropy across the boundaries of the Perm Anomaly as well as across a previously unsampled portion of the African LLSVP border. Our observations suggest that deformation is concentrated at the boundaries of both the Perm Anomaly and the African LLSVP.

Have I Been a Data Scientist from the Start? Parallels from the Geographic Information Science Community in the Early 1990s

NASA Astrophysics Data System (ADS)

Wright, D. J.

2013-12-01

In the early 1990s the author came of age as the technology driving the geographic information system or GIS was beginning to successfully 'handle' geospatial data at a range of scales and formats, and a wide array of information technology products emerged from an expanding GIS industry. However, that small community struggled to reflect the diverse research efforts at play in understanding the deeper issues surrounding geospatial data, and the impediments to that effective use of that data. It was from this need that geographic information science or GIScience arose, to ensure in part that GIS did not fall into the trap of being a technology in search of applications, a one-time, one-off, non-intellectual 'bag of tricks' with no substantive theory underpinning it, and suitable only for a static period of time (e.g., Goodchild, 1992). The community has since debated the issue of "tool versus science' which has also played a role in defining GIS as an actual profession. In turn, GIS has contributed to "methodological versus substantive" questions in science, leading to understandings of how the Earth works versus how the Earth should look. In the author's experience, the multidimensional structuring and scaling data, with integrative and innovative approaches to analyzing, modeling, and developing extensive and spatial data from selected places on land and at sea, have revealed how theory and application are in no way mutually exclusive, and it may often be application that advances theory, rather than vice versa. Increasingly, both the system and science of geographic information have welcomed strong collaborations among computer scientists, information scientists, and domain scientists to solve complex scientific questions. As such, they have paralleled the emergence and acceptance of "data science." And now that we are squarely in an era of regional- to global-scale observation and simulation of the Earth, produce data that are too big, move too fast, and do not fit the structures and processing capacity of conventional database systems, and the author reflects on how the potential of the GIS/GIScience world to contribute to the training and professional advancement of data science.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

PubMed

Seth-Smith, H M B; Busó, Leonor Sánchez; Livingstone, M; Sait, M; Harris, S R; Aitchison, K D; Vretou, Evangelia; Siarkou, V I; Laroucau, K; Sachse, K; Longbottom, D; Thomson, N R

2017-05-04

Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on C. abortus. Our aim was to investigate a broad collection of European isolates of C. abortus, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics. Whole genome sequencing was performed on our collection of 57 C. abortus isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the C. abortus species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for C. trachomatis and C. psittaci. No recombination was identified within C. abortus, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied. The diversity within C. abortus appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of Chlamydia may demonstrate different evolutionary dynamics, and that the genome of C. abortus is highly stable.

Research on spatial economic structure for different economic sectors from a perspective of a complex network

NASA Astrophysics Data System (ADS)

Hu, Sen; Yang, Hualei; Cai, Boliang; Yang, Chunxia

2013-09-01

The economy system is a complex system, and the complex network is a powerful tool to study its complexity. Here we calculate the economic distance matrices based on annual GDP of nine economic sectors from 1995-2010 in 31 Chinese provinces and autonomous regions,1 then build several spatial economic networks through the threshold method and the Minimal Spanning Tree method. After the analysis on the structure of the networks and the influence of geographic distance, some conclusions are drawn. First, connectivity distribution of a spatial economic network does not follow the power law. Second, according to the network structure, nine economic sectors could be divided into two groups, and there is significant discrepancy of network structure between these two groups. Moreover, the influence of the geographic distance plays an important role on the structure of a spatial economic network, network parameters are changed with the influence of the geographic distance. At last, 2000 km is the critical value for geographic distance: for real estate and finance, the spearman’s rho with l<2000 is bigger than that with l>2000, and the case is opposite for other economic sectors.

Variation and genetic structure of Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations based on ISSR pattern

PubMed Central

2010-01-01

For a study of diversity and genetic structuring in Melipona quadrifasciata, 61 colonies were collected in eight locations in the state of Minas Gerais, Brazil. By means of PCR analysis, 119 ISSR bands were obtained, 80 (68%) being polymorphic. He and H B were 0.20 and 0.16, respectively. Two large groups were obtained by the UPGMA method, one formed by individuals from Januária, Urucuia, Rio Vermelho and Caeté and the other by individuals from São João Del Rei, Barbacena, Ressaquinha and Cristiano Otoni. The Φst and θB values were 0.65 and 0.58, respectively, thereby indicating high population structuring. UPGMA grouping did not reveal genetic structuring of M. quadrifasciata in function of the tergite stripe pattern. The significant correlation between dissimilarity values and geographic distances (r = 0.3998; p < 0.05) implies possible geographic isolation. The genetic differentiation in population grouping was probably the result of an interruption in gene flow, brought about by geographic barriers between mutually close geographical locations. Our results also demonstrate the potential of ISSR markers in the study of Melipona quadrifasciata population structuring, possibly applicable to the studies of other bee species. PMID:21637500

Variation and genetic structure of Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations based on ISSR pattern.

PubMed

Nascimento, Marcília A; Batalha-Filho, Henrique; Waldschmidt, Ana M; Tavares, Mara G; Campos, Lucio A O; Salomão, Tânia M F

2010-04-01

For a study of diversity and genetic structuring in Melipona quadrifasciata, 61 colonies were collected in eight locations in the state of Minas Gerais, Brazil. By means of PCR analysis, 119 ISSR bands were obtained, 80 (68%) being polymorphic. H(e) and H (B) were 0.20 and 0.16, respectively. Two large groups were obtained by the UPGMA method, one formed by individuals from Januária, Urucuia, Rio Vermelho and Caeté and the other by individuals from São João Del Rei, Barbacena, Ressaquinha and Cristiano Otoni. The Φst and θ(B) values were 0.65 and 0.58, respectively, thereby indicating high population structuring. UPGMA grouping did not reveal genetic structuring of M. quadrifasciata in function of the tergite stripe pattern. The significant correlation between dissimilarity values and geographic distances (r = 0.3998; p < 0.05) implies possible geographic isolation. The genetic differentiation in population grouping was probably the result of an interruption in gene flow, brought about by geographic barriers between mutually close geographical locations. Our results also demonstrate the potential of ISSR markers in the study of Melipona quadrifasciata population structuring, possibly applicable to the studies of other bee species.

Dominant predators mediate the impact of habitat size on trophic structure in bromeliad invertebrate communities.

PubMed

Petermann, Jana S; Farjalla, Vinicius F; Jocque, Merlijn; Kratina, Pavel; MacDonald, A Andrew M; Marino, Nicholas A C; De Omena, Paula M; Piccoli, Gustavo C O; Richardson, Barbara A; Richardson, Michael J; Romero, Gustavo Q; Videla, Martin; Srivastava, Diane S

2015-02-01

Local habitat size has been shown to influence colonization and extinction processes of species in patchy environments. However, species differ in body size, mobility, and trophic level, and may not respond in the same way to habitat size. Thus far, we have a limited understanding of how habitat size influences the structure of multitrophic communities and to what extent the effects may be generalizable over a broad geographic range. Here, we used water-filled bromeliads of different sizes as a natural model system to examine the effects of habitat size on the trophic structure of their inhabiting invertebrate communities. We collected composition and biomass data from 651 bromeliad communities from eight sites across Central and South America differing in environmental conditions, species pools, and the presence of large-bodied odonate predators. We found that trophic structure in the communities changed dramatically with changes in habitat (bromeliad) size. Detritivore : resource ratios showed a consistent negative relationship with habitat size across sites. In contrast, changes in predator: detritivore (prey) ratios depended on the presence of odonates as dominant predators in the regional pool. At sites without odonates, predator: detritivore biomass ratios decreased with increasing habitat size. At sites with odonates, we found odonates to be more frequently present in large than in small bromeliads, and predator: detritivore biomass ratios increased with increasing habitat size to the point where some trophic pyramids became inverted. Our results show that the distribution of biomass amongst food-web levels depends strongly on habitat size, largely irrespective of geographic differences in environmental conditions or detritivore species compositions. However, the presence of large-bodied predators in the regional species pool may fundamentally alter this relationship between habitat size and trophic structure. We conclude that taking into account the response and multitrophic effects of dominant, mobile species may be critical when predicting changes in community structure along a habitat-size gradient.

Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici

PubMed Central

Ali, Sajid; Gladieux, Pierre; Leconte, Marc; Gautier, Angélique; Justesen, Annemarie F.; Hovmøller, Mogens S.; Enjalbert, Jérôme; de Vallavieille-Pope, Claude

2014-01-01

Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen. PMID:24465211

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

USGS Publications Warehouse

Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

2008-01-01

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

The roles of calving migration and climate change in the formation of the weak genetic structure in the Tibetan antelope (Pantholops hodgsonii).

PubMed

Chen, Jiarui; Lin, Gonghua; Qin, Wen; Yan, Jingyan; Zhang, Tongzuo; Su, Jianping

2018-05-31

Geographical barriers and distance can reduce gene exchange among animals, resulting in genetic divergence of geographically isolated populations. The habitats of Tibetan antelope (Pantholops hodgsonii) has a geographical range of approximately 1,600 km across the Qinghai-Tibet Plateau (QTP) with a series tall mountains and big rivers. However, previously studies indicated that there was little genetic differentiation among their geographically delineated populations. To better understand the genetic structure of P. hodgsonii populations, we collected 145 samples from the three major calving regions considering their various calving grounds and migration routes. We used a combination of mitochondrial sequences (Cyt b, ATPase, D-loop and COX I) to investigate the genetic structure and the evolutionary divergence of the populations. Significant, albeit weak, genetic differentiation was detected among the three geographical populations. Analysis of the genetic divergence process revealed that the animals gradually entered into a period of rapid genetic differentiation since approximately 60,000 years ago. The calving migration of P. hodgsonii cannot be the main cause of their weak genetic structure since such cannot fully homogenize the genetic pool. Instead, the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Identifying and modeling the structural discontinuities of human interactions

NASA Astrophysics Data System (ADS)

Grauwin, Sebastian; Szell, Michael; Sobolevsky, Stanislav; Hövel, Philipp; Simini, Filippo; Vanhoof, Maarten; Smoreda, Zbigniew; Barabási, Albert-László; Ratti, Carlo

2017-04-01

The idea of a hierarchical spatial organization of society lies at the core of seminal theories in human geography that have strongly influenced our understanding of social organization. Along the same line, the recent availability of large-scale human mobility and communication data has offered novel quantitative insights hinting at a strong geographical confinement of human interactions within neighboring regions, extending to local levels within countries. However, models of human interaction largely ignore this effect. Here, we analyze several country-wide networks of telephone calls - both, mobile and landline - and in either case uncover a systematic decrease of communication induced by borders which we identify as the missing variable in state-of-the-art models. Using this empirical evidence, we propose an alternative modeling framework that naturally stylizes the damping effect of borders. We show that this new notion substantially improves the predictive power of widely used interaction models. This increases our ability to understand, model and predict social activities and to plan the development of infrastructures across multiple scales.

Identifying and modeling the structural discontinuities of human interactions

PubMed Central

Grauwin, Sebastian; Szell, Michael; Sobolevsky, Stanislav; Hövel, Philipp; Simini, Filippo; Vanhoof, Maarten; Smoreda, Zbigniew; Barabási, Albert-László; Ratti, Carlo

2017-01-01

The idea of a hierarchical spatial organization of society lies at the core of seminal theories in human geography that have strongly influenced our understanding of social organization. Along the same line, the recent availability of large-scale human mobility and communication data has offered novel quantitative insights hinting at a strong geographical confinement of human interactions within neighboring regions, extending to local levels within countries. However, models of human interaction largely ignore this effect. Here, we analyze several country-wide networks of telephone calls - both, mobile and landline - and in either case uncover a systematic decrease of communication induced by borders which we identify as the missing variable in state-of-the-art models. Using this empirical evidence, we propose an alternative modeling framework that naturally stylizes the damping effect of borders. We show that this new notion substantially improves the predictive power of widely used interaction models. This increases our ability to understand, model and predict social activities and to plan the development of infrastructures across multiple scales. PMID:28443647

Identifying and modeling the structural discontinuities of human interactions.

PubMed

Grauwin, Sebastian; Szell, Michael; Sobolevsky, Stanislav; Hövel, Philipp; Simini, Filippo; Vanhoof, Maarten; Smoreda, Zbigniew; Barabási, Albert-László; Ratti, Carlo

2017-04-26

The idea of a hierarchical spatial organization of society lies at the core of seminal theories in human geography that have strongly influenced our understanding of social organization. Along the same line, the recent availability of large-scale human mobility and communication data has offered novel quantitative insights hinting at a strong geographical confinement of human interactions within neighboring regions, extending to local levels within countries. However, models of human interaction largely ignore this effect. Here, we analyze several country-wide networks of telephone calls - both, mobile and landline - and in either case uncover a systematic decrease of communication induced by borders which we identify as the missing variable in state-of-the-art models. Using this empirical evidence, we propose an alternative modeling framework that naturally stylizes the damping effect of borders. We show that this new notion substantially improves the predictive power of widely used interaction models. This increases our ability to understand, model and predict social activities and to plan the development of infrastructures across multiple scales.

Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy.

PubMed

du Toit, Nina; van Vuuren, Bettine Jansen; Matthee, Sonja; Matthee, Conrad A

2012-10-01

Within southern Africa, a link between past climatic changes and faunal diversification has been hypothesized for a diversity of taxa. To test the hypothesis that evolutionary divergences may be correlated to vegetation changes (induced by changes in climate), we selected the widely distributed four-striped mouse, Rhabdomys, as a model. Two species are currently recognized, the mesic-adapted R. dilectus and arid-adapted R. pumilio. However, the morphology-based taxonomy and the distribution boundaries of previously described subspecies remain poorly defined. The current study, which spans seven biomes, focuses on the spatial genetic structure of the arid-adapted R. pumilio (521 specimens from 31 localities), but also includes limited sampling of the mesic-adapted R. dilectus (33 specimens from 10 localities) to act as a reference for interspecific variation within the genus. The mitochondrial COI gene and four nuclear introns (Eef1a1, MGF, SPTBN1, Bfib7) were used for the construction of gene trees. Mitochondrial DNA analyses indicate that Rhabdomys consists of four reciprocally monophyletic, geographically structured clades, with three distinct lineages present within the arid-adapted R. pumilio. These monophyletic lineages differ by at least 7.9% (±0.3) and these results are partly confirmed by a multilocus network of the combined nuclear intron dataset. Ecological niche modeling in MaxEnt supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that the geographic clades diverged between 3.09 and 4.30Ma, supporting the hypothesis that the radiation within the genus coincides with paleoclimatic changes (and the establishment of the biomes) characterizing the Miocene-Pliocene boundary. Marked genetic divergence at the mitochondrial DNA level, coupled with strong nuclear and mtDNA signals of non-monophyly of R. pumilio, support the notion that a taxonomic revision of the genus is needed. Copyright © 2012 Elsevier Inc. All rights reserved.

Genetic structure of Flores island (Azores, Portugal) in the 19th century and in the present day: evidence from surname analysis.

PubMed

Santos, Cristina; Abade, Augusto; Cantons, Jordi; Mayer, Francine M; Aluja, M Pilar; Lima, Manuela

2005-06-01

The island of Flores is the most westerly of the Azores archipelago (Portugal). Despite its marked geographic isolation and reduced population size, biodemographic and genetic studies conducted so far do not support the idea that its population constitutes a genetic isolate. In this study we conducted a surname analysis of the Flores population for two time periods: the second half of the 19th century and the present day. Our main purposes were (1) to biodemographically and genetically characterize the island, taking into account the strong reduction in population observed from the middle of the 19th century to the present day; and (2) to analyze the influence that the effective population size and geographic distance have on the genetic structure of populations. For both periods analyzed, all indicators of diversity revealed a high level of surname diversity. Our results are in accordance with the diversity estimates obtained from both monoparental genetic markers located in the Y chromosome and frequencies of mtDNA haplogroups. Contrary to what could be expected, considering the strong reduction of population in the last 150 years, we observed that diversity was maintained and that microdifferentiation decreased. Both observations support a higher openness of parishes as a consequence of the increase in communication routes. From the first to the second period analyzed, a change in surname composition is evident, although the more frequent surnames in Flores are almost the same for both periods and some of them are reported to be surnames present in the first settlers of Flores. This result testifies to the impact of founders on the present-day gene pool of Flores island and allows us to infer that the genetic characterization of the present-day population of Flores could provide reliable information about the history of the peopling of the Azores.

Disparities in Temporal and Geographic Patterns of Declining Heart Disease Mortality by Race and Sex in the United States, 1973-2010.

PubMed

Vaughan, Adam S; Quick, Harrison; Pathak, Elizabeth B; Kramer, Michael R; Casper, Michele

2015-12-15

Examining small-area differences in the strength of declining heart disease mortality by race and sex provides important context for current racial and geographic disparities and identifies localities that could benefit from targeted interventions. We identified and described temporal trends in declining county-level heart disease mortality by race, sex, and geography between 1973 and 2010. Using a Bayesian hierarchical model, we estimated age-adjusted mortality with diseases of the heart listed as the underlying cause for 3099 counties. County-level percentage declines were calculated by race and sex for 3 time periods (1973-1985, 1986-1997, 1998-2010). Strong declines were statistically faster or no different than the total national decline in that time period. We observed county-level race-sex disparities in heart disease mortality trends. Continual (from 1973 to 2010) strong declines occurred in 73.2%, 44.6%, 15.5%, and 17.3% of counties for white men, white women, black men, and black women, respectively. Delayed (1998-2010) strong declines occurred in 15.4%, 42.0%, 75.5%, and 76.6% of counties for white men, white women, black men, and black women, respectively. Counties with the weakest patterns of decline were concentrated in the South. Since 1973, heart disease mortality has declined substantially for these race-sex groups. Patterns of decline differed by race and geography, reflecting potential disparities in national and local drivers of these declines. Better understanding of racial and geographic disparities in the diffusion of heart disease prevention and treatment may allow us to find clues to progress toward racial and geographic equity in heart disease mortality. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

Opportunities Seized and Squandered: An Analysis of Joint Union and Confederate Operations at New Madrid and Island Number Ten

DTIC Science & Technology

2016-06-10

install a command structure , and identify strategies for their geographic commanders. In the Western Theater of the war, both Northern and Southern...Federal and Confederate militaries had to mobilize forces, install a command structure , and identify strategies for their geographic commanders. In...Navy officers avoided these operations with their intermittent periods of importance. The lack of an enduring force structure and a consistent

Evaluating Progression in Students' Relational Thinking While Working on Tasks with Geospatial Technologies

ERIC Educational Resources Information Center

Favier, Tim; Van Der Schee, Joop

2014-01-01

One of the facets of geographic literacy is the ability to think in a structured way about geographic relationships. Geospatial technologies offer many opportunities to stimulate students' geographic relational thinking. The question is: How can these opportunities be effectuated? This paper discusses the results of a process-oriented experiment…

Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine

Treesearch

Anna W. Schoettle; Betsy A. Goodrich; Valerie Hipkins; Christopher Richards; Julie Kray

2012-01-01

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites...

Relative importance of pollen and seed dispersal across a Neotropical mountain landscape for an epiphytic orchid.

PubMed

Kartzinel, Tyler R; Shefferson, Richard P; Trapnell, Dorset W

2013-12-01

Populations of many species are isolated within narrow elevation bands of Neotropical mountain habitat, and how well dispersal maintains genetic connectivity is unknown. We asked whether genetic structure of an epiphytic orchid, Epidendrum firmum, corresponds to gaps between Costa Rican mountain ranges, and how these gaps influence pollen and seed flow. We predicted that significant genetic structure exists among mountain ranges due to different colonization histories and limited gene flow. Furthermore, we predicted that pollen movement contributes more to gene flow than seeds because seeds are released into strong winds perpendicular to the narrow northwest-southeast species distribution, while the likely pollinators are strong fliers. Individuals from 12 populations and three mountain ranges were genotyped with nuclear microsatellites (nDNA) and chloroplast sequences (cpDNA). Genetic diversity was high for both markers, while nDNA genetic structure was low (FSTn  = 0.020) and cpDNA structure was moderate (FSTc  = 0.443). Significant cpDNA barriers occurred within and among mountain ranges, but nDNA barriers were not significant after accounting for geographic distance. Consistent with these contrasting patterns of genetic structure, pollen contributes substantially more to gene flow among populations than seed (mp /ms  = 46). Pollinators mediated extensive gene flow, eroding nDNA colonization footprints, while seed flow was comparatively limited, possibly due to directional prevailing winds across linearly distributed populations. Dispersal traits alone may not accurately inform predictions about gene flow or genetic structure, supporting the need for research into the potentially crucial role of pollinators and landscape context in gene flow among isolated populations. © 2013 John Wiley & Sons Ltd.

Housing arrangement and location determine the likelihood of housing loss due to wildfire

USGS Publications Warehouse

Syphard, Alexandra D.; Keeley, Jon E.; Massada, Avi Bar; Brennan, Teresa J.; Radeloff, Volker C.

2012-01-01

Surging wildfires across the globe are contributing to escalating residential losses and have major social, economic, and ecological consequences. The highest losses in the U.S. occur in southern California, where nearly 1000 homes per year have been destroyed by wildfires since 2000. Wildfire risk reduction efforts focus primarily on fuel reduction and, to a lesser degree, on house characteristics and homeowner responsibility. However, the extent to which land use planning could alleviate wildfire risk has been largely missing from the debate despite large numbers of homes being placed in the most hazardous parts of the landscape. Our goal was to examine how housing location and arrangement affects the likelihood that a home will be lost when a wildfire occurs. We developed an extensive geographic dataset of structure locations, including more than 5500 structures that were destroyed or damaged by wildfire since 2001, and identified the main contributors to property loss in two extensive, fire-prone regions in southern California. The arrangement and location of structures strongly affected their susceptibility to wildfire, with property loss most likely at low to intermediate structure densities and in areas with a history of frequent fire. Rates of structure loss were higher when structures were surrounded by wildland vegetation, but were generally higher in herbaceous fuel types than in higher fuel-volume woody types. Empirically based maps developed using housing pattern and location performed better in distinguishing hazardous from non-hazardous areas than maps based on fuel distribution. The strong importance of housing arrangement and location indicate that land use planning may be a critical tool for reducing fire risk, but it will require reliable delineations of the most hazardous locations.

Geographic variation in resistance to nectar robbing and consequences for pollination.

PubMed

Adler, Lynn S; Leege, Lissa M; Irwin, Rebecca E

2016-10-01

Floral evolution is frequently ascribed to selection by pollinators, but may also be shaped by antagonists. However, remarkably few studies have examined geographic mosaics in resistance to floral antagonists or the consequences for other floral interactions. Gelsemium sempervirens experiences frequent nectar robbing in northern Georgia, but rarely in southern Georgia. We conducted common-garden experiments in both locations using genotypes from each region and measured robbing, pollinator attraction, floral attractive and defensive traits, and plant reproduction. Nectar robbing was more than four times higher in the north vs. south, and pollinator visits did not differ between gardens. Across both gardens, northern genotypes were half as likely to be nectar-robbed but received half as many pollinator visits as southern genotypes, suggesting evolution of resistance to robbing at a cost of reduced pollinator attraction. Plant-level traits, such as height and number of flowers, were more closely associated with resistance to robbing than floral size, shape, or chemistry. Northern genotypes had lower female and estimated male reproduction compared to southern genotypes at both locations, which could be due to costs of resistance to nectar robbing, or costs of adaptations to other biotic or abiotic differences between regions. Our study indicates that geographic variation can play a strong role structuring interactions with floral antagonists and mutualists and provides evidence consistent with the hypothesis that local resistance to nectar robbing imposes costs in terms of decreased pollinator attraction and reproduction. © 2016 Botanical Society of America.

Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices.

PubMed

Pellissier, Loïc; Oppliger, Anne; Hirzel, Alexandre H; Savova-Bianchi, Dessislava; Mbayo, Guilain; Mascher, Fabio; Kellenberger, Stefan; Niculita-Hirzel, Hélène

2016-01-29

Chronic exposure to airborne fungi has been associated with different respiratory symptoms and pathologies in occupational populations, such as grain workers. However, the homogeneity in the fungal species composition of these bioaerosols on a large geographical scale and the different drivers that shape these fungal communities remain unclear. In this study, the diversity of fungi in grain dust and in the aerosols released during harvesting was determined across 96 sites at a geographical scale of 560 km(2) along an elevation gradient of 500 m by tag-encoded 454 pyrosequencing of the internal transcribed spacer (ITS) sequences. Associations between the structure of fungal communities in the grain dust and different abiotic (farming system, soil characteristics, and geographic and climatic parameters) and biotic (wheat cultivar and previous crop culture) factors were explored. These analyses revealed a strong relationship between the airborne and grain dust fungal communities and showed the presence of allergenic and mycotoxigenic species in most samples, which highlights the potential contribution of these fungal species to work-related respiratory symptoms of grain workers. The farming system was the major driver of the alpha and beta phylogenetic diversity values of fungal communities. In addition, elevation and soil CaCO3 concentrations shaped the alpha diversity, whereas wheat cultivar, cropping history, and the number of freezing days per year shaped the taxonomic beta diversity of these communities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Maternal-child overweight/obesity and undernutrition in Kenya: a geographic analysis.

PubMed

Pawloski, Lisa R; Curtin, Kevin M; Gewa, Constance; Attaway, David

2012-11-01

The purpose of the study was to examine geographic relationships of nutritional status (BMI), including underweight, overweight and obesity, among Kenyan mothers and children. Spatial relationships were examined concerning BMI of the mothers and BMI-for-age percentiles of their children. These included spatial statistical measures of the clustering of segments of the population, in addition to inspection of co-location of significant clusters. Rural and urban areas of Kenya, including the cities of Nairobi and Mombasa, and the Kisumu region. Mother-child pairs from Demographic and Health Survey data including 1541 observations in 2003 and 1592 observations in 2009. These mother-child pairs were organized into 399 locational clusters. There is extremely strong evidence that high BMI values exhibit strong spatial clustering. There were co-locations of overweight mothers and overweight children only in the Nairobi region, while both underweight mothers and children tended to cluster in rural areas. In Mombasa clusters of overweight mothers were associated with normal-weight children, while in the Kisumu region clusters of overweight children were associated with normal-weight mothers. These findings show there is geographic variability as well as some defined patterns concerning the distribution of malnutrition among mothers and children in Kenya, and suggest the need for further geographic analyses concerning the potential factors which influence nutritional status in this population. In addition, the methods used in this research may be easily applied to other Demographic and Health Survey data in order to begin to understand the geographic determinants of health in low-income countries.

Analysis of co-occurrence toponyms in web pages based on complex networks

NASA Astrophysics Data System (ADS)

Zhong, Xiang; Liu, Jiajun; Gao, Yong; Wu, Lun

2017-01-01

A large number of geographical toponyms exist in web pages and other documents, providing abundant geographical resources for GIS. It is very common for toponyms to co-occur in the same documents. To investigate these relations associated with geographic entities, a novel complex network model for co-occurrence toponyms is proposed. Then, 12 toponym co-occurrence networks are constructed from the toponym sets extracted from the People's Daily Paper documents of 2010. It is found that two toponyms have a high co-occurrence probability if they are at the same administrative level or if they possess a part-whole relationship. By applying complex network analysis methods to toponym co-occurrence networks, we find the following characteristics. (1) The navigation vertices of the co-occurrence networks can be found by degree centrality analysis. (2) The networks express strong cluster characteristics, and it takes only several steps to reach one vertex from another one, implying that the networks are small-world graphs. (3) The degree distribution satisfies the power law with an exponent of 1.7, so the networks are free-scale. (4) The networks are disassortative and have similar assortative modes, with assortative exponents of approximately 0.18 and assortative indexes less than 0. (5) The frequency of toponym co-occurrence is weakly negatively correlated with geographic distance, but more strongly negatively correlated with administrative hierarchical distance. Considering the toponym frequencies and co-occurrence relationships, a novel method based on link analysis is presented to extract the core toponyms from web pages. This method is suitable and effective for geographical information retrieval.

Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species.

PubMed

Young, Emma F; Belchier, Mark; Hauser, Lorenz; Horsburgh, Gavin J; Meredith, Michael P; Murphy, Eugene J; Pascoal, Sonia; Rock, Jennifer; Tysklind, Niklas; Carvalho, Gary R

2015-06-01

Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.

Technologies and standards in the information systems of the soil-geographic database of Russia

NASA Astrophysics Data System (ADS)

Golozubov, O. M.; Rozhkov, V. A.; Alyabina, I. O.; Ivanov, A. V.; Kolesnikova, V. M.; Shoba, S. A.

2015-01-01

The achievements, problems, and challenges of the modern stage of the development of the Soil-Geographic Database of Russia (SGDBR) and the history of this project are outlined. The structure of the information system of the SGDBR as an internet-based resource to collect data on soil profiles and to integrate the geographic and attribute databases on the same platform is described. The pilot project in Rostov oblast illustrates the inclusion of regional information in the SGDBR and its application for solving practical problems. For the first time in Russia, the GeoRSS standard based on the structured hypertext representation of the geographic and attribute information has been applied in the state system for the agromonitoring of agricultural lands in Rostov oblast and information exchange through the internet.

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

Environmental versus geographical determinants of genetic structure in two subalpine conifers.

PubMed

Mosca, Elena; González-Martínez, Santiago C; Neale, David B

2014-01-01

Alpine ecosystems are facing rapid human-induced environmental changes, and so more knowledge about tree adaptive potential is needed. This study investigated the relative role of isolation by distance (IBD) versus isolation by adaptation (IBA) in explaining population genetic structure in Abies alba and Larix decidua, based on 231 and 233 single nucleotide polymorphisms (SNPs) sampled across 36 and 22 natural populations, respectively, in the Alps and Apennines. Genetic structure was investigated for both geographical and environmental groups, using analysis of molecular variance (AMOVA). For each species, nine environmental groups were defined using climate variables selected from a multiple factor analysis. Complementary methods were applied to identify outliers based on these groups, and to test for IBD versus IBA. AMOVA showed weak but significant genetic structure for both species, with higher values in L. decidua. Among the potential outliers detected, up to two loci were found for geographical groups and up to seven for environmental groups. A stronger effect of IBD than IBA was found in both species; nevertheless, once spatial effects had been removed, temperature and soil in A. alba, and precipitation in both species, were relevant factors explaining genetic structure. Based on our findings, in the Alpine region, genetic structure seems to be affected by both geographical isolation and environmental gradients, creating opportunities for local adaptation. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Onondaga Lake Watershed – A Geographic Information System Project Phase I – Needs assessment and spatial data framework

USGS Publications Warehouse

Freehafer, Douglas A.; Pierson, Oliver

2004-01-01

In the fall of 2002, the Onondaga Lake Partnership (OLP) formed a Geographic Information System (GIS) Planning Committee to begin the process of developing a comprehensive watershed geographic information system for Onondaga Lake. The goal of the Onondaga Lake Partnership geographic information system is to integrate the various types of spatial data used for scientific investigations, resource management, and planning and design of improvement projects in the Onondaga Lake Watershed. A needs-assessment survey was conducted and a spatial data framework developed to support the Onondaga Lake Partnership use of geographic information system technology. The design focused on the collection, management, and distribution of spatial data, maps, and internet mapping applications. A geographic information system library of over 100 spatial datasets and metadata links was assembled on the basis of the results of the needs assessment survey. Implementation options were presented, and the Geographic Information System Planning Committee offered recommendations for the management and distribution of spatial data belonging to Onondaga Lake Partnership members. The Onondaga Lake Partnership now has a strong foundation for building a comprehensive geographic information system for the Onondaga Lake watershed. The successful implementation of a geographic information system depends on the Onondaga Lake Partnership’s determination of: (1) the design and plan for a geographic information system, including the applications and spatial data that will be provided and to whom, (2) the level of geographic information system technology to be utilized and funded, and (3) the institutional issues of operation and maintenance of the system.

Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast

PubMed Central

El-Sibai, Mirvat; Platt, Daniel E.; Haber, Marc; Xue, Yali; Youhanna, Sonia C.; Wells, R. Spencer; Izaabel, Hassan; Sanyoura, May F.; Harmanani, Haidar; Bonab, Maziar Ashrafian; Behbehani, Jaafar; Hashwa, Fuad; Tyler-Smith, Chris; Zalloua, Pierre A.

2012-01-01

We have examined the male-specific phylogeography of the Levant and its surroundings by analyzing Y-chromosomal haplogroup distributions using 5,874 samples (885 new) from 23 countries. The diversity within some of these haplogroups was also examined. The Levantine populations showed clustering in SNP and STR analyses when considered against a broad Middle-East and North African background. However, we also found a coastal-inland, east-west pattern of diversity and frequency distribution in several haplogroups within the small region of the Levant. Since estimates of effective population size are similar in the two regions, this strong pattern is likely to have arisen mainly from differential migrations, with different lineages introduced from the east and west. PMID:19686289

Coastal Geographic Structures in Coastal-Marine Environmental Management

NASA Astrophysics Data System (ADS)

Baklanov, P. Ya.; Ganzei, K. S.; Ermoshin, V. V.

2018-01-01

It has been proposed to distinguish the coastal geographic structures consisting of a spatial combination of three interconnected and mutually conditioned parts (coastal-territorial, coastal, coastal-marine), which are interlinked with each other by the cumulative effect of real-energy flows. Distinguishing specific resource features of the coastal structures, by which they play a connecting role in the complex coastalmarine management, has been considered. The main integral resource feature of the coastal structures is their connecting functions, which form transitional parts mutually connecting the coastal-territorial and coastalmarine environmental management.

Geocoded data structures and their applications to Earth science investigations

NASA Technical Reports Server (NTRS)

Goldberg, M.

1984-01-01

A geocoded data structure is a means for digitally representing a geographically referenced map or image. The characteristics of representative cellular, linked, and hybrid geocoded data structures are reviewed. The data processing requirements of Earth science projects at the Goddard Space Flight Center and the basic tools of geographic data processing are described. Specific ways that new geocoded data structures can be used to adapt these tools to scientists' needs are presented. These include: expanding analysis and modeling capabilities; simplifying the merging of data sets from diverse sources; and saving computer storage space.

Recurrent hybridization and recent origin obscure phylogenetic relationships within the ‘white-headed’ gull (Larus sp.) complex

USGS Publications Warehouse

Sonsthagen, Sarah A.; Wilson, Robert E.; Chesser, Terry; Pons, Jean-Marc; Crochet, Pierre-Andre; Driscoll, Amy; Dove, Carla

2016-01-01

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian.

PubMed

Griffiths, Sarah M; Harrison, Xavier A; Weldon, Ché; Wood, Michael D; Pretorius, Abigail; Hopkins, Kevin; Fox, Graeme; Preziosi, Richard F; Antwis, Rachael E

2018-06-25

Amphibian populations worldwide are at risk of extinction from infectious diseases, including chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Amphibian cutaneous microbiomes interact with Bd and can confer protective benefits to the host. The composition of the microbiome itself is influenced by many environment- and host-related factors. However, little is known about the interacting effects of host population structure, genetic variation and developmental stage on microbiome composition and Bd prevalence across multiple sites. Here we explore these questions in Amietia hymenopus, a disease-affected frog in southern Africa. We use microsatellite genotyping and 16S amplicon sequencing to show that the microbiome associated with tadpole mouthparts is structured spatially, and is influenced by host genotype and developmental stage. We observed strong genetic structure in host populations based on rivers and geographic distances, but this did not correspond to spatial patterns in microbiome composition. These results indicate that demographic and host genetic factors affect microbiome composition within sites, but different factors are responsible for host population structure and microbiome structure at the between-site level. Our results help to elucidate complex within- and among- population drivers of microbiome structure in amphibian populations. That there is a genetic basis to microbiome composition in amphibians could help to inform amphibian conservation efforts against infectious diseases.

Contrasting effects of geographical separation on the genetic population structure of sympatric species of mites in avocado orchards.

PubMed

Guzman-Valencia, S; Santillán-Galicia, M T; Guzmán-Franco, A W; González-Hernández, H; Carrillo-Benítez, M G; Suárez-Espinoza, J

2014-10-01

Oligonychus punicae and Oligonychus perseae (Acari: Tetranychidae) are the most important mite species affecting avocado orchards in Mexico. Here we used nucleotide sequence data from segments of the nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes to assess the phylogenetic relationships between both sympatric mite species and, using only ITS sequence data, examine genetic variation and population structure in both species, to test the hypothesis that, although both species co-occur, their genetic population structures are different in both Michoacan state (main producer) and Mexico state. Phylogenetic analysis showed a clear separation between both species using ITS and COI sequence information. Haplotype network analysis done on 24 samples of O. punicae revealed low genetic diversity with only three haplotypes found but a significant geographical population structure confirmed by analysis of molecular variance (AMOVA) and Kimura-2-parameter (K2P) analyses. In addition, a Mantel test revealed that geographical isolation was a factor responsible for the genetic differentiation. In contrast, analyses of 22 samples of O. perseae revealed high genetic diversity with 15 haplotypes found but no geographical structure confirmed by the AMOVA, K2P and Mantel test analyses. We have suggested that geographical separation is one of the most important factors driving genetic variation, but that it affected each species differently. The role of the ecology of these species on our results, and the importance of our findings in the development of monitoring and control strategies are discussed.

Limited dispersal in mobile hunter–gatherer Baka Pygmies

PubMed Central

Verdu, Paul; Leblois, Raphaël; Froment, Alain; Théry, Sylvain; Bahuchet, Serge; Rousset, François; Heyer, Evelyne; Vitalis, Renaud

2010-01-01

Hunter–gatherer Pygmies from Central Africa are described as being extremely mobile. Using neutral genetic markers and population genetics theory, we explored the dispersal behaviour of the Baka Pygmies from Cameroon, one of the largest Pygmy populations in Central Africa. We found a strong correlation between genetic and geographical distances: a pattern of isolation by distance arising from limited parent–offspring dispersal. Our study suggests that mobile hunter–gatherers do not necessarily disperse over wide geographical areas. PMID:20427330

GIS-based poverty and population distribution analysis in China

NASA Astrophysics Data System (ADS)

Cui, Jing; Wang, Yingjie; Yan, Hong

2009-07-01

Geographically, poverty status is not only related with social-economic factors but also strongly affected by geographical environment. In the paper, GIS-based poverty and population distribution analysis method is introduced for revealing their regional differences. More than 100000 poor villages and 592 national key poor counties are chosen for the analysis. The results show that poverty distribution tends to concentrate in most of west China and mountainous rural areas of mid China. Furthermore, the fifth census data are overlaid to those poor areas in order to gain its internal diversity of social-economic characteristics. By overlaying poverty related social-economic parameters, such as sex ratio, illiteracy, education level, percentage of ethnic minorities, family composition, finding shows that poverty distribution is strongly correlated with high illiteracy rate, high percentage minorities, and larger family member.

Gene genealogies in geographically structured populations

Treesearch

Bryan K. Epperson

1999-01-01

Population genetics theory has dealt only with the spatial or geographic pattern of degrees of relatedness or genetic similarity separately for each point in time. However, a frequent goal of experimental studies is to infer migration patterns that occurred in the past or over extended periods of time. To fully understand how a present geographic pattern of genetic...

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse

PubMed Central

Lemieux, Jacob E.; Tran, Alice D.; Freimark, Lisa; Schaffner, Stephen F.; Goethert, Heidi; Andersen, Kristian G.; Bazner, Suzane; Li, Amy; McGrath, Graham; Sloan, Lynne; Vannier, Edouard; Milner, Dan; Pritt, Bobbi; Rosenberg, Eric; Telford, Sam; Bailey, Jeffrey A.; Sabeti, Pardis C.

2017-01-01

Human babesiosis caused by Babesia microti is an emerging tick-borne zoonosis of increasing importance due to rising incidence and expanding geographic range1. Infection with this organism, an intraerythrocytic parasite of the phylum Apicomplexa, causes a febrile syndrome similar to malaria2. Relapsing disease is common among immunocompromised and asplenic individuals3,4, and drug resistance has recently been reported5. To investigate the origin and genetic diversity of this parasite, we sequenced the complete genomes of 42 B. microti samples from around the world, including deep coverage of clinical infections at endemic sites in the continental United States. Samples from the continental US segregate into a Northeast lineage and a Midwest lineage, with subsequent divergence of subpopulations along geographic lines. We identify parasite variants that associate with relapsing disease, including amino acid substitutions in the atovaquone-binding regions of cytochrome b (cytb) and the azithromycin-binding region of ribosomal protein subunit L4 (rpl4). Our results shed light on the origin, diversity, and evolution of B. microti, suggest possible mechanisms for clinical relapse, and create the foundation for further research on this emerging pathogen. PMID:27572973

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse.

PubMed

Lemieux, Jacob E; Tran, Alice D; Freimark, Lisa; Schaffner, Stephen F; Goethert, Heidi; Andersen, Kristian G; Bazner, Suzane; Li, Amy; McGrath, Graham; Sloan, Lynne; Vannier, Edouard; Milner, Dan; Pritt, Bobbi; Rosenberg, Eric; Telford, Sam; Bailey, Jeffrey A; Sabeti, Pardis C

2016-06-13

Human babesiosis caused by Babesia microti is an emerging tick-borne zoonosis of increasing importance due to its rising incidence and expanding geographic range(1). Infection with this organism, an intraerythrocytic parasite of the phylum Apicomplexa, causes a febrile syndrome similar to malaria(2). Relapsing disease is common among immunocompromised and asplenic individuals(3,4) and drug resistance has recently been reported(5). To investigate the origin and genetic diversity of this parasite, we sequenced the complete genomes of 42 B. microti samples from around the world, including deep coverage of clinical infections at endemic sites in the continental USA. Samples from the continental USA segregate into a Northeast lineage and a Midwest lineage, with subsequent divergence of subpopulations along geographic lines. We identify parasite variants that associate with relapsing disease, including amino acid substitutions in the atovaquone-binding regions of cytochrome b (cytb) and the azithromycin-binding region of ribosomal protein subunit L4 (rpl4). Our results shed light on the origin, diversity and evolution of B. microti, suggest possible mechanisms for clinical relapse, and create the foundation for further research on this emerging pathogen.

Comparison of Thaumarchaeotal populations from four deep sea basins

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

Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T.

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. Wemore » demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.« less

Contrasting phylogeographic patterns in Sphagnum fimbriatum and Sphagnum squarrosum (Bryophyta, Sphagnopsida) in Europe.

PubMed

Szövényi, Péter; Hock, Zsófia; Urmi, Edwin; Schneller, Jakob J

2006-01-01

The chloroplast phylogeography of two peat mosses (Sphagnum fimbriatum and Sphagnum squarrosum) with similar distributions but different life history characteristics was investigated in Europe. Our main aim was to test whether similar distributions reflect similar phylogeographic and phylodemographic processes. Accessions covering the European distributions of the species were collected and approx. 2000 bp of the chloroplast genome of each species was sequenced. Maximum parsimony, statistical parsimony and phylodemographic analyses were used to address the question of whether these species with similar distributions show evidence of similar phylogeographic and phylodemographic processes. The chloroplast haplotypes of the currently spreading species S. fimbriatum showed strong geographic structure, whereas those of S. squarrosum, which has stable historical population sizes, showed only very weak geographic affinity and were widely distributed. We hypothesize that S. fimbriatum survived the last glaciations along the Atlantic coast of Europe, whereas S. squarrosum had numerous, scattered refugia in Europe. The dominance of one haplotype of S. fimbriatum across almost all of Europe suggests rapid colonization after the last glacial maximum. We hypothesize that high colonizing ability is an inherent characteristic of the species and its recent expansion in Europe is a response to climate change.

Spatial and temporal drivers of phenotypic diversity in polymorphic snakes.

PubMed

Cox, Christian L; Davis Rabosky, Alison R

2013-08-01

Color polymorphism in natural populations presents an ideal opportunity to study the evolutionary drivers of phenotypic diversity. Systems with striking spatial, temporal, and qualitative variation in color can be leveraged to study the mechanisms promoting the distribution of different types of variation in nature. We used the highly polymorphic ground snake (Sonora semiannulata), a putative coral snake mimic with both cryptic and conspicuous morphs, to compare patterns of neutral genetic variation and variation over space and time in color polymorphism to investigate the mechanistic drivers of phenotypic variation across scales. We found that strong selection promotes color polymorphism across spatial and temporal scales, with morph frequencies differing markedly between juvenile and adult age classes within a single population, oscillating over time within multiple populations, and varying drastically over the landscape despite minimal population genetic structure. However, we found no evidence that conspicuousness of morphs was related to which color pattern was favored by selection or to any geographic factors, including sympatry with coral snakes. We suggest that complex patterns of phenotypic variation in polymorphic systems may be a fundamental outcome of the conspicuousness of morphs and that explicit tests of temporal and geographic variation are critical to the interpretation of conspicuousness and mimicry.

Comparison of Thaumarchaeotal populations from four deep sea basins

DOE PAGES

Techtman, Stephen M.; Mahmoudi, Nagissa; Whitt, Kendall T.; ...

2017-10-03

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. Wemore » demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.« less

Population-genetic properties of differentiated copy number variations in cattle.

PubMed

Xu, Lingyang; Hou, Yali; Bickhart, Derek M; Zhou, Yang; Hay, El Hamidi Abdel; Song, Jiuzhou; Sonstegard, Tad S; Van Tassell, Curtis P; Liu, George E

2016-03-23

While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion, deletion and duplication of genomic sequence, is an informative type of genetic variation. CNVs have been shown to be both common in mammals and important for understanding the relationship between genotype and phenotype. However, CNV differentiation, selection and its population genetic properties are not well understood across diverse populations. We performed a population genetics survey based on CNVs derived from the BovineHD SNP array data of eight distinct cattle breeds. We generated high resolution results that show geographical patterns of variations and genome-wide admixture proportions within and among breeds. Similar to the previous SNP-based studies, our CNV-based results displayed a strong correlation of population structure and geographical location. By conducting three pairwise comparisons among European taurine, African taurine, and indicine groups, we further identified 78 unique CNV regions that were highly differentiated, some of which might be due to selection. These CNV regions overlapped with genes involved in traits related to parasite resistance, immunity response, body size, fertility, and milk production. Our results characterize CNV diversity among cattle populations and provide a list of lineage-differentiated CNVs.

Studies of Resurgent Bed Bugs: Population Genetic Structure, Impact of Aggregation on Development and Molecular Screening for Bartonella

NASA Astrophysics Data System (ADS)

Saenz, Virna Lisa

The recent resurgence of bed bugs (Cimex lectularius L.) has created an unprecedented demand for research on its biology. The main objectives of this dissertation research were to investigate several aspects of bed bug biology: infestation and dispersal dynamics at a large and small geographical scale using molecular markers, to determine the impact of aggregation on bed bug development and to screen bed bug populations for a re-emergent pathogen. First, we studied the infestation and dispersal dynamics of bed bugs at large geographical scale (e.g., across cities, states). Although bed bug infestations are on the rise, there is a poor understanding of their dispersal patterns and sources of infestation. We conducted a genetic study of 21 bed bug infestations from the eastern United States. We genotyped samples comprised of 8 - 10 individuals per infestation at nine polymorphic microsatellite loci. Despite high genetic diversity across all infestations, with 5 -- 17 alleles per locus (mean = 10.3), we found low genetic diversity (1 -- 4 alleles per locus) within all but one of the infestations. These results suggest that nearly all the studied infestations were started by a small propagule possibly consisting of a singly mated female and/or her progeny. All infestations were strongly genetically differentiated from each other (mean pairwise FST between populations = 0.68) and we did not find strong evidence of a geographic pattern of structuring. The high level of genetic diversity across infestations from the eastern United States together with the lack of geographically organized structure is consistent with multiple introductions into the United States from foreign sources. This work is described in Chapter 2 and was published in the Journal of Medical Entomology in 2012. Second, we investigated dispersal and infestation dynamics of bed bugs at a fine geographical scale within three multistory apartment buildings: one from Raleigh, NC and two from Jersey City, NJ. Here we describe the development of 24 high resolution microsatellite markers and their application to elucidate infestation dynamics within three multistory apartment buildings in the United States. Results reveal contrasting characteristics potentially representative of geographic or locale differences. In Raleigh, NC, an infestation within an apartment building seemed to have started from a single introduction followed by extensive spread throughout the building. In Jersey City, NJ, two or more introductions followed by extensive spread. Populations within single apartments in all buildings showed low levels of genetic diversity suggesting that few individuals are starting these infestations, possibly a singly mated female or her progeny. This work is described in Chapter 3 and was published in the Journal of Medical Entomology in 2012. Third, we studied the impact of aggregation in bed bug development. Although it is well known that bed bugs live in aggregations, the adaptive benefits of this behavior are not well understood. In this study, we reared first instars either in isolation or in groups of five from hatching to adult eclosion and recorded their development time. Additionally, we investigated the effects of group-housing on same age nymphs versus nymphs reared with adults. Nymphal development was 2.2 d faster in grouped nymphs than in solitary-housed nymphs, representing 7.3% faster overall development. However, this grouping effect did not appear to be influenced by group composition (nymphs vs. adults). Thus, similar to other gregarious insect species, nymph development in bed bugs is faster in aggregations than in isolation. This work is described in Chapter 4. Fourth, we investigated the prevalence of a re-emergent bacterial pathogen in United States bed bugs populations. Because reports of both bed bugs and Bartonella have been increasing in the United States, and because their host ranges can overlap, we investigated whether the resurgence of these two medically important species are linked by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent. We screened a total of 331 bed bugs from 39 unique collections in 30 geographic locations in 13 states for Bartonella spp. DNA using a polymerase chain reaction assay targeting the 16S-23S rRNA intergenic transcribed spacer region. Bartonella spp. DNA was not amplified from any bed bug, but five bed bugs from four different units of an elderly housing building in North Carolina contained Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector. This work is described in Chapter 5.

Local strong slow S-wave anomalies at western edge of Pacific LLSVP

NASA Astrophysics Data System (ADS)

Obayashi, M.; Niu, F.; Yoshimitsu, J.

2017-12-01

Seismic tomography studies have revealed two broad slow shear-wave speed anomalies regions beneath the Pacific and Africa called as LLSVPs (Large Low Seismic Velocity Provinces). There are geographic correlations between the LLSVPs and hotspots, and the LLSVPs could probably play an important role for convection throughout the mantle and thermal structure and evolution of the earth. The LLSVPs have been considered to be heterogeneous in composition since the boundaries between the normal mantle are sharp. To investigate the details of the sharp LLSVP edge we measure ScS-S and SKS-S differential traveltimes in the hypocentral distance of about 60°-90° using Japanese and Chinese seismic networks. We used 25events for the Chinese network and 16 events for Japanese network that occurred in Tonga-Kermadec region and obtained 3750 event-station pairs of ScS-S and 1500 pairs of SKS-S differential travel times. We found anomalously large (more than 5 sec) ScS-S travel times accompanying normal SKS-S travel times, suggesting local strong slow region in the vicinity of the ScS bounce points (red circles in Figure 1). Such ScS bounce points locate to the northeast of New Guinea Island extending over 20 degrees in NE-SW direction. However below New Guinea Island, both ScS-S and SKS-S travel times are normal (green circles in Figure 1), indicating abrupt end of the local strong slow anomalies. We inverted the ScS-S and SKS-S differential traveltimes for lowermost mantle S-wave speed structure, assuming isotropic mantle. The result shows very strong slow anomalies of more than 5% at western edge of Pacific LLSVP that extend vertically not more than 200 km from the core mantle boundary.

Vulnerability of animal trade networks to the spread of infectious diseases: a methodological approach applied to evaluation and emergency control strategies in cattle, France, 2005.

PubMed

Rautureau, S; Dufour, B; Durand, B

2011-04-01

Besides farming, trade of livestock is a major component of agricultural economy. However, the networks generated by live animal movements are the major support for the propagation of infectious agents between farms, and their structure strongly affects how fast a disease may spread. Structural characteristics may thus be indicators of network vulnerability to the spread of infectious disease. The method proposed here is based upon the analysis of specific subnetworks: the giant strongly connected components (GSCs). Their existence, size and geographic extent are used to assess network vulnerability. Their disappearance when targeted nodes are removed allows studying how network vulnerability may be controlled under emergency conditions. The method was applied to the cattle trade network in France, 2005. Giant strongly connected components were present and widely spread all over the country in yearly, monthly and weekly networks. Among several tested approaches, the most efficient way to make GSCs disappear was based on the ranking of nodes by decreasing betweenness centrality (the proportion of shortest paths between nodes on which a specific node lies). Giant strongly connected components disappearance was obtained after removal of <1% of network nodes. Under emergency conditions, suspending animal trade activities in a small subset of holdings may thus allow to control the spread of an infectious disease through the animal trade network. Nodes representing markets and dealers were widely affected by these simulated control measures. This confirms their importance as 'hubs' for infectious diseases spread. Besides emergency conditions, specific sensitization and preventive measures should be dedicated to this population. © 2010 Blackwell Verlag GmbH.

Multivariate approach to matrimonial mobility in Catalonia.

PubMed

Calafell, F; Hernández, M

1993-10-01

Matrimonial mobility in Catalonia was studied using 1986 census data. Comarca (a geographic division) of birth was used as the population unit, and a measure of affinity (a statistical distance) between comarques in spouse geographic origin was defined. This distance was analyzed with multivariate methods drawn from numerical taxonomy to detect any discontinuities in matrimonial mobility and gene flow between comarques. Results show a three-level pattern of gene flow in Catalonia: (1) a strong endogamy within comarques; (2) a 100-km matrimonial circle around every comarca; and (3) the capital, Barcelona, which attracts migrants from all over Catalonia. The regionalization in matrimonial mobility follows the geographically clear-cut groups of comarques almost exactly.

Eyjafjallajökull and 9/11: The Impact of Large-Scale Disasters on Worldwide Mobility

PubMed Central

Woolley-Meza, Olivia; Grady, Daniel; Thiemann, Christian; Bagrow, James P.; Brockmann, Dirk

2013-01-01

Large-scale disasters that interfere with globalized socio-technical infrastructure, such as mobility and transportation networks, trigger high socio-economic costs. Although the origin of such events is often geographically confined, their impact reverberates through entire networks in ways that are poorly understood, difficult to assess, and even more difficult to predict. We investigate how the eruption of volcano Eyjafjallajökull, the September 11th terrorist attacks, and geographical disruptions in general interfere with worldwide mobility. To do this we track changes in effective distance in the worldwide air transportation network from the perspective of individual airports. We find that universal features exist across these events: airport susceptibilities to regional disruptions follow similar, strongly heterogeneous distributions that lack a scale. On the other hand, airports are more uniformly susceptible to attacks that target the most important hubs in the network, exhibiting a well-defined scale. The statistical behavior of susceptibility can be characterized by a single scaling exponent. Using scaling arguments that capture the interplay between individual airport characteristics and the structural properties of routes we can recover the exponent for all types of disruption. We find that the same mechanisms responsible for efficient passenger flow may also keep the system in a vulnerable state. Our approach can be applied to understand the impact of large, correlated disruptions in financial systems, ecosystems and other systems with a complex interaction structure between heterogeneous components. PMID:23950904

Evidence of substantial recombination among Trypanosoma cruzi II strains from Minas Gerais.

PubMed

Baptista, Rodrigo de Paula; D'Ávila, Daniella Alchaar; Segatto, Marcela; do Valle, Ítalo Faria; Franco, Glória Regina; Valadares, Helder Magno Silva; Gontijo, Eliane Dias; Galvão, Lúcia Maria da Cunha; Pena, Sérgio Danilo Junho; Chiari, Egler; Machado, Carlos Renato; Macedo, Andréa Mara

2014-03-01

Due to the scarcity of evidence of sexuality in Trypanosoma cruzi, the causative agent of Chagas disease, it has been general accepted that the parasite reproduction is essentially clonal with infrequent genetic recombination. This assumption is mainly supported by indirect evidence, such as Hardy-Weinberg imbalances, linkage disequilibrium and a strong correlation between independent sets of genetic markers of T. cruzi populations. However, because the analyzed populations are usually isolated from different geographic regions, the possibility of population substructuring as generating these genetic marker imbalances cannot be eliminated. To investigate this possibility, we firstly compared the allele frequencies and haplotype networks using seven different polymorphic loci (two from mitochondrial and five from different nuclear chromosomes) in two groups of TcII strains: one including isolates obtained from different regions in Latin America and the other including isolates obtained only from patients of the Minas Gerais State in Brazil. Our hypothesis was that if the population structure is essentially clonal, Hardy-Weinberg disequilibrium and a sharp association between the clusters generated by analyzing independent markers should be observed in both strain groups, independent of the geographic origin of the samples. The results demonstrated that the number of microsatellite loci in linkage disequilibrium decreased from 4 to 1 when only strains from Minas Gerais were analyzed. Moreover, we did not observed any correlation between the clusters when analyzing the nuclear and mitochondrial loci, suggesting independent inheritance of these markers among the Minas Gerais strains. Besides, using a second subset of five physically linked microsatellite loci and the Minas Gerais strains, we could also demonstrate evidence of homologous recombination roughly proportional to the relative distance among them. Taken together, our results do not support a clonal population structure for T. cruzi, particularly in TcII, which coexists in the same geographical area, suggesting that genetic exchanges among these strains may occur more frequently than initially expected. Copyright © 2013 Elsevier B.V. All rights reserved.

Forest Restoration in a Fog Oasis: Evidence Indicates Need for Cultural Awareness in Constructing the Reference

PubMed Central

Balaguer, Luís; Arroyo-García, Rosa; Jiménez, Percy; Jiménez, María Dolores; Villegas, Luís; Cordero, Irene; Rubio de Casas, Rafael; Fernández-Delgado, Raúl; Ron, María Eugenia; Manrique, Esteban; Vargas, Pablo; Cano, Emilio; Pueyo, José J.; Aronson, James

2011-01-01

Background In the Peruvian Coastal Desert, an archipelago of fog oases, locally called lomas, are centers of biodiversity and of past human activity. Fog interception by a tree canopy, dominated by the legume tree tara (Caesalpinia spinosa), enables the occurrence in the Atiquipa lomas (southern Peru) of an environmental island with a diverse flora and high productivity. Although this forest provides essential services to the local population, it has suffered 90% anthropogenic reduction in area. Restoration efforts are now getting under way, including discussion as to the most appropriate reference ecosystem to use. Methodology/Principal Findings Genetic diversity of tara was studied in the Atiquipa population and over a wide geographical and ecological range. Neither exclusive plastid haplotypes to loma formations nor clear geographical structuring of the genetic diversity was found. Photosynthetic performance and growth of seedlings naturally recruited in remnant patches of loma forest were compared with those of seedlings recruited or planted in the adjacent deforested area. Despite the greater water and nitrogen availability under tree canopy, growth of forest seedlings did not differ from that of those recruited into the deforested area, and was lower than that of planted seedlings. Tara seedlings exhibited tight stomatal control of photosynthesis, and a structural photoprotection by leaflet closure. These drought-avoiding mechanisms did not optimize seedling performance under the conditions produced by forest interception of fog moisture. Conclusions/Significance Both weak geographic partitioning of genetic variation and lack of physiological specialization of seedlings to the forest water regime strongly suggest that tara was introduced to lomas by humans. Therefore, the most diverse fragment of lomas is the result of landscape management and resource use by pre-Columbian cultures. We argue that an appropriate reference ecosystem for ecological restoration of lomas should include sustainable agroforestry practices that emulate the outcomes of ancient uses. PMID:21829680

Using a Geographic Information System to Assess the Risk of Hurricane Hazards on the Maya Civilization

NASA Astrophysics Data System (ADS)

Weigel, A. M.; Griffin, R.; Sever, T.

2014-12-01

The extent of the Maya civilization spanned across portions of modern day Mexico, Belize, Guatemala, El Salvador and Honduras. Paleoclimatic studies suggest this region has been affected by strong hurricanes for the past six thousand years, reinforced by archeological evidence from Mayan records indicating they experienced strong storms. It is theorized hurricanes aided in the collapse of the Maya, damaging building structures, agriculture, and ceasing industry activities. Today, this region is known for its active tropical climatology, being hit by numerous strong storms including Hurricane Dean, Iris, Keith, and Mitch. This research uses a geographic information system (GIS) to model hurricane hazards, and assess the risk posed on the Maya civilization. GIS has the ability to handle various layer components making it optimal for combining parameters necessary for assessing the risk of experiencing hurricane related hazards. For this analysis, high winds, storm surge flooding, non-storm surge related flooding, and rainfall triggered landslides were selected as the primary hurricane hazards. Data sets used in this analysis include the National Climatic Data Center International Best Track Archive for Climate Stewardships (IBTrACS) hurricane tracks, Shuttle Radar Topography Mission Digital Elevation Model, WorldClim monthly accumulated precipitation, USGS HydroSHEDS river locations, Harmonized World Soil Database soil types, and known Maya site locations from the Electronic Atlas of Ancient Maya Sites. ArcGIS and ENVI software were utilized to process data and model hurricane hazards. To assess locations at risk of experiencing high winds, a model was created using ArcGIS Model Builder to map each storm's temporal wind profile, and adapted to simulate forward storm velocity, and storm frequency. Modeled results were then combined with physical land characteristics, meteorological, and hydrologic data to identify areas likely affected. Certain areas along the eastern edge of the Yucatan peninsula were found to be more prone to experiencing wind and flood related hurricane hazards. Novel methodologies developed from this analysis can be adapted for further hurricane risk assessment on archeological sites.

Spatiotemporal variation of the association between climate dynamics and HFRS outbreaks in Eastern China during 2005-2016 and its geographic determinants

PubMed Central

Wu, Jiaping; Cazelles, Bernard; Qian, Quan; Mu, Di; Wang, Yong; Yin, Wenwu; Zhang, Wenyi

2018-01-01

Background Hemorrhagic fever with renal syndrome (HFRS) is a rodent-associated zoonosis caused by hantavirus. The HFRS was initially detected in northeast China in 1931, and since 1955 it has been detected in many regions of the country. Global climate dynamics influences HFRS spread in a complex nonlinear way. The quantitative assessment of the spatiotemporal variation of the “HFRS infections-global climate dynamics” association at a large geographical scale and during a long time period is still lacking. Methods and findings This work is the first study of a recently completed dataset of monthly HFRS cases in Eastern China during the period 2005–2016. A methodological synthesis that involves a time-frequency technique, a composite space-time model, hotspot analysis, and machine learning is implemented in the study of (a) the association between HFRS incidence spread and climate dynamics and (b) the geographic factors impacting this association over Eastern China during the period 2005–2016. The results showed that by assimilating core and city-specific knowledge bases the synthesis was able to depict quantitatively the space-time variation of periodic climate-HFRS associations at a large geographic scale and to assess numerically the strength of this association in the area and period of interest. It was found that the HFRS infections in Eastern China has a strong association with global climate dynamics, in particular, the 12, 18 and 36 mos periods were detected as the three main synchronous periods of climate dynamics and HFRS distribution. For the 36 mos period (which is the period with the strongest association), the space-time correlation pattern of the association strength indicated strong temporal but rather weak spatial dependencies. The generated space-time maps of association strength and association hotspots provided a clear picture of the geographic variation of the association strength that often-exhibited cluster characteristics (e.g., the south part of the study area displays a strong climate-HFRS association with non-point effects, whereas the middle-north part displays a weak climate-HFRS association). Another finding of this work is the upward climate-HFRS coherency trend for the past few years (2013–2015) indicating that the climate impacts on HFRS were becoming increasingly sensitive with time. Lastly, another finding of this work is that geographic factors affect the climate-HFRS association in an interrelated manner through local climate or by means of HFRS infections. In particular, location (latitude, distance to coastline and longitude), grassland and woodland are the geographic factors exerting the most noticeable effects on the climate-HFRS association (e.g., low latitude has a strong effect, whereas distance to coastline has a wave-like effect). Conclusions The proposed synthetic quantitative approach revealed important aspects of the spatiotemporal variation of the climate-HFRS association in Eastern China during a long time period, and identified the geographic factors having a major impact on this association. Both findings could improve public health policy in an HFRS-torn country like China. Furthermore, the synthetic approach developed in this work can be used to map the space-time variation of different climate-disease associations in other parts of China and the World. PMID:29874263

Money circulation networks reveal emerging geographical communities

NASA Astrophysics Data System (ADS)

Brockmann, D.; Theis, F.; David, V.

2008-03-01

Geographical communities and their boundaries are key determinants of various spatially extended dynamical phenomena. Examples are migration dynamics of species, the spread of infectious diseases, bioinvasive processes, and the spatial evolution of language. We address the question to what extend multiscale human transportation networks encode geographical community structures, how they differ from geopolitical classifications, whether they are spatially coherent, and analyse their structure as a function of length scale. Our analysis is based on a proxy network for human transportation obtained from the geographic circulation of more than 10 million dollar bills in the United States recorded at the bill tracking website www.wheresgeorge.com. The data extends that of a previous study (Brockmann et al., Nature 2006) on the discovery of scaling laws of human travel by an order of magnitude and permits an approach to multiscale human transportation from a network perspective.

Evaluation of Geographic Indices Describing Health Care Utilization.

PubMed

Kim, Agnus M; Park, Jong Heon; Kang, Sungchan; Kim, Yoon

2017-01-01

The accurate measurement of geographic patterns of health care utilization is a prerequisite for the study of geographic variations in health care utilization. While several measures have been developed to measure how accurately geographic units reflect the health care utilization patterns of residents, they have been only applied to hospitalization and need further evaluation. This study aimed to evaluate geographic indices describing health care utilization. We measured the utilization rate and four health care utilization indices (localization index, outflow index, inflow index, and net patient flow) for eight major procedures (coronary artery bypass graft surgery, percutaneous transluminal coronary angioplasty, surgery after hip fracture, knee replacement surgery, caesarean sections, hysterectomy, computed tomography scans, and magnetic resonance imaging scans) according to three levels of geographic units in Korea. Data were obtained from the National Health Insurance database in Korea. We evaluated the associations among the health care utilization indices and the utilization rates. In higher-level geographic units, the localization index tended to be high, while the inflow index and outflow index were lower. The indices showed different patterns depending on the procedure. A strong negative correlation between the localization index and the outflow index was observed for all procedures. Net patient flow showed a moderate positive correlation with the localization index and the inflow index. Health care utilization indices can be used as a proxy to describe the utilization pattern of a procedure in a geographic unit.

Genetic effects of landscape, habitat preference and demography on three co-occurring turtle species.

PubMed

Reid, Brendan N; Mladenoff, David J; Peery, M Zachariah

2017-02-01

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life history strategies, habitat preferences and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation by distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and postsettlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long-lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co-occurring species. © 2016 John Wiley & Sons Ltd.

SINEs, evolution and genome structure in the opossum.

PubMed

Gu, Wanjun; Ray, David A; Walker, Jerilyn A; Barnes, Erin W; Gentles, Andrew J; Samollow, Paul B; Jurka, Jerzy; Batzer, Mark A; Pollock, David D

2007-07-01

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.

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.

Pollinator community structure and sources of spatial variation in plant--pollinator interactions in Clarkia xantiana ssp. xantiana.

PubMed

Moeller, David A

2005-01-01

The structure of diverse floral visitor assemblages and the nature of spatial variation in plant-pollinator interactions have important consequences for floral evolution and reproductive interactions among pollinator-sharing plant species. In this study, I use surveys of floral visitor communities across the geographic range of Clarkia xantiana ssp. xantiana (hereafter C. x. xantiana) (Onagraceae) to examine the structure of visitor communities, the specificity of the pollination system, and the role of variation in the abiotic vs. biotic environment in contributing to spatial variation in pollinator abundance and community composition. Although the assemblage of bee visitors to C. x. xantiana is very diverse (49 species), few were regular visitors and likely to act as pollinators. Seventy-four percent of visitor species accounted for only 11% of total visitor abundance and 69% were collected in three or fewer plant populations (of ten). Of the few reliable visitors, Clarkia pollen specialist bees were the most frequent visitors, carried more Clarkia pollen compared to generalist foragers, and were less likely to harbor foreign pollen. Overall, the core group of pollinators was obscured by high numbers of incidental visitors that are unlikely to contribute to pollination. In a geographic context, the composition of specialist pollinator assemblages varied considerably along the abiotic gradient spanning the subspecies' range. However, the overall abundance of specialist pollinators in plant populations was not influenced by the broad-scale abiotic gradient but strongly affected by local plant community associations. C. x. xantiana populations sympatric with pollinator-sharing congeners were visited twice as often by specialists compared to populations occurring alone. These positive indirect interactions among plant species may promote population persistence and species coexistence by enhancing individual reproductive success.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray–Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities. PMID:26943622

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.

Feasibility of using a bacteriophage-based structural color sensor for screening the geographical origins of agricultural products

NASA Astrophysics Data System (ADS)

Seol, Daun; Moon, Jong-Sik; Lee, Yujin; Han, Jiye; Jang, Daeil; Kang, Dong-Jin; Moon, Jiyoung; Jang, Eunjin; Oh, Jin-Woo; Chung, Hoeil

2018-05-01

An M13 bacteriophage-based color sensor, which can change its structural color upon interaction with a gaseous molecule, was evaluated as a screening tool for the discrimination of the geographical origins of three different agricultural products (garlic, onion, and perilla). Exposure of the color sensor to sample odors induced the self-assembled M13 bacteriophage bundles to swell by the interaction of amino acid residues (repeating units of four glutamates) on the bacteriophage with the odor components, resulting in a change in the structural color of the sensor. When the sensor was exposed to the odors of garlic and onion samples, the RGB color changes were considerable because of the strong interactions of the odor components such as disulfides with the glutamate residues on the sensor. Although the patterns of the color variations were generally similar between the domestic and imported samples, some degrees of dissimilarities in their intensities were also observed. Although the magnitude of color change decreased for perilla, the color change patterns between the two groups were somewhat different. With the acquired RGB data, a support vector machine was employed to distinguish the domestic and imported samples, and the resulting accuracies in the measurements of garlic, onion, and perilla samples were 94.1, 88.7, and 91.6%, respectively. The differences in the concentrations of the odor components between both groups and/or the presence of specific components exclusively in the odor of one group allowed the color sensor-based discrimination. The demonstrated color sensor was thus shown to be a potentially versatile and simple as an on-site screening tool. Strategies able to further improve the sensor performance were also discussed.

Feasibility of using a bacteriophage-based structural color sensor for screening the geographical origins of agricultural products.

PubMed

Seol, Daun; Moon, Jong-Sik; Lee, Yujin; Han, Jiye; Jang, Daeil; Kang, Dong-Jin; Moon, Jiyoung; Jang, Eunjin; Oh, Jin-Woo; Chung, Hoeil

2018-05-15

An M13 bacteriophage-based color sensor, which can change its structural color upon interaction with a gaseous molecule, was evaluated as a screening tool for the discrimination of the geographical origins of three different agricultural products (garlic, onion, and perilla). Exposure of the color sensor to sample odors induced the self-assembled M13 bacteriophage bundles to swell by the interaction of amino acid residues (repeating units of four glutamates) on the bacteriophage with the odor components, resulting in a change in the structural color of the sensor. When the sensor was exposed to the odors of garlic and onion samples, the RGB color changes were considerable because of the strong interactions of the odor components such as disulfides with the glutamate residues on the sensor. Although the patterns of the color variations were generally similar between the domestic and imported samples, some degrees of dissimilarities in their intensities were also observed. Although the magnitude of color change decreased for perilla, the color change patterns between the two groups were somewhat different. With the acquired RGB data, a support vector machine was employed to distinguish the domestic and imported samples, and the resulting accuracies in the measurements of garlic, onion, and perilla samples were 94.1, 88.7, and 91.6%, respectively. The differences in the concentrations of the odor components between both groups and/or the presence of specific components exclusively in the odor of one group allowed the color sensor-based discrimination. The demonstrated color sensor was thus shown to be a potentially versatile and simple as an on-site screening tool. Strategies able to further improve the sensor performance were also discussed. Copyright © 2018. Published by Elsevier B.V.

Genetic Population Structure of the Coral Reef Sea Star Linckia laevigata in the Western Indian Ocean and Indo-West Pacific.

PubMed

Otwoma, Levy Michael; Kochzius, Marc

2016-01-01

The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean.

Genetic Population Structure of the Coral Reef Sea Star Linckia laevigata in the Western Indian Ocean and Indo-West Pacific

PubMed Central

Kochzius, Marc

2016-01-01

The coral reef sea star Linckia laevigata is common on shallow water coral reefs of the Indo-West Pacific. Its large geographic distribution and comprehensive data from previous studies makes it suitable to examine genetic differentiation and connectivity over large geographical scales. Based on partial sequences of the mitochondrial cytochrome oxidase I (COI) gene this study investigates the genetic population structure and connectivity of L. laevigata in the Western Indian Ocean (WIO) and compares it to previous studies in the Indo-Malay-Philippines Archipelago (IMPA). A total of 138 samples were collected from nine locations in the WIO. AMOVA revealed a low but significant ΦST-value of 0.024 for the WIO populations. In the hierarchical AMOVA, the following grouping rejected the hypothesis of panmixia: (1) Kenya (Watamu, Mombasa, Diani) and Tanzanian Island populations (Misali and Jambiani) and (2) the rest of the WIO sites (mainland Tanzania and Madagascar; ΦCT = 0.03). The genetic population structure was stronger and more significant (ΦST = 0.13) in the comparative analysis of WIO and IMPA populations. Three clades were identified in the haplotype network. The strong genetic differentiation (ΦCT = 0.199, P < 0.001) suggests that Indo-West Pacific populations of L. laevigata can be grouped into four biogeographic regions: (1) WIO (2) Eastern Indian Ocean (3) IMPA and (4) Western Pacific. The findings of this study support the existence of a genetic break in the Indo-West Pacific consistent with the effect of lowered sea level during the Pleistocene, which limited gene flow between the Pacific and Indian Ocean. PMID:27798700

The significant surface-water connectivity of "geographically isolated wetlands"

USGS Publications Warehouse

Calhoun, Aram J.K.; Mushet, David M.; Alexander, Laurie C.; DeKeyser, Edward S.; Fowler, Laurie; Lane, Charles R.; Lang, Megan W.; Rains, Mark C.; Richter, Stephen; Walls, Susan

2017-01-01

We evaluated the current literature, coupled with our collective research expertise, on surface-water connectivity of wetlands considered to be “geographically isolated” (sensu Tiner Wetlands 23:494–516, 2003a) to critically assess the scientific foundation of grouping wetlands based on the singular condition of being surrounded by uplands. The most recent research on wetlands considered to be “geographically isolated” shows the difficulties in grouping an ecological resource that does not reliably indicate lack of surface water connectivity in order to meet legal, regulatory, or scientific needs. Additionally, the practice of identifying “geographically isolated wetlands” based on distance from a stream can result in gross overestimates of the number of wetlands lacking ecologically important surface-water connections. Our findings do not support use of the overly simplistic label of “geographically isolated wetlands”. Wetlands surrounded by uplands vary in function and surface-water connections based on wetland landscape setting, context, climate, and geographic region and should be evaluated as such. We found that the “geographically isolated” grouping does not reflect our understanding of the hydrologic variability of these wetlands and hence does not benefit conservation of the Nation’s diverse wetland resources. Therefore, we strongly discourage use of categorizations that provide overly simplistic views of surface-water connectivity of wetlands fully embedded in upland landscapes.

Geographically-based discrimination is a social determinant of mental health in a deprived or stigmatized area in Japan: a cross-sectional study.

PubMed

Tabuchi, Takahiro; Fukuhara, Hiroyuki; Iso, Hiroyasu

2012-09-01

Perceived discrimination has been shown to be associated with health. However, it is uncertain whether discrimination based on geographical place of residence (geographically-based discrimination), such as Buraku or Nishinari discrimination in Japan, is associated with health. We conducted a cross-sectional study (response rate = 52.3%) from February to March 2009 in a Buraku district of Nishinari ward in Osaka city, one of the most deprived areas in Japan. We implemented sex-stratified and education-stratified multivariate regression models to examine the association between geographically-based discrimination and two mental health outcomes (depressive symptoms and diagnosis of mental illness) with adjustment for age, socioeconomic status, social relationships and lifestyle factors. A total of 1994 persons aged 25-79 years (928 men and 1066 women) living in the district were analyzed. In the fully-adjusted model, perceived geographically-based discrimination was significantly associated with depressive symptoms and diagnosis of mental illness. It was more strongly associated among men or highly educated people than among women or among less educated people. The effect of geographically-based discrimination on mental health is independent of socioeconomic status, social relationship and lifestyle factors. Geographically-based discrimination may be one of the social determinants of mental health. Copyright © 2012. Published by Elsevier Ltd.

Energy gradients and the geographic distribution of local ant diversity.

PubMed

Kaspari, Michael; Ward, Philip S; Yuan, May

2004-08-01

Geographical diversity gradients, even among local communities, can ultimately arise from geographical differences in speciation and extinction rates. We evaluated three models--energy-speciation, energy-abundance, and area--that predict how geographic trends in net diversification rates generate trends in diversity. We sampled 96 litter ant communities from four provinces: Australia, Madagascar, North America, and South America. The energy-speciation hypothesis best predicted ant species richness by accurately predicting the slope of the temperature diversity curve, and accounting for most of the variation in diversity. The communities showed a strong latitudinal gradient in species richness as well as inter-province differences in diversity. The former vanished in the temperature-diversity residuals, suggesting that the latitudinal gradient arises primarily from higher diversification rates in the tropics. However, inter-province differences in diversity persisted in those residuals--South American communities remained more diverse than those in North America and Australia even after the effects of temperature were removed.

The geographical vector in distribution of genetic diversity for Clonorchis sinensis.

PubMed

Solodovnik, Daria A; Tatonova, Yulia V; Burkovskaya, Polina V

2018-01-01

Clonorchis sinensis, the causative agent of clonorchiasis, is one of the most important parasites that inhabit countries of East and Southeast Asia. In this study, we validated the existence of a geographical vector for C. sinensis using the partial cox1 mtDNA gene, which includes a conserved region. The samples of parasite were divided into groups corresponding to three river basins, and the size of the conserved region had a strong tendency to increase from the northernmost to the southernmost samples. This indicates the availability of the geographical vector in distribution of genetic diversity. A vector is a quantity that is characterized by magnitude and direction. Geographical vector obtained in cox1 gene of C. sinensis has both these features. The reasons for the occurrence of this feature, including the influence of intermediate and definitive hosts on vector formation, and the possibility of its use for clonorchiasis monitoring are discussed. Graphical abstract ᅟ.

A novel haplotype of spinocerebellar ataxia type 6 contributes to the highest prevalence in western Japan.

PubMed

Terasawa, Hideo; Oda, Masaya; Morino, Hiroyuki; Miyachi, Takafumi; Izumi, Yuishin; Maruyama, Hirofumi; Matsumoto, Masayasu; Kawakami, Hideshi

2004-03-25

The highest prevalence rate of spinocerebellar ataxia type 6 (SCA6) in the worldwide population is in the Chugoku and Kansai areas of Western Japan, but the reason of this geographic characteristics is unclear. We investigated the predisposing haplotypes and their geographic distribution. Genotyping of five microsatellite markers and three single nucleotide polymorphisms linked to the CACNA1A gene in 150 Japanese SCA6 patients from unrelated 118 families revealed three major haplotypes, carrying a pool of one common haplotype core. A founder chromosome was thought to have historically diverged into at least three types. One of the major haplotypes newly identified showed a strong geographical cluster around the Seto Inland Sea in the Chugoku and Kansai areas of Western Japan, whereas the others were widely distributed throughout Japan. The distribution of predisposing haplotypes contributes to the geographical differences in prevalence of SCA6.

Geographic variations of the bird-borne structural risk of West Nile virus circulation in Europe

PubMed Central

Durand, Benoit; Tran, Annelise; Balança, Gilles

2017-01-01

The structural risk of West Nile Disease results from the usual functioning of the socio-ecological system, which may favour the introduction of the pathogen, its circulation and the occurrence of disease cases. Its geographic variations result from the local interactions between three components: (i) reservoir hosts, (ii) vectors, both characterized by their diversity, abundance and competence, (iii) and the socio-economic context that impacts the exposure of human to infectious bites. We developed a model of bird-borne structural risk of West Nile Virus (WNV) circulation in Europe, and analysed the association between the geographic variations of this risk and the occurrence of WND human cases between 2002 and 2014. A meta-analysis of WNV serosurveys conducted in wild bird populations was performed to elaborate a model of WNV seropositivity in European bird species, considered a proxy for bird exposure to WNV. Several eco-ethological traits of bird species were linked to seropositivity and the statistical model adequately fitted species-specific seropositivity data (area under the ROC curve: 0.85). Combined with species distribution maps, this model allowed deriving geographic variations of the bird-borne structural risk of WNV circulation. The association between this risk, and the occurrence of WND human cases across the European Union was assessed. Geographic risk variations of bird-borne structural risk allowed predicting WND case occurrence in administrative districts of the EU with a sensitivity of 86% (95% CI: 0.79–0.92), and a specificity of 68% (95% CI: 0.66–0.71). Disentangling structural and conjectural health risks is important for public health managers as risk mitigation procedures differ according to risk type. The results obtained show promise for the prevention of WND in Europe. Combined with analyses of vector-borne structural risk, they should allow designing efficient and targeted prevention measures. PMID:29023472

A database paradigm for the management of DICOM-RT structure sets using a geographic information system

NASA Astrophysics Data System (ADS)

Shao, Weber; Kupelian, Patrick A.; Wang, Jason; Low, Daniel A.; Ruan, Dan

2014-03-01

We devise a paradigm for representing the DICOM-RT structure sets in a database management system, in such way that secondary calculations of geometric information can be performed quickly from the existing contour definitions. The implementation of this paradigm is achieved using the PostgreSQL database system and the PostGIS extension, a geographic information system commonly used for encoding geographical map data. The proposed paradigm eliminates the overhead of retrieving large data records from the database, as well as the need to implement various numerical and data parsing routines, when additional information related to the geometry of the anatomy is desired.

Small geographic range but not panmictic: how forests structure the endangered Point Arena mountain beaver (Aplodontia rufa nigra)

Treesearch

William J. Zielinski; Fredrick V. Schlexer; Sean A. Parks; Kristine L. Pilgrim; Michael K. Schwartz

2012-01-01

The landscape genetics framework is typically applied to broad regions that occupy only small portions of a species' range. Rarely is the entire range of a taxon the subject of study. We examined the landscape genetic structure of the endangered Point Arena mountain beaver (Aplodontia rufa nigra), whose isolated geographic range is found in a...

A Nationwide Learning-Style Assessment of Undergraduate Athletic Training Students in CAAHEP-Accredited Athletic Training Programs

PubMed Central

Stradley, Stephanie L.; Buckley, Bernadette D.; Kaminski, Thomas W.; Horodyski, MaryBeth; Fleming, David; Janelle, Christopher M.

2002-01-01

Objective: To identify the learning styles and preferred environmental characteristics of undergraduate athletic training students in Commission on Accreditation of Allied Health Education Programs (CAAHEP)-accredited athletic training education programs and to determine if learning-style differences existed among geographic regions of the country. Design and Setting: Fifty CAAHEP-accredited athletic training programs were randomly selected in proportion to the number of programs in each geographic region. Ten students from each school were selected to complete the Kolb Learning Style Inventory (LSI) and the Productivity Environmental Preference Survey (PEPS). Subjects: A total of 193 undergraduate athletic training students (84 men, 109 women) with a mean age of 22.3 ± 2.8 years completed the PEPS, while 188 students completed the LSI. Measurements: We used chi-square analyses to determine if differences existed in learning-style type and if these differences were based on geographic location. We calculated analysis of variance to determine if there were any geographic differences in the mean overall combination scores of the LSI. Descriptive statistics were used to evaluate the PEPS. Results: The overall return rate was 38%. The chi-square analyses revealed no significant difference in learning-style type for athletic training students, regardless of the geographic region. The LSI yielded a relatively even distribution of learning styles: 29.3% of the students were accommodators, 19.7% were divergers, 21.8% were convergers, and 29.3% were assimilators. The overall mean combination scores were 4.9 (abstract-concrete) and 4.9 (active-reflective), and analysis of variance indicated no significant difference in the mean combination scores among the geographic regions. The PEPS revealed that undergraduate athletic training students demonstrated a strong preference for learning in the afternoon. Conclusions: Undergraduate athletic training students demonstrated great diversity in learning style. Educators must strongly consider this diversity and incorporate teaching methods that will benefit all types of learners. PMID:12937535

A population genetic transect of Panicum hallii (Poaceae).

PubMed

Lowry, David B; Purmal, Colin T; Juenger, Thomas E

2013-03-01

Understanding the relationship between climate, adaptation, and population structure is of fundamental importance to botanists because these factors are crucial for the evolution of biodiversity and the response of species to future climate change. Panicum hallii is an emerging model system for perennial grass and bioenergy research, yet very little is known about the relationship between climate and population structure in this system. • We analyzed geographic population differentiation across 39 populations of P. hallii along a longitudinal transect from the savannas of central Texas through the deserts of Arizona and New Mexico. A combination of morphological and genetic (microsatellite) analysis was used to explore patterns of population structure. • We found strong differentiation between high elevation western desert populations and lower elevation eastern populations of P. hallii, with a pronounced break in structure occurring in western Texas. In addition, we confirmed that there are high levels of morphological and genetic structure between previous recognized varieties (var. hallii and var. filipes) within this species. • The results of this study suggest that patterns of population structure within P. hallii may be driven by climatic variation over space. Overall, this study lays the groundwork for future studies on the genetics of local adaptation and reproductive isolation in this system.

WIC program participation--a marketing approach.

PubMed Central

Buechner, J S; Scott, H D; Smith, J L; Humphrey, A B

1991-01-01

Recent evaluation studies have described the benefits accruing to low-income women and children who participate in the Special Supplemental Food Program for Women, Infants, and Children (WIC). However, participation is not uniform among all groups of eligible persons. This study examines the geographic variation in WIC participation rates of eligible pregnant women in Rhode Island to determine whether the program is effective in reaching the neediest segments of the population. Eight groups of small geographic areas in Rhode Island (census tracts) were formed on the basis of need for maternal and child health services, as determined from a statistical method employing factor and cluster analysis of existing health and sociodemographic data. Among these eight groups, participation rates in WIC during 1983-84 ranged from 46 percent to more than 100 percent of estimated eligible pregnant women. The rates were positively correlated with measures of need, strongly (r = 0.92) with an index of maternal risk, and less strongly (r = 0.79) with an index of birth outcomes. The results of this study have enabled the Rhode Island WIC Program to direct its outreach efforts more specifically to geographic areas where the need for the program's assistance is greatest. The procedures described in this report comprise a technique that can be generally applied to measure program effectiveness in marketing and outreach where relevant data are available by small geographic areas. The data requirements are (a) population-based estimates of program need and (b) program utilization measures. If these data can be aggregated to a common set of small geographic areas, the use of marketing analysis techniques becomes possible, and program benefits in the area of outreach and recruitment can be realized. PMID:1910189

Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago.

PubMed

Bottin, L; Verhaegen, D; Tassin, J; Olivieri, I; Vaillant, A; Bouvet, J M

2005-06-01

We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Mare to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautes, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci-population combinations (per population FIS = 0-0.03 on Grande-Terre and Ile des Pins, and 0-0.67 on Loyautes). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyaute and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum.

The relationships between electricity consumption and GDP in Asian countries, using hierarchical structure methods

NASA Astrophysics Data System (ADS)

Kantar, Ersin; Keskin, Mustafa

2013-11-01

This study uses hierarchical structure methods (minimal spanning tree (MST) and hierarchical tree (HT)) to examine the relationship between energy consumption and economic growth in a sample of 30 Asian countries covering the period 1971-2008. These countries are categorized into four panels based on the World Bank income classification, namely high, upper middle, lower middle, and low income. In particular, we use the data of electricity consumption and real gross domestic product (GDP) per capita to detect the topological properties of the countries. We show a relationship between electricity consumption and economic growth by using the MST and HT. We also use the bootstrap technique to investigate a value of the statistical reliability to the links of the MST. Finally, we use a clustering linkage procedure in order to observe the cluster structure. The results of the structural topologies of these trees are as follows: (i) we identified different clusters of countries according to their geographical location and economic growth, (ii) we found a strong relationship between energy consumption and economic growth for all income groups considered in this study and (iii) the results are in good agreement with the causal relationship between electricity consumption and economic growth.

50 CFR 216.211 - Specified activity and specified geographical region.

Code of Federal Regulations, 2012 CFR

2012-10-01

... and gas structure removal activities in areas within state and Federal waters in the U.S. Gulf of.... Gulf of Mexico § 216.211 Specified activity and specified geographical region. (a) Regulations in this...

Archaeological skeletons support a northwest European origin for Paget's disease of bone.

PubMed

Mays, Simon

2010-08-01

The strong genetic component in the etiology of Paget's disease of bone (PDB), together with marked geographic variation in its prevalence, with high frequencies in British populations, has led some to suggest that the disease originated in Britain and spread around the world in recent times by the migration and admixture of British populations. This study aims to investigate this hypothesis by studying the world geographic distribution of PDB cases identified in ancient skeletons excavated from archaeological sites. The methodology is a review of PDB cases described in the literature. There were 109 cases that met modern diagnostic criteria. All came from Western Europe, 94% from England. These data support the hypothesis that PDB originated in this geographic region.

Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?

PubMed Central

Marek, Paul E.

2017-01-01

For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we make several changes to the classification of the family, including transferring the rare state-threatened species Sigmoria whiteheadi Shelley, 1986 to the genus Apheloria Chamberlin, 1921—a relationship not readily apparent based on morphology alone. We show that while gonopod differences are a premier source of taxonomic characters to diagnose species pairwise, the traits should be viewed critically as taxonomic features uniting higher levels. PMID:29038750

Geographical differentiation of the floristic composition and structure of the herb layer of forest permanent plots in East Germany, Poland, and Belarus

Treesearch

Ewa Roo-Zielinska; Jerzy Solon

1998-01-01

The influences of a geographical location on floristic composition, horizontal structure, and biomass of the herb layer in pine and mixed pine forest communities along climatic and pollution gradients in East Germany, Poland, and Belarus were determined. Phytosociological records were collected in permanent plots in May 1995. Each record covered an area of 400 m

Geographic variation in Northwest Atlantic fin whale (Balaenoptera physalus) song: implications for stock structure assessment.

PubMed

Delarue, Julien; Todd, Sean K; Van Parijs, Sofie M; Di Iorio, Lucia

2009-03-01

Passive acoustic data are increasingly being used as a tool for helping to define marine mammal populations and stocks. Fin whale (Balaenoptera physalus) songs present a unique opportunity to determine interstock differences. Their highly stereotyped interpulse interval has been shown to vary between geographic areas and to remain stable over time in some areas. In this study the structure of songs recorded at two geographically close feeding aggregations in the Gulf of St. Lawrence (GSL) and Gulf of Maine (GoM) was compared. Recordings were made from September 2005 through February 2006 in the GSL and intermittently between January 2006 and September 2007 at two locations in the GoM. 6257 pulse intervals corresponding to 19 GSL and 29 GoM songs were measured to characterize songs from both areas. Classification trees showed that GSL songs differ significantly from those in the GoM. The results are consistent with those derived from other stock structure assessment methodologies, such as chemical signature and photoidentification analysis, suggesting that fin whales in these areas may form separate management stocks. Song structure analysis could therefore provide a useful and cost-efficient tool for defining conservation units over temporal and geographical scales relevant to management objectives in fin whales.

Population Explosion in the Yellow-Spined Bamboo Locust Ceracris kiangsu and Inferences for the Impact of Human Activity

PubMed Central

Fan, Zhou; Jiang, Guo-Fang; Liu, Yu-Xiang; He, Qi-Xin; Blanchard, Benjamin

2014-01-01

Geographic distance and geographical barriers likely play a considerable role in structuring genetic variation in species, although some migratory species may have less phylogeographic structure on a smaller spatial scale. Here, genetic diversity and the phylogenetic structure among geographical populations of the yellow-spined bamboo locust, Ceracris kiangsu, were examined with 16S rDNA and amplified fragment length polymorphisms (AFLPs). In this study, no conspicuous phylogeographical structure was discovered from either Maximum parsimony (MP) and Neighbor-joining (NJ) phylogenetic analyses. The effect of geographical isolation was not conspicuous on a large spatial scale.At smaller spatial scales local diversity of some populations within mountainous areas were detected using Nei's genetic distance and AMOVA. There is a high level of genetic diversity and a low genetic differentiation among populations in the C. kiangsu of South and Southeast China. Our analyses indicate that C. kiangsu is a monophyletic group. Our results also support the hypothesis that the C. kiangsu population is in a primary differentiation stage. Given the mismatch distribution, it is likely that a population expansion in C. kiangsu occurred about 0.242 Ma during the Quaternary interglaciation. Based on historical reports, we conjecture that human activities had significant impacts on the C. kiangsu gene flow. PMID:24603526

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish

PubMed Central

Torrente-Vilara, Gislene; Quilodran, Claudio; Rodrigues da Costa Doria, Carolina; Montoya-Burgos, Juan I.

2017-01-01

Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin. PMID:29261722

[EEG correlates of geno-phenotypical features of the brain development in children of the native and newcomers' population of the Russian North-East].

PubMed

Soroko, S I; Bekshaev, S S; Rozhkov, V P

2012-01-01

Traditional and original methods of EEG analysis were used to study the brain electrical activity maturation in 156 children and adolescents from 7 to 17 years old who represented the native (Koryaks and Evenks) and newcomers' populations living in severe climatic and geographic conditions of the Russian North-East. New data revealing age-, sex- and ethnic-related features in quantitative EEG parameters are presented. Markers are obtained that characterize alterations in the structure of interaction between different EEG rhythms. The results demonstrate age-dependent transformation of this structure separated in time for both different cortical areas and different EEG frequency bands. These alterations show time lag from 2 to 3 years in children of native population compared to the newcomers. The revealed differences are assumed to reflect geno-phenotypical features of morpho-functional CNS development in children of the native and newcomers' population that depend on strong adaptation tension for extreme environmental conditions.

Reptiles of Chubut province, Argentina: richness, diversity, conservation status and geographic distribution maps.

PubMed

Minoli, Ignacio; Morando, Mariana; Avila, Luciano Javier

2015-01-01

An accurate estimation of species and population geographic ranges is essential for species-focused studies and conservation and management plans. Knowledge of the geographic distributions of reptiles from Patagonian Argentina is in general limited and dispersed over manuscripts from a wide variety of topics. We completed an extensive review of reptile species of central Patagonia (Argentina) based on information from a wide variety of sources. We compiled and checked geographic distribution records from published literature and museum records, including extensive new data from the LJAMM-CNP (CENPAT-CONICET) herpetological collection. Our results show that there are 52 taxa recorded for this region and the highest species richness was seen in the families Liolaemidae and Dipsadidae with 31 and 10 species, respectively. The Patagónica was the phytogeographic province most diverse in species and Phymaturus was the genus of conservation concern most strongly associated with it. We present a detailed species list with geographical information, richness species, diversity analyses with comparisons across phytogeographical provinces, conservation status, taxonomic comments and distribution maps for all of these taxa.

Reptiles of Chubut province, Argentina: richness, diversity, conservation status and geographic distribution maps

PubMed Central

Minoli, Ignacio; Morando, Mariana; Avila, Luciano Javier

2015-01-01

Abstract An accurate estimation of species and population geographic ranges is essential for species-focused studies and conservation and management plans. Knowledge of the geographic distributions of reptiles from Patagonian Argentina is in general limited and dispersed over manuscripts from a wide variety of topics. We completed an extensive review of reptile species of central Patagonia (Argentina) based on information from a wide variety of sources. We compiled and checked geographic distribution records from published literature and museum records, including extensive new data from the LJAMM-CNP (CENPAT-CONICET) herpetological collection. Our results show that there are 52 taxa recorded for this region and the highest species richness was seen in the families Liolaemidae and Dipsadidae with 31 and 10 species, respectively. The Patagónica was the phytogeographic province most diverse in species and Phymaturus was the genus of conservation concern most strongly associated with it. We present a detailed species list with geographical information, richness species, diversity analyses with comparisons across phytogeographical provinces, conservation status, taxonomic comments and distribution maps for all of these taxa. PMID:25931966

Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles.

PubMed

Takacs-Vesbach, Cristina; Mitchell, Kendra; Jackson-Weaver, Olan; Reysenbach, Anna-Louise

2008-07-01

It has been suggested that the distribution of microorganisms should be cosmopolitan because of their enormous capacity for dispersal. However, recent studies have revealed that geographically isolated microbial populations do exist. Geographic distance as a barrier to dispersal is most often invoked to explain these distributions. Here we show that unique and diverse sequences of the bacterial genus Sulfurihydrogenibium exist in Yellowstone thermal springs, indicating that these sites are geographically isolated. Although there was no correlation with geographic distance or the associated geochemistry of the springs, there was a strong historical signal. We found that the Yellowstone calderas, remnants of prehistoric volcanic eruptions, delineate biogeographical provinces for the Sulfurihydrogenibium within Yellowstone (chi(2): 9.7, P = 0.002). The pattern of distribution that we have detected suggests that major geological events in the past 2 million years explain more of the variation in sequence diversity in this system than do contemporary factors such as habitat or geographic distance. These findings highlight the importance of historical legacies in determining contemporary microbial distributions and suggest that the same factors that determine the biogeography of macroorganisms are also evident among bacteria.

Range expansion of the jumbo squid in the NE Pacific: δ15N decrypts multiple origins, migration and habitat use.

PubMed

Ruiz-Cooley, Rocio I; Ballance, Lisa T; McCarthy, Matthew D

2013-01-01

Coincident with climate shifts and anthropogenic perturbations, the highly voracious jumbo squid Dosidicus gigas reached unprecedented northern latitudes along the NE Pacific margin post 1997-98. The physical or biological drivers of this expansion, as well as its ecological consequences remain unknown. Here, novel analysis from both bulk tissues and individual amino acids (Phenylalanine; Phe and Glutamic acid; Glu) in both gladii and muscle of D. gigas captured in the Northern California Current System (NCCS) documents for the first time multiple geographic origins and migration. Phe δ(15)N values, a proxy for habitat baseline δ(15)N values, confirm at least three different geographic origins that were initially detected by highly variable bulk δ(15)N values in gladii for squid at small sizes (<30 cm gladii length). In contrast, bulk δ(15)N values from gladii of large squid (>60 cm) converged, indicating feeding in a common ecosystem. The strong latitudinal gradient in Phe δ(15)N values from composite muscle samples further confirmed residency at a point in time for large squid in the NCCS. These results contrast with previous ideas, and indicate that small squid are highly migratory, move into the NCCS from two or more distinct geographic origins, and use this ecosystem mainly for feeding. These results represent the first direct information on the origins, immigration and habitat use of this key "invasive" predator in the NCCS, with wide implications for understanding both the mechanisms of periodic D. gigas population range expansions, and effects on ecosystem trophic structure.

Range Expansion of the Jumbo Squid in the NE Pacific: δ15N Decrypts Multiple Origins, Migration and Habitat Use

PubMed Central

Ruiz-Cooley, Rocio I.; Ballance, Lisa T.; McCarthy, Matthew D.

2013-01-01

Coincident with climate shifts and anthropogenic perturbations, the highly voracious jumbo squid Dosidicus gigas reached unprecedented northern latitudes along the NE Pacific margin post 1997–98. The physical or biological drivers of this expansion, as well as its ecological consequences remain unknown. Here, novel analysis from both bulk tissues and individual amino acids (Phenylalanine; Phe and Glutamic acid; Glu) in both gladii and muscle of D. gigas captured in the Northern California Current System (NCCS) documents for the first time multiple geographic origins and migration. Phe δ15N values, a proxy for habitat baseline δ15N values, confirm at least three different geographic origins that were initially detected by highly variable bulk δ15N values in gladii for squid at small sizes (<30 cm gladii length). In contrast, bulk δ15N values from gladii of large squid (>60 cm) converged, indicating feeding in a common ecosystem. The strong latitudinal gradient in Phe δ15N values from composite muscle samples further confirmed residency at a point in time for large squid in the NCCS. These results contrast with previous ideas, and indicate that small squid are highly migratory, move into the NCCS from two or more distinct geographic origins, and use this ecosystem mainly for feeding. These results represent the first direct information on the origins, immigration and habitat use of this key “invasive” predator in the NCCS, with wide implications for understanding both the mechanisms of periodic D. gigas population range expansions, and effects on ecosystem trophic structure. PMID:23527242

DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel

PubMed Central

Bedada, G; Westerbergh, A; Nevo, E; Korol, A; Schmid, K J

2014-01-01

Wild barley Hordeum spontaneum (L.) shows a wide geographic distribution and ecological diversity. A key question concerns the spatial scale at which genetic differentiation occurs and to what extent it is driven by natural selection. The Levant region exhibits a strong ecological gradient along the North–South axis, with numerous small canyons in an East–West direction and with small-scale environmental gradients on the opposing North- and South-facing slopes. We sequenced 34 short genomic regions in 54 accessions of wild barley collected throughout Israel and from the opposing slopes of two canyons. The nucleotide diversity of the total sample is 0.0042, which is about two-thirds of a sample from the whole species range (0.0060). Thirty accessions collected at ‘Evolution Canyon' (EC) at Nahal Oren, close to Haifa, have a nucleotide diversity of 0.0036, and therefore harbor a large proportion of the genetic diversity. There is a high level of genetic clustering throughout Israel and within EC, which roughly differentiates the slopes. Accessions from the hot and dry South-facing slope have significantly reduced genetic diversity and are genetically more distinct from accessions from the North-facing slope, which are more similar to accessions from other regions in Northern Israel. Statistical population models indicate that wild barley within the EC consist of three separate genetic clusters with substantial gene flow. The data indicate a high level of population structure at large and small geographic scales that shows isolation-by-distance, and is also consistent with ongoing natural selection contributing to genetic differentiation at a small geographic scale. PMID:24619177

Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study.

PubMed

Sun, Zhonglou; Pan, Tao; Wang, Hui; Pang, Mujia; Zhang, Baowei

2016-01-01

Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer ( Elaphodus cephalophus ) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline ( T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.

Geography-based structural analysis of the Internet

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

Kasiviswanathan, Shiva; Eidenbenz, Stephan; Yan, Guanhua

2010-01-01

In this paper, we study some geographic aspects of the Internet. We base our analysis on a large set of geolocated IP hop-level session data (including about 300,000 backbone routers, 150 million end hosts, and 1 billion sessions) that we synthesized from a variety of different input sources such as US census data, computer usage statistics, Internet market share data, IP geolocation data sets, CAJDA's Skitter data set for backbone connectivity, and BGP routing tables. We use this model to perform a nationwide and statewide geographic analysis of the Internet. Our main observations are: (1) There is a dominant coast-to-coastmore » pattern in the US Internet traffic. In fact, in many instances even if the end-devices are not near either coast, still the traffic between them takes a long detour through the coasts. (2) More than half of the Internet paths are inflated by 100% or more compared to their corresponding geometric straight-line distance. This circuitousness makes the average ratio between the routing distance and geometric distance big (around 10). (3) The weighted mean hop count is around 5, but the hop counts are very loosely correlated with the distances. The weighted mean AS count (number of ASes traversed) is around 3. (4) The AS size and the AS location number distributions are heavy-tailed and strongly correlated. Most of the ASes are medium sized and there is a wide variability in the geographic dispersion size (measured in terms of the convex hull area) of these ASes.« less

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

Polymorphic nuclear markers for coastal plant species with dynamic geographic distributions, the rock samphire (Crithmum maritimum) and the vulnerable dune pansy (Viola tricolor subsp. curtisii).

PubMed

Latron, Mathilde; Arnaud, Jean-François; Ferla, Héloïse; Godé, Cécile; Duputié, Anne

2018-06-01

Identifying spatial patterns of genetic differentiation across a species range is critical to set up conservation and restoration decision-making. This is especially timely, since global change triggers shifts in species' geographic distribution and in the geographical variation of mating system and patterns of genetic differentiation, with varying consequences at the trailing and leading edges of a species' distribution. Using 454 pyrosequencing, we developed nuclear microsatellite loci for two plant species showing a strictly coastal geographical distribution and contrasting range dynamics: the expanding rock samphire (Crithmum maritimum, 21 loci) and the highly endangered and receding dune pansy (Viola tricolor subsp. curtisii, 12 loci). Population genetic structure was then assessed by genotyping more than 100 individuals from four populations of each of the two target species. Rock samphire displayed high levels of genetic differentiation (F ST  = 0.38), and a genetic structure typical of a mostly selfing species (F IS ranging from 0.16 to 0.58). Populations of dune pansy showed a less pronounced level of population structuring (F ST  = 0.25) and a genotypic structure more suggestive of a mixed-mating system when excluding two loci with heterozygote excess. These results demonstrate that the genetic markers developed here are useful to assess the mating system of populations of these two species. They will be tools of choice to investigate phylogeographical patterns and variation in mating system over the geographical distribution ranges for two coastal plant species that are subject to dynamic evolution due to rapid contemporary global change.

[Family characteristics and the labor market in developed countries: a clear distinction between north and south].

PubMed

Barrere-maurisson, M; Marchand, O

1990-09-01

The relationship between family characteristics and the labor market is explored using data concerning 15 OECD countries. Several distinct geographical groupings are identified, including the Mediterranean countries, Scandinavia, North America, and Japan and West Germany. Belgium, France, the Netherlands, and the United Kingdom occupy a middle ground and are less specifically defined. Furthermore, "the statistical map shows a strong relationship which manifests itself in two opposite ways. On the one hand, it shows the link between a traditional family structure and a weak integration of women in the working population (Spain, Ireland), and, on the other hand, it shows a close link between a divided family and the fact women have a paying job, often just part time (Sweden, Denmark)." (SUMMARY IN ENG AND SPA) excerpt

North Atlantic Oscillation modulates total ozone winter trends

NASA Astrophysics Data System (ADS)

Appenzeller, Christof; Weiss, Andrea K.; Staehelin, Johannes

2000-04-01

The North Atlantic Oscillation (NAO) is modulating the Earth's ozone shield such that the calculated anthropogenic total ozone decrease is enhanced over Europe whereas over the North Atlantic region it is reduced (for the last 30 years). Including the NAO in a statistical model suggests a more uniform chemical winter trend compared to the strong longitudinal variation reported earlier. At Arosa (Switzerland) the trend is reduced to -2.4% per decade compared to -3.2% and at Reykjavik (Iceland) it is enhanced to -3.8% compared to 0%. The revised trend is slightly below the predictions by 2D chemical models. Decadal ozone variability is linked to variations in the dynamical structure of the atmosphere, as reflected in the tropopause pressure. The latter varies in concert with the NAO index with a distinct geographical pattern.

Advanced data structures for the interpretation of image and cartographic data in geo-based information systems

NASA Technical Reports Server (NTRS)

Peuquet, D. J.

1986-01-01

A growing need to usse geographic information systems (GIS) to improve the flexibility and overall performance of very large, heterogeneous data bases was examined. The Vaster structure and the Topological Grid structure were compared to test whether such hybrid structures represent an improvement in performance. The use of artificial intelligence in a geographic/earth sciences data base context is being explored. The architecture of the Knowledge Based GIS (KBGIS) has a dual object/spatial data base and a three tier hierarchial search subsystem. Quadtree Spatial Spectra (QTSS) are derived, based on the quadtree data structure, to generate and represent spatial distribution information for large volumes of spatial data.

Postglacial dispersal patterns and mitochondrial genetic structure of the Pyrenean desman (Galemys pyrenaicus) in the northwestern region of the Iberian Peninsula.

PubMed

Querejeta, Marina; Fernández-González, Angel; Romero, Rafael; Castresana, Jose

2017-06-01

The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman ( Galemys pyrenaicus ) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure. Thanks to different types of noninvasive samples, we obtained an extensive sampling of the Pyrenean desman from the northwestern region of the Iberian Peninsula and sequenced two mitochondrial DNA fragments. We then analyzed, using an isolation-by-distance approach, the correlation between phylogenetic distances and geographical distances measured along both river networks and land to infer the relative importance of river and overland dispersal. We found that the correlations in the whole area and in a large basin were consistent with an effect of overland dispersal, which may be due to the postglacial colonization of new territories using terrestrial corridors and, possibly, a more extensive fluvial network that may have been present during the Holocene. However, in a small basin, likely to be less influenced by the impact of ancient postglacial dispersal, the correlations suggested significant overall effects of both overland and river dispersal, as expected for a semiaquatic mammal. Therefore, different scales and geographical regions reflect different aspects of the evolutionary history and ecology of this semiaquatic species using this isolation-by-distance method. The results we obtained may have crucial implications for the conservation of the Pyrenean desman because they reinforce the importance of interbasin dispersal for this species in the studied area and the need to protect the whole riverine ecosystem, including rivers, upland streams and terrestrial corridors between basins.

A novel approach to parasite population genetics: experimental infection reveals geographic differentiation, recombination and host-mediated population structure in Pasteuria ramosa, a bacterial parasite of Daphnia.

PubMed

Andras, J P; Ebert, D

2013-02-01

The population structure of parasites is central to the ecology and evolution of host-parasite systems. Here, we investigate the population genetics of Pasteuria ramosa, a bacterial parasite of Daphnia. We used natural P. ramosa spore banks from the sediments of two geographically well-separated ponds to experimentally infect a panel of Daphnia magna host clones whose resistance phenotypes were previously known. In this way, we were able to assess the population structure of P. ramosa based on geography, host resistance phenotype and host genotype. Overall, genetic diversity of P. ramosa was high, and nearly all infected D. magna hosted more than one parasite haplotype. On the basis of the observation of recombinant haplotypes and relatively low levels of linkage disequilibrium, we conclude that P. ramosa engages in substantial recombination. Isolates were strongly differentiated by pond, indicating that gene flow is spatially restricted. Pasteuria ramosa isolates within one pond were segregated completely based on the resistance phenotype of the host-a result that, to our knowledge, has not been previously reported for a nonhuman parasite. To assess the comparability of experimental infections with natural P. ramosa isolates, we examined the population structure of naturally infected D. magna native to one of the two source ponds. We found that experimental and natural infections of the same host resistance phenotype from the same source pond were indistinguishable, indicating that experimental infections provide a means to representatively sample the diversity of P. ramosa while reducing the sampling bias often associated with studies of parasite epidemics. These results expand our knowledge of this model parasite, provide important context for the large existing body of research on this system and will guide the design of future studies of this host-parasite system. © 2012 Blackwell Publishing Ltd.

Evaluation of Geographic Indices Describing Health Care Utilization

PubMed Central

Park, Jong Heon

2017-01-01

Objectives The accurate measurement of geographic patterns of health care utilization is a prerequisite for the study of geographic variations in health care utilization. While several measures have been developed to measure how accurately geographic units reflect the health care utilization patterns of residents, they have been only applied to hospitalization and need further evaluation. This study aimed to evaluate geographic indices describing health care utilization. Methods We measured the utilization rate and four health care utilization indices (localization index, outflow index, inflow index, and net patient flow) for eight major procedures (coronary artery bypass graft surgery, percutaneous transluminal coronary angioplasty, surgery after hip fracture, knee replacement surgery, caesarean sections, hysterectomy, computed tomography scans, and magnetic resonance imaging scans) according to three levels of geographic units in Korea. Data were obtained from the National Health Insurance database in Korea. We evaluated the associations among the health care utilization indices and the utilization rates. Results In higher-level geographic units, the localization index tended to be high, while the inflow index and outflow index were lower. The indices showed different patterns depending on the procedure. A strong negative correlation between the localization index and the outflow index was observed for all procedures. Net patient flow showed a moderate positive correlation with the localization index and the inflow index. Conclusions Health care utilization indices can be used as a proxy to describe the utilization pattern of a procedure in a geographic unit. PMID:28173689

Transcontinental Phylogeography of the Daphnia pulex Species Complex

PubMed Central

Costanzo, Katie S.; Taylor, Derek J.

2012-01-01

Daphnia pulex is quickly becoming an attractive model species in the field of ecological genomics due to the recent release of its complete genome sequence, a wide variety of new genomic resources, and a rich history of ecological data. Sequences of the mitochondrial NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit 1 genes were used to assess the global phylogeography of this species, and to further elucidate its phylogenetic relationship to other members of the Daphnia pulex species complex. Using both newly acquired and previously published data, we analyzed 398 individuals from collections spanning five continents. Eleven strongly supported lineages were found within the D. pulex complex, and one lineage in particular, panarctic D. pulex, has very little phylogeographical structure and a near worldwide distribution. Mismatch distribution, haplotype network, and population genetic analyses are compatible with a North American origin for this lineage and subsequent spatial expansion in the Late Pleistocene. In addition, our analyses suggest that dispersal between North and South America of this and other species in the D. pulex complex has occurred multiple times, and is predominantly from north to south. Our results provide additional support for the evolutionary relationships of the eleven main mitochondrial lineages of the D. pulex complex. We found that the well-studied panarctic D. pulex is present on every continent except Australia and Antarctica. Despite being geographically very widespread, there is a lack of strong regionalism in the mitochondrial genomes of panarctic D. pulex – a pattern that differs from that of most studied cladocerans. Moreover, our analyses suggest recent expansion of the panarctic D. pulex lineage, with some continents sharing haplotypes. The hypothesis that hybrid asexuality has contributed to the recent and unusual geographic success of the panarctic D. pulex lineage warrants further study. PMID:23056371

Transcontinental phylogeography of the Daphnia pulex species complex.

PubMed

Crease, Teresa J; Omilian, Angela R; Costanzo, Katie S; Taylor, Derek J

2012-01-01

Daphnia pulex is quickly becoming an attractive model species in the field of ecological genomics due to the recent release of its complete genome sequence, a wide variety of new genomic resources, and a rich history of ecological data. Sequences of the mitochondrial NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit 1 genes were used to assess the global phylogeography of this species, and to further elucidate its phylogenetic relationship to other members of the Daphnia pulex species complex. Using both newly acquired and previously published data, we analyzed 398 individuals from collections spanning five continents. Eleven strongly supported lineages were found within the D. pulex complex, and one lineage in particular, panarctic D. pulex, has very little phylogeographical structure and a near worldwide distribution. Mismatch distribution, haplotype network, and population genetic analyses are compatible with a North American origin for this lineage and subsequent spatial expansion in the Late Pleistocene. In addition, our analyses suggest that dispersal between North and South America of this and other species in the D. pulex complex has occurred multiple times, and is predominantly from north to south. Our results provide additional support for the evolutionary relationships of the eleven main mitochondrial lineages of the D. pulex complex. We found that the well-studied panarctic D. pulex is present on every continent except Australia and Antarctica. Despite being geographically very widespread, there is a lack of strong regionalism in the mitochondrial genomes of panarctic D. pulex--a pattern that differs from that of most studied cladocerans. Moreover, our analyses suggest recent expansion of the panarctic D. pulex lineage, with some continents sharing haplotypes. The hypothesis that hybrid asexuality has contributed to the recent and unusual geographic success of the panarctic D. pulex lineage warrants further study.

Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region.

PubMed

Zhang, Yi; Lu, Yongfang; Yindee, Marnoch; Li, Kuan-Yi; Kuo, Hsiao-Yun; Ju, Yu-Ten; Ye, Shaohui; Faruque, Md Omar; Li, Qiang; Wang, Yachun; Cuong, Vu Chi; Pham, Lan Doan; Bouahom, Bounthong; Yang, Bingzhuang; Liang, Xianwei; Cai, Zhihua; Vankan, Dianne; Manatchaiworakul, Wallaya; Kowlim, Nonglid; Duangchantrasiri, Somphot; Wajjwalku, Worawidh; Colenbrander, Ben; Zhang, Yuan; Beerli, Peter; Lenstra, Johannes A; Barker, J Stuart F

2016-04-01

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock. © 2015 John Wiley & Sons Ltd.

Do larvae from deep-sea hydrothermal vents disperse in surface waters?

PubMed

Yahagi, Takuya; Kayama Watanabe, Hiromi; Kojima, Shigeaki; Kano, Yasunori

2017-06-01

Larval dispersal significantly contributes to the geographic distribution, population dynamics, and evolutionary processes of animals endemic to deep-sea hydrothermal vents. Little is known as to the extent that their larvae migrate vertically to shallower waters and experience stronger currents and richer food supplies. Here, we first provide evidence from early life-history traits and population genetics for the surface dispersal of a vent species. Planktotrophic larvae of a red blood limpet, Shinkailepas myojinensis (Gastropoda: Neritimorpha: Phenacolepadidae), were cultured to observe their swimming behavior and to evaluate the effects of temperature on survival and growth. In addition, the population structure was analyzed based on 1.2-kbp mitochondrial DNA sequences from 77 specimens that cover the geographic and bathymetric distributions of the species (northwest Pacific, 442-1,227 m in depth). Hatched larvae constantly swam upward at 16.6-44.2 mm/min depending on temperature. Vertical migration from hydrothermal vents to the surface, calculated to take ~4-43 d, is attainable given their lengthy survival time without feeding. Fed larvae best survived and grew at 25°C (followed by 20°C), which approximates the sea surface temperature in the geographic range of the species. Little or no growth was observed at the temperature of the vent habitat where adult limpets occur (≤15°C). Population genetic analyses showed no differentiation among localities that are <1,350 km apart. The larvae of S. myojinensis most likely migrate to the surface water, where high phytoplankton biomass and strong currents enable their growth and long distance dispersal over many months. Sea surface temperature may represent a critical factor in determining the geographic distribution of many vent endemic species with a planktotrophic early development, and in turn the faunal composition of individual vent sites and regions. © 2017 by the Ecological Society of America.

Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species

PubMed Central

Young, Emma F; Belchier, Mark; Hauser, Lorenz; Horsburgh, Gavin J; Meredith, Michael P; Murphy, Eugene J; Pascoal, Sonia; Rock, Jennifer; Tysklind, Niklas; Carvalho, Gary R

2015-01-01

Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a ‘seascape genetics’ approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts. PMID:26029262

Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific.

PubMed

Gao, Tianxiang; Wan, Zhenzhen; Song, Na; Zhang, Xiumei; Han, Zhiqiang

2014-12-01

A number of evolutionary mechanisms have been suggested for generating significant genetic structuring among marine fish populations in Northwestern Pacific. We used mtDNA control region to assess the factors in shaping the genetic structure of Japanese grenadier anchovy, Coilia nasus, an anadromous and estuarine coastal species, in Northwestern Pacific. Sixty seven individuals from four locations in Northwestern Pacific were sequenced for mitochondrial control region, detecting 61 haplotypes. The length of amplified control region varied from 677 to 754 bp. This length variability was due to the presence of varying numbers of a 38-bp tandemly repeated sequence. Two distinct lineages were detected, which might have diverged during Pleistocene low sea levels. There were strong differences in the geographical distribution of the two lineages. Analyses of molecular variance and the population statistic ΦST revealed significant genetic structure between China and Ariake Bay populations. Based on the frequency distribution of tandem repeat units, significant genetic differentiation was also detected between China and Ariake Bay populations. Isolation by distance seems to be the main factor driving present genetic structuring of C. nasus populations, indicating coastal dispersal pattern in this coastal species. Such an evolutionary process agrees well with some of the biological features characterizing this species.

Genetic diversity of Diaphorina citri and its endosymbionts across east and south-east Asia.

PubMed

Wang, Yanjing; Xu, Changbao; Tian, Mingyi; Deng, Xiaoling; Cen, Yijing; He, Yurong

2017-10-01

Diaphorina citri is the vector of 'Candidatus Liberibacter asiaticus', the most widespread pathogen associated huanglongbing, the most serious disease of citrus. To enhance our understanding of the distribution and origin of the psyllid, we investigated the genetic diversity and population structures of 24 populations in Asia and one from Florida based on the mtCOI gene. Simultaneously, genetic diversity and population structures of the primary endosymbiont (P-endosymbiont) 'Candidatus Carsonella ruddii' and secondary endosymbiont (S-endosymbiont) 'Candidatus Profftella armatura' of D. citri were determined with the housekeeping genes. AMOVA analysis indicated that populations of D. citri and its endosymbionts in east and south-east Asia were genetically distinct from populations in Pakistan and Florida. Furthermore, P-endosymbiont populations displayed a strong geographical structure across east and south-east Asia, while low genetic diversity indicated the absence of genetic structure among the populations of D. citri and its S-endosymbiont across these regions. The 'Ca. C. ruddii' is more diverse and structured than the D. citri and the 'Ca. P. armatura' across east and south-east Asia. Multiple introductions of the psyllid have occurred in China. Management application for controlling the pest is proposed based on the genetic information of D. citri and its endosymbionts. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Advancing the Hypothesis that Geographic Variations in Risk Factors Contribute Relatively Little to Observed Geographic Variations in Heart Disease and Stroke Mortality

PubMed Central

Howard, George; Cushman, Mary; Prineas, Ronald J.; Howard, Virginia J.; Moy, Claudia S.; Sullivan, Lisa M.; D’Agostino, Ralph B.; McClure, Leslie A.; Pulley, Lea Vonne; Safford, Monika M.

2009-01-01

Purpose Geographic variation in risk factors may underlie geographic disparities in coronary heart disease (CHD) and stroke mortality. Methods Framingham CHD Risk Score (FCRS) and Stroke Risk Score (FSRS) were calculated for 25,770 stroke-free and 22,247 CHD-free participants from the REasons for Geographic And Racial Differences in Stroke cohort. Vital statistics provided age-adjusted CHD and stroke mortality rates. In an ecologic analysis, the age-adjusted, race-sex weighted, average state-level risk factor levels were compared to state-level mortality rates. Results There was no relationship between CHD and stroke mortality rates (r = 0.04; p = 0.78), but there was between CHD and stroke risk scores at the individual (r = 0.68; p < 0.0001) and state (r = 0.64, p < 0.0001) level. There was a stronger (p < 0.0001) association between state-level FCRS and state-level CHD mortality (r = 0.28, p = 0.18), than between FSRS and stroke mortality (r = 0.12, p = 0.56). Conclusions Weak associations between CHD and stroke mortality and strong associations between CHD and stroke risk scores suggest geographic variation in risk factors may not underlie geographic variations in stroke and CHD mortality. The relationship between risk factor scores and mortality was stronger for CHD than stroke. PMID:19285103

Distinct population structure for co-occurring Anopheles goeldii and Anopheles triannulatus in Amazonian Brazil

PubMed Central

McKeon, Sascha Naomi; Moreno, Marta; Sallum, Maria Anise; Povoa, Marinete Marins; Conn, Jan Evelyn

2013-01-01

To evaluate whether environmental heterogeneity contributes to the genetic heterogeneity in Anopheles triannulatus, larval habitat characteristics across the Brazilian states of Roraima and Pará and genetic sequences were examined. A comparison with Anopheles goeldii was utilised to determine whether high genetic diversity was unique to An. triannulatus. Student t test and analysis of variance found no differences in habitat characteristics between the species. Analysis of population structure of An. triannulatus and An. goeldii revealed distinct demographic histories in a largely overlapping geographic range. Cytochrome oxidase I sequence parsimony networks found geographic clustering for both species; however nuclear marker networks depicted An. triannulatus with a more complex history of fragmentation, secondary contact and recent divergence. Evidence of Pleistocene expansions suggests both species are more likely to be genetically structured by geographic and ecological barriers than demography. We hypothesise that niche partitioning is a driving force for diversity, particularly in An. triannulatus. PMID:23903977

Structural and geographic shifts in the Washington warehousing industry : transportation impacts for the Green River Valley.

DOT National Transportation Integrated Search

2009-07-01

Establishment level employment data indicate that the warehousing industry has experienced rapid growth and : restructuring since 1998. This restructuring has resulted in geographic shifts at the national, regional, and local scales. : Uneven growth ...

Population genetics at three spatial scales of a rare sponge living in fragmented habitats

PubMed Central

2010-01-01

Background Rare species have seldom been studied in marine habitats, mainly because it is difficult to formally assess the status of rare species, especially in patchy benthic organisms, for which samplings are often assumed to be incomplete and, thus, inappropriate for establishing the real abundance of the species. However, many marine benthic invertebrates can be considered rare, due to the fragmentation and rarity of suitable habitats. Consequently, studies on the genetic connectivity of rare species in fragmented habitats are basic for assessing their risk of extinction, especially in the context of increased habitat fragmentation by human activities. Sponges are suitable models for studying the intra- and inter-population genetic variation of rare invertebrates, as they produce lecitotrophic larvae and are often found in fragmented habitats. Results We investigated the genetic structure of a Mediterranean sponge, Scopalina lophyropoda (Schmidt), using the allelic size variation of seven specific microsatellite loci. The species can be classified as "rare" because of its strict habitat requirements, the low number of individuals per population, and the relatively small size of its distribution range. It also presents a strong patchy distribution, philopatric larval dispersal, and both sexual and asexual reproduction. Classical genetic-variance-based methods (AMOVA) and differentiation statistics revealed that the genetic diversity of S. lophyropoda was structured at the three spatial scales studied: within populations, between populations of a geographic region, and between isolated geographic regions, although some stochastic gene flow might occur among populations within a region. The genetic structure followed an isolation-by-distance pattern according to the Mantel test. However, despite philopatric larval dispersal and fission events in the species, no single population showed inbreeding, and the contribution of clonality to the population makeup was minor (only ca. 4%). Conclusions The structure of the S. lophyropoda populations at all spatial scales examined confirms the philopatric larval dispersal that has been reported. Asexual reproduction does not seem to play a relevant role in the populations. The heterozygote excess and the lack of inbreeding could be interpreted as a hitherto unknown outcrossing strategy of the species. The envisaged causes for this strategy are sperm dispersal, a strong selection against the mating of genetically related individuals to avoid inbreeding depression or high longevity of genets combined with stochastic recruitment events by larvae from other populations. It should be investigated whether this strategy could also explain the genetic diversity of many other patchy marine invertebrates whose populations remain healthy over time, despite their apparent rarity. PMID:20074333

Geographically Modified PageRank Algorithms: Identifying the Spatial Concentration of Human Movement in a Geospatial Network.

PubMed

Chin, Wei-Chien-Benny; Wen, Tzai-Hung

2015-01-01

A network approach, which simplifies geographic settings as a form of nodes and links, emphasizes the connectivity and relationships of spatial features. Topological networks of spatial features are used to explore geographical connectivity and structures. The PageRank algorithm, a network metric, is often used to help identify important locations where people or automobiles concentrate in the geographical literature. However, geographic considerations, including proximity and location attractiveness, are ignored in most network metrics. The objective of the present study is to propose two geographically modified PageRank algorithms-Distance-Decay PageRank (DDPR) and Geographical PageRank (GPR)-that incorporate geographic considerations into PageRank algorithms to identify the spatial concentration of human movement in a geospatial network. Our findings indicate that in both intercity and within-city settings the proposed algorithms more effectively capture the spatial locations where people reside than traditional commonly-used network metrics. In comparing location attractiveness and distance decay, we conclude that the concentration of human movement is largely determined by the distance decay. This implies that geographic proximity remains a key factor in human mobility.

Geographical assemblages of European raptors and owls

NASA Astrophysics Data System (ADS)

López-López, Pascual; Benavent-Corai, José; García-Ripollés, Clara

2008-09-01

In this work we look for geographical structure patterns in European raptors (Order: Falconiformes) and owls (Order: Strigiformes). For this purpose we have conducted our research using freely available tools such as statistical software and databases. To perform the study, presence-absence data for the European raptors and owl species (Class Aves) were downloaded from the BirdLife International website. Using the freely available "pvclust" R-package, we applied similarity Jaccard index and cluster analysis in order to delineate biogeographical relationships for European countries. According to the cluster of similarity, we found that Europe is structured into two main geographical assemblages. The larger length branch separated two main groups: one containing Iceland, Greenland and the countries of central, northern and northwestern Europe, and the other group including the countries of eastern, southern and southwestern Europe. Both groups are divided into two main subgroups. According to our results, the European raptors and owls could be considered structured into four meta-communities well delimited by suture zones defined by Remington (1968) [Remington, C.L., 1968. Suture-zones of hybrid interaction between recently joined biotas. Evol. Biol. 2, 321-428]. Climatic oscillations during the Quaternary Ice Ages could explain at least in part the modern geographical distribution of the group.

Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences.

PubMed

Che, Xianli; Zhang, Min; Zhao, Yanyan; Zhang, Qiang; Quan, Qing; Møller, Anders; Zou, Fasheng

2018-01-19

Ecological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.

Paternity analysis reveals wide pollen dispersal and high multiple paternity in a small isolated population of the bird-pollinated Eucalyptus caesia (Myrtaceae).

PubMed

Bezemer, N; Krauss, S L; Phillips, R D; Roberts, D G; Hopper, S D

2016-12-01

Optimal foraging behaviour by nectavores is expected to result in a leptokurtic pollen dispersal distribution and predominantly near-neighbour mating. However, complex social interactions among nectarivorous birds may result in different mating patterns to those typically observed in insect-pollinated plants. Mating system, realised pollen dispersal and spatial genetic structure were examined in the bird-pollinated Eucalyptus caesia, a species characterised by small, geographically disjunct populations. Nine microsatellite markers were used to genotype an entire adult stand and 181 seeds from 28 capsules collected from 6 trees. Mating system analysis using MLTR revealed moderate to high outcrossing (t m =0.479-0.806) and low estimates of correlated paternity (r p =0.136±s.e. 0.048). Paternity analysis revealed high outcrossing rates (mean=0.72) and high multiple paternity, with 64 different sires identified for 181 seeds. There was a significant negative relationship between the frequency of outcross mating and distance between mating pairs. Realised mating events were more frequent than expected with random mating for plants <40 m apart. The overall distribution of pollen dispersal distances was platykurtic. Despite extensive pollen dispersal within the stand, three genetic clusters were detected by STRUCTURE analysis. These genetic clusters were strongly differentiated yet geographically interspersed, hypothesised to be a consequence of rare recruitment events coupled with extreme longevity. We suggest that extensive polyandry and pollen dispersal is a consequence of pollination by highly mobile honeyeaters and may buffer E. caesia against the loss of genetic diversity predicted for small and genetically isolated populations.

Paternity analysis reveals wide pollen dispersal and high multiple paternity in a small isolated population of the bird-pollinated Eucalyptus caesia (Myrtaceae)

PubMed Central

Bezemer, N; Krauss, S L; Phillips, R D; Roberts, D G; Hopper, S D

2016-01-01

Optimal foraging behaviour by nectavores is expected to result in a leptokurtic pollen dispersal distribution and predominantly near-neighbour mating. However, complex social interactions among nectarivorous birds may result in different mating patterns to those typically observed in insect-pollinated plants. Mating system, realised pollen dispersal and spatial genetic structure were examined in the bird-pollinated Eucalyptus caesia, a species characterised by small, geographically disjunct populations. Nine microsatellite markers were used to genotype an entire adult stand and 181 seeds from 28 capsules collected from 6 trees. Mating system analysis using MLTR revealed moderate to high outcrossing (tm=0.479–0.806) and low estimates of correlated paternity (rp=0.136±s.e. 0.048). Paternity analysis revealed high outcrossing rates (mean=0.72) and high multiple paternity, with 64 different sires identified for 181 seeds. There was a significant negative relationship between the frequency of outcross mating and distance between mating pairs. Realised mating events were more frequent than expected with random mating for plants <40 m apart. The overall distribution of pollen dispersal distances was platykurtic. Despite extensive pollen dispersal within the stand, three genetic clusters were detected by STRUCTURE analysis. These genetic clusters were strongly differentiated yet geographically interspersed, hypothesised to be a consequence of rare recruitment events coupled with extreme longevity. We suggest that extensive polyandry and pollen dispersal is a consequence of pollination by highly mobile honeyeaters and may buffer E. caesia against the loss of genetic diversity predicted for small and genetically isolated populations. PMID:27530908

Fluid spatial dynamics of West Nile virus in the USA: Rapid spread in a permissive host environment

USGS Publications Warehouse

Di Giallonardo , Francesca; Geoghegan, Jemma L.; Docherty, Douglas E.; McLean, Robert G.; Zody, Michael C.; Qu, James; Yang, Xiao; Birren, Bruce W.; Malboeuf, Christine M.; Newman, R.; Ip, Hon S.; Holmes, Edward C.

2016-01-01

The introduction of West Nile virus (WNV) into North America in 1999 is a classical example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology we sequenced the complete genomes of approximately 300 avian isolates sampled across the USA between 2001-2012. Phylogenetic analysis revealed a relatively ‘star-like' tree structure, indicative of explosive viral spread in US, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well sampled avian species. The genome sequence data analysed here also contain relatively little evidence for adaptive evolution, particularly on structural proteins, suggesting that most viral lineages are of similar fitness, and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the USA. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers.

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.

Genetic Drift Linked to Heterogeneous Landscape and Ecological Specialization Drives Diversification in the Alpine Endemic Columbine Aquilegia thalictrifolia.

PubMed

Lega, Margherita; Fior, Simone; Li, Mingai; Leonardi, Stefano; Varotto, Claudio

2014-01-01

The European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia represents a textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographic area are still widely unexplored. In this work, we used 9 microsatellite loci to study the genetic structure and diversity of 11 populations of Aquilegia thalictrifolia Schott & Kotschy, an alpine taxon characterized by a marked ecological specificity. We found that, despite the endemic and fragmented distribution, A. thalictrifolia has overall high levels of heterozygosity, which is consistent to the substantial inbreeding depression that characterizes the genus. Strong spatial genetic structuring of populations suggests a historical prevalence of genetic drift over gene flow, with natural barriers and ecological niche hindering migration. An analytical comparison of fixation and population differentiation indexes allowed us to infer hypotheses of the postglacial history and more recent demographic events that have influenced the genetics of the species. Overall, our results indicate allopatry as a major force of differentiation in the European scenario, likely to underlie the development of taxonomic boundaries in a broader geographic context. This adds to previous notions on the primary evolutionary forces shaping the Aquilegia radiation in Europe. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana

PubMed Central

Colosimo, Giuliano; Knapp, Charles R.; Wallace, Lisa E.; Welch, Mark E.

2014-01-01

Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA) indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p0.01). These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes. PMID:25229344

Palaeo-islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae).

PubMed

Mairal, M; Sanmartín, I; Aldasoro, J J; Culshaw, V; Manolopoulou, I; Alarcón, M

2015-08-01

Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable 'palaeo-islands' of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between-islands. We argue that volcanic eruptions and landslides after the merging of the palaeo-islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo-islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago. © 2015 John Wiley & Sons Ltd.

Advanced techniques for the storage and use of very large, heterogeneous spatial databases. The representation of geographic knowledge: Toward a universal framework. [relations (mathematics)

NASA Technical Reports Server (NTRS)

Peuquet, Donna J.

1987-01-01

A new approach to building geographic data models that is based on the fundamental characteristics of the data is presented. An overall theoretical framework for representing geographic data is proposed. An example of utilizing this framework in a Geographic Information System (GIS) context by combining artificial intelligence techniques with recent developments in spatial data processing techniques is given. Elements of data representation discussed include hierarchical structure, separation of locational and conceptual views, and the ability to store knowledge at variable levels of completeness and precision.

The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

PubMed Central

2011-01-01

Background While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m) may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot Cyanoliseus patagonus (Aves, Psittaciformes) across its wide distributional range in Chile and Argentina. Results Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data. Conclusions Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations. PMID:21672266

Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique.

PubMed

Bartáková, Veronika; Reichard, Martin; Janko, Karel; Polačik, Matej; Blažek, Radim; Reichwald, Kathrin; Cellerino, Alessandro; Bryja, Josef

2013-09-12

Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.

Spatio-Temporal Patterns of the International Merger and Acquisition Network.

PubMed

Dueñas, Marco; Mastrandrea, Rossana; Barigozzi, Matteo; Fagiolo, Giorgio

2017-09-07

This paper analyses the world web of mergers and acquisitions (M&As) using a complex network approach. We use data of M&As to build a temporal sequence of binary and weighted-directed networks for the period 1995-2010 and 224 countries (nodes) connected according to their M&As flows (links). We study different geographical and temporal aspects of the international M&A network (IMAN), building sequences of filtered sub-networks whose links belong to specific intervals of distance or time. Given that M&As and trade are complementary ways of reaching foreign markets, we perform our analysis using statistics employed for the study of the international trade network (ITN), highlighting the similarities and differences between the ITN and the IMAN. In contrast to the ITN, the IMAN is a low density network characterized by a persistent giant component with many external nodes and low reciprocity. Clustering patterns are very heterogeneous and dynamic. High-income economies are the main acquirers and are characterized by high connectivity, implying that most countries are targets of a few acquirers. Like in the ITN, geographical distance strongly impacts the structure of the IMAN: link-weights and node degrees have a non-linear relation with distance, and an assortative pattern is present at short distances.

An Ancient Divide in a Contiguous Rainforest: Endemic Earthworms in the Australian Wet Tropics.

PubMed

Moreau, Corrie S; Hugall, Andrew F; McDonald, Keith R; Jamieson, Barrie G M; Moritz, Craig

2015-01-01

Understanding the factors that shape current species diversity is a fundamental aim of ecology and evolutionary biology. The Australian Wet Tropics (AWT) are a system in which much is known about how the rainforests and the rainforest-dependent organisms reacted to late Pleistocene climate changes, but less is known about how events deeper in time shaped speciation and extinction in this highly endemic biota. We estimate the phylogeny of a species-rich endemic genus of earthworms (Terrisswalkerius) from the region. Using DEC and DIVA historical biogeography methods we find a strong signal of vicariance among known biogeographical sub-regions across the whole phylogeny, congruent with the phylogeography of less diverse vertebrate groups. Absolute dating estimates, in conjunction with relative ages of major biogeographic disjunctions across Australia, indicate that diversification in Terrisswalkerius dates back before the mid-Miocene shift towards aridification, into the Paleogene era of isolation of mesothermal Gondwanan Australia. For the Queensland endemic Terrisswalkerius earthworms, the AWT have acted as both a museum of biological diversity and as the setting for continuing geographically structured diversification. These results suggest that past events affecting organismal diversification can be concordant across phylogeographic to phylogenetic levels and emphasize the value of multi-scale analysis, from intra- to interspecies, for understanding the broad-scale processes that have shaped geographic diversity.

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

PubMed

Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

2017-01-01

Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Structures data collection for The National Map using volunteered geographic information

USGS Publications Warehouse

Poore, Barbara S.; Wolf, Eric B.; Korris, Erin M.; Walter, Jennifer L.; Matthews, Greg D.

2012-01-01

The U.S. Geological Survey (USGS) has historically sponsored volunteered data collection projects to enhance its topographic paper and digital map products. This report describes one phase of an ongoing project to encourage volunteers to contribute data to The National Map using online editing tools. The USGS recruited students studying geographic information systems (GIS) at the University of Colorado Denver and the University of Denver in the spring of 2011 to add data on structures - manmade features such as schools, hospitals, and libraries - to four quadrangles covering metropolitan Denver. The USGS customized a version of the online Potlatch editor created by the OpenStreetMap project and populated it with 30 structure types drawn from the Geographic Names Information System (GNIS), a USGS database of geographic features. The students corrected the location and attributes of these points and added information on structures that were missing. There were two rounds of quality control. Student volunteers reviewed each point, and an in-house review of each point by the USGS followed. Nine-hundred and thirty-eight structure points were initially downloaded from the USGS database. Editing and quality control resulted in 1,214 structure points that were subsequently added to The National Map. A post-project analysis of the data shows that after student edit and peer review, 92 percent of the points contributed by volunteers met National Map Accuracy Standards for horizontal accuracy. Lessons from this project will be applied to later phases. These include: simplifying editing tasks and the user interfaces, stressing to volunteers the importance of adding structures that are missing, and emphasizing the importance of conforming to editorial guidelines for formatting names and addresses of structures. The next phase of the project will encompass the entire State of Colorado and will allow any citizen to contribute structures data. Volunteers will benefit from this project by engaging with their local geography and contributing to a national resource of topographic information that remains in the public domain for anyone to download.

Cooperation and Patience: The Key To A High Quality, Sustainable GIS

DOT National Transportation Integrated Search

1998-09-16

Geographic Information Systems (GIS) provides a powerful tool to transportation : planners and engineers for a variety of analytical tasks. However, even with : the advent of PC-based GIS systems and strong state and federal support, : transportation...

Microbial evolution of sulphate reduction when lateral gene transfer is geographically restricted.

PubMed

Chi Fru, E

2011-07-01

Lateral gene transfer (LGT) is an important mechanism by which micro-organisms acquire new functions. This process has been suggested to be central to prokaryotic evolution in various environments. However, the influence of geographical constraints on the evolution of laterally acquired genes in microbial metabolic evolution is not yet well understood. In this study, the influence of geographical isolation on the evolution of laterally acquired dissimilatory sulphite reductase (dsr) gene sequences in the sulphate-reducing micro-organisms (SRM) was investigated. Sequences on four continental blocks related to SRM known to have received dsr by LGT were analysed using standard phylogenetic and multidimensional statistical methods. Sequences related to lineages with large genetic diversity correlated positively with habitat divergence. Those affiliated to Thermodesulfobacterium indicated strong biogeographical delineation; hydrothermal-vent sequences clustered independently from hot-spring sequences. Some of the hydrothermal-vent and hot-spring sequences suggested to have been acquired from a common ancestral source may have diverged upon isolation within distinct habitats. In contrast, analysis of some Desulfotomaculum sequences indicated they could have been transferred from different ancestral sources but converged upon isolation within the same niche. These results hint that, after lateral acquisition of dsr genes, barriers to gene flow probably play a strong role in their subsequent evolution.

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies

PubMed Central

Bao, Wenquan; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-e

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%–36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau. PMID:29186199

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies.

PubMed

Bao, Wenquan; Wuyun, Tana; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-E

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.

Genetic Structure in the Seabuckthorn Carpenter Moth (Holcocerus hippophaecolus) in China: The Role of Outbreak Events, Geographical and Host Factors

PubMed Central

Tao, Jing; Chen, Min; Zong, Shi-Xiang; Luo, You-Qing

2012-01-01

Understanding factors responsible for structuring genetic diversity is of fundamental importance in evolutionary biology. The seabuckthorn carpenter moth (Holcocerus hippophaecolus Hua) is a native species throughout the north of China and is considered the main threat to seabuckthorn, Hippophae rhamnoides L. We assessed the influence of outbreaks, environmental factors and host species in shaping the genetic variation and structure of H. hippophaecolus by using Amplified Fragment Length Polymorphism (AFLP) markers. We rejected the hypothesis that outbreak-associated genetic divergence exist, as evidenced by genetic clusters containing a combination of populations from historical outbreak areas, as well as non-outbreak areas. Although a small number of markers (4 of 933 loci) were identified as candidates under selection in response to population densities. H. hippophaecolus also did not follow an isolation-by-distance pattern. We rejected the hypothesis that outbreak and drought events were driving the genetic structure of H. hippophaecolus. Rather, the genetic structure appears to be influenced by various confounding bio-geographical factors. There were detectable genetic differences between H. hippophaecolus occupying different host trees from within the same geographic location. Host-associated genetic divergence should be confirmed by further investigation. PMID:22291983

Early childhood gut microbiomes show strong geographic differences among subjects at high risk for type 1 diabetes.

PubMed

Kemppainen, Kaisa M; Ardissone, Alexandria N; Davis-Richardson, Austin G; Fagen, Jennie R; Gano, Kelsey A; León-Novelo, Luis G; Vehik, Kendra; Casella, George; Simell, Olli; Ziegler, Anette G; Rewers, Marian J; Lernmark, Åke; Hagopian, William; She, Jin-Xiong; Krischer, Jeffrey P; Akolkar, Beena; Schatz, Desmond A; Atkinson, Mark A; Triplett, Eric W

2015-02-01

Gut microbiome dysbiosis is associated with numerous diseases, including type 1 diabetes. This pilot study determines how geographical location affects the microbiome of infants at high risk for type 1 diabetes in a population of homogenous HLA class II genotypes. High-throughput 16S rRNA sequencing was performed on stool samples collected from 90 high-risk, nonautoimmune infants participating in The Environmental Determinants of Diabetes in the Young (TEDDY) study in the U.S., Germany, Sweden, and Finland. Study site-specific patterns of gut colonization share characteristics across continents. Finland and Colorado have a significantly lower bacterial diversity, while Sweden and Washington state are dominated by Bifidobacterium in early life. Bacterial community diversity over time is significantly different by geographical location. The microbiome of high-risk infants is associated with geographical location. Future studies aiming to identify the microbiome disease phenotype need to carefully consider the geographical origin of subjects. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

Prediction of Pig Trade Movements in Different European Production Systems Using Exponential Random Graph Models.

PubMed

Relun, Anne; Grosbois, Vladimir; Alexandrov, Tsviatko; Sánchez-Vizcaíno, Jose M; Waret-Szkuta, Agnes; Molia, Sophie; Etter, Eric Marcel Charles; Martínez-López, Beatriz

2017-01-01

In most European countries, data regarding movements of live animals are routinely collected and can greatly aid predictive epidemic modeling. However, the use of complete movements' dataset to conduct policy-relevant predictions has been so far limited by the massive amount of data that have to be processed (e.g., in intensive commercial systems) or the restricted availability of timely and updated records on animal movements (e.g., in areas where small-scale or extensive production is predominant). The aim of this study was to use exponential random graph models (ERGMs) to reproduce, understand, and predict pig trade networks in different European production systems. Three trade networks were built by aggregating movements of pig batches among premises (farms and trade operators) over 2011 in Bulgaria, Extremadura (Spain), and Côtes-d'Armor (France), where small-scale, extensive, and intensive pig production are predominant, respectively. Three ERGMs were fitted to each network with various demographic and geographic attributes of the nodes as well as six internal network configurations. Several statistical and graphical diagnostic methods were applied to assess the goodness of fit of the models. For all systems, both exogenous (attribute-based) and endogenous (network-based) processes appeared to govern the structure of pig trade network, and neither alone were capable of capturing all aspects of the network structure. Geographic mixing patterns strongly structured pig trade organization in the small-scale production system, whereas belonging to the same company or keeping pigs in the same housing system appeared to be key drivers of pig trade, in intensive and extensive production systems, respectively. Heterogeneous mixing between types of production also explained a part of network structure, whichever production system considered. Limited information is thus needed to capture most of the global structure of pig trade networks. Such findings will be useful to simplify trade networks analysis and better inform European policy makers on risk-based and more cost-effective prevention and control against swine diseases such as African swine fever, classical swine fever, or porcine reproductive and respiratory syndrome.

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

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

Geographic variation in mixed-conifer forest fire regimes in California

Treesearch

Beaty R. Matthew; Taylor Alan H.

2008-01-01

This paper reviews recent research from California on geographic variability in mixed conifer(MC) forest fire regimes. MC forests are typically described as having experienced primarilyfrequent, low to moderate severity burns prior to fire suppression that created a mosaic ofvegetation patches with variable structure. Research...

Tropical Aquatic Archaea Show Environment-Specific Community Composition

PubMed Central

Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

2013-01-01

The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota , a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

Changes to zooplankton community structure following colonization of a small lake by Leptodora kindti

USGS Publications Warehouse

McNaught, A.S.; Kiesling, R.L.; Ghadouani, A.

2004-01-01

The predaceous cladoceran Leptodora kindti (Focke) became established in Third Sister Lake, Michigan, after individuals escaped from experimental enclosures in 1987. By 1988, the Leptodora population exhibited seasonal dynamics characteristic of natural populations. The maximum seasonal abundance of Leptodora increased to 85 individuals m-3 3 yr following the introduction. After the appearance of Leptodora, small-bodied cladocerans (Ceriodaphnia and Bosmina) virtually disappeared from the lake. There were strong seasonal shifts in the dominance patterns of both cladocerans and copepods, and Daphnia species diversity increased. Results from this unplanned introduction suggest that invertebrate predators can have a rapid and lasting effect on prey populations, even in the presence of planktivorous fish. Small-scale (<20 km) geographic barriers might be as important as large-scale barriers to dispersal of planktonic animals.

Seismic High Attenuation Beneath Southern New England Indicates High Asthenospheric Temperature and No Melt

NASA Astrophysics Data System (ADS)

Dong, M. T.; Menke, W. H.

2017-12-01

Seismic attenuation exhibits strong geographic variability in northeastern North America, with the highest values associated with the previously-recognized Northern Appalachian Anomaly (NAA) in southern New England. The shear wave quality factor at 100 km depth is 14s<25, the ratio of P-wave and S-wave quality factors is QP/Qs=1.2±0.03, and the frequency dependence parameter is α=0.39±0.025. The high values of Qp/Qs and α are compatible with laboratory measurements of unmelted rock and incompatible with widespread melting. The low Qs (high shear attenuation) implies high mantle temperatures ( 1550-1650°C) at 100 km depth (assuming no melt). Small-scale variations in attenuation suggests structural heterogeneity within the NAA, possibly due to lithospheric delamination caused by directional asthenospheric flow.

Geographically Modified PageRank Algorithms: Identifying the Spatial Concentration of Human Movement in a Geospatial Network

PubMed Central

2015-01-01

A network approach, which simplifies geographic settings as a form of nodes and links, emphasizes the connectivity and relationships of spatial features. Topological networks of spatial features are used to explore geographical connectivity and structures. The PageRank algorithm, a network metric, is often used to help identify important locations where people or automobiles concentrate in the geographical literature. However, geographic considerations, including proximity and location attractiveness, are ignored in most network metrics. The objective of the present study is to propose two geographically modified PageRank algorithms—Distance-Decay PageRank (DDPR) and Geographical PageRank (GPR)—that incorporate geographic considerations into PageRank algorithms to identify the spatial concentration of human movement in a geospatial network. Our findings indicate that in both intercity and within-city settings the proposed algorithms more effectively capture the spatial locations where people reside than traditional commonly-used network metrics. In comparing location attractiveness and distance decay, we conclude that the concentration of human movement is largely determined by the distance decay. This implies that geographic proximity remains a key factor in human mobility. PMID:26437000

The Sampling Scheme Matters: Pan troglodytes troglodytes and P. t. schweinfurthii Are Characterized by Clinal Genetic Variation Rather Than a Strong Subspecies Break

PubMed Central

Fünfstück, Tillmann; Arandjelovic, Mimi; Morgan, David B.; Sanz, Crickette; Reed, Patricia; Olson, Sarah H.; Cameron, Ken; Ondzie, Alain; Peeters, Martine; Vigilant, Linda

2015-01-01

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. PMID:25330245

Stronger tests of mechanisms underlying geographic gradients of biodiversity: insights from the dimensionality of biodiversity.

PubMed

Stevens, Richard D; Tello, J Sebastián; Gavilanez, María Mercedes

2013-01-01

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km(2) grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota.

A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica.

PubMed

Ortiz-Rodriguez, Andrés Ernesto; Ornelas, Juan Francisco; Ruiz-Sanchez, Eduardo

2018-05-01

The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions. Copyright © 2018 Elsevier Inc. All rights reserved.

Stronger Tests of Mechanisms Underlying Geographic Gradients of Biodiversity: Insights from the Dimensionality of Biodiversity

PubMed Central

Stevens, Richard D.; Tello, J. Sebastián; Gavilanez, María Mercedes

2013-01-01

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km2 grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota. PMID:23451099

The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break.

PubMed

Fünfstück, Tillmann; Arandjelovic, Mimi; Morgan, David B; Sanz, Crickette; Reed, Patricia; Olson, Sarah H; Cameron, Ken; Ondzie, Alain; Peeters, Martine; Vigilant, Linda

2015-02-01

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. Copyright © 2014 Wiley Periodicals, Inc.

Investigating the capabilities of semantic enrichment of 3D CityEngine data

NASA Astrophysics Data System (ADS)

Solou, Dimitra; Dimopoulou, Efi

2016-08-01

In recent years the development of technology and the lifting of several technical limitations, has brought the third dimension to the fore. The complexity of urban environments and the strong need for land administration, intensify the need of using a three-dimensional cadastral system. Despite the progress in the field of geographic information systems and 3D modeling techniques, there is no fully digital 3D cadastre. The existing geographic information systems and the different methods of three-dimensional modeling allow for better management, visualization and dissemination of information. Nevertheless, these opportunities cannot be totally exploited because of deficiencies in standardization and interoperability in these systems. Within this context, CityGML was developed as an international standard of the Open Geospatial Consortium (OGC) for 3D city models' representation and exchange. CityGML defines geometry and topology for city modeling, also focusing on semantic aspects of 3D city information. The scope of CityGML is to reach common terminology, also addressing the imperative need for interoperability and data integration, taking into account the number of available geographic information systems and modeling techniques. The aim of this paper is to develop an application for managing semantic information of a model generated based on procedural modeling. The model was initially implemented in CityEngine ESRI's software, and then imported to ArcGIS environment. Final goal was the original model's semantic enrichment and then its conversion to CityGML format. Semantic information management and interoperability seemed to be feasible by the use of the 3DCities Project ESRI tools, since its database structure ensures adding semantic information to the CityEngine model and therefore automatically convert to CityGML for advanced analysis and visualization in different application areas.

Genetic differentiation associated with host plants and geography among six widespread species of South American Blepharoneura fruit flies (Tephritidae).

PubMed

Ottens, K; Winkler, I S; Lewis, M L; Scheffer, S J; Gomes-Costa, G A; Condon, M A; Forbes, A A

2017-04-01

Tropical herbivorous insects are astonishingly diverse, and many are highly host-specific. Much evidence suggests that herbivorous insect diversity is a function of host plant diversity; yet, the diversity of some lineages exceeds the diversity of plants. Although most species of herbivorous fruit flies in the Neotropical genus Blepharoneura are strongly host-specific (they deposit their eggs in a single host plant species and flower sex), some species are collected from multiple hosts or flowers and these may represent examples of lineages that are diversifying via changes in host use. Here, we investigate patterns of diversification within six geographically widespread Blepharoneura species that have been collected and reared from at least two host plant species or host plant parts. We use microsatellites to (1) test for evidence of local genetic differentiation associated with different sympatric hosts (different plant species or flower sexes) and (2) examine geographic patterns of genetic differentiation across multiple South American collection sites. In four of the six fly species, we find evidence of local genetic differences between flies collected from different hosts. All six species show evidence of geographic structure, with consistent differences between flies collected in the Guiana Shield and flies collected in Amazonia. Continent-wide analyses reveal - in all but one instance - that genetically differentiated flies collected in sympatry from different host species or different sex flowers are not one another's closest relatives, indicating that genetic differences often arise in allopatry before, or at least coincident with, the evolution of novel host use. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Multilocus analyses indicate a mosaic distribution of hybrid populations in ground squirrels (genus Ictidomys)

PubMed Central

Thompson, Cody W; Anwarali Khan, Faisal Ali; Stangl, Frederick B; Baker, Robert J; Bradley, Robert D

2013-01-01

DNA sequence data from mitochondrial cytochrome-b (Cytb) and Y-linked structural maintenance of chromosomes (SmcY) genes were combined with 478 nuclear loci obtained from amplified fragment length polymorphisms (AFLP) to assess the extent of hybridization and genetic spatial structure of populations in two hybridizing species of ground squirrel (Ictidomys parvidens and Ictidomys tridecemlineatus). Based on AFLP analyses of 134 individuals from 28 populations, 10 populations were identified that possessed hybrid individuals. Overall estimates of FST values revealed strong support for population structure in the Cytb data set; however, analyses of the SmcY gene and the AFLP data indicated ongoing gene flow between species. Pairwise FST comparisons of populations were not significant for the SmcY gene; although they were significant for the Cytb gene, indicating that these populations were structured and that gene flow was minimal. Therefore, gene flow between I. parvidens and I. tridecemlineatus appeared to be restricted to populations that exhibited hybridization. In addition, the fragmented nature of the geographic landscape suggested limited gene flow between populations. As a result, the distributional pattern of interspersed parental and hybrid populations were compatible with a mosaic hybrid zone model. Because ground squirrels display female philopatry and male-biased dispersal, the ecology of these species is compatible with this hypothesis. PMID:24340186

Genetic variation and phylogeographic structure of the cotton aphid, Aphis gossypii, based on mitochondrial DNA and microsatellite markers.

PubMed

Wang, Xing-Ya; Yang, Xian-Ming; Lu, Bin; Zhou, Li-Hong; Wu, Kong-Ming

2017-05-15

Aphis gossypii, one of the most important agricultural pests in the world, can cause serious economic losses in the main crop-producing areas. To clarify issues such as the genetic differentiation, genetic structure, and demographic history of A. gossypii populations, we used 10 nuclear microsatellite loci (SSR) and two mitochondrial gene sequences (COI and Cytb) to investigate genetic diversity and population structure of A. gossypii populations that were collected from 33 sampling sites in China from different climatic zones. SSR and mtDNA data suggested low to moderate levels of genetic diversity. A star-shaped network of mtDNA haplotypes indicated that the maternal ancestor of China cotton aphids likely originated in Xinjiang. The POPTREE, STRUCTURE and principal coordinate analysis (PCoA) revealed two genetic clusters: an eastern and a western region group. Isolation by distance (IBD) results showed a positive correlation between geographic distance and genetic distance in the vast eastern region but not in the western region. Neutrality testing and mismatch distribution analysis provided strong evidence for a recent rapid expansion in most populations. Genetic bottleneck was not detected in A. gossypii populations of China. The present work can help us to develop strategies for managing this pest.

Factors that influence the beta-diversity of spider communities in northwestern Argentinean Grasslands

PubMed Central

Rodriguez-Artigas, Sandra M.; Ballester, Rodrigo

2016-01-01

Beta-diversity, defined as spatial replacement in species composition, is crucial to the understanding of how local communities assemble. These changes can be driven by environmental or geographic factors (such as geographic distance), or a combination of the two. Spiders have been shown to be good indicators of environmental quality. Accordingly, spiders are used in this work as model taxa to establish whether there is a decrease in community similarity that corresponds to geographic distance in the grasslands of the Campos & Malezales ecoregion (Corrientes). Furthermore, the influence of climactic factors and local vegetation heterogeneity (environmental factors) on assemblage composition was evaluated. Finally, this study evaluated whether the differential dispersal capacity of spider families is a factor that influences their community structure at a regional scale. Spiders were collected with a G-Vac from vegetation in six grassland sites in the Campos & Malezales ecoregion that were separated by a minimum of 13 km. With this data, the impact of alpha-diversity and different environmental variables on the beta-diversity of spider communities was analysed. Likewise, the importance of species replacement and nesting on beta-diversity and their contribution to the regional diversity of spider families with different dispersion capacities was evaluated. The regional and site-specific inventories obtained were complete. The similarity between spider communities declined as the geographic distance between sites increased. Environmental variables also influenced community composition; stochastic events and abiotic forces were the principal intervening factors in assembly structure. The differential dispersal capacity of spider groups also influenced community structure at a regional scale. The regional beta-diversity, as well as species replacement, was greater in high and intermediate vagility spiders; while nesting was greater in spiders with low dispersion capacity. Geographic distance, among other factors (climate, and active and passive dispersion capacity), explains assembly structure and the decrease spider community similarity between geographically distant sites. Spiders with the highest dispersal capacity showed greater species replacement. This may be due to the discontinuity (both natural and anthropic) of the grasslands in this ecoregion, which limits the dispersal capacity of these spiders, and their close dependence on microhabitats. The dispersal capacity of the least vagile spiders is limited by geographic distance and biotic factors, such as competition, which could explain the nesting observed between their communities. PMID:27123380

Research on Russian National Character

ERIC Educational Resources Information Center

Na, Zhuo

2008-01-01

The special geographical location Russia lies in creates the unique character of the Russian nation. Based on the dual nature of the Russian national character, the Russian geographical environment and the analysis of its social structure, this text tries to explore the reasons of the dual nature of Russian national character.

Predictors of Satisfaction in Geographically Close and Long-Distance Relationships

ERIC Educational Resources Information Center

Lee, Ji-yeon; Pistole, M. Carole

2012-01-01

In this study, the authors examined geographically close (GCRs) and long-distance (LDRs) romantic relationship satisfaction as explained by insecure attachment, self-disclosure, gossip, and idealization. After college student participants (N = 536) completed a Web survey, structural equation modeling (SEM) multigroup analysis revealed that the GCR…

50 CFR 216.211 - Specified activity and specified geographical region.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Specified activity and specified... Activities Conducted During Offshore Structure Removal Operations on the Outer Continental Shelf in the U.S. Gulf of Mexico § 216.211 Specified activity and specified geographical region. (a) Regulations in this...

50 CFR 216.211 - Specified activity and specified geographical region.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Specified activity and specified... Activities Conducted During Offshore Structure Removal Operations on the Outer Continental Shelf in the U.S. Gulf of Mexico § 216.211 Specified activity and specified geographical region. (a) Regulations in this...

Using Educational Tourism in Geographical Education

ERIC Educational Resources Information Center

Prakapiene, Dalia; Olberkyte, Loreta

2013-01-01

The article analyses and defines the concept of educational tourism, presents the structure of the concept and looks into the opportunities for using educational tourism in geographical education. In order to reveal such opportunities a research was carried out in the Lithuanian national and regional parks using the qualitative method of content…

Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine

USDA-ARS?s Scientific Manuscript database

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations and is threatened by multiple stresses, including rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and pop...

Propagule pressure, genetic structure, and geographic origins of Chondrilla juncea (Asteraceae): An apomictic invader on three continents

USDA-ARS?s Scientific Manuscript database

Assessing the propagule pressure and geographic origins of invasive populations using molecular markers provides insights into the invasion process. Rush skeletonweed (Chondrilla juncea) is an apomictic perennial plant that is invasive in Australia, Argentina, Canada and the USA. Invasive biotypes...

The geographic distribution of HMOF and TTF revenues and allocations in Virginia : FY 93 update.

DOT National Transportation Integrated Search

1993-01-01

This report is an update of the report, The Geographic Distribution of HMOF and TTF Revenues and Allocations in Virginia From FY 88 through FY 92. As such, it describes the current structure of transportation finance in the Commonwealth. The financia...

Size and shape in Melipona quadrifasciata anthidioides Lepeletier, 1836 (Hymenoptera; Meliponini).

PubMed

Nunes, L A; Passos, G B; Carvalho, C A L; Araújo, E D

2013-11-01

This study aimed to identify differences in wing shape among populations of Melipona quadrifasciata anthidioides obtained in 23 locations in the semi-arid region of Bahia state (Brazil). Analysis of the Procrustes distances among mean wing shapes indicated that population structure did not determine shape variation. Instead, populations were structured geographically according to wing size. The Partial Mantel Test between morphometric (shape and size) distance matrices and altitude, taking geographic distances into account, was used for a more detailed understanding of size and shape determinants. A partial Mantel test between morphometris (shape and size) variation and altitude, taking geographic distances into account, revealed that size (but not shape) is largely influenced by altitude (r = 0.54 p < 0.01). These results indicate greater evolutionary constraints for the shape variation, which must be directly associated with aerodynamic issues in this structure. The size, however, indicates that the bees tend to have larger wings in populations located at higher altitudes.

A planktonic diatom displays genetic structure over small spatial scales.

PubMed

Sefbom, Josefin; Kremp, Anke; Rengefors, Karin; Jonsson, Per R; Sjöqvist, Conny; Godhe, Anna

2018-04-03

Marine planktonic microalgae have potentially global dispersal, yet reduced gene flow has been confirmed repeatedly for several species. Over larger distances (>200 km) geographic isolation and restricted oceanographic connectivity have been recognized as instrumental in driving population divergence. Here we investigated whether similar patterns, that is, structured populations governed by geographic isolation and/or oceanographic connectivity, can be observed at smaller (6-152 km) geographic scales. To test this we established 425 clonal cultures of the planktonic diatom Skeletonema marinoi collected from 11 locations in the Archipelago Sea (northern Baltic Sea). The region is characterized by a complex topography, entailing several mixing regions of which four were included in the sampling area. Using eight microsatellite markers and conventional F-statistics, significant genetic differentiation was observed between several sites. Moreover, Bayesian cluster analysis revealed the co-occurrence of two genetic groups spread throughout the area. However, geographic isolation and oceanographic connectivity could not explain the genetic patterns observed. Our data reveal hierarchical genetic structuring whereby despite high dispersal potential, significantly diverged populations have developed over small spatial scales. Our results suggest that biological characteristics and historical events may be more important in generating barriers to gene flow than physical barriers at small spatial scales. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Large stationary wave features appearing repeatedly at the cloud top of Venus

NASA Astrophysics Data System (ADS)

Kouyama, Toru; Imamura, Takeshi; Taguchi, Makoto; Fukuhara, Tetsuya; Sato, Takao M.; Hashimoto, George L.; Futaguchi, Masahiko; Takamura, Mao; Yamada, Takeru; Satoh, Takehiko; Nakamura, Masato; Akatsuki Science Team

2017-10-01

At the first observation sequence after Akatsuki’s Venus orbiter re-insertion (VOI-R) on December 7, 2015, Akatsuki revealed an existence of a large-scale “bow-shaped” feature staying at almost same geographic location (above Aphrodite Terra) at the cloud top level with the Longwave Infrared Camera (LIR) and Ultra Violet Imager (UVI). It expanded ~10,000 km from south to north and bended to downstream side of the super-rotation of Venus. A numerical calculation in Fukuhara et al. (2017) suggested that a gravity wave generated in the lower atmosphere can propagate upward to the cloud top and reproduce the observed bow-shape structure. Because the wave can transport momentum to the upper atmosphere which possibly decelerates the super-rotation, it is an interesting topic whether the stationary wave event is regular or just an occasional event. For more than three Venus years, or four Venus solar days, Akatsuki has observed huge stationary wave features in LIR images again and again since the VOI-R. It has been confirmed that four high-altitude regions, east and west part of Aphrodite Terra, Atra Regio, and Beta Regio, accompany with the large stationary features. All four regions are located in lower latitudes (< 30°), while no clear stationary feature has been confirmed above Maxwell Mountain, which is the highest mountain but located at a high latitude (60°), indicating geographical and latitudinal dependencies of the generation of the stationary waves. Akatsuki also reveals the stationary features can be considered as "daily" phenomena in Venus atmosphere. At every timing when the four high-altitude regions were passing afternoon region of Venus, huge stationary waves became clearer. On the other hand, when the high mountains were located around mid-night and morning, stationary features were much weaker than that in afternoon, or cannot be confirmed, indicating strong local time dependency of the appearance. Since lower latitude has more incident solar flux and afternoon area experiences longer solar heating than morning area, the geographical and the local time dependencies indicate that interaction between mountains and solar heating or solar fixed atmospheric structure may cause the large-scale features.

Mitochondrial and nuclear sequence polymorphisms reveal geographic structuring in Amazonian populations of Echinococcus vogeli (Cestoda: Taeniidae).

PubMed

Santos, Guilherme B; Soares, Manoel do C P; de F Brito, Elisabete M; Rodrigues, André L; Siqueira, Nilton G; Gomes-Gouvêa, Michele S; Alves, Max M; Carneiro, Liliane A; Malheiros, Andreza P; Póvoa, Marinete M; Zaha, Arnaldo; Haag, Karen L

2012-12-01

To date, nothing is known about the genetic diversity of the Echinococcus neotropical species, Echinococcus vogeli and Echinococcus oligarthrus. Here we used mitochondrial and nuclear DNA sequence polymorphisms to uncover the genetic structure, transmission and history of E. vogeli in the Brazilian Amazon, based on a sample of 38 isolates obtained from human and wild animal hosts. We confirm that the parasite is partially synanthropic and show that its populations are diverse. Furthermore, significant geographical structuring is found, with western and eastern populations being genetically divergent. Copyright © 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Geographical aspects of a territory and the velocity of liquidation natural-technical emergency situations' consequences (the case of Leningradskaya oblast in Russia)

NASA Astrophysics Data System (ADS)

Vashalova, Tatiana; Gavrilova, Sofia

2013-04-01

The velocity of liquidation of consequences of emergency situation or natural hazards is on of two main components of nonmonetized evaluation of their graveness. Besides the level of technical and economical securance of repair works the big role in their differentiation plays macro and mesolocation of the repaire object in phisical- and economicalgeographical space. The enlistment of theses factors differs very much for the accidents of various origin and for various territories with their own combination of phisical- and economicalgeographical conditions. In this work the first attempt of analysis of influence of the phisical- and economicalgeographical conditions on the duration of repair the electricity supplies, broken down by the hazardous hydrometeorological phenomena in Leneigradskaya oblast in Russia was made. This region, situated on north-west of the country, outstands with variety of phisical- and economicalgeographical conditions. In this project the data of Laboratory of snow avalanches and mudflows (geographical faculty, MSU), open-sourced map data and the archive of newspapers of Leningradskaya oblast were used. It is very important to understand, that the transportation of the electricity by electric power lines is the main way of transportation energy in Russia. The interruption of power supply, caused by dangerous phenomena, happens in majority cases because of kinking or break of the cable. The break takes places during the strong winds and fall of the trees on the cable or icing and their break during the strong winds. The frequency of strong winds in the terms of one sinoptical cicle (5-7 days) appears as an independent factor of elongation of terms of repairing the power supply. Such phisicogeographical singularities of landscape of Leningradkaya oblast as the grade of loiss soil and swampiness of different districts apears as a factor, wgich modulate the dependence of the velocity of repairing the power supply from the characteristics of economical geographical space. Economical-geograhical characteristics of the space according to concered tipes of accidents should be estimate in macro and meso scale. In macro scale the social-economical status of Saint-Petersburg and accumbens cities and districts is essential. This city determins the creation of technical conditious, providing the protection of these objects from natural hazards. In meso scale the significant factors are the rank of the village, the presence of objects of life necessities and social-significant objects, the number of population, the distance to the closest "central place" and the quality of the transport arteria. In some cases the size of "the zone of responsobilitiy" plays a role. The investigation allowes to determine the principals of estimation geographical structure of the territory as a factor of differentation the velocity if liquadation the consequence of accidents and natural hazards. The analysis of causes and conditions, that influence the velocity of liquadation the consequence of accidents on a power supply make possible the zoning of Leningradskaya oblast. The conformation of achieved connections on other regions will make possible the development of methods of evaluation the value of appreciation the maintaining the life in regions of Russia on a certain level of life.

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.

Land surveys show regional variability of historical fire regimes and dry forest structure of the western United States.

PubMed

Baker, William L; Williams, Mark A

2018-03-01

An understanding of how historical fire and structure in dry forests (ponderosa pine, dry mixed conifer) varied across the western United States remains incomplete. Yet, fire strongly affects ecosystem services, and forest restoration programs are underway. We used General Land Office survey reconstructions from the late 1800s across 11 landscapes covering ~1.9 million ha in four states to analyze spatial variation in fire regimes and forest structure. We first synthesized the state of validation of our methods using 20 modern validations, 53 historical cross-validations, and corroborating evidence. These show our method creates accurate reconstructions with low errors. One independent modern test reported high error, but did not replicate our method and made many calculation errors. Using reconstructed parameters of historical fire regimes and forest structure from our validated methods, forests were found to be non-uniform across the 11 landscapes, but grouped together in three geographical areas. Each had a mixture of fire severities, but dominated by low-severity fire and low median tree density in Arizona, mixed-severity fire and intermediate to high median tree density in Oregon-California, and high-severity fire and intermediate median tree density in Colorado. Programs to restore fire and forest structure could benefit from regional frameworks, rather than one size fits all. © 2018 by the Ecological Society of America.

Genetic diversity and phylogeographic structure of Bactrian camels shown by mitochondrial sequence variations.

PubMed

Ming, L; Yi, L; Sa, R; Wang, Z X; Wang, Z; Ji, R

2017-04-01

The Bactrian camel includes various domestic (Camelus bactrianus) and wild (Camelus ferus) breeds that are important for transportation and for their nutritional value. However, there is a lack of extensive information on their genetic diversity and phylogeographic structure. Here, we studied these parameters by examining an 809-bp mtDNA fragment from 113 individuals, representing 11 domestic breeds, one wild breed and two hybrid individuals. We found 15 different haplotypes, and the phylogenetic analysis suggests that domestic and wild Bactrian camels have two distinct lineages. The analysis of molecular variance placed most of the genetic variance (90.14%, P < 0.01) between wild and domestic camel lineages, suggesting that domestic and wild Bactrian camel do not have the same maternal origin. The analysis of domestic Bactrian camels from different geographical locations found there was no significant genetic divergence in China, Russia and Mongolia. This suggests a strong gene flow due to wide movement of domestic Bactrian camels. © 2016 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

The Development and Validation of the Mood-based Indoor Tanning Scale.

PubMed

Carcioppolo, Nick; Chen, Yixin; John, Kevin K; Gonzalez, Andrea Martinez; King, Andy J; Morgan, Susan E; Hu, Shasa

2017-01-01

Research indicates that mood-based motivations may be an important predictor of indoor tanning bed use and may be related to indoor tanning dependence. Problematically, little research has been conducted to develop a psychometric measure of mood-based tanning motivations. The current study seeks to develop and validate the moodbased indoor tanning scale (MITS). Two studies were conducted to identify and verify the MITS factor structure as well as assess construct validity. Study 1 was conducted at 5 geographically diverse universities in the United States. Study 2 was conducted by using a national online sample in the United States. Results from study 1 specified the factor structure of the MITS. Results from study 2 suggest that a one-point increase in the MITS measure corresponds with using indoor tanning beds 11 more times in the past year. These findings demonstrate that moodbased tanning motivations are a strong predictor of indoor tanning intentions and behavior. Further, they suggest that health behavior researchers and healthcare practitioners can use the MITS to assess the extent to which mood-based motivations impact indoor tanning bed use.

Palaeopolyploidy, spatial structure and conservation genetics of the narrow steppe plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae).

PubMed

Pérez-Collazos, Ernesto; Catalán, Pilar

2006-04-01

Vella pseudocytisus subsp. paui (Cruciferae) is a narrow endemic plant to the Teruel province (eastern Spain), which is listed in the National Catalogue of Endangered Species. Two distinct ploidy levels (diploid, 2n = 34, and tetraploid, 2n = 68) have been reported for this taxon that belongs to the core subtribe Vellinae, a western Mediterranean group of shrubby taxa with a chromosome base number of x = 17. Allozyme and AFLP analyses were conducted (a) to test for the ploidy and putative palaeo-allopolyploid origin of this taxon, (b) to explore levels of genetic diversity and spatial structure of its populations, and (c) to address in-situ and ex-situ strategies for its conservation. Six populations that covered the entire geographical range of this taxon were sampled and examined for 19 allozyme loci and three AFLP primer pair combinations. In addition, the gametic progenies of five individuals were analysed for two allozyme loci that showed fixed heterozygosity. Multiple banded allozyme profiles for most of the surveyed loci indicated the polyploidy of this taxon. Co-inherited fixed heterozygous patterns were exhibited by the gametophytic tissues of the mother plants. Both allozyme and AFLP markers detected high levels of genetic diversity, and a strong micro-spatial genetic structure was recovered from AFLP phenetic analyses and Mantel correlograms. Allozyme data support the hypothesis of an allotetraploid origin of Vella pseudocytisus subsp. paui that could be representative of other taxa of the core Vellinae group. AFLP data distinguished three geographically distinct groups with no genetic interaction among them. Allotetraploidy and outcrossing reproduction have probably contributed to maintenance of high levels of genetic variability of the populations, whereas habitat fragmentation may have enhanced the high genetic isolation observed among groups. In-situ microgenetic reserves and a selective sampling of germplasm stocks for ex-situ conservation of this taxon are proposed.

Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran

PubMed Central

Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

2016-01-01

Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among Iranian P. pectinatus than previously observed for temperate European regions, due to regional differences across mountain ranges over long distances. PMID:27560947

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

PubMed Central

2013-01-01

Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species. PMID:23311925

Contrasting Genetic Structure among Populations of Two Amphidromous Fish Species (Sicydiinae) in the Central West Pacific

PubMed Central

Taillebois, Laura; Castelin, Magalie; Ovenden, Jennifer R.; Bonillo, Céline; Keith, Philippe

2013-01-01

Both present-day and past processes can shape connectivity of populations. Pleistocene vicariant events and dispersal have shaped the present distribution and connectivity patterns of aquatic species in the Indo-Pacific region. In particular, the processes that have shaped distribution of amphidromous goby species still remain unknown. Previous studies show that phylogeographic breaks are observed between populations in the Indian and Pacific Oceans where the shallow Sunda shelf constituted a geographical barrier to dispersal, or that the large spans of open ocean that isolate the Hawaiian or Polynesian Islands are also barriers for amphidromous species even though they have great dispersal capacity. Here we assess past and present genetic structure of populations of two amphidromous fish (gobies of the Sicydiinae) that are widely distributed in the Central West Pacific and which have similar pelagic larval durations. We analysed sections of mitochondrial COI, Cytb and nuclear Rhodospine genes in individuals sampled from different locations across their entire known range. Similar to other Sicydiinae fish, intraspecific mtDNA genetic diversity was high for all species (haplotype diversity between 0.9–0.96). Spatial analyses of genetic variation in Sicyopus zosterophorum demonstrated strong isolation across the Torres Strait, which was a geologically intermittent land barrier linking Australia to Papua New Guinea. There was a clear genetic break between the northwestern and the southwestern clusters in Si. zosterophorum (φST = 0.67502 for COI) and coalescent analyses revealed that the two populations split at 306 Kyr BP (95% HPD 79–625 Kyr BP), which is consistent with a Pleistocene separation caused by the Torres Strait barrier. However, this geographical barrier did not seem to affect Sm. fehlmanni. Historical and demographic hypotheses are raised to explain the different patterns of population structure and distribution between these species. Strategies aiming to conserve amphidromous fish should consider the presence of cryptic evolutionary lineages to prevent stock depletion. PMID:24130714

Palaeopolyploidy, Spatial Structure and Conservation Genetics of the Narrow Steppe Plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae)

PubMed Central

PÉREZ-COLLAZOS, ERNESTO; CATALÁN, PILAR

2006-01-01

• Background and Aims Vella pseudocytisus subsp. paui (Cruciferae) is a narrow endemic plant to the Teruel province (eastern Spain), which is listed in the National Catalogue of Endangered Species. Two distinct ploidy levels (diploid, 2n = 34, and tetraploid, 2n = 68) have been reported for this taxon that belongs to the core subtribe Vellinae, a western Mediterranean group of shrubby taxa with a chromosome base number of x = 17. Allozyme and AFLP analyses were conducted (a) to test for the ploidy and putative palaeo-allopolyploid origin of this taxon, (b) to explore levels of genetic diversity and spatial structure of its populations, and (c) to address in-situ and ex-situ strategies for its conservation. • Methods Six populations that covered the entire geographical range of this taxon were sampled and examined for 19 allozyme loci and three AFLP primer pair combinations. In addition, the gametic progenies of five individuals were analysed for two allozyme loci that showed fixed heterozygosity. • Key Results Multiple banded allozyme profiles for most of the surveyed loci indicated the polyploidy of this taxon. Co-inherited fixed heterozygous patterns were exhibited by the gametophytic tissues of the mother plants. Both allozyme and AFLP markers detected high levels of genetic diversity, and a strong micro-spatial genetic structure was recovered from AFLP phenetic analyses and Mantel correlograms. • Conclusions Allozyme data support the hypothesis of an allotetraploid origin of Vella pseudocytisus subsp. paui that could be representative of other taxa of the core Vellinae group. AFLP data distinguished three geographically distinct groups with no genetic interaction among them. Allotetraploidy and outcrossing reproduction have probably contributed to maintenance of high levels of genetic variability of the populations, whereas habitat fragmentation may have enhanced the high genetic isolation observed among groups. In-situ microgenetic reserves and a selective sampling of germplasm stocks for ex-situ conservation of this taxon are proposed. PMID:16495317

Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

PubMed

Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

2016-01-01

Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among Iranian P. pectinatus than previously observed for temperate European regions, due to regional differences across mountain ranges over long distances.

Trade-offs between constitutive and induced defences drive geographical and climatic clines in pine chemical defences.

PubMed

Moreira, Xoaquín; Mooney, Kailen A; Rasmann, Sergio; Petry, William K; Carrillo-Gavilán, Amparo; Zas, Rafael; Sampedro, Luis

2014-05-01

There is increasing evidence that geographic and climatic clines drive the patterns of plant defence allocation and defensive strategies. We quantified early growth rate and both constitutive and inducible chemical defences of 18 Pinaceae species in a common greenhouse environment and assessed their defensive allocation with respect to each species' range across climatic gradients spanning 31° latitude and 2300 m elevation. Constitutive defences traded-off with induced defences, and these defensive strategies were associated with growth rate such that slow-growing species invested more in constitutive defence, whereas fast-growing species invested more in inducible defence. The position of each pine species along this trade-off axis was in turn associated with geography; moving poleward and to higher elevations, growth rate and inducible defences decreased, while constitutive defence increased. These geographic patterns in plant defence were most strongly associated with variation in temperature. Climatic and geographical clines thus act as drivers of defence profiles by mediating the constraints imposed by trade-offs, and this dynamic underlays global patterns of defence allocation.

[European Community Respiratory Health Survey in Adults (ECRHS)].

PubMed

Heinrich, J; Richter, K; Frye, C; Meyer, I; Wölke, G; Wjst, M; Nowak, D; Magnussen, H; Wichmann, H E

2002-05-01

The European Community Respiratory Health Survey (ECRHS) was the first study to assess the geographical variation in asthma, allergy, and allergic sensitization in adults using the same instruments and definitions. The database of the ECRHS includes information from approximately 140 000 individuals aged 20 - 44 years from 22 countries. The aim of this review is to summarize the results of the ECRHS and to present the specific contribution of the German centers in Hamburg and Erfurt. The prevalence ranged from 2.0 - 11.9 % for asthma, 9.5 - 40.9 % for allergic rhinitis, 4.0 - 32.0 % for wheeze, 3.4 - 27.9 % for bronchial hyperreactivity, and 16.2 - 44.5 % for allergic sensitisation against common aeroallergens. Although the prevalence of these atopic disorders were found to be consistently higher for the Hamburg center compared to the Erfurt center, strong regional differences in the prevalences were also found within several other European countries. Overall Europe, the lowest prevalences were seen in the Eastern and Middle European countries with the center Erfurt, followed by the Mediterranean region. The highest prevalences were reported for all English speaking centers. Strong geographic variation was reported for medication for asthma. Asthma seems to be undertreated in several countries. Environmental exposures and in particular indoor factors, and exposures at the workplace are playing a major role for asthma in adulthood. Furthermore, protective effects on atopy were found for exposures to pets (dogs) and a large number of siblings in early childhood. In conclusion, the ECRHS has shown that the prevalence of asthma varies widely. The fact that the geographical pattern is consistent with the distribution of atopy and bronchial responsiveness supports the conclusion that the geographical variations in the prevalence of asthma are true and likely due to environmental factors.

Genetic variation and bill size dimorphism in a passerine bird, the reed bunting Emberiza schoeniclus.

PubMed

Grapputo, A; Pilastro, A; Marin, G

1998-09-01

In passerine birds morphological differentiation in bill size within species is not commonly observed. Bill size is usually associated with a trophic niche, and strong differences in it may reflect the process of genetic differentiation and, possibly, speciation. We used both mitochondrial DNA (mtDNA) and nuclear microsatellites to study genetic variation between two subspecies of reed bunting, Emberiza schoeniclus schoeniclus and E.s. intermedia, along their distributional boundary in western Europe. These two subspecies are characterized by a high dimorphism in bill size and, although breeding populations of the two subspecies are found very close to each other in northern Italy, apparently no interbreeding occurs. The observed morphological pattern between the two subspecies may be maintained by geographically varying selective forces or, alternatively, may be the result of a long geographical separation followed by a secondary contact. MtDNA sequences of cytochrome b and ND5 (515 bp) showed little variation and did not discriminate between the two subspecies, indicating a divergence time of less than 500 000 years. The analysis of four microsatellite loci suggested a clear, although weak, degree of genetic differentiation in the large- and small-billed populations, as indicated by FST and RST values and genetic distances. The correlation between bill size and genetic distance between populations remained significant after accounting for the geographical distances between sampling localities. Altogether, these results indicate a very recent genetic differentiation between the two bill morphs and suggest that a strong selection for large bills in the southern part of the breeding range is probably involved in maintaining the geographical differentiation of this species.

Phytogeographical Analysis of Seed Plant Genera in China

PubMed Central

QIAN, HONG; WANG, SILONG; HE, JIN-SHENG; ZHANG, JUNLI; WANG, LISONG; WANG, XIANLI; GUO, KE

2006-01-01

• Background and Aims A central goal of biogeography and ecology is to uncover and understand distributional patterns of organisms. China has long been a focus of attention because of its rich biota, especially with respect to plants. Using 290 floras from across China, this paper quantitatively characterizes the composition of floristic elements at multiple scales (i.e. national, provincial and local), and explores the extent to which climatic and geographical factors associated with each flora can jointly and independently explain the variation in floristic elements in local floras. • Methods A study was made of 261 local floras, 28 province-level floras and one national-level flora across China. Genera of seed plants in each flora were assigned to 14 floristic elements according to their worldwide geographical distributions. The composition of floristic elements was related to climatic and geographical factors. • Key Results and Conclusions Variations in percentages of cosmopolitan, tropical and temperate genera among local floras tend to be greater at higher latitudes than at lower latitudes. Latitude is strongly correlated with the proportions of 13 of the 14 floristic elements. Correlations of the proportions of floristic elements with longitude are much weaker than those with latitude. Climate represented by the first principal component of a principal component analysis was strongly correlated with the proportions of floristic elements in local floras (|r| = 0·75 ± 0·18). Geographical coordinates independently explained about four times as much variation in floristic elements as did climate. Further research is necessary to examine the roles of water–energy dynamics, geology, soils, biotic interactions, and historical factors such as land connections between continents in the past and at present in creating observed floristic patterns. PMID:16945946

Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States

USGS Publications Warehouse

Lee, Soo-Rang; Jo, Yeong-Seok; Park, Chan-Ho; Friedman, Jonathan M.; Olson, Matthew S.

2018-01-01

Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.

The Conservation of North Carolina's Natural Resources.

ERIC Educational Resources Information Center

Washington City Board of Education, NC.

This is a course designed specifically for use in eastern North Carolina or a similar geographic region but this does not preclude the use of its concepts and basic structure for other geographic regions. Plans and activities are student-centered and many are problem-solving oriented and, therefore, may be modified without disrupting the…

A geographic comparison of selected large-scale planetary surface features

NASA Technical Reports Server (NTRS)

Meszaros, S. P.

1984-01-01

Photographic and cartographic comparisons of geographic features on Mercury, the Moon, Earth, Mars, Ganymede, Callisto, Mimas, and Tethys are presented. Planetary structures caused by impacts, volcanism, tectonics, and other natural forces are included. Each feature is discussed individually and then those of similar origin are compared at the same scale.

Mathematical Ecology Analysis of Geographical Distribution of Soybean-Nodulating Bradyrhizobia in Japan

PubMed Central

Saeki, Yuichi; Shiro, Sokichi; Tajima, Toshiyuki; Yamamoto, Akihiro; Sameshima-Saito, Reiko; Sato, Takashi; Yamakawa, Takeo

2013-01-01

We characterized the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia from weakly acidic soils in Japan and their geographical distribution in an ecological study of indigenous soybean rhizobia. We isolated bradyrhizobia from three kinds of Rj-genotype soybeans. Their genetic diversity and community structure were analyzed by PCR-RFLP analysis of the 16S–23S rRNA gene internal transcribed spacer (ITS) region with 11 Bradyrhizobium USDA strains as references. We used data from the present study and previous studies to carry out mathematical ecological analyses, multidimensional scaling analysis with the Bray-Curtis index, polar ordination analysis, and multiple regression analyses to characterize the relationship between soybean-nodulating bradyrhizobial community structures and their geographical distribution. The mathematical ecological approaches used in this study demonstrated the presence of ecological niches and suggested the geographical distribution of soybean-nodulating bradyrhizobia to be a function of latitude and the related climate, with clusters in the order Bj123, Bj110, Bj6, and Be76 from north to south in Japan. PMID:24240318

Lyssavirus in Indian Flying Foxes, Sri Lanka.

PubMed

Gunawardena, Panduka S; Marston, Denise A; Ellis, Richard J; Wise, Emma L; Karawita, Anjana C; Breed, Andrew C; McElhinney, Lorraine M; Johnson, Nicholas; Banyard, Ashley C; Fooks, Anthony R

2016-08-01

A novel lyssavirus was isolated from brains of Indian flying foxes (Pteropus medius) in Sri Lanka. Phylogenetic analysis of complete virus genome sequences, and geographic location and host species, provides strong evidence that this virus is a putative new lyssavirus species, designated as Gannoruwa bat lyssavirus.

Quantifying the Impact of geographically isolated wetlands on the downstream hydrology of a Canadian Prairie watershed

NASA Astrophysics Data System (ADS)

Muhammad, A.; Evenson, G. R.; Boluwade, A.; Jha, S. K.; Rasmussen, P. F.

2016-12-01

Hydrological processes are highly complex and strongly nonlinear and cannot be represented through simple means. Models are built to replicate these processes. However, models due to various sources of uncertainty including their structural capability often lead to inaccurate results. The aim of this study is to setup the soil water assessment tool (SWAT) for a watershed that is dominated by potholes in the Prairie region of Canada. The potholes not connected to the stream, also known as geographically isolated wetlands (GIWs), are dynamic in nature leading to a fill and spill situation due to varying surface runoff conditions. Significant land use changes have resulted in almost 70% of wetlands being lost and have posed threat of flooding to downstream areas. While some studies were devoted to identify the presence of potholes only few have explored the impacts of wetlands on the downstream hydrology. In this study, we follow Evenson et al., (2016) approach of modifying SWAT model. The modification enhances structural capability of SWAT while depicting the dynamics of wetlands at HRUs level. Redefining the formation of HRUs in such way effectively captures the spatial presence of potholes. We then routed the potholes' fill and spill hydrology to direct the flow to the potholes immediately downstream. The model was calibrated for 2005-2008 and verified over 2009-2011 at a daily time step. We tested our model with three land use change scenarios by varying the presence of potholes and evaluated its impact on the downstream hydrograph. We foresee a significant improvement in replicating stream flow using this novel approach. We believe that it will effectively improve the predictive power of SWAT for this highly complex sub basin (Upper Assiniboine catchment at Kamsack) located in Canadian Prairie.

Recent radiation and dispersal of an ancient lineage: The case of Fouquieria (Fouquiericeae, Ericales) in North American deserts.

PubMed

De-Nova, José Arturo; Sánchez-Reyes, Luna L; Eguiarte, Luis E; Magallón, Susana

2018-09-01

Arid biomes are particularly prominent in the Neotropics providing some of its most emblematic landscapes and a substantial part of its species diversity. To understand some of the evolutionary processes underlying the speciation of lineages in the Mexican Deserts, the diversification of Fouquieria is investigated, which includes eleven species, all endemic to the warm deserts and dry subtropical regions of North America. Using a phylogeny from plastid DNA sequences with samples of individuals from populations of all the species recognized in Fouquieria, we estimate divergence times, test for temporal diversification heterogeneity, test for geographical structure, and conduct ancestral area reconstruction. Fouquieria is an ancient lineage that diverged from Polemoniaceae ca. 75.54 Ma. A Mio-Pliocene diversification of Fouquieria with vicariance, associated with Neogene orogenesis underlying the early development of regional deserts is strongly supported. Test for temporal diversification heterogeneity indicates that during its evolutionary history, Fouquieria had a drastic diversification rate shift at ca.12.72 Ma, agreeing with hypotheses that some of the lineages in North American deserts diversified as early as the late Miocene to Pliocene, and not during the Pleistocene. Long-term diversification dynamics analyses suggest that extinction also played a significant role in Fouquieria's evolution, with a very high rate at the onset of the process. From the late Miocene onwards, Fouquieria underwent substantial diversification change, involving high speciation decreasing to the present and negligible extinction, which is congruent with its scant fossil record during this period. Geographic phylogenetic structure and the pattern of most sister species inhabiting different desert nucleus support that isolation by distance could be the main driver of speciation. Copyright © 2018 Elsevier Inc. All rights reserved.

Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow.

PubMed

Gryseels, S; Goüy de Bellocq, J; Makundi, R; Vanmechelen, K; Broeckhove, J; Mazoch, V; Šumbera, R; Zima, J; Leirs, H; Baird, S J E

2016-10-01

Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to humans and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180-km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city (Morogoro). We sampled M. natalensis across 10 localities and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the isolation-with-migration model implemented in IMa2, we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2N e M = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Phylogeography of an Australian termite, Amitermes laurensis (Isoptera, Termitidae), with special reference to the variety of mound shapes.

PubMed

Ozeki, Masato; Isagi, Yuji; Tsubota, Hiromi; Jacklyn, Peter; Bowman, David M J S

2007-01-01

In northern Australia, the debris-feeding termite Amitermes laurensis builds tall, wedge-shaped mounds in the northern part of Cape York Peninsula and Arnhem Land, where their habitats are seasonally flooded, and small dome shaped mounds in the southeastern part of Cape York Peninsula, where their habitats are well-drained. Phylogeographic analyses were conducted in 238 individuals from 30 populations using the mitochondrial cytochrome oxidase II (COII) gene. DNA sequences of 50 haplotypes were used to construct NJ, MP and ML trees. Phylogenetic trees for 16 Amitermes species showed monophyly of A. laurensis and the variation of A. laurensis mounds did not strongly correspond to the intraspecific phylogeny. It was observed that mounds with the same shape were constructed by phylogenetically different groups under similar environmental conditions and different mounds shapes were built by phylogenetically closely related groups under the different environmental conditions. Thus, phylogenetically close groups of A. laurensis, in different habitats, may adapt to environmental conditions by constructing different mound shapes. We also investigated the phylogeographic structure of A. laurensis. The significant positive correlation between genetic and geographic distances indicated isolation by distance, reflecting restricted dispersal ability of alates. Although the overall genetic structure of A. laurensis showed isolation by distance, we also identified two exceptions: (i) secondary contacts of genetically divergent lineages in southern Cape York Peninsula, and (ii) low genetic differences between geographically separated populations of Cape York Peninsula and Arnhem Land. Therefore, the phylogeography of A. laurensis may reflect continuous gene flow restricted to short distances and past changes of gene flow associated with the fluctuation of environmental conditions accompanying the changing sea levels in the Quaternary.

Phylogeography and spatial structure of the lowland tapir (Tapirus terrestris, Perissodactyla: Tapiridae) in South America.

PubMed

Ruiz-García, Manuel; Vásquez, Catalina; Sandoval, Sergio; Kaston, Franz; Luengas-Villamil, Kelly; Shostell, Joseph Mark

2016-07-01

We sequenced the mitochondrial cytochrome b gene of 141 lowland tapirs (Tapirus terrestris) - representing the largest geographical distribution sample of this species studied across of South America to date. We compare our new data regard to two previous works on population structure and molecular systematics of T. terrestris. Our data agree with the Thoisy et al.'s work in (1) the Northern Western Amazon basin was the area with the highest gene diversity levels in T. terrestris, being probably the area of initial diversification; (2) there was no clear association between haplogroups and specific geographical areas; (3) there were clear population decreases during the last glacial maximum for the different haplogroups detected, followed by population expansions during the Holocene; and (4) our temporal splits among different T. terrestris haplogroups coincided with the first molecular clock approach carried out by these authors (fossil calibration). Nevertheless, our study disagreed regard to other aspects of the Thoisy et al.'s claims: (1) meanwhile, they detected four relevant clades in their data, we put forward six different relevant clades; (2) the Amazon River was not a strong barrier for haplotype dispersion in T. terrestris; and (3) we found reciprocal monophyly between T. terrestris and T. pinchaque. Additionally, we sequenced 42 individuals (T. terrestris, T. pinchaque, T. bairdii, and the alleged "new species", T. kabomani) for three concatenated mitochondrial genes (Cyt-b, COI, and COII) agreeing quite well with the view of Voss et al., and against of the claims of Cozzuol et al. Tapirus kabomani should be not considered as a full species with the results obtained throughout the mitochondrial sequences.

A pilot GIS database of active faults of Mt. Etna (Sicily): A tool for integrated hazard evaluation

NASA Astrophysics Data System (ADS)

Barreca, Giovanni; Bonforte, Alessandro; Neri, Marco

2013-02-01

A pilot GIS-based system has been implemented for the assessment and analysis of hazard related to active faults affecting the eastern and southern flanks of Mt. Etna. The system structure was developed in ArcGis® environment and consists of different thematic datasets that include spatially-referenced arc-features and associated database. Arc-type features, georeferenced into WGS84 Ellipsoid UTM zone 33 Projection, represent the five main fault systems that develop in the analysed region. The backbone of the GIS-based system is constituted by the large amount of information which was collected from the literature and then stored and properly geocoded in a digital database. This consists of thirty five alpha-numeric fields which include all fault parameters available from literature such us location, kinematics, landform, slip rate, etc. Although the system has been implemented according to the most common procedures used by GIS developer, the architecture and content of the database represent a pilot backbone for digital storing of fault parameters, providing a powerful tool in modelling hazard related to the active tectonics of Mt. Etna. The database collects, organises and shares all scientific currently available information about the active faults of the volcano. Furthermore, thanks to the strong effort spent on defining the fields of the database, the structure proposed in this paper is open to the collection of further data coming from future improvements in the knowledge of the fault systems. By layering additional user-specific geographic information and managing the proposed database (topological querying) a great diversity of hazard and vulnerability maps can be produced by the user. This is a proposal of a backbone for a comprehensive geographical database of fault systems, universally applicable to other sites.

Genetic Structure and Demographic History Reveal Migration of the Diamondback Moth Plutella xylostella (Lepidoptera: Plutellidae) from the Southern to Northern Regions of China

PubMed Central

Wei, Shu-Jun; Shi, Bao-Cai; Gong, Ya-Jun; Jin, Gui-Hua; Chen, Xue-Xin; Meng, Xiang-Feng

2013-01-01

The diamondback moth Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) is one of the most destructive insect pests of cruciferous plants worldwide. Biological, ecological and genetic studies have indicated that this moth is migratory in many regions around the world. Although outbreaks of this pest occur annually in China and cause heavy damage, little is known concerning its migration. To better understand its migration pattern, we investigated the population genetic structure and demographic history of the diamondback moth by analyzing 27 geographical populations across China using four mitochondrial genes and nine microsatellite loci. The results showed that high haplotype diversity and low nucleotide diversity occurred in the diamondback moth populations, a finding that is typical for migratory species. No genetic differentiation among all populations and no correlation between genetic and geographical distance were found. However, pairwise analysis of the mitochondrial genes has indicated that populations from the southern region were more differentiated than those from the northern region. Gene flow analysis revealed that the effective number of migrants per generation into populations of the northern region is very high, whereas that into populations of the southern region is quite low. Neutrality testing, mismatch distribution and Bayesian Skyline Plot analyses based on mitochondrial genes all revealed that deviation from Hardy-Weinberg equilibrium and sudden expansion of the effective population size were present in populations from the northern region but not in those from the southern region. In conclusion, all our analyses strongly demonstrated that the diamondback moth migrates within China from the southern to northern regions with rare effective migration in the reverse direction. Our research provides a successful example of using population genetic approaches to resolve the seasonal migration of insects. PMID:23565158

History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico

PubMed Central

Via, Marc; Gignoux, Christopher R.; Roth, Lindsey A.; Fejerman, Laura; Galanter, Joshua; Choudhry, Shweta; Toro-Labrador, Gladys; Viera-Vera, Jorge; Oleksyk, Taras K.; Beckman, Kenneth; Ziv, Elad; Risch, Neil

2011-01-01

Contemporary genetic variation among Latin Americans human groups reflects population migrations shaped by complex historical, social and economic factors. Consequently, admixture patterns may vary by geographic regions ranging from countries to neighborhoods. We examined the geographic variation of admixture across the island of Puerto Rico and the degree to which it could be explained by historic and social events. We analyzed a census-based sample of 642 Puerto Rican individuals that were genotyped for 93 ancestry informative markers (AIMs) to estimate African, European and Native American ancestry. Socioeconomic status (SES) data and geographic location were obtained for each individual. There was significant geographic variation of ancestry across the island. In particular, African ancestry demonstrated a decreasing East to West gradient that was partially explained by historical factors linked to the colonial sugar plantation system. SES also demonstrated a parallel decreasing cline from East to West. However, at a local level, SES and African ancestry were negatively correlated. European ancestry was strongly negatively correlated with African ancestry and therefore showed patterns complementary to African ancestry. By contrast, Native American ancestry showed little variation across the island and across individuals and appears to have played little social role historically. The observed geographic distributions of SES and genetic variation relate to historical social events and mating patterns, and have substantial implications for the design of studies in the recently admixed Puerto Rican population. More generally, our results demonstrate the importance of incorporating social and geographic data with genetics when studying contemporary admixed populations. PMID:21304981

Correlation Assessment of Climate and Geographic Distribution of Tuberculosis Using Geographical Information System (GIS).

PubMed

Beiranvand, Reza; Karimi, Asrin; Delpisheh, Ali; Sayehmiri, Kourosh; Soleimani, Samira; Ghalavandi, Shahnaz

2016-01-01

Tuberculosis (TB) spread pattern is influenced by geographic and social factors. Nowadays Geographic Information System (GIS) is one of the most important epidemiological instrumentation identifying high-risk population groups and geographic areas of TB. The aim of this study was to determine the correlation between climate and geographic distribution of TB in Khuzestan Province using GIS during 2005-2012. Through an ecological study, all 6363 patients with definite diagnosis of TB from 2005 until the end of September 2012 in Khuzestan Province, southern Iran were diagnosed. Data were recorded using TB- Register software. Tuberculosis incidence based on the climate and the average of annual rain was evaluated using GIS. Data were analyzed through SPSS software. Independent t-test, ANOVA, Linear regression, Pearson and Eta correlation coefficient with a significance level of less than 5% were used for the statistical analysis. The TB incidence was different in various geographic conditions. The highest mean of TB cumulative incidence rate was observed in extra dry areas (P= 0.017). There was a significant inverse correlation between annual rain rate and TB incidence rate (R= -0.45, P= 0.001). The lowest TB incidence rate (0-100 cases per 100,000) was in areas with the average of annual rain more than 1000 mm (P= 0.003). The risk of TB has a strong relationship with climate and the average of annual rain, so that the risk of TB in areas with low annual rainfall and extra dry climate is more than other regions. Services and special cares to high-risk regions of TB are recommended.

Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.

PubMed

Hoh, Boon-Peng; Deng, Lian; Julia-Ashazila, Mat Jusoh; Zuraihan, Zakaria; Nur-Hasnah, Ma'amor; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Endom, Ismail; Zilfalil, Bin Alwi; Khalid, Yusoff; Xu, Shuhua

2015-07-22

Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.

Geographical and taxonomic biases in invasion ecology.

PubMed

Pysek, Petr; Richardson, David M; Pergl, Jan; Jarosík, Vojtech; Sixtová, Zuzana; Weber, Ewald

2008-05-01

Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.

Geographic clustering of elderly people with above-norm anthropometric measurements and blood chemistry.

PubMed

Mena, Carlos; Fuentes, Eduardo; Ormazábal, Yony; Palomo, Iván

2017-05-11

The global percentage of people over 60 is strongly increasing and estimated to exceed 20% by 20,150, which means that there will be an increase in many pathological conditions related to aging. Mapping of the location of aging people and identification of their needs can be extremely valuable from a social-economic point of view. Participants in this study were 148 randomly selected adults from Talca City, Chile aged 60-74 at baseline. Geographic information systems (GIS) analyses were performed using ArcGIS software through its module Spatial Autocorrelation. In this study, we demonstrated that elderly people show geographic clustering according to above-norm results of anthropometric measurements and blood chemistry. The spatial identifications found would facilitate exploring the impact of treatment programmes in communities where many aging people live, thereby improving their quality of life as well as reducing overall costs.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift.

PubMed

Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

2014-11-01

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. © 2014 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift

PubMed Central

Moura, Andre E; Kenny, John G; Chaudhuri, Roy; Hughes, Margaret A; J Welch, Andreanna; Reisinger, Ryan R; de Bruyn, P J Nico; Dahlheim, Marilyn E; Hall, Neil; Hoelzel, A Rus

2014-01-01

The evolution of diversity in the marine ecosystem is poorly understood, given the relatively high potential for connectivity, especially for highly mobile species such as whales and dolphins. The killer whale (Orcinus orca) has a worldwide distribution, and individual social groups travel over a wide geographic range. Even so, regional populations have been shown to be genetically differentiated, including among different foraging specialists (ecotypes) in sympatry. Given the strong matrifocal social structure of this species together with strong resource specializations, understanding the process of differentiation will require an understanding of the relative importance of both genetic drift and local adaptation. Here we provide a high-resolution analysis based on nuclear single-nucleotide polymorphic markers and inference about differentiation at both neutral loci and those potentially under selection. We find that all population comparisons, within or among foraging ecotypes, show significant differentiation, including populations in parapatry and sympatry. Loci putatively under selection show a different pattern of structure compared to neutral loci and are associated with gene ontology terms reflecting physiologically relevant functions (e.g. related to digestion). The pattern of differentiation for one ecotype in the North Pacific suggests local adaptation and shows some fixed differences among sympatric ecotypes. We suggest that differential habitat use and resource specializations have promoted sufficient isolation to allow differential evolution at neutral and functional loci, but that the process is recent and dependent on both selection and drift. PMID:25244680

Mitochondrial DNA variability among six South American Amerindian villages from the Pano linguistic group.

PubMed

Mendes-Junior, Celso T; Simoes, Aguinaldo L

2014-01-01

Although scattered throughout a large geographic area, the members of the Pano linguistic group present strong ethnic, linguistic, and cultural homogeneity, a feature that causes them to be considered components of a same "Pano" tribe. Nevertheless, the genetic homogeneity between Pano villages has not yet been examined. To study the genetic structure of the Pano linguistic group, four major Native American mitochondrial DNA (mtDNA) founder haplogroups were analyzed in 77 Amerindians from six villages of four Pano tribes (Katukina, Kaxináwa, Marúbo, and Yaminawa) located in the Brazilian Amazon. The central position of these tribes in the continent makes them relevant for attempts to reconstruct population movements in South America. Except for a single individual that presented an African haplogroup L, all remaining individuals presented one of the four Native American haplogroups. Significant heterogeneity was observed across the six Pano villages. Although Amerindian populations are usually characterized by considerable interpopulational diversity, the high heterogeneity level observed is unexpected if the strong ethnic, linguistic, and cultural homogeneity of the Pano linguistic group is taken into account. The present findings indicate that the ethnic, linguistic, and cultural homogeneity does not imply genetic homogeneity. Even though the genetic heterogeneity uncovered may be a female-specific process, the most probable explanation for that is the joint action of isolation and genetic drift as major factors influencing the genetic structure of the Pano linguistic group. Copyright © 2014 Wayne State University Press, Detroit, Michigan 48201-1309.

Soil factors involved in the diversity and structure of soil bacterial communities in commercial organic olive orchards in Southern Spain.

PubMed

Landa, B B; Montes-Borrego, M; Aranda, S; Soriano, M A; Gómez, J A; Navas-Cortés, J A

2014-04-01

Nowadays, there is a tendency in olive production systems to reduce tillage or keep a vegetative cover to reduce soil erosion and degradation. However, there is scarce information on the effects of different soil management systems (SMS) in soil bacterial community composition of olive groves. In this study, we have evaluated the effects of soil type and different SMS implemented to control weeds in the structure and diversity of bacterial communities of 58 soils in the two geographic areas that best represent the organic olive production systems in Spain. Bacterial community composition assessed by frequency and intensity of occurrence of terminal restriction profiles (TRFs) derived from terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S ribosomal deoxyribonucleic acid were strongly correlated with soil type/field site (Eutric/Calcaric) that differed mainly in soil particle size distribution and soil pH, followed by a strong effect of SMS, in that order. Canonical discriminant (CD) analysis of TRFs properly classified all of the olive orchard soils as belonging to their respective soil type or SMS. Furthermore, only a small set of TRFs were enough to clearly and significantly differentiate soil samples according to soil type or SMS. Those specific TRFs could be used as bioindicators to assess the effect of changes in SMS aimed to enhance soil quality in olive production systems. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Combined Analyses of Bacterial, Fungal and Nematode Communities in Andosolic Agricultural Soils in Japan

PubMed Central

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols. PMID:22223474

Combined analyses of bacterial, fungal and nematode communities in andosolic agricultural soils in Japan.

PubMed

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.

Improvement of the F-Perceptory Approach Through Management of Fuzzy Complex Geographic Objects

NASA Astrophysics Data System (ADS)

Khalfi, B.; de Runz, C.; Faiz, S.; Akdag, H.

2015-08-01

In the real world, data is imperfect and in various ways such as imprecision, vagueness, uncertainty, ambiguity and inconsistency. For geographic data, the fuzzy aspect is mainly manifested in time, space and the function of objects and is due to a lack of precision. Therefore, the researchers in the domain emphasize the importance of modeling data structures in GIS but also their lack of adaptation to fuzzy data. The F-Perceptory approachh manages the modeling of imperfect geographic information with UML. This management is essential to maintain faithfulness to reality and to better guide the user in his decision-making. However, this approach does not manage fuzzy complex geographic objects. The latter presents a multiple object with similar or different geographic shapes. So, in this paper, we propose to improve the F-Perceptory approach by proposing to handle fuzzy complex geographic objects modeling. In a second step, we propose its transformation to the UML modeling.

Structural barriers to comprehensive, coordinated HIV care: geographic accessibility in the US South.

PubMed

Kimmel, April D; Masiano, Steven P; Bono, Rose S; Martin, Erika G; Belgrave, Faye Z; Adimora, Adaora A; Dahman, Bassam; Galadima, Hadiza; Sabik, Lindsay M

2018-05-30

Structural barriers to HIV care are particularly challenging in the US South, which has higher HIV diagnosis rates, poverty, uninsurance, HIV stigma, and rurality, and fewer comprehensive public health programs versus other US regions. Focusing on one structural barrier, we examined geographic accessibility to comprehensive, coordinated HIV care (HIVCCC) in the US South. We integrated publicly available data to study travel time to HIVCCC in 16 Southern states and District of Columbia. We geocoded HIVCCC service locations and estimated drive time between the population-weighted county centroid and closest HIVCCC facility. We evaluated drive time in aggregate, and by county-level HIV prevalence quintile, urbanicity, and race/ethnicity. Optimal drive time was ≤30 min, a common primary care accessibility threshold. We identified 228 service locations providing HIVCCC across 1422 Southern counties, with median drive time to care of 70 min (IQR 64 min). For 368 counties in the top HIV prevalence quintile, median drive time is 50 min (IQR 61 min), exceeding 60 min in over one-third of these counties. Among counties in the top HIV prevalence quintile, drive time to care is six-folder higher for rural versus super-urban counties. Counties in the top HIV prevalence quintiles for non-Hispanic Blacks and for Hispanics have >50% longer drive time to care versus for non-Hispanic Whites. Including another potential care source-publicly-funded health centers serving low-income populations-could double the number of high-HIV burden counties with drive time ≤30 min, representing nearly 35,000 additional people living with HIV with accessible HIVCCC. Geographic accessibility to HIVCCC is inadequate in the US South, even in high HIV burden areas, and geographic and racial/ethnic disparities exist. Structural factors, such as geographic accessibility to care, may drive disparities in health outcomes. Further research on programmatic policies, and evidence-based alternative HIV care delivery models improving access to care, is critical.

Geographic information modeling of Econet of Northwestern Federal District territory on graph theory basis

NASA Astrophysics Data System (ADS)

Kopylova, N. S.; Bykova, A. A.; Beregovoy, D. N.

2018-05-01

Based on the landscape-geographical approach, a structural and logical scheme for the Northwestern Federal District Econet has been developed, which can be integrated into the federal and world ecological network in order to improve the environmental infrastructure of the region. The method of Northwestern Federal District Econet organization on the basis of graph theory by means of the Quantum GIS geographic information system is proposed as an effective mean of preserving and recreating the unique biodiversity of landscapes, regulation of the sphere of environmental protection.

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

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.

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

PubMed Central

Banaticla-Hilario, Maria Celeste N; van den Berg, Ronald G; Hamilton, Nigel Ruaraidh Sackville; McNally, Kenneth L

2013-01-01

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by FST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (HE = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (HE = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species. PMID:24101993

An Ancient Divide in a Contiguous Rainforest: Endemic Earthworms in the Australian Wet Tropics

PubMed Central

Moreau, Corrie S.; Hugall, Andrew F.; McDonald, Keith R.; Jamieson, Barrie G. M.; Moritz, Craig

2015-01-01

Understanding the factors that shape current species diversity is a fundamental aim of ecology and evolutionary biology. The Australian Wet Tropics (AWT) are a system in which much is known about how the rainforests and the rainforest-dependent organisms reacted to late Pleistocene climate changes, but less is known about how events deeper in time shaped speciation and extinction in this highly endemic biota. We estimate the phylogeny of a species-rich endemic genus of earthworms (Terrisswalkerius) from the region. Using DEC and DIVA historical biogeography methods we find a strong signal of vicariance among known biogeographical sub-regions across the whole phylogeny, congruent with the phylogeography of less diverse vertebrate groups. Absolute dating estimates, in conjunction with relative ages of major biogeographic disjunctions across Australia, indicate that diversification in Terrisswalkerius dates back before the mid-Miocene shift towards aridification, into the Paleogene era of isolation of mesothermal Gondwanan Australia. For the Queensland endemic Terrisswalkerius earthworms, the AWT have acted as both a museum of biological diversity and as the setting for continuing geographically structured diversification. These results suggest that past events affecting organismal diversification can be concordant across phylogeographic to phylogenetic levels and emphasize the value of multi-scale analysis, from intra- to interspecies, for understanding the broad-scale processes that have shaped geographic diversity. PMID:26366862

Lyssavirus in Indian Flying Foxes, Sri Lanka

PubMed Central

Gunawardena, Panduka S.; Marston, Denise A.; Ellis, Richard J.; Wise, Emma L.; Karawita, Anjana C.; Breed, Andrew C.; McElhinney, Lorraine M.; Johnson, Nicholas; Banyard, Ashley C.

2016-01-01

A novel lyssavirus was isolated from brains of Indian flying foxes (Pteropus medius) in Sri Lanka. Phylogenetic analysis of complete virus genome sequences, and geographic location and host species, provides strong evidence that this virus is a putative new lyssavirus species, designated as Gannoruwa bat lyssavirus. PMID:27434858

Temporal and spatial correlation patterns of air pollutants in Chinese cities

PubMed Central

Dai, Yue-Hua

2017-01-01

As a huge threat to the public health, China’s air pollution has attracted extensive attention and continues to grow in tandem with the economy. Although the real-time air quality report can be utilized to update our knowledge on air quality, questions about how pollutants evolve across time and how pollutants are spatially correlated still remain a puzzle. In view of this point, we adopt the PMFG network method to analyze the six pollutants’ hourly data in 350 Chinese cities in an attempt to find out how these pollutants are correlated temporally and spatially. In terms of time dimension, the results indicate that, except for O3, the pollutants have a common feature of the strong intraday patterns of which the daily variations are composed of two contraction periods and two expansion periods. Besides, all the time series of the six pollutants possess strong long-term correlations, and this temporal memory effect helps to explain why smoggy days are always followed by one after another. In terms of space dimension, the correlation structure shows that O3 is characterized by the highest spatial connections. The PMFGs reveal the relationship between this spatial correlation and provincial administrative divisions by filtering the hierarchical structure in the correlation matrix and refining the cliques as the tinny spatial clusters. Finally, we check the stability of the correlation structure and conclude that, except for PM10 and O3, the other pollutants have an overall stable correlation, and all pollutants have a slight trend to become more divergent in space. These results not only enhance our understanding of the air pollutants’ evolutionary process, but also shed lights on the application of complex network methods into geographic issues. PMID:28832599

Speciation in the Derrida-Higgs model with finite genomes and spatial populations

NASA Astrophysics Data System (ADS)

de Aguiar, Marcus A. M.

2017-02-01

The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it for finite genomes, focusing on the question of how many genes it actually takes to trigger neutral sympatric speciation. We find that, for typical parameters used in the original model, it takes the order of 105 genes. We compare the results with a similar spatially explicit model where about 100 genes suffice for speciation. We show that when the number of genes is small the species that emerge are strongly segregated in space. For a larger number of genes, on the other hand, the spatial structure of the population is less important and the species distribution overlap considerably.

Seismic High Attenuation Region Observed Beneath Southern New England From Teleseismic Body Wave Spectra: Evidence for High Asthenospheric Temperature Without Melt

NASA Astrophysics Data System (ADS)

Dong, Mingduo T.; Menke, William H.

2017-11-01

Seismic attenuation exhibits strong geographic variability in northeastern North America, with the highest values associated with the previously recognized Northern Appalachian Anomaly (NAA) in southern New England. The shear wave quality factor at 100 km depth is 14 < QS < 25, the ratio of P wave and S wave quality factors is QP/QS = 1.2 ± 0.03 (95%), and the frequency dependence parameter is α = 0.39 ± 0.025 (95%). The high values of QP/QS and α are compatible with laboratory measurements of unmelted rock and, in the case of α, incompatible with widespread melting. The low QS implies high mantle temperatures ( 1,550-1,650°C) at 100 km depth (assuming no melt). Small-scale variations in attenuation suggest structural heterogeneity within the NAA, possibly due to lithospheric delamination caused by asthenospheric flow.

Does human migration affect international trade? A complex-network perspective.

PubMed

Fagiolo, Giorgio; Mastrorillo, Marina

2014-01-01

This paper explores the relationships between international human migration and merchandise trade, using a complex-network approach. We firstly compare the topological structure of worldwide networks of human migration and bilateral trade over the period 1960-2000. Next, we ask whether the position of any pair of countries in the migration network affects their bilateral trade flows. We show that: (i) both weighted and binary versions of the networks of international migration and trade are strongly correlated; (ii) such correlations can be mostly explained by country economic/demographic size and geographical distance; and (iii) pairs of countries that are more central in the international-migration network trade more. Our findings suggest that bilateral trade between any two countries is not only affected by the presence of migrants from either countries but also by their relative embeddedness in the complex web of corridors making up the network of international human migration.

Does Human Migration Affect International Trade? A Complex-Network Perspective

PubMed Central

Fagiolo, Giorgio; Mastrorillo, Marina

2014-01-01

This paper explores the relationships between international human migration and merchandise trade using a complex-network approach. We firstly compare the topological structure of worldwide networks of human migration and bilateral trade over the period 1960–2000. Next, we ask whether pairs of countries that are more central in the migration network trade more. We show that: (i) the networks of international migration and trade are strongly correlated, and such correlation can be mostly explained by country economic/demographic size and geographical distance; (ii) centrality in the international-migration network boosts bilateral trade; (iii) intensive forms of country centrality are more trade enhancing than their extensive counterparts. Our findings suggest that bilateral trade between any two countries is not only affected by the presence of migrants from either countries, but also by their relative embeddedness in the complex web of corridors making up the network of international human migration. PMID:24828376

Business cycles' correlation and systemic risk of the Japanese supplier-customer network.

PubMed

Krichene, Hazem; Chakraborty, Abhijit; Inoue, Hiroyasu; Fujiwara, Yoshi

2017-01-01

This work aims to study and explain the business cycle correlations of the Japanese production network. We consider the supplier-customer network, which is a directed network representing the trading links between Japanese firms (links from suppliers to customers). The community structure of this network is determined by applying the Infomap algorithm. Each community is defined by its GDP and its associated business cycle. Business cycle correlations between communities are estimated based on copula theory. Then, based on firms' attributes and network topology, these correlations are explained through linear econometric models. The results show strong evidence of business cycle correlations in the Japanese production network. A significant systemic risk is found for high negative or positive shocks. These correlations are explained mainly by the sector and by geographic similarities. Moreover, our results highlight the higher vulnerability of small communities and small firms, which is explained by the disassortative mixing of the production network.

Business cycles’ correlation and systemic risk of the Japanese supplier-customer network

PubMed Central

Chakraborty, Abhijit; Inoue, Hiroyasu; Fujiwara, Yoshi

2017-01-01

This work aims to study and explain the business cycle correlations of the Japanese production network. We consider the supplier-customer network, which is a directed network representing the trading links between Japanese firms (links from suppliers to customers). The community structure of this network is determined by applying the Infomap algorithm. Each community is defined by its GDP and its associated business cycle. Business cycle correlations between communities are estimated based on copula theory. Then, based on firms’ attributes and network topology, these correlations are explained through linear econometric models. The results show strong evidence of business cycle correlations in the Japanese production network. A significant systemic risk is found for high negative or positive shocks. These correlations are explained mainly by the sector and by geographic similarities. Moreover, our results highlight the higher vulnerability of small communities and small firms, which is explained by the disassortative mixing of the production network. PMID:29059233

Genomic analysis of local variation and recent evolution in Plasmodium vivax

PubMed Central

Pearson, Richard D; Miotto, Olivo; Almagro-Garcia, Jacob; Amaratunga, Chanaki; Suon, Seila; Mao, Sivanna; Noviyanti, Rintis; Trimarsanto, Hidayat; Marfurt, Jutta; Anstey, Nicholas M; William, Timothy; Boni, Maciej F; Dolecek, Christiane; Hien, Tinh Tran; White, Nicholas J; Michon, Pascal; Siba, Peter; Tavul, Livingstone; Harrison, Gabrielle; Barry, Alyssa; Mueller, Ivo; Ferreira, Marcelo U; Karunaweera, Nadira; Randrianarivelojosia, Milijaona; Gao, Qi; Hubbart, Christina; Hart, Lee; Jeffery, Ben; Drury, Eleanor; Mead, Daniel; Kekre, Mihir; Campino, Susana; Manske, Magnus; Cornelius, Victoria J; MacInnis, Bronwyn; Rockett, Kirk A; Miles, Alistair; Rayner, Julian C; Fairhurst, Rick M; Nosten, Francois; Price, Ric N; Kwiatkowski, Dominic P

2016-01-01

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination. PMID:27348299

Between activity and solidarity: Comprehending retirement and extended working lives in Swedish rural areas.

PubMed

Lundgren, Anna Sofia; Liliequist, Evelina; Sjöstedt Landén, Angelika

2018-03-01

The expected costs of population ageing have generally led to perceived needs to postpone the age of retirement. Drawing on 20 semi-structured interviews, the aim of this paper is to describe the ways that the possibility of an extended working life is comprehended by persons over the age of 60 living in sparsely populated areas in northern Sweden. While defining themselves as active, the interviewees argued strongly in favour of the right to retire. What are often described as opposing retiree subject positions - healthy and active vs. vulnerable and dependent - were partly transgressed in the interviews. The interviewees performed a solidarity that had the potential of including their future selves as possible objects of solidarity. Another important result was that in comprehending the possibility of an extended working life, morally charged notions of geographic place became central. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Geography has more influence than language on maternal genetic structure of various northeastern Thai ethnicities.

PubMed

Kutanan, Wibhu; Ghirotto, Silvia; Bertorelle, Giorgio; Srithawong, Suparat; Srithongdaeng, Kanokpohn; Pontham, Nattapon; Kangwanpong, Daoroong

2014-09-01

Several literatures have shown the influence of geographic and linguistic factors in shaping genetic variation patterns, but their relative impact, if any, in the very heterogeneous northeastern region of Thailand has not yet been studied. This area, called Isan, is geographically structured in two wide basins, the Sakon Nakorn Basin and the Korat Basin, serving today as home to diverse ethnicities encompassing two different linguistic families, that is, the Austro-Asiatic; Suay (Kui), Mon, Chaobon (Nyahkur), So and Khmer, and the Tai-Kadai; Saek, Nyaw, Phu Tai, Kaleung and Lao Isan. In this study, we evaluated the relative role of geographic distance and barriers as well as linguistic differences as possible causes affecting the maternal genetic distances among northeastern Thai ethnicities. A 596-bp segment of the hypervariable region I mitochondrial DNA was utilized to elucidate the genetic structure and biological affinity from 433 individuals. Different statistical analyses agreed in suggesting that most ethnic groups in the Sakon Nakorn Basin are closely related. Mantel test revealed that genetic distances were highly associated to geographic (r = 0.445, P<0.01) but not to linguistic (r = 0.001, P>0.01) distances. Three evolutionary models were compared by Approximate Bayesian Computation. The posterior probability of the scenario, which assumed an initial population divergence possibly related to reduced gene flow among basins, was equal or higher than 0.87. All analyses exhibited concordant results supporting that geography was the most relevant factor in determining the maternal genetic structure of northeastern Thai populations.

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.

Mapping Vegetation Structure in Kakadu National Park: An AIRSAR and GIS Application in Conservation

NASA Technical Reports Server (NTRS)

Imhoff, Marc L.; Sisk, Thomas D.; Hampton, Haydee; Milne, Anthony K.

1999-01-01

Airborne Synthetic Aperture Radar (AIRSAR) data were used to map vegetation structure in Kakadu National Park Australia as part of the PACRIM project. SAR data were co-registered with Landsat TM, aerial photos, and map data in a geographic information system for a small test area consisting of mangrove, floodplain grasslands, lowland tropical evergreen forest and upland mixed deciduous and evergreen tropical forest near the South Alligator River. Landsat (Thematic Mapper) TM very clearly showed the floristic composition and burn scars from the previous years fires and the AIRSAR data provided a profile of vegetation structure. Extensive field data on vegetation species composition and structure were collected across a series of transects in cooperation with a survey of avifauna in an effort to link the habitat edge structure with bird species responses. A test site was found that contained two types of habitat edges: 1) A structure specific edge - characterized by the appearance of a very strong structural change in the forest canopy occurring in the absence of a substantial turnover in floristics. 2) Floristic edge - a sharp transition in vegetation genetic composition with a mixed set of structural changes. Specific polarization combinations were selected that were highly correlated to a set of desired structural parameters found in the field data. Classification routines were employed to group radar pixels into 3 structural classes based on: the Surface Area to Volume ratio (SA/V) of the stems, the SA/V of the branches, and the leaf area index of the canopy. Separate canopy structure maps were then entered into the GIS and bird responses were observed relative to the classes and their boundaries. Follow-on work will consist of extending this approach to neighboring areas, generating structure maps, predicting bird responses across the edges, and make accuracy assessments.

Cost-effective age structure and geographical distribution of boreal forest reserves.

PubMed

Lundström, Johanna; Ohman, Karin; Perhans, Karin; Rönnqvist, Mikael; Gustafsson, Lena; Bugman, Harald

2011-02-01

1. Forest reserves are established to preserve biodiversity, and to maintain natural functions and processes. Today there is heightened focus on old-growth stages, with less attention given to early successional stages. The biodiversity potential of younger forests has been overlooked, and the cost-effectiveness of incorporating different age classes in reserve networks has not yet been studied.2. We performed a reserve selection analysis in boreal Sweden using the Swedish National Forest Inventory plots. Seventeen structural variables were used as biodiversity indicators, and the cost of protecting each plot as a reserve was assessed using the Heureka system. A goal programming approach was applied, which allowed inclusion of several objectives and avoided a situation in which common indicators affected the result more than rare ones. The model was limited either by budget or area.3. All biodiversity indicators were found in all age classes, with more than half having the highest values in ages ≥ 100 years. Several large-tree indicators and all deadwood indicators had higher values in forests 0-14 years than in forests 15-69 years.4. It was most cost-effective to protect a large proportion of young forests since they generally have a lower net present value compared to older forests, but still contain structures of importance for biodiversity. However, it was more area-effective to protect a large proportion of old forests since they have a higher biodiversity potential per area.5. The geographical distribution of reserves selected with the budget-constrained model was strongly biassed towards the north-western section of boreal Sweden, with a large proportion of young forest, whereas the area-constrained model focussed on the south-eastern section, with dominance by the oldest age class.6.Synthesis and applications. We show that young forests with large amounts of structures important to biodiversity such as dead wood and remnant trees are cheap and cost-efficient to protect. This suggests that reserve networks should incorporate sites with high habitat quality of different forest ages. Since young forests are generally neglected in conservation, our approach is of interest also to other forest biomes where biodiversity is adapted to disturbance regimes resulting in open, early successional stages.

Sequence homology and structural analysis of plasmepsin 4 isolated from Indian Plasmodium vivax isolates.

PubMed

Rawat, Manmeet; Vijay, Sonam; Gupta, Yash; Dixit, Rajnikant; Tiwari, P K; Sharma, Arun

2011-07-01

Plasmodium vivax malaria is a globally widespread disease responsible for 50% of human malaria cases in Central and South America, South East Asia and Indian subcontinent. The rising severity of the disease and emerging resistance of the parasite has emphasized the need for the search of novel therapeutic targets to combat P. vivax malaria. Plasmepsin 4 (PM4) a food vacuole aspartic protease is essential in parasite functions and viability such as initiating hemoglobin digestion and processing of proteins and is being looked upon as potential drug target. Although the plasmepsins of Plasmodium falciparum have been extensively studied, the plasmepsins of P. vivax are not well characterized. This is the first report detailing complete PM4 gene analysis from Indian P. vivax isolates. Blast results of sequences of P. vivax plasmepsin 4 (PvPM4) shows 100% homology among isolates of P. vivax collected from different geographical regions of India. All of the seven Indian isolates did not contain intron within the coding region. Interestingly, PvPM4 sequence analysis showed a very high degree of homology with all other sequences of Plasmodium species available in the genebank. Our results strongly suggest that PvPM4 are highly conserved except a small number of amino acid substitutions that did not modify key motifs at active site formation for the function or the structure of the enzymes. Furthermore, our study shows that PvPM4 occupies unique phylogenetic status within Plasmodium group and sufficiently differ from the most closely related human aspartic protease, cathepsin D. The analysis of 3D model of PM4 showed a typical aspartic protease structure with bi-lobed, compact and distinct peptide binding cleft in both P. vivax and P. falciparum. In order to validate appropriate use of PM4 as potential anti-malarial drug target, studies on genetic and structural variations among P. vivax plasmepsins (PvPMs) from different geographical regions are of utmost importance for drugs and vaccine designs for anti-malarial strategies. Copyright © 2011 Elsevier B.V. All rights reserved.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level.

PubMed

Urrestarazu, Jorge; Denancé, Caroline; Ravon, Elisa; Guyader, Arnaud; Guisnel, Rémi; Feugey, Laurence; Poncet, Charles; Lateur, Marc; Houben, Patrick; Ordidge, Matthew; Fernandez-Fernandez, Felicidad; Evans, Kate M; Paprstein, Frantisek; Sedlak, Jiri; Nybom, Hilde; Garkava-Gustavsson, Larisa; Miranda, Carlos; Gassmann, Jennifer; Kellerhals, Markus; Suprun, Ivan; Pikunova, Anna V; Krasova, Nina G; Torutaeva, Elnura; Dondini, Luca; Tartarini, Stefano; Laurens, François; Durel, Charles-Eric

2016-06-08

The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

What Influences Geography Teachers' Usage of Geographic Information Systems? A Structural Equation Analysis

ERIC Educational Resources Information Center

Lay, Jinn-Guey; Chi, Yu-Lin; Hsieh, Yeu-Sheng; Chen, Yu-Wen

2013-01-01

Understanding the usage of the geographic information system (GIS) among geography teachers is a crucial step in evaluating the current dissemination of GIS knowledge and skills in Taiwan's educational system. The primary contribution of this research is to further our understanding of the factors that affect teachers' GIS usage. The structural…

Designing a Structured and Interactive Learning Environment Based on GIS for Secondary Geography Education

ERIC Educational Resources Information Center

Liu, Suxia; Zhu, Xuan

2008-01-01

Geographic information systems (GIS) are computer-based tools for geographic data analysis and spatial visualization. They have become one of the information and communications technologies for education at all levels. This article reviews the current status of GIS in schools, analyzes the requirements of a GIS-based learning environment from…

Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

PubMed Central

Shanks, Orin C.; Newton, Ryan J.; Kelty, Catherine A.; Huse, Susan M.; Sogin, Mitchell L.

2013-01-01

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States. PMID:23435885

Microsatellite Analyses of Blacktip Reef Sharks (Carcharhinus melanopterus) in a Fragmented Environment Show Structured Clusters

PubMed Central

Vignaud, Thomas; Clua, Eric; Mourier, Johann; Maynard, Jeffrey; Planes, Serge

2013-01-01

The population dynamics of shark species are generally poorly described because highly mobile marine life is challenging to investigate. Here we investigate the genetic population structure of the blacktip reef shark (Carcharhinus melanopterus) in French Polynesia. Five demes were sampled from five islands with different inter-island distances (50–1500 km). Whether dispersal occurs between islands frequently enough to prevent moderate genetic structure is unknown. We used 11 microsatellites loci from 165 individuals and a strong genetic structure was found among demes with both F-statistics and Bayesian approaches. This differentiation is correlated with the geographic distance between islands. It is likely that the genetic structure seen is the result of all or some combination of the following: low gene flow, time since divergence, small effective population sizes, and the standard issues with the extent to which mutation models actually fit reality. We suggest low levels of gene flow as at least a partial explanation of the level of genetic structure seen among the sampled blacktip demes. This explanation is consistent with the ecological traits of blacktip reef sharks, and that the suitable habitat for blacktips in French Polynesia is highly fragmented. Evidence for spatial genetic structure of the blacktip demes we studied highlights that similar species may have populations with as yet undetected or underestimated structure. Shark biology and the market for their fins make them highly vulnerable and many species are in rapid decline. Our results add weight to the case that total bans on shark fishing are a better conservation approach for sharks than marine protected area networks. PMID:23585872

The National Map - Orthoimagery Layer

USGS Publications Warehouse

,

2007-01-01

Many Federal, State, and local agencies use a common set of framework geographic information databases as a tool for economic and community development, land and natural resource management, and health and safety services. Emergency management and homeland security applications rely on this information. Private industry, nongovernmental organizations, and individual citizens use the same geographic data. Geographic information underpins an increasingly large part of the Nation's economy. The U.S. Geological Survey (USGS) is developing The National Map to be a seamless, continually maintained, and nationally consistent set of online, public domain, framework geographic information databases. The National Map will serve as a foundation for integrating, sharing, and using data easily and consistently. The data will be the source of revised paper topographic maps. The National Map includes digital orthorectified imagery; elevation data; vector data for hydrography, transportation, boundary, and structure features; geographic names; and land cover information.

Biofouling community composition across a range of environmental conditions and geographical locations suitable for floating marine renewable energy generation.

PubMed

Macleod, Adrian K; Stanley, Michele S; Day, John G; Cook, Elizabeth J

2016-01-01

Knowledge of biofouling typical of marine structures is essential for engineers to define appropriate loading criteria in addition to informing other stakeholders about the ecological implications of creating novel artificial environments. There is a lack of information regarding biofouling community composition (including weight and density characteristics) on floating structures associated with future marine renewable energy generation technologies. A network of navigation buoys were identified across a range of geographical areas, environmental conditions (tidal flow speed, temperature and salinity), and deployment durations suitable for future developments. Despite the perceived importance of environmental and temporal factors, geographical location explained the greatest proportion of the observed variation in community composition, emphasising the importance of considering geography when assessing the impact of biofouling on device functioning and associated ecology. The principal taxa associated with variation in biofouling community composition were mussels (Mytilus edulis), which were also important when determining loading criteria.

Interplay between geo-population factors and hierarchy of cities in multilayer urban networks.

PubMed

Makarov, Vladimir V; Hramov, Alexander E; Kirsanov, Daniil V; Maksimenko, Vladimir A; Goremyko, Mikhail V; Ivanov, Alexey V; Yashkov, Ivan A; Boccaletti, Stefano

2017-12-08

Only taking into consideration the interplay between processes occurring at different levels of a country can provide the complete social and geopolitical plot of its urban system. We study the interaction of the administrative structure and the geographical connectivity between cities with the help of a multiplex network approach. We found that a spatially-distributed geo-network imposes its own ranking to the hierarchical administrative network, while the latter redistributes the shortest paths between nodes in the geographical layer. Using both real demographic data of population censuses of the Republic of Kazakhstan and theoretical models, we show that in a country-scale urban network and for each specific city, the geographical neighbouring with highly populated areas is more important than its political setting. Furthermore, the structure of political subordination is instead crucial for the wealth of transportation network and communication between populated regions of the country.

Report from a forum on US heart allocation policy.

PubMed

Kobashigawa, J A; Johnson, M; Rogers, J; Vega, J D; Colvin-Adams, M; Edwards, L; Meyer, D; Luu, M; Reinsmoen, N; Dipchand, A I; Feldman, D; Kormos, R; Mancini, D; Webber, S

2015-01-01

Since the latest revision in US heart allocation policy (2006), the landscape and volume of transplant waitlists have changed considerably. Advances in mechanical circulatory support (MCS) prolong survival, but Status 1A mortality remains high. Several patient subgroups may be disadvantaged by current listing criteria and geographical disparity remains in waitlist time. This forum on US heart allocation policy was organized to discuss these issues and highlight concepts for consideration in the policy development process. A 25-question survey on heart allocation policy was conducted. Among attendees/respondents were 84 participants with clinical/published experience in heart transplant representing 51 US transplant centers, and OPTN/UNOS and SRTR representatives. The survey results and forum discussions demonstrated very strong interest in change to a further-tiered system, accounting for disadvantaged subgroups and lowering use of exceptions. However, a heart allocation score is not yet viable due to the long-term viability of variables (used in the score) in an ever-developing field. There is strong interest in more refined prioritization of patients with MCS complications, highly sensitized patients and those with severe arrhythmias or restrictive physiology. There is also strong interest in distribution by geographic boundaries modified according to population. Differences of opinion exist between small and large centers.

School Desegregation, the Philadelphia Experience.

ERIC Educational Resources Information Center

Herron, William P.

The Philadelphia experience very strongly indicates that at least in Philadelphia, and very probably in most large cities in the northeastern U.S., several factors--notably the geographic separation of the races within the city and the existence of a sizable non-public school system (Usually (Usually parochial)--preclude the effective…

Genetics of the pig tapeworm in Madagascar reveal a history of human dispersal and colonization

USDA-ARS?s Scientific Manuscript database

An intricate history of human dispersal and geographic colonization has strongly affected the distribution of obligate parasites circulating among people. Among these parasites, the pig tapeworm Taenia solium occurs throughout the world as the causative agent of cysticercosis, one of the most serio...

The evolution of cooperation on geographical networks

NASA Astrophysics Data System (ADS)

Li, Yixiao; Wang, Yi; Sheng, Jichuan

2017-11-01

We study evolutionary public goods game on geographical networks, i.e., complex networks which are located on a geographical plane. The geographical feature effects in two ways: In one way, the geographically-induced network structure influences the overall evolutionary dynamics, and, in the other way, the geographical length of an edge influences the cost when the two players at the two ends interact. For the latter effect, we design a new cost function of cooperators, which simply assumes that the longer the distance between two players, the higher cost the cooperator(s) of them have to pay. In this study, network substrates are generated by a previous spatial network model with a cost-benefit parameter controlling the network topology. Our simulations show that the greatest promotion of cooperation is achieved in the intermediate regime of the parameter, in which empirical estimates of various railway networks fall. Further, we investigate how the distribution of edges' geographical costs influences the evolutionary dynamics and consider three patterns of the distribution: an approximately-equal distribution, a diverse distribution, and a polarized distribution. For normal geographical networks which are generated using intermediate values of the cost-benefit parameter, a diverse distribution hinders the evolution of cooperation, whereas a polarized distribution lowers the threshold value of the amplification factor for cooperation in public goods game. These results are helpful for understanding the evolution of cooperation on real-world geographical networks.

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.

Extreme deconstruction supports niche conservatism driving New World bird diversity

NASA Astrophysics Data System (ADS)

Diniz-Filho, José Alexandre Felizola; Rangel, Thiago Fernando; dos Santos, Mariana Rocha

2012-08-01

It is expected that if environment fully establishes the borders of species geographic distribution, then richness patterns will arise simple by changing parameters on how environment affect each of the species. However, if other mechanisms (i.e., non-equilibrium of species' distributions with climate and historical contingency, shifts in adaptive peaks or biotic interactions) are driving species geographic distribution, models for species distribution and richness will not entirely match. Here we used the extreme deconstruction principle to test how niche conservatism keeping species geographic distributions in certain parts of environmental space drives richness patterns in New World birds, under tropical niche conservatism. Eight environmental variables were used to model the geographic distribution of 2790 species within 28 bird families using a GLM. Spatial patterns in richness for each of these families were also modeled as a function of these same variables using a standard OLS regression. Fit of these two types of models (mean MacFadden's ρ2 for GLM and R2 of OLS) across families and the match between GLM and OLS standardized slopes within and among bird families were then compared. We found a positive and significant correlation between GLM and OLS model fit (r = 0.601; P < 0.01), indicating that when environment strongly determine richness of a family, it also explains its species geographic distributions. The match between GLM and OLS slopes is significantly correlated with families' phylogenetic root distance (r = -0.467; P = 0.012), so that more basal families tend to have a better match between environmental drivers of richness and geographic distribution models. This is expected under tropical niche conservatism model and provides an integrated explanation on how processes at a lower hierarchical level (species' geographic distribution) drive diversity patterns.

WebEQ: a web-GIS System to collect, display and query data for the management of the earthquake emergency in Central Italy

NASA Astrophysics Data System (ADS)

Carbone, Gianluca; Cosentino, Giuseppe; Pennica, Francesco; Moscatelli, Massimiliano; Stigliano, Francesco

2017-04-01

After the strong earthquakes that hit central Italy in recent months, the Center for Seismic Microzonation and its applications (CentroMS) was commissioned by the Italian Department of Civil Protection to conduct the study of seismic microzonation of the territories affected by the earthquake of August 24, 2016. As part of the activities of microzonation, IGAG CNR has created WebEQ, a management tool of the data that have been acquired by all participants (i.e., more than twenty research institutes and university departments). The data collection was organized and divided into sub-areas, assigned to working groups with multidisciplinary expertise in geology, geophysics and engineering. WebEQ is a web-GIS System that helps all the subjects involved in the data collection activities, through tools aimed at data uploading and validation, and with a simple GIS interface to display, query and download geographic data. WebEQ is contributing to the creation of a large database containing geographical data, both vector and raster, from various sources and types: - Regional Technical Map em Geological and geomorphological maps em Data location maps em Maps of microzones homogeneous in seismic perspective and seismic microzonation maps em National strong motion network location. Data loading is done through simple input masks that ensure consistency with the database structure, avoiding possible errors and helping users to interact with the map through user-friendly tools. All the data are thematized through standardized symbologies and colors (Gruppo di lavoro MS 2008), in order to allow the easy interpretation by all users. The data download tools allow data exchange between working groups and the scientific community to benefit from the activities. The seismic microzonation activities are still ongoing. WebEQ is enabling easy management of large amounts of data and will form a basis for the development of tools for the management of the upcoming seismic emergencies.

Learned Vocal Variation Is Associated with Abrupt Cryptic Genetic Change in a Parrot Species Complex

PubMed Central

Ribot, Raoul F. H.; Buchanan, Katherine L.; Endler, John A.; Joseph, Leo; Bennett, Andrew T. D.; Berg, Mathew L.

2012-01-01

Contact zones between subspecies or closely related species offer valuable insights into speciation processes. A typical feature of such zones is the presence of clinal variation in multiple traits. The nature of these traits and the concordance among clines are expected to influence whether and how quickly speciation will proceed. Learned signals, such as vocalizations in species having vocal learning (e.g. humans, many birds, bats and cetaceans), can exhibit rapid change and may accelerate reproductive isolation between populations. Therefore, particularly strong concordance among clines in learned signals and population genetic structure may be expected, even among continuous populations in the early stages of speciation. However, empirical evidence for this pattern is often limited because differences in vocalisations between populations are driven by habitat differences or have evolved in allopatry. We tested for this pattern in a unique system where we may be able to separate effects of habitat and evolutionary history. We studied geographic variation in the vocalizations of the crimson rosella (Platycercus elegans) parrot species complex. Parrots are well known for their life-long vocal learning and cognitive abilities. We analysed contact calls across a ca 1300 km transect encompassing populations that differed in neutral genetic markers and plumage colour. We found steep clinal changes in two acoustic variables (fundamental frequency and peak frequency position). The positions of the two clines in vocal traits were concordant with a steep cline in microsatellite-based genetic variation, but were discordant with the steep clines in mtDNA, plumage and habitat. Our study provides new evidence that vocal variation, in a species with vocal learning, can coincide with areas of restricted gene flow across geographically continuous populations. Our results suggest that traits that evolve culturally can be strongly associated with reduced gene flow between populations, and therefore may promote speciation, even in the absence of other barriers. PMID:23227179

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.

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

PubMed

Bracco, Mariana; Cascales, Jimena; Hernández, Julián Cámara; Poggio, Lidia; Gottlieb, Alexandra M; Lia, Verónica V

2016-08-26

Maize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure. Bayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models. Our results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.

Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.

PubMed

Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M

2009-02-01

The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.

Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations.

PubMed

Ben Halim, Nizar; Hsouna, Sana; Lasram, Khaled; Chargui, Mariem; Khemira, Laaroussi; Saidane, Rachid; Abdelhak, Sonia; Kefi, Rym

2018-02-01

Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (n = 4857) were compiled from previous studies. The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.

Spatial variation of natural radiation and childhood leukaemia incidence in Great Britain.

PubMed

Richardson, S; Monfort, C; Green, M; Draper, G; Muirhead, C

This paper describes an analysis of the geographical variation of childhood leukaemia incidence in Great Britain over a 15 year period in relation to natural radiation (gamma and radon). Data at the level of the 459 district level local authorities in England, Wales and regional districts in Scotland are analysed in two complementary ways: first, by Poisson regressions with the inclusion of environmental covariates and a smooth spatial structure; secondly, by a hierarchical Bayesian model in which extra-Poisson variability is modelled explicitly in terms of spatial and non-spatial components. From this analysis, we deduce a strong indication that a main part of the variability is accounted for by a local neighbourhood 'clustering' structure. This structure is furthermore relatively stable over the 15 year period for the lymphocytic leukaemias which make up the majority of observed cases. We found no evidence of a positive association of childhood leukaemia incidence with outdoor or indoor gamma radiation levels. There is no consistent evidence of any association with radon levels. Indeed, in the Poisson regressions, a significant positive association was only observed for one 5-year period, a result which is not compatible with a stable environmental effect. Moreover, this positive association became clearly non-significant when over-dispersion relative to the Poisson distribution was taken into account.

Knowing what and where: TMS evidence for the dual neural basis of geographical knowledge.

PubMed

Hoffman, Paul; Crutch, Sebastian

2016-02-01

All animals acquire knowledge about the topography of their immediate environment through direct exploration. Uniquely, humans also acquire geographical knowledge indirectly through exposure to maps and verbal information, resulting in a rich database of global geographical knowledge. We used transcranial magnetic stimulation to investigate the structure and neural basis of this critical but poorly understood component of semantic knowledge. Participants completed tests of geographical knowledge that probed either information about spatial locations (e.g., France borders Spain) or non-spatial taxonomic information (e.g., France is a country). TMS applied to the anterior temporal lobe, a region that codes conceptual knowledge for words and objects, had a general disruptive effect on the geographical tasks. In contrast, stimulation of the intraparietal sulcus (IPS), a region involved in the coding of spatial and numerical information, had a highly selective effect on spatial geographical decisions but no effect on taxonomic judgements. Our results establish that geographical concepts lie at the intersection of two distinct neural representation systems, and provide insights into how the interaction of these systems shape our understanding of the world. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Effects of English admixture and geographic distance on anthropometric variation and genetic structure in 19th-century Ireland.

PubMed

Relethford, J H

1988-05-01

The analysis of anthropometric data often allows investigation of patterns of genetic structure in historical populations. This paper focuses on interpopulational anthropometric variation in seven populations in Ireland using data collected in the 1890s. The seven populations were located within a 120-km range along the west coast of Ireland and include islands and mainland isolates. Two of the populations (the Aran Islands and Inishbofin) have a known history of English admixture in earlier centuries. Ten anthropometric measures (head length, breadth, and height; nose length and breadth; bizygomatic and bigonial breadth; stature; hand length; and forearm length) on 259 adult Irish males were analyzed following age adjustment. Discriminant and canonical variates analysis were used to determine the degree and pattern of among-group variation. Mahalanobis' distance measure, D2, was computed between each pair of populations and compared to distance measures based on geographic distance and English admixture (a binary measure indicating whether either of a pair of populations had historical indications of admixture). In addition, surname frequencies were used to construct distance measures based on random isonymy. Correlations were computed between distance measures, and their probabilities were derived using the Mantel matrix permutation method. English admixture has the greatest effect on anthropometric variation among these populations, followed by geographic distance. The correlation between anthropometric distance and geographic distance is not significant (r = -0.081, P = .590), but the correlation of admixture and anthropometric distance is significant (r = 0.829, P = .047). When the two admixed populations are removed from the analysis the correlation between geographic and anthropometric distance becomes significant (r = 0.718, P = .025). Isonymy distance shows a significant correlation with geographic distance (r = 0.425, P = .046) but not with admixture distance (r = -0.052, P = .524). The fact that anthropometrics show past patterns of gene flow and surnames do not reflects the greater impact of stochastic processes on surnames, along with the continued extinction of surnames. This study shows that 1) anthropometrics can be extremely useful in assessing population structure and history, 2) differential gene flow into populations can have a major impact on local genetic structure, and 3) microevolutionary processes can have different effects on biological characters and surnames.

Discordant genetic diversity and geographic patterns between Crassicutis cichlasomae (Digenea: Apocreadiidae) and its cichlid host, "Cichlasoma" urophthalmus (Osteichthyes: Cichlidae), in Middle-America.

PubMed

Razo-Mendivil, Ulises; Vázquez-Domínguez, Ella; de León, Gerardo Pérez-Ponce

2013-12-01

Genetic analyses of hosts and their parasites are key to understand the evolutionary patterns and processes that have shaped host-parasite associations. We evaluated the genetic structure of the digenean Crassicutis cichlasomae and its most common host, the Mayan cichlid "Cichlasoma" urophthalmus, encompassing most of their geographical range in Middle-America (river basins in southeastern Mexico, Belize, and Guatemala together with the Yucatan Peninsula). Genetic diversity and structure analyses were done based on 167 cytochrome c oxidase subunit 1 sequences (330 bp) for C. cichlasomae from 21 populations and 161 cytochrome b sequences (599 bp) for "C." urophthalmus from 26 populations. Analyses performed included phylogenetic tree estimation under Bayesian inference and maximum likelihood analysis, genetic diversity, distance and structure estimates, haplotype networks, and demographic evaluations. Crassicutis cichlasomae showed high genetic diversity values and genetic structuring, corresponding with 4 groups clearly differentiated and highly divergent. Conversely, "C." urophthalmus showed low levels of genetic diversity and genetic differentiation, defined as 2 groups with low divergence and with no correspondence with geographical distribution. Our results show that species of cichlids parasitized by C. cichlasomae other than "C." urophthalmus, along with multiple colonization events and subsequent isolation in different basins, are likely factors that shaped the genetic structure of the parasite. Meanwhile, historical long-distance dispersal and drought periods during the Holocene, with significant population size reductions and fragmentations, are factors that could have shaped the genetic structure of the Mayan cichlid.

Legal disputes as a proxy for regional conflicts over water rights in Chile

NASA Astrophysics Data System (ADS)

Rivera, Diego; Godoy-Faúndez, Alex; Lillo, Mario; Alvez, Amaya; Delgado, Verónica; Gonzalo-Martín, Consuelo; Menasalvas, Ernestina; Costumero, Roberto; García-Pedrero, Ángel

2016-04-01

Water demand and climate variability increases competition and tension between water users -agricultural, industrial, mining, hydropower- and local communities. Since 1981, the Water Code has regulated water allocation through private individual property rights, fostering markets as the distribution mechanism among users. When legal conflicts occur between parties, it is the responsibility of the courts to settle the conflict. The aim of this research is twofold: first, to apply a geographical approach by mapping water conflicts using legal disputes reaching the higher courts as a proxy for conflict intensity and second, to explain the diversity of water disputes and how they vary regionally. We built a representative database with a sample of 1000 legal records corresponding to decisions issued by the Supreme Court and 17 courts of appeal throughout the country from 1981 to 2014. For geo-tagging, all records were transformed to plain text and analyzed to find words matching the entries of a geographical thesaurus, allowing records to be linked to geographical locations. The geo-tagging algorithm is capable of automatically populating a searchable database. Several maps were constructed using a color scale to visualize conflict intensity. Legal disputes represent different types of conflicts among water users, such as competition between agriculture and hydropower. Processed data allowed the identification of the regional variation of conflicts. The spatial pattern for the intensity of conflicts related to specific sections of the Water Code is explained in terms of the main geographical, climatic and productive characteristics of Chile. Geo-tagging legal records shows a strong potential to understand and define regional variation of water conflicts. However, data availability would become a barrier if measures to improve data management were not taken. Regarding the institutional framework, the same regulations for water management rules are applied throughout the highly diverse ecosystems of the country, impeding the resolution of conflicts that are strongly related to the local geographical context. This leads to a collision of interests and visions around water resources of both a public and private, extractive and non-extractive uses, national, and international nature of individuals, aboriginal communities, and corporations, especially mining industries.

Geographical variations in seasonal mortality across the United States: A bioclimatological approach

NASA Astrophysics Data System (ADS)

Kalkstein, Adam

2008-10-01

Human mortality exhibits a strong seasonal pattern with deaths in winter far exceeding those in the summer. Surprisingly, this seasonal trend is evident in all major cities across the United States, seemingly independent of climate. While the pattern itself is clear, its magnitude varies considerably across space, and it is not known if there is regional homogeneity among cities. Additionally, the causal mechanisms relating to pattern variability are not clearly understood. The goal of this study is to conduct a comprehensive geographic analysis of seasonal mortality across the United States, to uncover systematic regional differences in such mortality, and to determine what role weather plays in impacting seasonal mortality rates. Unique seasonal mortality curves were created for 28 Metropolitan Statistical Areas across the United States, and the amplitude and timing of mortality peaks were determined. In addition, seasonality was calculated for different demographic groups and causes of death. Meteorological factors were also evaluated as possible causal mechanisms. The findings here indicate that the seasonality of mortality exhibits strong spatial variation with the largest seasonal mortality amplitudes found in the southwestern United States and the smallest in the North, along with South Florida. In addition, there have been changes in the timing of seasonal mortality; the date of maximum mortality is occurring increasingly early in the year. Demographics also play an important role with women, Whites, and the elderly exhibiting the strongest seasonality in mortality. There is a strong connection between respiratory disease and other causes of death, implying a cause-effect relationship. Meteorology also plays an important role in seasonal mortality; variations in the frequency of certain air masses were associated with changes in the timing and amplitude of seasonal mortality. Finally, there were strong intra-regional similarities that exist among the examined cities, implying that environmental factors are more important than social factors in determining seasonal mortality response. This work begins to fill a large gap within the scientific literature concerning the causes, geographic variation, and meteorological influences on seasonal mortality. Additionally, these results will increase the forecasting capabilities of determining when and where winter mortality will reach unusually high levels.

The Importance of the Geographic Level of Analysis in the Assessment of the Quality of Life: The Case of Spain

ERIC Educational Resources Information Center

Gonzalez, Eduardo; Carcaba, Ana; Ventura, Juan

2011-01-01

There is a growing literature on the assessment of quality of life conditions in geographically and/or politically divided regions. Sometimes these territories are countries within a specified supranational structure, such as the European Union, for instance, and sometimes they are regions within countries. There is also some research that focuses…

Community Health Coalitions in Context: Associations between Geographic Context, Member Type and Length of Membership with Coalition Functions

ERIC Educational Resources Information Center

Sánchez, V.; Sanders, M.; Andrews, M. L.; Hale, R.; Carrillo, C.

2014-01-01

The coalition literature recognizes context (geography, demographics and history) as a variable of interest, yet few coalition evaluation studies have focused on it. This study explores the association between geographic context and structures (e.g. member type) with functional characteristics (e.g. decision making or levels of conflict) in a…

Geographic patterns of genetic variation, population structure and adaptive traits in Pinus aristata, Rocky Mountain bristlecone pine

Treesearch

Anna W. Schoettle; Betsy A. Goodrich; Valerie Hipkins; Christopher Richards; Julie Kray

2011-01-01

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow geographic and elevational distribution and occurs in disjunct mountain-top populations throughout Colorado and New Mexico in its core range. The species' unique aesthetic and ecological traits combined with the threats of the exotic disease white pine blister rust (WPBR), climate change in high...

The organisation, operational dynamics and structure of female sex work in Pakistan.

PubMed

Emmanuel, Faran; Thompson, Laura H; Athar, Uzma; Salim, Momina; Sonia, Altaf; Akhtar, Naeem; Blanchard, James F

2013-09-01

Pakistan is known to have large populations of female sex workers (FSWs) with considerable geographic heterogeneity in their characteristics. In this paper, we describe the social organisation and structural patterns of female sex work in different geographic regions of Pakistan. We report geographic and network mapping data collected among FSWs in 15 cities across Pakistan in 2011 as part of the Canada-Pakistan HIV/AIDS Surveillance Project. A total number of 89 178 FSWs were estimated in the target cities for an average of 7.2 FSWs per 1000 adult males. 55% of the estimated number of FSWs concentrated in Karachi and Lahore. Based on the operations of female sex work, two major typologies of FSWs were identified: establishment-based and non-establishment-based. FSWs were further subtyped into those operating through brothels, homes, kothikhanas, streets and by cell phone. Cities varied considerably in terms of predominance of different FSW typologies. There is considerable heterogeneity among FSWs in Pakistan, geographically and in terms of operational typology. Understanding the social organisation of sex work and the influence of social-cultural and legal factors in Pakistan is essential for the design of HIV prevention programmes and other services for FSWs.

Population structure and cultural geography of a folktale in Europe

PubMed Central

Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

2013-01-01

Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

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.

The evolution of traditional knowledge: environment shapes medicinal plant use in Nepal

PubMed Central

Saslis-Lagoudakis, C. Haris; Hawkins, Julie A.; Greenhill, Simon J.; Pendry, Colin A.; Watson, Mark F.; Tuladhar-Douglas, Will; Baral, Sushim R.; Savolainen, Vincent

2014-01-01

Traditional knowledge is influenced by ancestry, inter-cultural diffusion and interaction with the natural environment. It is problematic to assess the contributions of these influences independently because closely related ethnic groups may also be geographically close, exposed to similar environments and able to exchange knowledge readily. Medicinal plant use is one of the most important components of traditional knowledge, since plants provide healthcare for up to 80% of the world's population. Here, we assess the significance of ancestry, geographical proximity of cultures and the environment in determining medicinal plant use for 12 ethnic groups in Nepal. Incorporating phylogenetic information to account for plant evolutionary relatedness, we calculate pairwise distances that describe differences in the ethnic groups' medicinal floras and floristic environments. We also determine linguistic relatedness and geographical separation for all pairs of ethnic groups. We show that medicinal uses are most similar when cultures are found in similar floristic environments. The correlation between medicinal flora and floristic environment was positive and strongly significant, in contrast to the effects of shared ancestry and geographical proximity. These findings demonstrate the importance of adaptation to local environments, even at small spatial scale, in shaping traditional knowledge during human cultural evolution. PMID:24523269

The evolution of traditional knowledge: environment shapes medicinal plant use in Nepal.

PubMed

Saslis-Lagoudakis, C Haris; Hawkins, Julie A; Greenhill, Simon J; Pendry, Colin A; Watson, Mark F; Tuladhar-Douglas, Will; Baral, Sushim R; Savolainen, Vincent

2014-04-07

Traditional knowledge is influenced by ancestry, inter-cultural diffusion and interaction with the natural environment. It is problematic to assess the contributions of these influences independently because closely related ethnic groups may also be geographically close, exposed to similar environments and able to exchange knowledge readily. Medicinal plant use is one of the most important components of traditional knowledge, since plants provide healthcare for up to 80% of the world's population. Here, we assess the significance of ancestry, geographical proximity of cultures and the environment in determining medicinal plant use for 12 ethnic groups in Nepal. Incorporating phylogenetic information to account for plant evolutionary relatedness, we calculate pairwise distances that describe differences in the ethnic groups' medicinal floras and floristic environments. We also determine linguistic relatedness and geographical separation for all pairs of ethnic groups. We show that medicinal uses are most similar when cultures are found in similar floristic environments. The correlation between medicinal flora and floristic environment was positive and strongly significant, in contrast to the effects of shared ancestry and geographical proximity. These findings demonstrate the importance of adaptation to local environments, even at small spatial scale, in shaping traditional knowledge during human cultural evolution.

Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses

PubMed Central

Castel, Guillaume; Razzauti, Maria; Jousselin, Emmanuelle; Kergoat, Gael J.; Cosson, Jean-François

2014-01-01

In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus) using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local). We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space. PMID:24618811

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

PubMed

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-08-11

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

Evidence for Geographic Isolation and Signs of Endemism within a Protistan Morphospecies†

PubMed Central

Boenigk, Jens; Pfandl, Karin; Garstecki, Tobias; Harms, Hauke; Novarino, Gianfranco; Chatzinotas, Antonis

2006-01-01

The possible existence of endemism among microorganisms resulting from and preserved by geographic isolation is one of the most controversial topics in microbial ecology. We isolated 31 strains of “Spumella-like” flagellates from remote sampling sites from all continents, including Antarctica. These and another 23 isolates from a former study were characterized morphologically and by small-subunit rRNA gene sequence analysis and tested for the maximum temperature tolerance. Only a minority of the Spumella morpho- and phylotypes from the geographically isolated Antarctic continent follow the worldwide trend of a linear correlation between ambient (air) temperature during strain isolation and heat tolerance of the isolates. A high percentage of the Antarctic isolates, but none of the isolates from locations on all other continents, were obligate psychrophilic, although some of the latter were isolated at low ambient temperatures. The drastic deviation of Antarctic representatives of Spumella from the global trend of temperature adaptation of this morphospecies provides strong evidence for geographic transport restriction of a microorganism; i.e., Antarctic protistan communities are less influenced by transport of protists to and from the Antarctic continent than by local adaptation, a subtle form of endemism. PMID:16885260

Socioeconomic Status Accounts for Rapidly Increasing Geographic Variation in the Incidence of Poor Fetal Growth

PubMed Central

Ball, Stephen J.; Jacoby, Peter; Zubrick, Stephen R.

2013-01-01

Fetal growth is an important risk factor for infant morbidity and mortality. In turn, socioeconomic status is a key predictor of fetal growth; however, other sociodemographic factors and environmental effects may also be important. This study modelled geographic variation in poor fetal growth after accounting for socioeconomic status, with a fixed effect for socioeconomic status and a combination of spatially-correlated and spatially-uncorrelated random effects. The dataset comprised 88,246 liveborn singletons, aggregated within suburbs in Perth, Western Australia. Low socioeconomic status was strongly associated with an increased risk of poor fetal growth. An increase in geographic variation of poor fetal growth from 1999–2001 (interquartile odds ratio among suburbs = 1.20) to 2004–2006 (interquartile odds ratio = 1.40) indicated a widening risk disparity by socioeconomic status. Low levels of residual spatial patterns strengthen the case for targeting policies and practices in areas of low socioeconomic status for improved outcomes. This study indicates an alarming increase in geographic inequalities in poor fetal growth in Perth which warrants further research into the specific aspects of socioeconomic status that act as risk factors. PMID:23799513

phylogeo: an R package for geographic analysis and visualization of microbiome data.

PubMed

Charlop-Powers, Zachary; Brady, Sean F

2015-09-01

We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language. phylogeo is documented and freely available http://zachcp.github.io/phylogeo : zcharlop@rockefeller.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Geographic variation and genetic structure in Spotted Owls

USGS Publications Warehouse

Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

2001-01-01

We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (FST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccarda??s distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of FST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

Population genetic structure of the rock outcrop species Encholirium spectabile (Bromeliaceae): The role of pollination vs. seed dispersal and evolutionary implications.

PubMed

Gonçalves-Oliveira, Rodrigo C; Wöhrmann, Tina; Benko-Iseppon, Ana M; Krapp, Florian; Alves, Marccus; Wanderley, Maria das Graças L; Weising, Kurt

2017-06-01

Inselbergs are terrestrial, island-like rock outcrop environments that present a highly adapted flora. The epilithic bromeliad Encholirium spectabile is a dominant species on inselbergs in the Caatinga of northeastern Brazil. We conducted a population genetic analysis to test whether the substantial phenotypic diversity of E. spectabile could be explained by limited gene flow among populations and to assess the relative impact of pollen vs. seed dispersal on the genetic structure of the species. Nuclear and chloroplast microsatellite markers were used to genotype E. spectabile individuals from 20 rock outcrop locations, representing four geographic regions: northern Espinhaço Range, Borborema Plateau, southwestern Caatinga and southeastern Caatinga. F -statistics, structure, and other tools were applied to evaluate the genetic makeup of populations. Considerable levels of genetic diversity were revealed. Genetic structuring among populations was stronger on the plastid as compared with the nuclear level, indicating higher gene flow via bat pollination as compared with seed dispersal by wind. structure and AMOVA analyses of the nuclear data suggested a high genetic differentiation between two groups, one containing all populations from the southeastern Caatinga and the other one comprising all remaining samples. The strong genetic differentiation between southeastern Caatinga and the remaining regions may indicate the occurrence of a cryptic species in E. spectabile . The unique genetic composition of each inselberg population suggests in situ conservation as the most appropriate protection measure for this plant lineage. © 2017 Botanical Society of America.

Resources and obstacles to developing and implementing a structural intervention to prevent HIV in San Salvador, El Salvador

PubMed Central

Corbett, A. Michelle; Bodnar, Gloria; Rodriguez, Karla; Guevara, Carmen E

2009-01-01

HIV prevention researchers have increasingly advocated structural interventions that address factors in the social, political and economic context to reduce disparities of HIV/AIDS among disadvantaged populations. This paper draws on data collected in three different types of low-income communities (n=6) in the San Salvador metropolitan area in El Salvador. Nine focus group discussions were conducted between January 2006 - July 2007, six with community leaders, and three with crack cocaine users, as well as in-depth interviews with 20 crack users and crack dealers. We explore opportunities and barriers to the implementation of a community-level, structural intervention. We first analyze the different forms of leadership, and other community resources including existing HIV prevention activities that could potentially be used to address the related problems of crack use and HIV in the communities, and the structural factors that may act as barriers to capitalizing on communities’ strengths in interventions. Each of the communities studied demonstrated different resources that stem from each community's unique history and geographic location. HIV testing and prevention resources varied widely among the communities, with resources concentrated in one Older Central community despite a strong need in all communities. In many communities, fear of gang violence and non-responsiveness by government agencies to communities’ needs have discouraged community organizing. In the discussion, we offer concrete suggestions for developing and implementing structural interventions to reduce HIV risks that use communities’ different but complementary resources. PMID:19910099

Population genomics and the causes of local differentiation.

PubMed

Tonsor, Stephen J

2012-11-01

Exactly 50 years ago, a revolution in empirical population genetics began with the introduction of methods for detecting allelic variation using protein electrophoresis (Throckmorton 1962; Hubby 1963; Lewontin & Hubby 1966). These pioneering scientists showed that populations are chock-full of genetic variation. This variation was a surprise that required a re-thinking of evolutionary genetic heuristics. Understanding the causes for the maintenance of this variation became and remains a major area of research. In the process of addressing the causes, this same group of scientists documented geographical genetic structure (Prakash et al. 1969), spawning the continued accumulation of what is now a huge case study catalogue of geographical differentiation (e.g. Loveless & Hamrick 1984; Linhart & Grant 1996). Geographical differentiation is clearly quite common. Yet, a truly general understanding of the patterns in and causes of spatial genetic structure across the genome remains elusive. To what extent is spatial structure driven by drift and phylogeography vs. geographical differences in environmental sources of selection? What proportion of the genome participates? A general understanding requires range-wide data on spatial patterning of variation across the entire genome. In this issue of Molecular Ecology, Lasky et al. (2012) make important strides towards addressing these issues, taking advantage of three contemporary revolutions in evolutionary biology. Two are technological: high-throughput sequencing and burgeoning computational power. One is cultural: open access to data from the community of scientists and especially data sets that result from large collaborative efforts. Together, these developments may at last put answers within reach.

Niger-wide assessment of in situ sorghum genetic diversity with microsatellite markers.

PubMed

Deu, M; Sagnard, F; Chantereau, J; Calatayud, C; Hérault, D; Mariac, C; Pham, J-L; Vigouroux, Y; Kapran, I; Traore, P S; Mamadou, A; Gerard, B; Ndjeunga, J; Bezançon, G

2008-05-01

Understanding the geographical, environmental and social patterns of genetic diversity on different spatial scales is key to the sustainable in situ management of genetic resources. However, few surveys have been conducted on crop genetic diversity using exhaustive in situ germplasm collections on a country scale and such data are missing for sorghum in sub-Saharan Africa, its centre of origin. We report here a genetic analysis of 484 sorghum varieties collected in 79 villages evenly distributed across Niger, using 28 microsatellite markers. We found a high level of SSR diversity in Niger. Diversity varied between eastern and western Niger, and allelic richness was lower in the eastern part of the country. Genetic differentiation between botanical races was the first structuring factor (Fst = 0.19), but the geographical distribution and the ethnic group to which farmers belonged were also significantly associated with genetic diversity partitioning. Gene pools are poorly differentiated among climatic zones. The geographical situation of Niger, where typical western African (guinea), central African (caudatum) and eastern Sahelian African (durra) sorghum races converge, explained the high observed genetic diversity and was responsible for the interactions among the ethnic, geographical and botanical structure revealed in our study. After correcting for the structure of botanical races, spatial correlation of genetic diversity was still detected within 100 km, which may hint at limited seed exchanges between farmers. Sorghum domestication history, in relation to the spatial organisation of human societies, is therefore key information for sorghum in situ conservation programs in sub-Saharan Africa.

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.

Measuring geographical accessibility to palliative and end of life (PEoLC) related facilities: a comparative study in an area with well-developed specialist palliative care (SPC) provision.

PubMed

Pearson, Clare; Verne, Julia; Wells, Claudia; Polato, Giovanna M; Higginson, Irene J; Gao, Wei

2017-01-26

Geographical accessibility is important in accessing healthcare services. Measuring it has evolved alongside technological and data analysis advances. High correlations between different methods have been detected, but no comparisons exist in the context of palliative and end of life care (PEoLC) studies. To assess how geographical accessibility can affect PEoLC, selection of an appropriate method to capture it is crucial. We therefore aimed to compare methods of measuring geographical accessibility of decedents to PEoLC-related facilities in South London, an area with well-developed SPC provision. Individual-level death registration data in 2012 (n = 18,165), from the Office for National Statistics (ONS) were linked to area-level PEoLC-related facilities from various sources. Simple and more complex measures of geographical accessibility were calculated using the residential postcodes of the decedents and postcodes of the nearest hospital, care home and hospice. Distance measures (straight-line, travel network) and travel times along the road network were compared using geographic information system (GIS) mapping and correlation analysis (Spearman rho). Borough-level maps demonstrate similarities in geographical accessibility measures. Strong positive correlation exist between straight-line and travel distances to the nearest hospital (rho = 0.97), care home (rho = 0.94) and hospice (rho = 0.99). Travel times were also highly correlated with distance measures to the nearest hospital (rho range = 0.84-0.88), care home (rho = 0.88-0.95) and hospice (rho = 0.93-0.95). All correlations were significant at p < 0.001 level. Distance-based and travel-time measures of geographical accessibility to PEoLC-related facilities in South London are similar, suggesting the choice of measure can be based on the ease of calculation.

Diversification and spatial structuring in the mutualism between Ficus septica and its pollinating wasps in insular South East Asia.

PubMed

Rodriguez, Lillian Jennifer; Bain, Anthony; Chou, Lien-Siang; Conchou, Lucie; Cruaud, Astrid; Gonzales, Regielene; Hossaert-McKey, Martine; Rasplus, Jean-Yves; Tzeng, Hsy-Yu; Kjellberg, Finn

2017-08-29

Interspecific interactions have long been assumed to play an important role in diversification. Mutualistic interactions, such as nursery pollination mutualisms, have been proposed as good candidates for diversification through co-speciation because of their intricate nature. However, little is known about how speciation and diversification proceeds in emblematic nursery pollination systems such as figs and fig wasps. Here, we analyse diversification in connection with spatial structuring in the obligate mutualistic association between Ficus septica and its pollinating wasps throughout the Philippines and Taiwan. Ceratosolen wasps pollinating F. septica are structured into a set of three vicariant black coloured species, and a fourth yellow coloured species whose distribution overlaps with those of the black species. However, two black pollinator species were found to co-occur on Lanyu island. Microsatellite data on F. septica indicates the presence of three gene pools that broadly mirrors the distribution of the three black clades. Moreover, receptive fig odours, the specific message used by pollinating wasps to locate their host tree, varied among locations. F. septica and its black pollinator clades exhibited similar geographic structuring. This could be due originally to geographic barriers leading to isolation, local adaptation, and finally co-structuring. Nevertheless, the co-occurrence of two black pollinator species on Lanyu island suggests that the parapatric distribution of the black clades is now maintained by the inability of migrating individuals of black pollinators to establish populations outside their range. On the other hand, the distribution of the yellow clade strongly suggests an initial case of character displacement followed by subsequent range extension: in our study system, phenotypic or microevolutionary plasticity has allowed the yellow clade to colonise hosts presenting distinct odours. Hence, while variation in receptive fig odours allows specificity in the interaction, this variation does not necessarily lead to coevolutionary plant-insect diversification. Globally, our results evidence evolutionary plasticity in the fig-fig wasp mutualism. This is the first documentation of the presence of two distinct processes in pollinating fig wasp diversification on a host species: the formation of vicariant species and the co-occurrence of other species over large parts of their ranges probably made possible by character displacement.

Extinction and the spatial dynamics of biodiversity

PubMed Central

Jablonski, David

2008-01-01

The fossil record amply shows that the spatial fabric of extinction has profoundly shaped the biosphere; this spatial dimension provides a powerful context for integration of paleontological and neontological approaches. Mass extinctions evidently alter extinction selectivity, with many factors losing effectiveness except for a positive relation between survivorship and geographic range at the clade level (confirmed in reanalyses of end-Cretaceous extinction data). This relation probably also holds during “normal” times, but changes both slope and intercept with increasing extinction. The strong geographical component to clade dynamics can obscure causation in the extinction of a feature or a clade, owing to hitchhiking effects on geographic range, so that multifactorial analyses are needed. Some extinctions are spatially complex, and regional extinctions might either reset a diversity ceiling or create a diversification debt open to further diversification or invasion. Evolutionary recoveries also exhibit spatial dynamics, including regional differences in invasibilty, and expansion of clades from the tropics fuels at least some recoveries, as well as biodiversity dynamics during normal times. Incumbency effects apparently correlate more closely with extinction intensities than with standing diversities, so that regions with higher local and global extinctions are more subject to invasion; the latest Cenozoic temperate zones evidently received more invaders than the tropics or poles, but this dynamic could shift dramatically if tropical diversity is strongly depleted. The fossil record can provide valuable insights, and their application to present-day issues will be enhanced by partitioning past and present-day extinctions by driving mechanism rather than emphasizing intensity. PMID:18695229

The impact of preventive screening resource distribution on geographic and population-based disparities in colorectal cancer in Mississippi.

PubMed

Faruque, Fazlay S; Zhang, Xu; Nichols, Elizabeth N; Bradley, Denae L; Reeves-Darby, Royce; Reeves-Darby, Vonda; Duhé, Roy J

2015-09-08

The state of Mississippi has the highest colorectal cancer (CRC) mortality rate in the USA. The geographic distribution of CRC screening resources and geographic- and population-based CRC characteristics in Mississippi are investigated to reveal the geographic disparity in CRC screening. The primary practice sites of licensed gastroenterologists and the addresses of licensed medical facilities offering on-site colonoscopies were verified via telephone surveys, then these CRC screening resource data were geocoded and analyzed using Geographic Information Systems. Correlation analyses were performed to detect the strength of associations between CRC screening resources, CRC screening behavior and CRC outcome data. Age-adjusted colorectal cancer incidence rates, mortality rates, mortality-to-incidence ratios, and self-reported endoscopic screening rates from the years 2006 through 2010 were significantly different for Black and White Mississippians; Blacks fared worse than Whites in all categories throughout all nine Public Health Districts. CRC screening rates were negatively correlated with CRC incidence rates and CRC mortality rates. The availability of gastroenterologists varied tremendously throughout the state; regions with the poorest CRC outcomes tended to be underserved by gastroenterologists. Significant population-based and geographic disparities in CRC screening behaviors and CRC outcomes exist in Mississippi. The effects of CRC screening resources are related to CRC screening behaviors and outcomes at a regional level, whereas at the county level, socioeconomic factors are more strongly associated with CRC outcomes. Thus, effective control of CRC in rural states with high poverty levels requires both adequate preventive CRC screening capacity and a strategy to address fundamental causes of health care disparities.

Observations of geographically correlated orbit errors for TOPEX/Poseidon using the global positioning system

NASA Technical Reports Server (NTRS)

Christensen, E. J.; Haines, B. J.; Mccoll, K. C.; Nerem, R. S.

1994-01-01

We have compared Global Positioning System (GPS)-based dynamic and reduced-dynamic TOPEX/Poseidon orbits over three 10-day repeat cycles of the ground-track. The results suggest that the prelaunch joint gravity model (JGM-1) introduces geographically correlated errors (GCEs) which have a strong meridional dependence. The global distribution and magnitude of these GCEs are consistent with a prelaunch covariance analysis, with estimated and predicted global rms error statistics of 2.3 and 2.4 cm rms, respectively. Repeating the analysis with the post-launch joint gravity model (JGM-2) suggests that a portion of the meridional dependence observed in JGM-1 still remains, with global rms error of 1.2 cm.

Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

PubMed Central

Drovetski, Sergei V.; Raković, Marko; Semenov, Georgy; Fadeev, Igor V.; Red’kin, Yaroslav A.

2014-01-01

Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species. PMID:24498139

A CONCEPTUAL FRAMEWORK FOR SELECTING AND ANALYZING STRESSOR DATA TO STUDY SPECIES RICHNESS AT LARGE SPATIAL SCALES

EPA Science Inventory

In this paper we develop a conceptual framework for selecting stressor data and anlyzing their relationship to geographic patterns of species richness at large spatial scales. Aspects of climate and topography, which are not stressors per se, have been most strongly linked with g...

Geospatial Technologies as a Vehicle for Enhancing Graduate Education and Promoting the Value of Geography

ERIC Educational Resources Information Center

Oberle, Alex P.; Joseph, Sue A.; May, David W.

2010-01-01

Geospatial technologies (GSTs), such as geographic information systems, global positioning systems and remote sensing, present an avenue for expanding the already strong interdisciplinary nature of geography. This paper discusses how GSTs served as a common thread for a crosscutting faculty institute that was established to enhance graduate…

Promoting Academic, Business, and Community Partnerships in Rural Areas.

ERIC Educational Resources Information Center

Morelli, Peg

Rural community colleges are faced with issues similar to their urban counterparts, but many challenges for rural schools are further exacerbated by limited resources, geographic isolation, and a static economy. This paper argues that the difference between success and failure can be the ability to create strong partnerships. Of the 15 colleges in…

Scale-free correlations in the geographical spreading of obesity

NASA Astrophysics Data System (ADS)

Gallos, Lazaros; Barttfeld, Pablo; Havlin, Shlomo; Sigman, Mariano; Makse, Hernan

2012-02-01

Obesity levels have been universally increasing. A crucial problem is to determine the influence of global and local drivers behind the obesity epidemic, to properly guide effective policies. Despite the numerous factors that affect the obesity evolution, we show a remarkable regularity expressed in a predictable pattern of spatial long-range correlations in the geographical spreading of obesity. We study the spatial clustering of obesity and a number of related health and economic indicators, and we use statistical physics methods to characterize the growth of the resulting clusters. The resulting scaling exponents allow us to broadly classify these indicators into two separate universality classes, weakly or strongly correlated. Weak correlations are found in generic human activity such as population distribution and the growth of the whole economy. Strong correlations are recovered, among others, for obesity, diabetes, and the food industry sectors associated with food consumption. Obesity turns out to be a global problem where local details are of little importance. The long-range correlations suggest influence that extends to large scales, hinting that the physical model of obesity clustering can be mapped to a long-range correlated percolation process.

Land-use changes in Illinois, USA: The influence of landscape attributes on current and historic land use

Treesearch

Louis R. Iverson; Louis R. Iverson

1988-01-01

The Illinois Geographic Information System was used to compare the soil and landscape attributes of the State with its historic vegetation, current land use, and patterns of land-use change over the past 160 years. Patch structural characteristics among land types in four geographic zones were also compared. The assessment of patch characteristics revealed a highly...

Evidence for progenitor–derivative speciation in sexually deceptive orchids

PubMed Central

Schlüter, Philipp M.; Ruas, Paulo M.; Kohl, Gudrun; Ruas, Claudete F.; Stuessy, Tod F.; Paulus, Hannes F.

2011-01-01

Background and Aims Sexually deceptive orchids of the genus Ophrys use mimicry of pollinator females to attract specific pollinators. Pollinator shifts may drive speciation in Ophrys, since novel pollinators may in principle act as isolating factors immediately. It is thus possible that evolution of novel species occurs rapidly and with a progenitor–derivative pattern. The aims of this study are to compare genetic structure and diversity among widespread and geographically restricted Ophrys taxa, to test whether genetic structure is associated with specific pollinators, and to investigate whether any widespread species may have acted as a progenitor for the evolution of more restricted taxa. Methods Genetic differentiation and diversity were investigated in O. leucadica and O. cinereophila, the two taxa of the Ophrys fusca sensu lato complex widespread in the Aegean, and three geographically restricted taxa from Rhodes, O. attaviria, O. parvula and O. persephonae, all differing in their specific pollinators. This was done using amplified fragment length polymorphism (AFLP) DNA fingerprinting, and sequencing of the low-copy nuclear gene LEAFY (LFY). Key Results All taxa were found to be separate genetic entities, with O. leucadica forming two geographic groups from the west and east of the Aegean. Genetic structure was significantly shaped by pollinators and geography, and comparison of sequence and AFLP data revealed ancestral polymorphisms shared among several taxa. Among the sampled taxa, O. leucadica harbours the greatest genetic differentiation and geographic structure, and the highest genetic diversity. Part of the genome of O. parvula, endemic to Rhodes, may be derived from O. leucadica. Conclusions Pollinators probably influence the genetic structure of the investigated Ophrys species. The genetic pattern identified is consistent with O. leucadica being the oldest of the sampled taxa, making O. leucadica a candidate progenitor species from which more restricted taxa such as O. parvula may have evolved. PMID:21890487

Geographic variation in the advertisement calls of Hyla eximia and its possible explanations

PubMed Central

Rodríguez-Tejeda, Ruth E.; Méndez-Cárdenas, María Guadalupe; Islas-Villanueva, Valentina

2014-01-01

Populations of species occupying large geographic ranges are often phenotypically diverse as a consequence of variation in selective pressures and drift. This applies to attributes involved in mate choice, particularly when both geographic range and breeding biology overlap between related species. This condition may lead to interference of mating signals, which would in turn promote reproductive character displacement (RCD). We investigated whether variation in the advertisement call of the mountain treefrog (Hyla eximia) is linked to geographic distribution with respect to major Mexican river basins (Panuco, Lerma, Balsas and Magdalena), or to coexistence with its sister (the canyon treefrog, Hyla arenicolor) or another related species (the dwarf treefrog, Tlalocohyla smithii). We also evaluated whether call divergence across the main river basins could be linked to genetic structure. We found that the multidimensional acoustic space of calls from two basins where H. eximia currently interacts with T. smithii, was different from the acoustic space of calls from H. eximia elsewhere. Individuals from these two basins were also distinguishable from the rest by both the phylogeny inferred from mitochondrial sequences, and the genetic structure inferred from nuclear markers. The discordant divergence of H. eximia advertisement calls in the two separate basins where its geographic range overlaps that of T. smithii can be interpreted as the result of two independent events of RCD, presumably as a consequence of acoustic interference in the breeding choruses, although more data are required to evaluate this possibility. PMID:25024904

Interactive map communication: pilot study of the visual perceptions and preferences of public health practitioners.

PubMed

Koenig, A; Samarasundera, E; Cheng, T

2011-08-01

To conduct a pilot study into the comprehension and visualisation preferences of geographic information by public health practitioners (PHPs), particularly in the context of interactive, Internet-based atlases. Structured human-computer interaction interviews. Seven academia-based PHPs were interviewed as information service users based on a structured questionnaire to assess their understanding of geographic representations of morbidity data, and identify their visualisation preferences in a geographic information systems environment. Awareness of area-based deprivation indices and the Index of Multiple Deprivation 2007 health and disability domain was near-universal. However, novice users of disease maps had difficulties in interpreting data classifications, in understanding supplementary information in the form of box plots and histograms, and in making use of links between interactive tabular and cartographic information. Choices for colour plans when viewing maps showed little agreement between users, although pre-viewing comments showed preferences for red-blue diverging schema. PHPs new to geographic information would benefit from enhanced interpretive support documentation to meet their needs when using Internet-based, interactive public health atlases, which are rarely provided at such sites. Technical, software-related support alone is insufficient. Increased interaction between PHPs and mapmakers would be beneficial to maximise the potential of the current growth in interactive, electronic atlases, and improve geographic information support for public health decision-making and informing the wider public. Copyright © 2011 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Geographic variation in the advertisement calls of Hyla eximia and its possible explanations.

PubMed

Rodríguez-Tejeda, Ruth E; Méndez-Cárdenas, María Guadalupe; Islas-Villanueva, Valentina; Macías Garcia, Constantino

2014-01-01

Populations of species occupying large geographic ranges are often phenotypically diverse as a consequence of variation in selective pressures and drift. This applies to attributes involved in mate choice, particularly when both geographic range and breeding biology overlap between related species. This condition may lead to interference of mating signals, which would in turn promote reproductive character displacement (RCD). We investigated whether variation in the advertisement call of the mountain treefrog (Hyla eximia) is linked to geographic distribution with respect to major Mexican river basins (Panuco, Lerma, Balsas and Magdalena), or to coexistence with its sister (the canyon treefrog, Hyla arenicolor) or another related species (the dwarf treefrog, Tlalocohyla smithii). We also evaluated whether call divergence across the main river basins could be linked to genetic structure. We found that the multidimensional acoustic space of calls from two basins where H. eximia currently interacts with T. smithii, was different from the acoustic space of calls from H. eximia elsewhere. Individuals from these two basins were also distinguishable from the rest by both the phylogeny inferred from mitochondrial sequences, and the genetic structure inferred from nuclear markers. The discordant divergence of H. eximia advertisement calls in the two separate basins where its geographic range overlaps that of T. smithii can be interpreted as the result of two independent events of RCD, presumably as a consequence of acoustic interference in the breeding choruses, although more data are required to evaluate this possibility.

The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat

PubMed Central

Puechmaille, Sébastien J.; Gouilh, Meriadeg Ar; Piyapan, Piyathip; Yokubol, Medhi; Mie, Khin Mie; Bates, Paul J.; Satasook, Chutamas; Nwe, Tin; Bu, Si Si Hla; Mackie, Iain J.; Petit, Eric J.; Teeling, Emma C.

2011-01-01

The sensory drive theory of speciation predicts that populations of the same species inhabiting different environments can differ in sensory traits, and that this sensory difference can ultimately drive speciation. However, even in the best-known examples of sensory ecology driven speciation, it is uncertain whether the variation in sensory traits is the cause or the consequence of a reduction in levels of gene flow. Here we show strong genetic differentiation, no gene flow and large echolocation differences between the allopatric Myanmar and Thai populations of the world's smallest mammal, Craseonycteris thonglongyai, and suggest that geographic isolation most likely preceded sensory divergence. Within the geographically continuous Thai population, we show that geographic distance has a primary role in limiting gene flow rather than echolocation divergence. In line with sensory-driven speciation models, we suggest that in C. thonglongyai, limited gene flow creates the suitable conditions that favour the evolution of sensory divergence via local adaptation. PMID:22146392

Geographical gradients in selection can reveal genetic constraints for evolutionary responses to ocean acidification

PubMed Central

Gaitán-Espitia, Juan Diego; Marshall, Dustin; Dupont, Sam; Bacigalupe, Leonardo D.; Bodrossy, Levente; Hobday, Alistair J.

2017-01-01

Geographical gradients in selection can shape different genetic architectures in natural populations, reflecting potential genetic constraints for adaptive evolution under climate change. Investigation of natural pH/pCO2 variation in upwelling regions reveals different spatio-temporal patterns of natural selection, generating genetic and phenotypic clines in populations, and potentially leading to local adaptation, relevant to understanding effects of ocean acidification (OA). Strong directional selection, associated with intense and continuous upwellings, may have depleted genetic variation in populations within these upwelling regions, favouring increased tolerances to low pH but with an associated cost in other traits. In contrast, diversifying or weak directional selection in populations with seasonal upwellings or outside major upwelling regions may have resulted in higher genetic variances and the lack of genetic correlations among traits. Testing this hypothesis in geographical regions with similar environmental conditions to those predicted under climate change will build insights into how selection may act in the future and how populations may respond to stressors such as OA. PMID:28148831

Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?

PubMed Central

Zepeda-Paulo, Francisca; Lavandero, Blas; Mahéo, Frédérique; Dion, Emilie; Outreman, Yannick; Simon, Jean-Christophe; Figueroa, Christian C

2015-01-01

Host recognition and use in female parasitoids strongly relies on host fidelity, a plastic behavior which can significantly restrict the host preferences of parasitoids, thus reducing the gene flow between parasitoid populations attacking different insect hosts. However, the effect of migrant males on the genetic differentiation of populations has been frequently ignored in parasitoids, despite its known impact on gene flow between populations. Hence, we studied the extent of gene flow mediated by female and male parasitoids by assessing sibship relationships among parasitoids within and between populations, and its impact on geographic and host-associated differentiation in the aphid parasitoid Aphidius ervi. We report evidences of a high gene flow among parasitoid populations on different aphid hosts and geographic locations. The high gene flow among parasitoid populations was found to be largely male mediated, suggested by significant differences in the distribution of full-sib and paternal half-sib dyads of parasitoid populations. PMID:26078852

Automatic Correction Algorithm of Hyfrology Feature Attribute in National Geographic Census

NASA Astrophysics Data System (ADS)

Li, C.; Guo, P.; Liu, X.

2017-09-01

A subset of the attributes of hydrologic features data in national geographic census are not clear, the current solution to this problem was through manual filling which is inefficient and liable to mistakes. So this paper proposes an automatic correction algorithm of hydrologic features attribute. Based on the analysis of the structure characteristics and topological relation, we put forward three basic principles of correction which include network proximity, structure robustness and topology ductility. Based on the WJ-III map workstation, we realize the automatic correction of hydrologic features. Finally, practical data is used to validate the method. The results show that our method is highly reasonable and efficient.

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges

PubMed Central

Carotenuto, Francesco; Diniz-Filho, José Alexandre F.

2016-01-01

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes—speciation, extinction and dispersal—in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. PMID:26977061

Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges.

PubMed

Villalobos, Fabricio; Carotenuto, Francesco; Raia, Pasquale; Diniz-Filho, José Alexandre F

2016-04-05

Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes--speciation, extinction and dispersal--in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. © 2016 The Author(s).

Geographic authentication of Asian rice (Oryza sativa L.) using multi-elemental and stable isotopic data combined with multivariate analysis.

PubMed

Chung, Ill-Min; Kim, Jae-Kwang; Lee, Kyoung-Jin; Park, Sung-Kyu; Lee, Ji-Hee; Son, Na-Young; Jin, Yong-Ik; Kim, Seung-Hyun

2018-02-01

Rice (Oryza sativa L.) is the world's third largest food crop after wheat and corn. Geographic authentication of rice has recently emerged asan important issue for enhancing human health via food safety and quality assurance. Here, we aimed to discriminate rice of six Asian countries through geographic authentication using combinations of elemental/isotopic composition analysis and chemometric techniques. Principal components analysis could distinguish samples cultivated from most countries, except for those cultivated in the Philippines and Japan. Furthermore, orthogonal projection to latent structure-discriminant analysis provided clear discrimination between rice cultivated in Korea and other countries. The major common variables responsible for differentiation in these models were δ 34 S, Mn, and Mg. Our findings contribute to understanding the variations of elemental and isotopic compositions in rice depending on geographic origins, and offer valuable insight into the control of fraudulent labeling regarding the geographic origins of rice traded among Asian countries. Copyright © 2017 Elsevier Ltd. All rights reserved.

A multilevel model for comorbid outcomes: obesity and diabetes in the US.

PubMed

Congdon, Peter

2010-02-01

Multilevel models are overwhelmingly applied to single health outcomes, but when two or more health conditions are closely related, it is important that contextual variation in their joint prevalence (e.g., variations over different geographic settings) is considered. A multinomial multilevel logit regression approach for analysing joint prevalence is proposed here that includes subject level risk factors (e.g., age, race, education) while also taking account of geographic context. Data from a US population health survey (the 2007 Behavioral Risk Factor Surveillance System or BRFSS) are used to illustrate the method, with a six category multinomial outcome defined by diabetic status and weight category (obese, overweight, normal). The influence of geographic context is partly represented by known geographic variables (e.g., county poverty), and partly by a model for latent area influences. In particular, a shared latent variable (common factor) approach is proposed to measure the impact of unobserved area influences on joint weight and diabetes status, with the latent variable being spatially structured to reflect geographic clustering in risk.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

PubMed

Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

2017-11-01

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

PubMed Central

Baker, K H; Gray, H W I; Ramovs, V; Mertzanidou, D; Akın Pekşen, Ç; Bilgin, C C; Sykes, N; Hoelzel, A R

2017-01-01

Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented by Anatolia, Italy and Iberia. Understanding modern patterns of diversity depends on understanding these historical population dynamics. Traditionally, European fallow deer (Dama dama dama) are thought to have been restricted to refugia in Anatolia and possibly Sicily and the Balkans. However, the distribution of this species was also greatly influenced by human-mediated translocations. We focus on fallow deer to better understand the relative influence of these natural and anthropogenic processes. We compared modern fallow deer putative populations across a broad geographic range using microsatellite and mitochondrial DNA loci. The results revealed highly insular populations, depauperate of genetic variation and significantly differentiated from each other. This is consistent with the expectations of drift acting on populations founded by small numbers of individuals, and reflects known founder populations in the north. However, there was also evidence for differentiation among (but not within) physically isolated regions in the south, including Iberia. In those regions we find evidence for a stronger influence from natural processes than may be expected for a species with such strong, known anthropogenic influence. PMID:28353685

Rock outcrop orchids reveal the genetic connectivity and diversity of inselbergs of northeastern Brazil.

PubMed

Pinheiro, Fábio; Cozzolino, Salvatore; Draper, David; de Barros, Fábio; Félix, Leonardo P; Fay, Michael F; Palma-Silva, Clarisse

2014-03-15

Because of their fragmented nature, inselberg species are interesting biological models for studying the genetic consequences of disjoint populations. Inselbergs are commonly compared with oceanic islands, as most of them display a marked ecological isolation from the surrounding area. The isolation of these rock outcrops is reflected in the high number of recorded endemic species and the strong floristic differences between individual inselbergs and adjacent habitats. We examined the genetic connectivity of orchids Epidendrum cinnabarinum and E. secundum adapted to Neotropical inselbergs of northeastern Brazil. Our goals were to identify major genetic divergences or disjunctions across the range of the species and to investigate potential demographic and evolutionary mechanisms leading to lineage divergence in Neotropical mountain ecosystems. Based on plastid markers, high genetic differentiation was found for E. cinnabarinum (FST = 0.644) and E. secundum (FST = 0.636). Haplotypes were not geographically structured in either taxon, suggesting that restricted gene flow and genetic drift may be significant factors influencing the diversification of these inselberg populations. Moreover, strong differentiation was found between populations over short spatial scales, indicating substantial periods of isolation among populations. For E. secundum, nuclear markers indicated higher gene flow by pollen than by seeds. The comparative approach adopted in this study contributed to the elucidation of patterns in both species. Our results confirm the ancient and highly isolated nature of inselberg populations. Both species showed similar patterns of genetic diversity and structure, highlighting the importance of seed-restricted gene flow and genetic drift as drivers of plant diversification in terrestrial islands such as inselbergs.

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

USGS Publications Warehouse

Sonsthagen, Sarah A.; Talbot, Sandra L.; Scribner, Kim T.; McCracken, Kevin G.

2011-01-01

Aim  Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post-glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice-free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north-west Norway.Location  Alaska, Canada, Norway and Sweden.Methods  Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F-statistics, analyses of molecular variance, and multilocus coalescent analyses.Results  Significant inter-population variation in allelic and haplotypic frequencies were observed (nuclear DNA FST = 0.004–0.290; mtDNA ΦST = 0.051–0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter-population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene-flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post-glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post-glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium.Main conclusions  Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.

Geographic variation and sociodemographic disparity in the use of oxaliplatin-containing chemotherapy in patients with stage III colon cancer.

PubMed

Panchal, Janki M; Lairson, David R; Chan, Wenyaw; Du, Xianglin L

2013-06-01

This study examined the geographic variation and sociodemographic disparities in the use of oxaliplatin chemotherapy, which has not been widely studied in the past. Our results suggest that chemotherapy use varies across geographic regions. Patterns of use that relate specifically to oxaliplatin-containing chemotherapy can inform providers and researchers how newer regimens are being used as standard chemotherapy in a real-world setting. According to the National Cancer Comprehensive Network (NCCN), oxaliplatin with 5-fluorouracil and leucovorin (5-FU/LV) is the recommended adjuvant chemotherapy for patients with resected stage III colon cancer. Age and race are considered strong predictors of chemotherapy receipt, whereas geographic disparity has received minimal attention. The purpose of this study was to examine geographic variation and sociodemographic disparity in the use of chemotherapy in patients with stage III colon cancer, focusing specifically on oxaliplatin. A retrospective cohort of 4106 Medicare patients was identified from the Surveillance, Epidemiology and End Results (SEER)/Medicare linked database. Descriptive statistics show how oxaliplatin-containing chemotherapy was used in various geographic regions among different age and racial groups. Multiple logistic regression analysis was performed to examine the relationship between receipt of oxaliplatin-containing chemotherapy and geographic region while adjusting for other sociodemographic and tumor characteristics. Only 49% of the patients with stage III disease received adjuvant chemotherapy within 3 to 6 months of colon cancer-specific surgery. Patients aged 66 to 70 years were 78% more likely to receive chemotherapy than were those aged 80 years and older (P<.001). Patients in less urban regions were approximately 42% less likely to receive oxaliplatin chemotherapy than those residing in a big metro region (odds ratio [OR], 0.58; P=.008). Chemotherapy use varies across geographic regions, especially for new chemotherapy drugs like oxaliplatin. Further research is needed to identify the causes of this geographic disparity and ways to provide high-quality cancer care to all patients according to their preferences and needs. Copyright © 2013 Elsevier Inc. All rights reserved.