Population genetics of the westernmost distribution of the glaciations-surviving black truffle Tuber melanosporum.

PubMed

García-Cunchillos, Iván; Sánchez, Sergio; Barriuso, Juan José; Pérez-Collazos, Ernesto

2014-04-01

The black truffle (Tuber melanosporum Vittad.) is an important natural resource due to its relevance as a delicacy in gastronomy. Different aspects of this hypogeous fungus species have been studied, including population genetics of French and Italian distribution ranges. Although those studies include some Spanish populations, this is the first time that the genetic diversity and genetic structure of the wide geographical range of the natural Spanish populations have been analysed. To achieve this goal, 23 natural populations were sampled across the Spanish geographical distribution. ISSR technique demonstrated its reliability and capability to detect high levels of polymorphism in the species. Studied populations showed high levels of genetic diversity (h N  = 0.393, h S  = 0.678, Hs = 0.418), indicating a non threatened genetic conservation status. These high levels may be a consequence of the wide distribution range of the species, of its spore dispersion by animals, and by its evolutionary history. AMOVA analysis showed a high degree of genetic structure among populations (47.89%) and other partitions as geographical ranges. Bayesian genetic structure analyses differentiated two main Spanish groups separated by the Iberian Mountain System, and showed the genetic uniqueness of some populations. Our results suggest the survival of some of these populations during the last glaciation, the Spanish southern distribution range perhaps surviving as had occurred in France and Italy, but it is also likely that specific northern areas may have acted as a refugia for the later dispersion to other calcareous areas in the Iberian Peninsula and probably France.

[Urbanization and its consequences for socio-demographic structures in Tunisia].

PubMed

Taamallah, M

1986-01-01

Comparisons are made between rural and urban populations in Tunisia in terms of selected demographic and social factors using official and other published data for the late 1970s and early 1980s. The focus is on the consequences of imbalances created by Tunisia's urbanization for population composition, health, economic development, and certain social structures. The history of urbanization in Tunisia since the end of the nineteenth century is outlined. Urban and rural populations are compared on the basis of sex distribution, age distribution, mortality, and fertility. The relationships among urbanization and economic development, public health, and family structure are considered.

Plague Circulation and Population Genetics of the Reservoir Rattus rattus: The Influence of Topographic Relief on the Distribution of the Disease within the Madagascan Focus

PubMed Central

Brouat, Carine; Rahelinirina, Soanandrasana; Loiseau, Anne; Rahalison, Lila; Rajerison, Minoariso; Laffly, Dominique; Handschumacher, Pascal; Duplantier, Jean-Marc

2013-01-01

Background Landscape may affect the distribution of infectious diseases by influencing the population density and dispersal of hosts and vectors. Plague (Yersinia pestis infection) is a highly virulent, re-emerging disease, the ecology of which has been scarcely studied in Africa. Human seroprevalence data for the major plague focus of Madagascar suggest that plague spreads heterogeneously across the landscape as a function of the relief. Plague is primarily a disease of rodents. We therefore investigated the relationship between disease distribution and the population genetic structure of the black rat, Rattus rattus, the main reservoir of plague in Madagascar. Methodology/Principal Findings We conducted a comparative study of plague seroprevalence and genetic structure (15 microsatellite markers) in rat populations from four geographic areas differing in topology, each covering about 150–200 km2 within the Madagascan plague focus. The seroprevalence levels in the rat populations mimicked those previously reported for humans. As expected, rat populations clearly displayed a more marked genetic structure with increasing relief. However, the relationship between seroprevalence data and genetic structure differs between areas, suggesting that plague distribution is not related everywhere to the effective dispersal of rats. Conclusions/Significance Genetic diversity estimates suggested that plague epizootics had only a weak impact on rat population sizes. In the highlands of Madagascar, plague dissemination cannot be accounted for solely by the effective dispersal of the reservoir. Human social activities may also be involved in spreading the disease in rat and human populations. PMID:23755317

A thermally driven differential mutation approach for the structural optimization of large atomic systems

NASA Astrophysics Data System (ADS)

Biswas, Katja

2017-09-01

A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations. With just a population size of six systems, energetically very low structures are obtained. While each of the structures represents a distinctly different arrangement of the atoms, their properties, such as energy, distribution of rings, radial distribution function, coordination number, and distribution of bond angles, are very similar.

Towards population-level conservation in the critically endangered Antarctic blue whale: the number and distribution of their populations

PubMed Central

Attard, Catherine R. M.; Beheregaray, Luciano B.; Möller, Luciana M.

2016-01-01

Population-level conservation is required to prevent biodiversity loss within a species, but it first necessitates determining the number and distribution of populations. Many whale populations are still depleted due to 20th century whaling. Whales are one of the most logistically difficult and expensive animals to study because of their mobility, pelagic lifestyle and often remote habitat. We tackle the question of population structure in the Antarctic blue whale (Balaenoptera musculus intermedia) – a critically endangered subspecies and the largest extant animal – by capitalizing on the largest genetic dataset to date for Antarctic blue whales. We found evidence of three populations that are sympatric in the Antarctic feeding grounds and likely occupy separate breeding grounds. Our study adds to knowledge of population structure in the Antarctic blue whale. Future research should invest in locating the breeding grounds and migratory routes of Antarctic blue whales through satellite telemetry to confirm their population structure and allow population-level conservation. PMID:26951747

Towards population-level conservation in the critically endangered Antarctic blue whale: the number and distribution of their populations

NASA Astrophysics Data System (ADS)

Attard, Catherine R. M.; Beheregaray, Luciano B.; Möller, Luciana M.

2016-03-01

Population-level conservation is required to prevent biodiversity loss within a species, but it first necessitates determining the number and distribution of populations. Many whale populations are still depleted due to 20th century whaling. Whales are one of the most logistically difficult and expensive animals to study because of their mobility, pelagic lifestyle and often remote habitat. We tackle the question of population structure in the Antarctic blue whale (Balaenoptera musculus intermedia) - a critically endangered subspecies and the largest extant animal - by capitalizing on the largest genetic dataset to date for Antarctic blue whales. We found evidence of three populations that are sympatric in the Antarctic feeding grounds and likely occupy separate breeding grounds. Our study adds to knowledge of population structure in the Antarctic blue whale. Future research should invest in locating the breeding grounds and migratory routes of Antarctic blue whales through satellite telemetry to confirm their population structure and allow population-level conservation.

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

PubMed

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

2018-06-22

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

Genetic structure of the world's polar bear populations.

PubMed

Paetkau, D; Amstrup, S C; Born, E W; Calvert, W; Derocher, A E; Garner, G W; Messier, F; Stirling, I; Taylor, M K; Wiig, O; Strobeck, C

1999-10-01

We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

Genetic structure of the world's polar bear populations

USGS Publications Warehouse

Paetkau, David; Amstrup, Steven C.; Born, E.W.; Calvert, W.; Derocher, A.E.; Garner, G.W.; Messier, F.; Stirling, I.; Taylor, M.K.; Wiig, O.; Strobeck, C.

1999-01-01

We studied genetic structure in polar bear (Ursus maritimus) populations by typing a sample of 473 individuals spanning the species distribution at 16 highly variable microsatellite loci. No genetic discontinuities were found that would be consistent with evolutionarily significant periods of isolation between groups. Direct comparison of movement data and genetic data from the Canadian Arctic revealed a highly significant correlation. Genetic data generally supported existing population (management unit) designations, although there were two cases where genetic data failed to differentiate between pairs of populations previously resolved by movement data. A sharp contrast was found between the minimal genetic structure observed among populations surrounding the polar basin and the presence of several marked genetic discontinuities in the Canadian Arctic. The discontinuities in the Canadian Arctic caused the appearance of four genetic clusters of polar bear populations. These clusters vary in total estimated population size from 100 to over 10 000, and the smallest may merit a relatively conservative management strategy in consideration of its apparent isolation. We suggest that the observed pattern of genetic discontinuities has developed in response to differences in the seasonal distribution and pattern of sea ice habitat and the effects of these differences on the distribution and abundance of seals.

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

PubMed Central

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

2017-01-01

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

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.

Phylogeographical structure inferred from cpDNA sequence variation of Zygophyllum xanthoxylon across north-west China.

PubMed

Shi, Xiao-Jun; Zhang, Ming-Li

2015-03-01

Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.

A demographic study of the exponential distribution applied to uneven-aged forests

Treesearch

Jeffrey H. Gove

2016-01-01

A demographic approach based on a size-structured version of the McKendrick-Von Foerster equation is used to demonstrate a theoretical link between the population size distribution and the underlying vital rates (recruitment, mortality and diameter growth) for the population of individuals whose diameter distribution is negative exponential. This model supports the...

Ecological and genetic determinants of plasmid distribution in Escherichia coli.

PubMed

Medaney, Frances; Ellis, Richard J; Raymond, Ben

2016-11-01

Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, little is known of the determinants of plasmid distribution in bacterial populations. Here the factors affecting the diversity and distribution of the large plasmids of Escherichia coli were explored in cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, the population genetic structure of bacterial hosts was chararacterized. This revealed structured E. coli populations with high diversity between sites and individuals but low diversity within cattle hosts. Plasmid profiles, however, varied considerably within the same E. coli genotype. Both ecological and genetic factors affected plasmid distribution: plasmid profiles were affected by site, E. coli diversity, E. coli genotype and the presence of other large plasmids. Notably 3/26 E. coli serotypes accounted for half the observed plasmid-free isolates indicating that within species variation can substantially affect carriage of the major conjugative plasmids. The observed population structure suggest that most of the opportunities for within species plasmid transfer occur between different individuals of the same genotype and support recent experimental work indicating that plasmid-host coevolution, and epistatic interactions on fitness costs are likely to be important in determining occupancy. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Contrasting patterns of population history and seed-mediated gene flow in two endemic Costa Rican oak species.

PubMed

Rodríguez-Correa, Hernando; Oyama, Ken; Quesada, Mauricio; Fuchs, Eric J; González-Rodríguez, Antonio

2018-03-02

Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in two partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. Phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.

Glaciation Effects on the Phylogeographic Structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the Southern Andes

PubMed Central

Palma, R. Eduardo; Boric-Bargetto, Dusan; Torres-Pérez, Fernando; Hernández, Cristián E.; Yates, Terry L.

2012-01-01

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, Bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000–13,000 years ago). Neutrality tests and the “g” parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats. PMID:22396751

Glaciation effects on the phylogeographic structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the southern Andes.

PubMed

Palma, R Eduardo; Boric-Bargetto, Dusan; Torres-Pérez, Fernando; Hernández, Cristián E; Yates, Terry L

2012-01-01

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000-13,000 years ago). Neutrality tests and the "g" parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats.

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

PubMed Central

Besnier, Francois; Glover, Kevin A.

2013-01-01

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

Does beekeeping reduce genetic variability in Melipona scutellaris (Apidae, Meliponini)?

PubMed

Carvalho-Zilse, G A; Costa-Pinto, M F F; Nunes-Silva, C G; Kerr, W E

2009-06-30

Many factors have contributed to reductions in wild populations of stingless bees, such as: deforestation, displacement and destruction of nests by honey gatherers, as well as use of insecticides and other agrochemicals. All of these can potentially affect the populational structure of native species. We analyzed genetic variability and populational structure of Melipona scutellaris, based on five microsatellite loci, using heterologous primers of M. bicolor. Samples were taken from 43 meliponaries distributed among 30 sites of four northeastern states of Brazil (Pernambuco, Alagoas, Sergipe, and Bahia). Thirty-one alleles were found to be well distributed among the populations, with sizes ranging from 85 to 146 bp. In general, there was a variable distribution and frequency of alleles among populations, with either exclusive and/or fixed alleles at some sites. The population of Pernambuco was the most polymorphic, followed by Bahia, Alagoas and Sergipe. The heterozygosity was Ho = 0.36 on average, much lower than what has been reported for M. bicolor (Ho = 0.65). Most populations were not under Hardy-Weinberg equilibrium. We found a higher variation within rather than among populations, indicating no genetic structuring in those bees maintained in meliponaries. This apparent homogenization may be due to intense beekeeping activity, including exchange of genetic material among beekeepers. Based on our findings, we recommend more studies of meliponaries and of wild populations in order to help orient management and conservation of these native pollinators.

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

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

PubMed

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

2017-01-10

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

Small-scale distribution characteristics of Munida spp. populations (Decapoda: Anomura) off the Catalan coasts (western Mediterranean)

NASA Astrophysics Data System (ADS)

Huguet, Carme; Maynou, Francesc; Abelló, Pere

2005-04-01

The small-scale distribution characteristics of three species of the anomuran genus Munida, namely Munida rutllanti, Munida intermedia and Munida tenuimana, have been studied on the lower shelf and upper-middle continental slope near the coasts of Tarragona and the Ebro delta region in the western Mediterranean. The differential bathymetric distribution showed that a fair degree of overlap exists between M. rutllanti and M. intermedia, with the former being mainly found at shallower depths. The size population structure of the three species showed that polymodality, as indicative of a longer life-span and of a higher degree of population structuring was more evident in the deeper-living species, whereas unimodality, as an indication of a recruitment dependent population, was more evident in the shallowest-occurring species. Geostatistics have been applied to determine the degree of spatial variability occurring in M. intermedia abundance, the better-sampled species. The Mantel test has been used to assess the significance of the overlap between the three species distributions as well as the relation between certain population parameters. A discussion on the population characteristics of M. rutllanti is made in relation with its expansion along the western Mediterranean in the last decades.

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

PubMed Central

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

2015-01-01

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

The mutation-drift balance in spatially structured populations.

PubMed

Schneider, David M; Martins, Ayana B; de Aguiar, Marcus A M

2016-08-07

In finite populations the action of neutral mutations is balanced by genetic drift, leading to a stationary distribution of alleles that displays a transition between two different behaviors. For small mutation rates most individuals will carry the same allele at equilibrium, whereas for high mutation rates of the alleles will be randomly distributed with frequencies close to one half for a biallelic gene. For well-mixed haploid populations the mutation threshold is μc=1/2N, where N is the population size. In this paper we study how spatial structure affects this mutation threshold. Specifically, we study the stationary allele distribution for populations placed on regular networks where connected nodes represent potential mating partners. We show that the mutation threshold is sensitive to spatial structure only if the number of potential mates is very small. In this limit, the mutation threshold decreases substantially, increasing the diversity of the population at considerably low mutation rates. Defining kc as the degree of the network for which the mutation threshold drops to half of its value in well-mixed populations we show that kc grows slowly as a function of the population size, following a power law. Our calculations and simulations are based on the Moran model and on a mapping between the Moran model with mutations and the voter model with opinion makers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genetic structure of local populations of Lutzomyia longipalpis (Diptera: Psychodidae) in central Colombia.

PubMed

Munstermann, L E; Morrison, A C; Ferro, C; Pardo, R; Torres, M

1998-01-01

Lutzomyia longipalpis (Lutz & Neiva), the sand fly vector of American visceral leishmaniasis in the New World tropics, has a broad but discontinuous geographical distribution from southern Mexico to Argentina. A baseline for population genetic structure and genetic variability for this species was obtained by analyzing 5 local, peridomestic populations at the approximate center of its distribution, the Magdalena River Valley of central Colombia. Three populations of L. longipalpis from El Callejón, a small rural community, were compared with 2 populations from neighboring areas 12 and 25 km distant for genetic variation at 15 isoenzyme loci. The mean heterozygosity ranged from 11 to 16%, with 1.2 to 2.3 alleles detected per locus. Nei's genetic distances among the populations were very low, ranging from 0.001 to 0.007. Gene flow estimates based on FST indicated high levels of gene flow among local L. longipalpis populations, with minimal population substructuring.

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.

A size-structured model of bacterial growth and reproduction.

PubMed

Ellermeyer, S F; Pilyugin, S S

2012-01-01

We consider a size-structured bacterial population model in which the rate of cell growth is both size- and time-dependent and the average per capita reproduction rate is specified as a model parameter. It is shown that the model admits classical solutions. The population-level and distribution-level behaviours of these solutions are then determined in terms of the model parameters. The distribution-level behaviour is found to be different from that found in similar models of bacterial population dynamics. Rather than convergence to a stable size distribution, we find that size distributions repeat in cycles. This phenomenon is observed in similar models only under special assumptions on the functional form of the size-dependent growth rate factor. Our main results are illustrated with examples, and we also provide an introductory study of the bacterial growth in a chemostat within the framework of our model.

A general modeling framework for describing spatially structured population dynamics

USGS Publications Warehouse

Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

2017-01-01

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles

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...

77 FR 13097 - Endangered Species; File Nos. 15661, 10027, and 15685

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-05

... population structure, size class composition, foraging ecology, and migration patterns for green and... of green and hawksbill sea turtles focusing on distribution and abundance, ecology, health, and... and population structure, foraging ecology, habitat use, and movements. Researchers may capture...

Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci.

Treesearch

P. Spruell; A.R. Hemmingsen; P.J. Howell; N. Kanda; F.W. Allendorf

2003-01-01

We describe the genetic population structure of 65 bull trout (Salvelinus confluentus) populations from the northwestern United States using four microsatellite loci. The distribution of genetic variation as measured by microsatellites is consistent with previous allozyme and mitochondrial DNA analysis. There is relatively little genetic variation...

Risky business: The impact of climate and climate variability on human population dynamics in Western Europe during the Last Glacial Maximum

NASA Astrophysics Data System (ADS)

Burke, Ariane; Kageyama, Masa; Latombe, Guilllaume; Fasel, Marc; Vrac, Mathieu; Ramstein, Gilles; James, Patrick M. A.

2017-05-01

The extent to which climate change has affected the course of human evolution is an enduring question. The ability to maintain spatially extensive social networks and a fluid social structure allows human foragers to ;map onto; the landscape, mitigating the impact of ecological risk and conferring resilience. But what are the limits of resilience and to which environmental variables are foraging populations sensitive? We address this question by testing the impact of a suite of environmental variables, including climate variability, on the distribution of human populations in Western Europe during the Last Glacial Maximum (LGM). Climate variability affects the distribution of plant and animal resources unpredictably, creating an element of risk for foragers for whom mobility comes at a cost. We produce a model of habitat suitability that allows us to generate predictions about the probable distribution of human populations and discuss the implications of these predictions for the structure of human populations and their social and cultural evolution during the LGM.

[Spatial structure analysis and distribution simulation of Therioaphis trifolii population based on geostatistics and GIS].

PubMed

Zhang, Rong; Leng, Yun-fa; Zhu, Meng-meng; Wang, Fang

2007-11-01

Based on geographic information system and geostatistics, the spatial structure of Therioaphis trifolii population of different periods in Yuanzhou district of Guyuan City, the southern Ningxia Province, was analyzed. The spatial distribution of Therioaphis trifolii population was also simulated by ordinary Kriging interpretation. The results showed that Therioaphis trifolii population of different periods was correlated spatially in the study area. The semivariograms of Therioaphis trifolii could be described by exponential model, indicating an aggregated spatial arrangement. The spatial variance varied from 34.13%-48.77%, and the range varied from 8.751-12.049 km. The degree and direction of aggregation showed that the trend was increased gradually from southwest to northeast. The dynamic change of Therioaphis trifolii population in different periods could be analyzed intuitively on the simulated maps of the spatial distribution from the two aspects of time and space, The occurrence position and degree of Therioaphis trifolii to a state of certain time could be determined easily.

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

PubMed

Najafi, Nargess; Akmali, Vahid; Sharifi, Mozafar

2018-04-26

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

Genetic structure among continental and island populations of gyrfalcons.

PubMed

Johnson, Jeff A; Burnham, Kurt K; Burnham, William A; Mindell, David P

2007-08-01

Little is known about the possible influence that past glacial events have had on the phylogeography and population structure of avian predators in the Arctic and sub-Arctic. In this study, we use microsatellite and mitochondrial control region DNA variation to investigate the population genetic structure of gyrfalcons (Falco rusticolus) throughout a large portion of their circumpolar distribution. In most locations sampled, the mtDNA data revealed little geographic structure; however, five out of eight mtDNA haplotypes were unique to a particular geographic area (Greenland, Iceland, or Alaska) and the Iceland population differed from others based on haplotype frequency differences (F(ST)). With the microsatellite results, significant population structure (F(ST), principal components analysis, and cluster analysis) was observed identifying Greenland and Iceland as separate populations, while Norway, Alaska and Canada were identified as a single population consistent with contemporary gene flow across Russia. Within Greenland, differing levels of gene flow between western and eastern sampling locations was indicated with apparent asymmetric dispersal in western Greenland from north to south. This dispersal bias is in agreement with the distribution of plumage colour variants with white gyrfalcons in much higher proportion in northern Greenland. Lastly, because the mtDNA control region sequence differed by only one to four nucleotides from a common haplotype among all gyrfalcons, we infer that the observed microsatellite population genetic structure has developed since the last glacial maximum. This conclusion is further supported by our finding that a closely related species, the saker falcon (Falco cherrug), has greater genetic heterogeneity, including mtDNA haplotypes differing by 1-16 nucleotide substitutions from a common gyrfalcon haplotype. This is consistent with gyrfalcons having expanded rapidly from a single glacial-age refugium to their current circumpolar distribution. Additional sampling of gyrfalcons from Fennoscandia and Russia throughout Siberia is necessary to test putative gene flow between Norway and Alaska and Canada as suggested by this study.

Genetic Diversity and Distribution of Blastocystis Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico

PubMed Central

Serrano-Vázquez, Angélica; Pérez-Juárez, Horacio; Poot-Hernández, Augusto C.; González, Enrique; Hernández, Eric; Nieves-Ramírez, Miriam E.; Magaña, Ulises; Eguiarte, Luis E.; Piñero, Daniel

2018-01-01

Blastocystis subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of Blastocystis ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of Blastocystis ST3 from other regions of the planet. Our analyses reveled that diversity of Blastocystis ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity of Blastocystis ST3 worldwide. PMID:29744356

Genetic Diversity and Distribution of Blastocystis Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico.

PubMed

Rojas-Velázquez, Liliana; Morán, Patricia; Serrano-Vázquez, Angélica; Fernández, Leonardo D; Pérez-Juárez, Horacio; Poot-Hernández, Augusto C; Portillo, Tobías; González, Enrique; Hernández, Eric; Partida-Rodríguez, Oswaldo; Nieves-Ramírez, Miriam E; Magaña, Ulises; Torres, Javier; Eguiarte, Luis E; Piñero, Daniel; Ximénez, Cecilia

2018-01-01

Blastocystis subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of Blastocystis ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of Blastocystis ST3 from other regions of the planet. Our analyses reveled that diversity of Blastocystis ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity of Blastocystis ST3 worldwide.

Electron acoustic nonlinear structures in planetary magnetospheres

NASA Astrophysics Data System (ADS)

Shah, K. H.; Qureshi, M. N. S.; Masood, W.; Shah, H. A.

2018-04-01

In this paper, we have studied linear and nonlinear propagation of electron acoustic waves (EAWs) comprising cold and hot populations in which the ions form the neutralizing background. The hot electrons have been assumed to follow the generalized ( r , q ) distribution which has the advantage that it mimics most of the distribution functions observed in space plasmas. Interestingly, it has been found that unlike Maxwellian and kappa distributions, the electron acoustic waves admit not only rarefactive structures but also allow the formation of compressive solitary structures for generalized ( r , q ) distribution. It has been found that the flatness parameter r , tail parameter q , and the nonlinear propagation velocity u affect the propagation characteristics of nonlinear EAWs. Using the plasmas parameters, typically found in Saturn's magnetosphere and the Earth's auroral region, where two populations of electrons and electron acoustic solitary waves (EASWs) have been observed, we have given an estimate of the scale lengths over which these nonlinear waves are expected to form and how the size of these structures would vary with the change in the shape of the distribution function and with the change of the plasma parameters.

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Using satellite telemetry to define spatial population structure in polar bears in the Norwegian and western Russian Arctic

USGS Publications Warehouse

Mauritzen, Mette; Derocher, Andrew E.; Wiig, Øystein; Belikov, Stanislav; Boltunov, Andrei N.; Garner, Gerald W.

2002-01-01

1. Animal populations, defined by geographical areas within a species’ distribution where population dynamics are largely regulated by births and deaths rather than by migration from surrounding areas, may be the correct unit for wildlife management. However, in heterogeneous landscapes varying habitat quality may yield subpopulations with distinct patterns in resource use and demography significant to the dynamics of populations.2. To define the spatial population structure of polar bears Ursus maritimus in the Norwegian and western Russian Arctic, and to assess the existence of a shared population between the two countries, we analysed satellite telemetry data obtained from 105 female polar bears over 12 years.3. Using both cluster analyses and home-range estimation methods, we identified five population units inhabiting areas with different sea-ice characteristics and prey availability.4. The continuous distribution of polar bear positions indicated that the different subpopulations formed one continuous polar bear population in the Norwegian and western Russian Arctic. Hence, Norway and Russia have a shared management responsibility.5. The spatial population structure identified will provide a guide for evaluating geographical patterns in polar bear ecology, the dynamics of polar bear–seal relationships and the effects of habitat alteration due to climate change. The work illustrates the importance of defining population borders and subpopulation structure in understanding the dynamics and management of larger animals.

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

PubMed Central

Kang, Hongzhang; Sun, Xiao; Yin, Shan; Du, Hongmei; Yamanaka, Norikazu; Gapare, Washington; Wu, Harry X.; Liu, Chunjiang

2012-01-01

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N ST = 0.751> G ST = 0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s FS indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia. PMID:23115642

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

PubMed

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

2015-04-01

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

Genetic structure of the carnivorous plant Pinguicula moranensis (Lentibulariaceae) on the transvolcanic Mexican belt.

PubMed

Alcalá, Raúl E; Domínguez, César A

2012-06-01

Most species of Pinguicula present a montane distribution with populations located at high altitudes. In this context, we proposed that populations of Pinguicula species could be genetically differentiated even at a local scale. This study supported that prediction, as a RAPD-based analysis of molecular variance revealed a high degree of genetic structure (Φ (st) = 0.157, P = 0.001) and low gene flow (Nm = 1.0) among four central populations of Pinguicula moranensis in Mexico, with a maximum geographic separation of about 140 km. The four populations also exhibited high levels of genetic diversity (mean Nei's genetic diversity = 0.3716; % polymorphism = 95.45%). The evolutionary implications of the genetic structure found in P. moranensis for other species in the genus are discussed in the context of the naturally fragmented distribution and a set of life history traits shared by most Pinguicula species that could promote geographic isolation and limited gene flow.

Dynamics of a Stochastic Predator-Prey Model with Stage Structure for Predator and Holling Type II Functional Response

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Alsaedi, Ahmed

2018-01-01

In this paper, we develop and study a stochastic predator-prey model with stage structure for predator and Holling type II functional response. First of all, by constructing a suitable stochastic Lyapunov function, we establish sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the positive solutions to the model. Then, we obtain sufficient conditions for extinction of the predator populations in two cases, that is, the first case is that the prey population survival and the predator populations extinction; the second case is that all the prey and predator populations extinction. The existence of a stationary distribution implies stochastic weak stability. Numerical simulations are carried out to demonstrate the analytical results.

Dynamics of a Stochastic Predator-Prey Model with Stage Structure for Predator and Holling Type II Functional Response

NASA Astrophysics Data System (ADS)

Liu, Qun; Jiang, Daqing; Hayat, Tasawar; Alsaedi, Ahmed

2018-06-01

In this paper, we develop and study a stochastic predator-prey model with stage structure for predator and Holling type II functional response. First of all, by constructing a suitable stochastic Lyapunov function, we establish sufficient conditions for the existence and uniqueness of an ergodic stationary distribution of the positive solutions to the model. Then, we obtain sufficient conditions for extinction of the predator populations in two cases, that is, the first case is that the prey population survival and the predator populations extinction; the second case is that all the prey and predator populations extinction. The existence of a stationary distribution implies stochastic weak stability. Numerical simulations are carried out to demonstrate the analytical results.

Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides).

PubMed

Friedman, Michael; Schaffer, Les

2011-02-01

BACKGROUND AND AIMS. With the goal of assessing population structure and geographic distribution of haplotype lineages among Lampropeltis elapsoides, we sequenced the ND4 mitochondrial DNA locus from 96 specimens of this snake across its area of distribution. MATERIALS AND METHODS. We relied heavily on formalin-fixed museum specimens to accomplish this analysis. RESULTS. The sequence alignment consisted of 491 bp of the selected gene, with 28% missing data. A simulation used to assess the effect of missing data on population genetic and phylogenetic resolution indicated increased character conflict, but with minimal loss of phylogenetic structure. CONCLUSION. This limited dataset suggests that L. elapsoides constitutes a largely unstructured population, with both widespread haplotypes and large number of private haplotypes, a moderate level of nucleotide diversity, and a low, but significant, degree of north-south population differentiation. Haplotype structure and frequency, nucleotide frequency, and values for Tajima's D and Fu's F(S) indicate a recent range or population expansion following a historic bottleneck.

Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation.

PubMed

Leite, K C E; Seixas, G H F; Berkunsky, I; Collevatti, R G; Caparroz, R

2008-09-09

The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit.

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.

Fine-scale population genetic structure of a wildlife disease vector: The southern house mosquito on the island of Hawaii

USGS Publications Warehouse

Keyghobadi, N.; LaPointe, D.; Fleischer, R.C.; Fonseca, D.M.

2006-01-01

The southern house mosquito, Culex quinquefasciatus, is a widespread tropical and subtropical disease vector. In the Hawaiian Islands, where it was introduced accidentally almost two centuries ago, it is considered the primary vector of avian malaria and pox. Avian malaria in particular has contributed to the extinction and endangerment of Hawaii's native avifauna, and has altered the altitudinal distribution of native bird populations. We examined the population genetic structure of Cx. quinquefasciatus on the island of Hawaii at a smaller spatial scale than has previously been attempted, with particular emphasis on the effects of elevation on population genetic structure. We found significant genetic differentiation among populations and patterns of isolation by distance within the island. Elevation per se did not have a limiting effect on gene flow; however, there was significantly lower genetic diversity among populations at mid elevations compared to those at low elevations. A recent sample taken from just above the predicted upper altitudinal distribution of Cx. quinquefasciatus on the island of Hawaii was confirmed as being a temporary summer population and appeared to consist of individuals from more than one source population. Our results indicate effects of elevation gradients on genetic structure that are consistent with known effects of elevation on population dynamics of this disease vector. ?? 2006 The Authors.

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

PubMed

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

2017-12-01

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

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

Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil.

PubMed

Clozato, Camila L; Miranda, Flávia R; Lara-Ruiz, Paula; Collevatti, Rosane G; Santos, Fabrício R

2017-01-01

The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b) and two nuclear markers (AMELY and RAG2). We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

Spatial genetic structure of the cyprinid fish Onychostoma lepturum on Hainan Island.

PubMed

Zhou, Tian-Qi; Lin, Hung-Du; Hsu, Kui-Ching; Kuo, Po-Hsun; Wang, Wei-Kuang; Tang, Wen-Qiao; Liu, Dong; Yang, Jin-Quan

2017-11-01

Population genetic structure of Onychostoma lepturum on Hainan Island was investigated based on mitochondrial CR + cyt b region in 63 specimens collected from four populations. Population analyses indicated significant genetic structure (F ST  = 0.749) and displayed a significant relationship between phylogeny and geography (N ST  = 0.750 and G ST  = 0.140). Thirty-one mtDNA haplotypes were classified into four lineages, and these lineages had an almost allopatric distribution. The results of a statistical dispersal-vicariance analysis suggest that the ancestral populations were distributed widely on Hainan Island, and the rising of the central mountainous area of Hainan Island, the Wuzhi and Yinggeling Mountain Range, separated these four drainages into independent lineages. According to a spatial analysis of molecular variance analysis, we divided these populations into three units: ND, CH and WQ + LS, running into Qiongzhou Strait, the Gulf of Tokin and the South China Sea, respectively. According to our study, the exposure of straits and shelf under water retreat gave chances for population dispersion during the glaciations.

Spatio-temporal variation in age structure and abundance of the endangered snail kite: Pooling across regions masks a declining and aging population

USGS Publications Warehouse

Reichert, Brian E.; Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

2016-01-01

While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species.

Genetic Variation and Population Differentiation in a Medical Herb Houttuynia cordata in China Revealed by Inter-Simple Sequence Repeats (ISSRs)

PubMed Central

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. PMID:22942696

Genetic variation and population differentiation in a medical herb Houttuynia cordata in China revealed by inter-simple sequence repeats (ISSRs).

PubMed

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included.

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

PubMed

Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

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

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

PubMed Central

Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

Relationship between ancient bridges and population dynamics in the lower Yangtze River Basin, China.

PubMed

Zhao, Yang; Jia, Xin; Lee, Harry F; Zhao, Hongqiang; Cai, Shuliang; Huang, Xianjin

2017-01-01

It has been suggested that population growth dynamics may be revealed by the geographic distribution and the physical structure of ancient bridges. Yet, this relationship has not been empirically verified. In this study, we applied the archaeological records for ancient bridges to reveal the population growth dynamics in the lower Yangtze River Basin in late imperial China. We investigated 89 ancient bridges in Yixing that were built during the Ming and Qing dynasties (AD1368-1911). Global Position System information and structure (length, width, and span) of those bridges was measured during our field investigations. Their distribution density was calculated by ArcGIS. The historical socio-economic dynamics of Yixing was inferred from the distribution and structure of ancient bridges. Based on the above information, the population growth dynamics in Yixing was projected. Our results show that 77 bridges were built in Yixing during the Qing dynasty, which is 6.41 times more than the number built during the Ming dynasty. In the Ming dynasty, bridges were built on pivotal routes; in the Qing dynasty, bridges were scattered across various places. Over the period, the density distribution of bridges shifted northwestward, while the average length and width of bridges decreased. The increasing number of bridges corresponded to population growth, largely attributable to massive clan migration from northern China during the Little Ice Age. The shift in the density distribution of bridges corresponded to the formation of settlements of large clans and the blossoming of Yixing Teapot handicrafts. The scattering and the reduction in average length and width of bridges was due to the dispersal of population and the associated formation of small settlements in the latter period. Our approach is innovative and robust, and could be employed to recover long-term historical population growth dynamics in other parts of China.

Relationship between ancient bridges and population dynamics in the lower Yangtze River Basin, China

PubMed Central

Zhao, Yang; Lee, Harry F.; Zhao, Hongqiang; Cai, Shuliang; Huang, Xianjin

2017-01-01

It has been suggested that population growth dynamics may be revealed by the geographic distribution and the physical structure of ancient bridges. Yet, this relationship has not been empirically verified. In this study, we applied the archaeological records for ancient bridges to reveal the population growth dynamics in the lower Yangtze River Basin in late imperial China. We investigated 89 ancient bridges in Yixing that were built during the Ming and Qing dynasties (AD1368–1911). Global Position System information and structure (length, width, and span) of those bridges was measured during our field investigations. Their distribution density was calculated by ArcGIS. The historical socio-economic dynamics of Yixing was inferred from the distribution and structure of ancient bridges. Based on the above information, the population growth dynamics in Yixing was projected. Our results show that 77 bridges were built in Yixing during the Qing dynasty, which is 6.41 times more than the number built during the Ming dynasty. In the Ming dynasty, bridges were built on pivotal routes; in the Qing dynasty, bridges were scattered across various places. Over the period, the density distribution of bridges shifted northwestward, while the average length and width of bridges decreased. The increasing number of bridges corresponded to population growth, largely attributable to massive clan migration from northern China during the Little Ice Age. The shift in the density distribution of bridges corresponded to the formation of settlements of large clans and the blossoming of Yixing Teapot handicrafts. The scattering and the reduction in average length and width of bridges was due to the dispersal of population and the associated formation of small settlements in the latter period. Our approach is innovative and robust, and could be employed to recover long-term historical population growth dynamics in other parts of China. PMID:28792976

Genetic Population Structure of Tectura paleacea: Implications for the Mechanisms Regulating Population Structure in Patchy Coastal Habitats

PubMed Central

Begovic, Emina; Lindberg, David R.

2011-01-01

The seagrass limpet Tectura paleacea (Gastropoda; Patellogastropoda) belongs to a seagrass obligate lineage that has shifted from the Caribbean in the late Miocene, across the Isthmus of Panama prior to the closing of the Panamanian seaway, and then northward to its modern Baja California – Oregon distribution. To address whether larval entrainment by seagrass beds contributes to population structuring, populations were sampled at six California/Oregon localities approximately 2 degrees latitude apart during two post-settlement periods in July 2002 and June 2003. Partial cytochrome oxidase b (Cytb) sequences were obtained from 20 individuals (10 per year) from each population in order to determine the levels of population subdivision/connectivity. From the 120 individuals sequenced, there were eighty-one unique haplotypes, with the greatest haplotype diversity occurring in southern populations. The only significant genetic break detected was consistent with a peri-Point Conception (PPC) biogeographic boundary while populations north and south of Point Conception were each panmictic. The data further indicate that populations found south of the PPC biogeographic boundary originated from northern populations. This pattern of population structure suggests that seagrass patches are not entraining the larvae of T. paleacea by altering flow regimes within their environment; a process hypothesized to produce extensive genetic subdivision on fine geographic scales. In contrast to the haplotype data, morphological patterns vary significantly over very fine geographic scales that are inconsistent with the observed patterns of genetic population structure, indicating that morphological variation in T. paleacea might be attributed to differential ecophenotypic expression in response to local habitat variability throughout its distribution. These results suggest that highly localized conservation efforts may not be as effective as large-scale conservation efforts in near shore marine environments. PMID:21490969

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

PubMed

Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

2017-09-01

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population differentiation highlight the conservation value of large populations throughout the species' range, particularly in light of climate change and direct human threats.

Structure of velocity distributions in shock waves in granular gases with extension to molecular gases.

PubMed

Vilquin, A; Boudet, J F; Kellay, H

2016-08-01

Velocity distributions in normal shock waves obtained in dilute granular flows are studied. These distributions cannot be described by a simple functional shape and are believed to be bimodal. Our results show that these distributions are not strictly bimodal but a trimodal distribution is shown to be sufficient. The usual Mott-Smith bimodal description of these distributions, developed for molecular gases, and based on the coexistence of two subpopulations (a supersonic and a subsonic population) in the shock front, can be modified by adding a third subpopulation. Our experiments show that this additional population results from collisions between the supersonic and subsonic subpopulations. We propose a simple approach incorporating the role of this third intermediate population to model the measured probability distributions and apply it to granular shocks as well as shocks in molecular gases.

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species' global distribution: Combining classical population genetics and network analyses.

PubMed

Rodger, Yael S; Greenbaum, Gili; Silver, Micha; Bar-David, Shirli; Winters, Gidon

2018-01-01

Genetic diversity and structure of populations at the edge of the species' spatial distribution are important for potential adaptation to environmental changes and consequently, for the long-term survival of the species. Here, we combined classical population genetic methods with newly developed network analyses to gain complementary insights into the genetic structure and diversity of Acacia tortilis, a keystone desert tree, at the northern edge of its global distribution, where the population is under threat from climatic, ecological, and anthropogenic changes. We sampled A. tortilis from 14 sites along the Dead Sea region and the Arava Valley in Israel and in Jordan. In addition, we obtained samples from Egypt and Sudan, the hypothesized origin of the species. Samples from all sites were genotyped using six polymorphic microsatellite loci.Our results indicate a significant genetic structure in A. tortilis along the Arava Valley. This was detected at different hierarchical levels-from the basic unit of the subpopulation, corresponding to groups of trees within ephemeral rivers (wadis), to groups of subpopulations (communities) that are genetically more connected relative to others. The latter structure mostly corresponds to the partition of the major drainage basins in the area. Network analyses, combined with classical methods, allowed for the identification of key A. tortilis subpopulations in this region, characterized by their relatively high level of genetic diversity and centrality in maintaining gene flow in the population. Characterizing such key subpopulations may enable conservation managers to focus their efforts on certain subpopulations that might be particularly important for the population's long-term persistence, thus contributing to species conservation within its peripheral range.

A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

PubMed

Ornelas, Juan Francisco; Gándara, Etelvina; Vásquez-Aguilar, Antonio Acini; Ramírez-Barahona, Santiago; Ortiz-Rodriguez, Andrés Ernesto; González, Clementina; Mejía Saules, María Teresa; Ruiz-Sanchez, Eduardo

2016-04-12

Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate Bayesian Computation (ABC) analyses strongly supported a scenario of simultaneous divergence among the three groups isolated recently. Our results provide support for the predominant role of isolation and environmental factors in driving genetic differentiation of Mesoamerican parrot-flower mistletoes. The ABC results are consistent with a scenario of post-glacial mistletoe invasion, independent of host identity, and that habitat types recently isolated P. schiedeanus populations, accumulating slight phenotypic differences among genetic groups due to recent migration across habitats. Under this scenario, climatic fluctuations throughout the Pleistocene would have altered the distribution of suitable habitat for mistletoes throughout Mesoamerica leading to variation in population continuity and isolation. Our findings add to an understanding of the role of recent isolation and colonization in shaping cloud forest communities in the region.

Structure, Spatial and Temporal Distribution of the Culex pipiens Complex in Shanghai, China

PubMed Central

Gao, Qiang; Xiong, Chenglong; Su, Fei; Cao, Hui; Zhou, Jianjun; Jiang, Qingwu

2016-01-01

Background: Culex pipiens molestus was first reported in Shanghai in 2010. The population structures and seasonal distributions of Culex pipiens subspecies C. p. molestus, Culex pipiens pallens, and Culex pipiens quinquefasciatus are not well known. Methods: From late February to November 2013, we conducted daily field surveillance of mosquitoes at eight sites at two green lands and three residential areas in downtown Shanghai. Morphological comparison and DV/D ratios (DV/D is an indicator of mosquito taxonomy) were used to identify adult mosquitoes. Results: The distribution curves of the Culex pipiens complex members indicated seasonal fluctuations. The temperature range of 20–25 °C was the most suitable for adult activity. Micro-environmental factors may differentiate the complex population structures. Hybridization between C. p. pallens and C. p. quinquefasciatus was common and neither “DV/D = 0.40” nor “DV/D = 0.50” can distinguish these subspecies and their hybrids. Conclusion: the population structure of the Culex pipiens complex is complex and characterized by significant hybridization. Measures other than DV/D ratios are needed for the discrimination of subspecies. The C. p. molestus invasion might result in the transmission of novel vector-borne diseases in Shanghai. PMID:27869687

Iowa Population Trends.

ERIC Educational Resources Information Center

Tait, John L.; Johnson, Arthur H.

The trends in population distribution and the composition of Iowa's population are reported in this document in order to provide the leaders and citizens of Iowa with information to assist them in making decisions relating to growth and development. Birth and death rates, rural and urban residence, population by race, and age structure are…

Genetic Diversity and Population Structure of the Rare and Endangered Plant Species Pulsatilla patens (L.) Mill in East Central Europe.

PubMed

Szczecińska, Monika; Sramko, Gabor; Wołosz, Katarzyna; Sawicki, Jakub

2016-01-01

Pulsatilla patens s.s. is a one of the most endangered plant species in Europe. The present range of this species in Europe is highly fragmented and the size of the populations has been dramatically reduced in the past 50 years. The rapid disappearance of P. patens localities in Europe has prompted the European Commission to initiate active protection of this critically endangered species. The aim of this study was to estimate the degree and distribution of genetic diversity within European populations of this endangered species. We screened 29 populations of P. patens using a set of six microsatellite primers. The results of our study indicate that the analyzed populations are characterized by low levels of genetic diversity (Ho = 0.005) and very high levels of inbreeding (FIS = 0.90). These results suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species. Private allelic richness was very low, being as low as 0.00 for most populations. Average genetic diversity over loci and mean number of alleles in P. patens populations were significantly correlated with population size, suggesting severe genetic drift. The results of AMOVA point to higher levels of variation within populations than between populations.The results of Structure and PCoA analyses suggest that the genetic structure of the studied P. patens populations fall into three clusters corresponding to geographical regions. The most isolated populations (mostly from Romania) formed a separate group with a homogeneous gene pool located at the southern, steppic part of the distribution range. Baltic, mostly Polish, populations fall into two genetic groups which were not fully compatible with their geographic distribution.Our results indicate the serious genetic depauperation of P. patens in the western part of its range, even hinting at an ongoing extinction vortex. Therefore, special conservation attention is required to maintain the populations of this highly endangered species of European Community interest.

On the relationship between cell cycle analysis with ergodic principles and age-structured cell population models.

PubMed

Kuritz, K; Stöhr, D; Pollak, N; Allgöwer, F

2017-02-07

Cyclic processes, in particular the cell cycle, are of great importance in cell biology. Continued improvement in cell population analysis methods like fluorescence microscopy, flow cytometry, CyTOF or single-cell omics made mathematical methods based on ergodic principles a powerful tool in studying these processes. In this paper, we establish the relationship between cell cycle analysis with ergodic principles and age structured population models. To this end, we describe the progression of a single cell through the cell cycle by a stochastic differential equation on a one dimensional manifold in the high dimensional dataspace of cell cycle markers. Given the assumption that the cell population is in a steady state, we derive transformation rules which transform the number density on the manifold to the steady state number density of age structured population models. Our theory facilitates the study of cell cycle dependent processes including local molecular events, cell death and cell division from high dimensional "snapshot" data. Ergodic analysis can in general be applied to every process that exhibits a steady state distribution. By combining ergodic analysis with age structured population models we furthermore provide the theoretic basis for extensions of ergodic principles to distribution that deviate from their steady state. Copyright © 2016 Elsevier Ltd. All rights reserved.

Population, genetic, and antigenic diversity of the apicomplexan Eimeria tenella and their relevance to vaccine development

PubMed Central

Blake, Damer P.; Clark, Emily L.; Macdonald, Sarah E.; Thenmozhi, Venkatachalam; Kundu, Krishnendu; Garg, Rajat; Jatau, Isa D.; Ayoade, Simeon; Kawahara, Fumiya; Moftah, Abdalgader; Reid, Adam James; Adebambo, Ayotunde O.; Álvarez Zapata, Ramón; Srinivasa Rao, Arni S. R.; Thangaraj, Kumarasamy; Banerjee, Partha S.; Dhinakar-Raj, G.; Raman, M.; Tomley, Fiona M.

2015-01-01

The phylum Apicomplexa includes serious pathogens of humans and animals. Understanding the distribution and population structure of these protozoan parasites is of fundamental importance to explain disease epidemiology and develop sustainable controls. Predicting the likely efficacy and longevity of subunit vaccines in field populations relies on knowledge of relevant preexisting antigenic diversity, population structure, the likelihood of coinfection by genetically distinct strains, and the efficiency of cross-fertilization. All four of these factors have been investigated for Plasmodium species parasites, revealing both clonal and panmictic population structures with exceptional polymorphism associated with immunoprotective antigens such as apical membrane antigen 1 (AMA1). For the coccidian Toxoplasma gondii only genomic diversity and population structure have been defined in depth so far; for the closely related Eimeria species, all four variables are currently unknown. Using Eimeria tenella, a major cause of the enteric disease coccidiosis, which exerts a profound effect on chicken productivity and welfare, we determined population structure, genotype distribution, and likelihood of cross-fertilization during coinfection and also investigated the extent of naturally occurring antigenic diversity for the E. tenella AMA1 homolog. Using genome-wide Sequenom SNP-based haplotyping, targeted sequencing, and single-cell genotyping, we show that in this coccidian the functionality of EtAMA1 appears to outweigh immune evasion. This result is in direct contrast to the situation in Plasmodium and most likely is underpinned by the biology of the direct and acute coccidian life cycle in the definitive host. PMID:26354122

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

PubMed Central

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

2009-01-01

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

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico.

PubMed

Domínguez-Contreras, José F; Munguia-Vega, Adrian; Ceballos-Vázquez, Bertha P; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J; Culver, Melanie; Reyes-Bonilla, Hector

2018-01-01

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides . These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

3-D habitat suitability of jack mackerel Trachurus murphyi in the Southeastern Pacific, a comprehensive study

NASA Astrophysics Data System (ADS)

Bertrand, Arnaud; Habasque, Jérémie; Hattab, Tarek; Hintzen, Niels T.; Oliveros-Ramos, Ricardo; Gutiérrez, Mariano; Demarcq, Hervé; Gerlotto, François

2016-08-01

South Pacific jack mackerel, Trachurus murphyi, has an ocean-scale distribution, from the South American coastline to New Zealand and Tasmania. This fish, captured by Humans since the Holocene, is nowadays heavily exploited and its population has decreased substantially since the mid-1990s. The uncertainty associated to jack mackerel population structure currently hampers management. Several hypotheses have been proposed from a single population up to several discrete populations. Still no definitive answer was given. Determining how environmental conditions drive jack mackerel distribution can provide insights on its population structure. To do so, here we performed in three steps. First, we used satellite data to develop a statistical model of jack mackerel horizontal habitat suitability. Model predictions based on interaction between temperature and chlorophyll-a match the observed jack mackerel distribution, even during extreme El Niño event. Second, we studied the impact of oxygen and show that jack mackerel distribution and abundance is correlated to oxygen over a wide variety of scales and avoid low oxygen areas and periods. Third, on the basis of the above we built a conceptual 3D model of jack mackerel habitat in the Southeastern Pacific. We reveal the presence of a low suitable habitat along the Chilean and Peruvian coast, figuratively presenting a closed door caused by a gap in the horizontal habitat at ∼19-22°S and a shallow oxycline off south-centre Peru. This kind of situation likely occurs on a seasonal basis, in austral summer but also at longer temporal scales. A lack of exchanges at some periods/seasons partially isolate jack mackerel distributed off Peru. On the other hand the continuity in the habitat during most of the year explains why exchanges occur. We conclude that the more likely population structure for jack mackerel is a pelagic metapopulation.

Genetic Variability and Distribution of Mating Type Alleles in Field Populations of Leptosphaeria maculans from France

PubMed Central

Gout, Lilian; Eckert, Maria; Rouxel, Thierry; Balesdent, Marie-Hélène

2006-01-01

Leptosphaeria maculans is the most ubiquitous fungal pathogen of Brassica crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of L. maculans in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m2 field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All L. maculans field populations had a high level of gene diversity (H = 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m2 field plots. Population differentiation among the four field populations was low (GST < 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of L. maculans suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used. PMID:16391041

Comparison of Campylobacter jejuni isolates from human, food, veterinary and environmental sources in Iceland using PFGE, MLST and fla-SVR sequencing.

PubMed

Magnússon, S H; Guðmundsdóttir, S; Reynisson, E; Rúnarsson, A R; Harðardóttir, H; Gunnarson, E; Georgsson, F; Reiersen, J; Marteinsson, V Th

2011-10-01

Campylobacter jejuni isolates from various sources in Iceland were genotyped with the aim of assessing the genetic diversity, population structure, source distribution and campylobacter transmission routes to humans. A collection of 584 Campylobacter isolates were collected from clinical cases, food, animals and environment in Iceland in 1999-2002, during a period of national Campylobacter epidemic in Iceland. All isolates were characterized by pulse field gel electrophoresis (PFGE), and selected subset of 52 isolates representing the diversity of the identified PFGE types was further genotyped using multilocus sequence typing (MLST) and fla-SVR sequencing to gain better insight into the population structure. The results show a substantial diversity within the Icelandic Campylobacter population. Majority of the human Campylobacter infections originated from domestic chicken and cattle isolates. MLST showed the isolates to be distributed among previously reported and common sequence type complexes in the MLST database. The genotyping of Campylobacter from various sources has not previously been reported from Iceland, and the results of the study gave a valuable insight into the population structure of Camp. jejuni in Iceland, source distribution and transmission routes to humans. The geographical isolation of Iceland in the north Atlantic provides new information on Campylobacter population dynamics on a global scale. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology No claim to Icelandic Government works.

Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda

PubMed Central

Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D.; Goffredo, Stefano

2015-01-01

Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa. PMID:26544963

Population Structure of Montastraea cavernosa on Shallow versus Mesophotic Reefs in Bermuda.

PubMed

Goodbody-Gringley, Gretchen; Marchini, Chiara; Chequer, Alex D; Goffredo, Stefano

2015-01-01

Mesophotic coral reef ecosystems remain largely unexplored with only limited information available on taxonomic composition, abundance and distribution. Yet, mesophotic reefs may serve as potential refugia for shallow-water species and thus understanding biodiversity, ecology and connectivity of deep reef communities is integral for resource management and conservation. The Caribbean coral, Montastraea cavernosa, is considered a depth generalist and is commonly found at mesophotic depths. We surveyed abundance and size-frequency of M. cavernosa populations at six shallow (10m) and six upper mesophotic (45m) sites in Bermuda and found population structure was depth dependent. The mean surface area of colonies at mesophotic sites was significantly smaller than at shallow sites, suggesting that growth rates and maximum colony surface area are limited on mesophotic reefs. Colony density was significantly higher at mesophotic sites, however, resulting in equal contributions to overall percent cover. Size-frequency distributions between shallow and mesophotic sites were also significantly different with populations at mesophotic reefs skewed towards smaller individuals. Overall, the results of this study provide valuable baseline data on population structure, which indicate that the mesophotic reefs of Bermuda support an established population of M. cavernosa.

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

Ecotoxicology and spatial modeling in population dynamics: an illustration with brown trout.

PubMed

Chaumot, Arnaud; Charles, Sandrine; Flammarion, Patrick; Auger, Pierre

2003-05-01

We developed a multiregion matrix population model to explore how the demography of a hypothetical brown trout population living in a river network varies in response to different spatial scenarios of cadmium contamination. Age structure, spatial distribution, and demographic and migration processes are taken into account in the model. Chronic or acute cadmium concentrations affect the demographic parameters at the scale of the river range. The outputs of the model constitute population-level end points (the asymptotic population growth rate, the stable age structure, and the asymptotic spatial distribution) that allow comparing the different spatial scenarios of contamination regarding the demographic response at the scale of the whole river network. An analysis of the sensitivity of these end points to lower order parameters enables us to link the local effects of cadmium to the global demographic behavior of the brown trout population. Such a link is of broad interest in the point of view of ecotoxicological management.

World Virtual Observatory Organization

NASA Astrophysics Data System (ADS)

Ignatyev, Mikhail; Pinigin, Gennadij

On the base of experience of our Unoversity and Observatory we investigate the seven blocks model of virtual organization for consolidation of resources. This model consists of the next blocks: 1.Population-scientists students robots and agents. 2.Aspiration of population groups. 3.Territory. 4.Production. 5.Ecology and safety. 6.Finance. 7. External relations - input and output flows of population information resources.The world virtual observatory is the virtual world which consists of three groups of variables - appearances essences and structured uncertainty which defines the number and distribution of arbitrary coefficients in equivalent equations. The consolodation of recources permit to create the large telescopes with distributed structure on our planet and cosmos. Virtual instruments can have the best characteristics by means of collective effects which have investigated in our paper.

Hierarchical population structure in greater sage-grouse provides insight into management boundary delineation

Treesearch

Todd B. Cross; David E. Naugle; John C. Carlson; Michael K. Schwartz

2016-01-01

Understanding population structure is important for guiding ongoing conservation and restoration efforts. The greater sage-grouse (Centrocercus urophasianus) is a species of concern distributed across 1.2 million km2 of western North America. We genotyped 1499 greater sagegrouse from 297 leks across Montana, North Dakota and South Dakota using a 15 locus...

Age structure and age-related performance of sulfur cinquefoil (Potentilla recta).

Treesearch

Dana L. Perkins; Catherine G. Parks; Kathleen A. Dwire; Bryan A. Endress; Kelsi L. Johnson

2006-01-01

Age distributions of sulfur cinquefoil populations were determined on sites that were historically grazed, cultivated, and mechanically disturbed. From 12 sites, a total of 279 reproductively active plants were collected and aged by using herbchronology (counting rings in the secondary root xylem of the root crown) to (1) estimate the age structure of the populations...

Young Alu insertions within the MHC class I region in native American populations: insights into the origin of the MHC-Alu repeats.

PubMed

Gómez-Pérez, Luis; Alfonso-Sánchez, Miguel A; Dipierri, José E; Sánchez, Dora; Espinosa, Ibone; De Pancorbo, Marian M; Peña, José A

2013-01-01

Genetic heterogeneity of two Amerindian populations (Jujuy province, Argentina, and Waorani tribe, Ecuador) was characterized by analyzing data on polymorphic Alu insertions within the human major histocompatibility complex (MHC) class I region (6p21.31), which are completely nonexistent in Native Americans. We further evaluated the haplotype distribution and genetic diversity among continental ancestry groups and their potential implications for the dating of the origin of MHC-Alus. Five MHC-Alu elements (AluMicB, AluTF, AluHJ, AluHG, and AluHF) were typed in samples from Jujuy (N = 108) and Waorani (N = 36). Allele and haplotype frequency data on worldwide populations were compiled to explore spatial structuring of the MHC-Alu diversity through AMOVA tests. We utilized the median-joining network approach to illustrate the continental distribution of the MHC-Alu haplotypes and their phylogenetic relationships. Allele and haplotype distributions differed significantly between Jujuy and Waorani. The Waorani featured a low average heterozygosity attributable to strong population isolation. Overall, Alu markers showed great genetic heterogeneity both within and among populations. The haplotype distribution was distinctive of each continental ancestry group. Contrary to expectations, Africans showed the lowest MHC-Alu diversity. Genetic drift mainly associated to population bottlenecks seems to be reflected in the low MHC-Alu diversity of the Amerindians, mainly in Waorani. Geographical structuring of the haplotype distribution supports the efficiency of the MHC-Alu loci as lineage (ancestry) markers. The markedly low Alu diversity of African populations relative to other continental clusters suggests that these MHC-Alus might have arisen after the anatomically modern humans expanded out of Africa. Copyright © 2013 Wiley Periodicals, Inc.

Study of Aggregation of Janus Ellipsoids

NASA Astrophysics Data System (ADS)

Ruth, Donovan; Li, Wei; Khadka, Shreeya; Rickman, Jeffrey; Gunton, James

2013-03-01

We perform numerical simulations of a quasi-square well potential model of one-patch colloidal particles to investigate the collective structure of a system of Janus ellipsoids. We show that for Janus ellipsoids such that one half is an attractive patch, while the entire ellipsoid has a hardcore repulsion, the system organizes into a distribution of orientationally ordered micelles and vesicles. We analyze the cluster distribution at several temperatures and low densities and show that below certain temperatures the system is populated by stable clusters and depending on temperature and density the system is populated by either vesicles or micelle structures.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan.

PubMed

Thormann, Imke; Reeves, Patrick; Reilley, Ann; Engels, Johannes M M; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan

PubMed Central

Reeves, Patrick; Reilley, Ann; Engels, Johannes M. M.; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M.

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum. PMID:27513459

X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations

PubMed Central

Laan, Maris; Wiebe, Victor; Khusnutdinova, Elza; Remm, Maido; Pääbo, Svante

2005-01-01

Linkage disequilibrium structure is still unpredictable because the interplay of regional recombination rate and demographic history is poorly understood. We have compared the distribution of LD across two genomic regions differing in crossing-over activity – Xq13 (0.166 cM/Mb) and Xp22 (1.3 cM/Mb) – in 15 Eurasian populations. Demographic events predicted to increase the LD level – genetic drift, bottleneck and admixture – had a very strong impact on extent and patterns of regional LD across Xq13 compared to Xp22. The haplotype distribution of the DXS1225-DXS8082 microsatellites from Xq13 exhibiting strong association in all populations was remarkably influenced by population history. European populations shared one common haplotype with a frequency of 25-40%. The Volga-Ural populations studied, living at the geographic borderline of Europe, showed elevated LD as well as harboring a significant fraction of haplotypes originating from East Asia, thus reflecting their past migrations and admixture. In the young Kuusamo isolate from Finland, a bottleneck has led to allelic associations between loci and shifted the haplotype distribution, but has much less affected single microsatellite allele frequencies compared to the main Finnish population. The data show that the footprint of a demographic event is longer preserved in haplotype distribution within a region of low crossing-over rate, than in the information content of a single marker, or between actively recombining markers. As the knowledge of LD patterns is often chosen to assist association mapping of common disease, our conclusions emphasise the importance of understanding the history, structure and variation of a study population. PMID:15657606

Seascape Genetics of a Globally Distributed, Highly Mobile Marine Mammal: The Short-Beaked Common Dolphin (Genus Delphinus)

PubMed Central

Amaral, Ana R.; Beheregaray, Luciano B.; Bilgmann, Kerstin; Boutov, Dmitri; Freitas, Luís; Robertson, Kelly M.; Sequeira, Marina; Stockin, Karen A.; Coelho, M. Manuela; Möller, Luciana M.

2012-01-01

Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna. PMID:22319634

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

PubMed

Zinck, John W R; Rajora, Om P

2016-03-02

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

Living in isolation - population structure, reproduction, and genetic variation of the endangered plant species Dianthus gratianopolitanus (Cheddar pink).

PubMed

Putz, Christina M; Schmid, Christoph; Reisch, Christoph

2015-09-01

The endangered plant species Dianthus gratianopolitanus exhibits a highly fragmented distribution range comprising many isolated populations. Based upon this pattern of distribution, we selected a study region in Switzerland with a lower magnitude of isolation (Swiss Jura) and another study region in Germany with a higher degree of isolation (Franconian Jura). In each region, we chose ten populations to analyze population structure, reproduction, and genetic variation in a comparative approach. Therefore, we determined population density, cushion size, and cushion density to analyze population structure, investigated reproductive traits, including number of flowers, capsules, and germination rate, and analyzed amplified fragment length polymorphisms to study genetic variation. Population and cushion density were credibly higher in German than in Swiss populations, whereas reproductive traits and genetic variation within populations were similar in both study regions. However, genetic variation among populations and isolation by distance were stronger in Germany than in Switzerland. Generally, cushion size and density as well as flower and capsule production increased with population size and density, whereas genetic variation decreased with population density. In contrast to our assumptions, we observed denser populations and cushions in the region with the higher magnitude of isolation, whereas reproductive traits and genetic variation within populations were comparable in both regions. This corroborates the assumption that stronger isolation must not necessarily result in the loss of fitness and genetic variation. Furthermore, it supports our conclusion that the protection of strongly isolated populations contributes essentially to the conservation of a species' full evolutionary potential.

Analysis of the population structure of Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) in the Palaearctic region using microsatellite markers

PubMed Central

Sanchez, Juan Antonio; Spina, Michelangelo La; Perera, Omaththage P

2012-01-01

Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) is widely distributed throughout the Palaearctic region. The aim was to explain the current geographic distribution of the species by investigating its genetic population structure. Samples of M. pygmaeus were collected in 15 localities through its range of distribution. A sample from a commercial producer was also analyzed. A total of 367 M. pygmaeus were genotyped for nine microsatellite loci. Isolation by distance was tested by Mantel's test. The molecular structure of M. pygmaeus populations was inferred by UPGMA, AMOVA, Principal component and Bayesian analyses. The average number of alleles per locus per population was 5.5 (range: 3.1–7.8). Istanbul (Turkey) and Nimes (France) had the lowest (0.291) and the highest (0.626) expected heterozygosity (He), respectively. There was an increase in He from the Canary Islands to Nimes, and a progressive decrease thereafter. A significant negative correlation was found between allelic richness and He, and the distance of each population to the easternmost locality (Canary Islands). Significant linkage disequilibrium was observed in the populations from Turkey. FST (0.004–0.334) indicated a high population differentiation, with isolation by distance supported by a high correlation. Bayesian analyses, PCA, and UPGMA pointed to three main clusters: (1) Greece and Turkey, (2) Italy and France, and (3) southern Iberia and the Canary Islands. The recent evolutionary history of M. pygmaeus is inferred from the data as follows: (1) the reduction in the geographic distribution of the species to the Iberian, Italian, and Balkan peninsulas, and possibly southern France, during glaciations and re-colonization of northern Europe from its southern refuges; (2) the maintenance of high diversity in Iberia and Italy (and possibly southern France) during contraction periods, and bottlenecks in the Balkans; (3) introgression of the Italian–French lineage in northern Spain, naturally or through trade. PMID:23301179

Comparative phylogeographic study of Hosta sieboldiana and Hosta albomarginata (Asparagaceae) in Japan

PubMed Central

Lee, Sangryong; Maki, Masayuki

2013-01-01

We analyzed variations in chloroplast DNA (cpDNA) in the widespread herbaceous species Hosta sieboldiana and Hosta albomarginata across large portions of their geographic ranges in the Japanese archipelago. Our objective was to compare the phylogeographic histories and phylogeographic structures of the two congeneric species in the Japanese archipelago. The location of the study is Japanese archipelago. We sequenced 1380 bp of noncoding cpDNA from 45 populations of H. sieboldiana (n = 362) and 55 populations of H. albomarginata (n = 436) to assess genetic variations within and among populations across almost the entire distributions of the species in Japan. Extant patterns of geographic structure were analyzed using statistical parsimony networks and spatial analysis of molecular variance (SAMOVA). We also used Monmonier's algorithm to detect genetic barriers between regions. Relationships between the populations were examined using a neighbor-joining (NJ) method. Four haplotypes were found for H. sieboldiana, whereas eight haplotypes were identified for H. albomarginata. Total genetic haplotype diversity (hT) and within-population haplotype diversity (hS) for H. sieboldiana were 0.352 and 0.040, respectively, while the values for H. albomarginata were 0.529 and 0.085, respectively. The population differentiations (GST) for H. sieboldiana and H. albomarginata were 0.839 and 0.886, respectively. The SAMOVA analysis revealed two clusters in H. sieboldiana and four clusters in H. albomarginata. Differentiations between and among the clusters were supported by the BARRIER analysis and the NJ tree. We detected differences in the population genetic structure between the two species. We found that H. sieboldiana had lower haplotype diversity than H. albomarginata. These results may be partially explained by the difference in ecological habitats and geographic distributions between the species. Hosta albomarginata is more widely distributed than H. sieboldiana in East Asia including Russia, and this large distribution range would enable more chances to intraspecific gene flow. PMID:24363903

Analysis of the population structure of Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) in the Palaearctic region using microsatellite markers.

PubMed

Sanchez, Juan Antonio; Spina, Michelangelo La; Perera, Omaththage P

2012-12-01

Macrolophus pygmaeus (Rambur) (Hemiptera: Miridae) is widely distributed throughout the Palaearctic region. The aim was to explain the current geographic distribution of the species by investigating its genetic population structure. Samples of M. pygmaeus were collected in 15 localities through its range of distribution. A sample from a commercial producer was also analyzed. A total of 367 M. pygmaeus were genotyped for nine microsatellite loci. Isolation by distance was tested by Mantel's test. The molecular structure of M. pygmaeus populations was inferred by UPGMA, AMOVA, Principal component and Bayesian analyses. The average number of alleles per locus per population was 5.5 (range: 3.1-7.8). Istanbul (Turkey) and Nimes (France) had the lowest (0.291) and the highest (0.626) expected heterozygosity (H(e)), respectively. There was an increase in H(e) from the Canary Islands to Nimes, and a progressive decrease thereafter. A significant negative correlation was found between allelic richness and H(e), and the distance of each population to the easternmost locality (Canary Islands). Significant linkage disequilibrium was observed in the populations from Turkey. F(ST) (0.004-0.334) indicated a high population differentiation, with isolation by distance supported by a high correlation. Bayesian analyses, PCA, and UPGMA pointed to three main clusters: (1) Greece and Turkey, (2) Italy and France, and (3) southern Iberia and the Canary Islands. The recent evolutionary history of M. pygmaeus is inferred from the data as follows: (1) the reduction in the geographic distribution of the species to the Iberian, Italian, and Balkan peninsulas, and possibly southern France, during glaciations and re-colonization of northern Europe from its southern refuges; (2) the maintenance of high diversity in Iberia and Italy (and possibly southern France) during contraction periods, and bottlenecks in the Balkans; (3) introgression of the Italian-French lineage in northern Spain, naturally or through trade.

Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations.

PubMed

Szövényi, P; Terracciano, S; Ricca, M; Giordano, S; Shaw, A J

2008-12-01

Several lines of evidence suggest that recent long-distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi-Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (IM and MIGRATE) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F(ST) = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long-range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000-289,000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi-Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.

Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae).

PubMed

Cosendai, A-C; Wagner, J; Ladinig, U; Rosche, C; Hörandl, E

2013-06-01

Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations.

Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)

PubMed Central

Cosendai, A-C; Wagner, J; Ladinig, U; Rosche, C; Hörandl, E

2013-01-01

Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations. PMID:23403961

Molecular and morphological data of the freshwater fish Glandulocauda melanopleura (Characiformes: Characidae) provide evidences of river captures and local differentiation in the Brazilian Atlantic Forest

PubMed Central

Menezes, Naércio Aquino; Costa-Silva, Guilherme José; Oliveira, Claudio

2018-01-01

The current distribution of freshwater fishes across multiple basins along Eastern Brazil can be associated to two main events: river captures or temporary paleoconnections. Apparently, river captures had a more significant role on distribution and structuring of species from upland areas, such as Glandulocauda melanopleura. Populations of this species are found in contiguous drainages in presently isolated upper parts of Rio Tietê and the coastal basins of Guaratuba, Itatinga, Itanháem, and Ribeira de Iguape, in the Atlantic Forest domain. The allopatric and disjoint distribution of G. melanopleura associated with variation of morphological characters detected among geographically isolated populations stimulated this study. Thus, an integrative approach was undertaken, including morphological and molecular data, to better understand the evolutionary history of the species and the area where it occurs. Molecular analyses based on two mitochondrial markers revealed a strong genetic structure within G. melanopleura, that allowed recognition of two lineages, one distributed in both the upper Tietê and Itanhaém and the other in the Guaratuba. Overall, morphological data revealed some intraspecific overlapping variation, indicating that all samples are conspecific. Phylogenetic and phylogeographic analyses allied to divergence times and geomorphological information indicate that the current distribution of G. melanopleura is a result of relatively recent river captures involving the Tietê and some other coastal drainages. Although of recent origin, they occurred long enough to completely isolate these populations, since there are no haplotypes sharing between them. The conservation status of this species is also discussed, and our results corroborate the need to understand population structure for conservation planning. PMID:29579069

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae).

PubMed

da Silva, Marjorie; Noll, Fernando Barbosa; E Castro, Adriana C Morales-Corrêa

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks.

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae)

PubMed Central

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks. PMID:29538451

Phylogeography and Post-Glacial Recolonization in Wolverines (Gulo gulo) from across Their Circumpolar Distribution

PubMed Central

Zigouris, Joanna; Schaefer, James A.; Fortin, Clément; Kyle, Christopher J.

2013-01-01

Interglacial-glacial cycles of the Quaternary are widely recognized in shaping phylogeographic structure. Patterns from cold adapted species can be especially informative - in particular, uncovering additional glacial refugia, identifying likely recolonization patterns, and increasing our understanding of species’ responses to climate change. We investigated phylogenetic structure of the wolverine, a wide-ranging cold adapted carnivore, using a 318 bp of the mitochondrial DNA control region for 983 wolverines (n = 209 this study, n = 774 from GenBank) from across their full Holarctic distribution. Bayesian phylogenetic tree reconstruction and the distribution of observed pairwise haplotype differences (mismatch distribution) provided evidence of a single rapid population expansion across the wolverine’s Holarctic range. Even though molecular evidence corroborated a single refugium, significant subdivisions of population genetic structure (0.01< ΦST <0.99, P<0.05) were detected. Pairwise ΦST estimates separated Scandinavia from Russia and Mongolia, and identified five main divisions within North America - the Central Arctic, a western region, an eastern region consisting of Ontario and Quebec/Labrador, Manitoba, and California. These data are in contrast to the nearly panmictic structure observed in northwestern North America using nuclear microsatellites, but largely support the nuclear DNA separation of contemporary Manitoba and Ontario wolverines from northern populations. Historic samples (c. 1900) from the functionally extirpated eastern population of Quebec/Labrador displayed genetic similarities to contemporary Ontario wolverines. To understand these divergence patterns, four hypotheses were tested using Approximate Bayesian Computation (ABC). The most supported hypothesis was a single Beringia incursion during the last glacial maximum that established the northwestern population, followed by a west-to-east colonization during the Holocene. This pattern is suggestive of colonization occurring in accordance with glacial retreat, and supports expansion from a single refugium. These data are significant relative to current discussions on the conservation status of this species across its range. PMID:24386287

Phylogeography and post-glacial recolonization in wolverines (Gulo gulo) from across their circumpolar distribution.

PubMed

Zigouris, Joanna; Schaefer, James A; Fortin, Clément; Kyle, Christopher J

2013-01-01

Interglacial-glacial cycles of the Quaternary are widely recognized in shaping phylogeographic structure. Patterns from cold adapted species can be especially informative - in particular, uncovering additional glacial refugia, identifying likely recolonization patterns, and increasing our understanding of species' responses to climate change. We investigated phylogenetic structure of the wolverine, a wide-ranging cold adapted carnivore, using a 318 bp of the mitochondrial DNA control region for 983 wolverines (n=209 this study, n=774 from GenBank) from across their full Holarctic distribution. Bayesian phylogenetic tree reconstruction and the distribution of observed pairwise haplotype differences (mismatch distribution) provided evidence of a single rapid population expansion across the wolverine's Holarctic range. Even though molecular evidence corroborated a single refugium, significant subdivisions of population genetic structure (0.01< ΦST <0.99, P<0.05) were detected. Pairwise ΦST estimates separated Scandinavia from Russia and Mongolia, and identified five main divisions within North America - the Central Arctic, a western region, an eastern region consisting of Ontario and Quebec/Labrador, Manitoba, and California. These data are in contrast to the nearly panmictic structure observed in northwestern North America using nuclear microsatellites, but largely support the nuclear DNA separation of contemporary Manitoba and Ontario wolverines from northern populations. Historic samples (c. 1900) from the functionally extirpated eastern population of Quebec/Labrador displayed genetic similarities to contemporary Ontario wolverines. To understand these divergence patterns, four hypotheses were tested using Approximate Bayesian Computation (ABC). The most supported hypothesis was a single Beringia incursion during the last glacial maximum that established the northwestern population, followed by a west-to-east colonization during the Holocene. This pattern is suggestive of colonization occurring in accordance with glacial retreat, and supports expansion from a single refugium. These data are significant relative to current discussions on the conservation status of this species across its range.

Morphology and Structures of Nearby Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Seo, Mira; Ann, H. B.

2016-08-01

We applied GALFIT and STARLIGHT to the r-band images and spectra, respectively, of ~1,100 dwarf galaxies to analyze the structural properties and stellar populations. In most cases, single component with n = 1 ~ 1.5 well describes the luminosity distribution of dwarf galaxies. However, a large fraction of dS0, dE bc , and dE blue galaxies show sub-structures such as spiral arms and rings. There is a bimodal distributions of stellar ages in dS0 galaxies. But other sub-types of dwarf galaxies show a single peak in the stellar distributions.

Toxoplasma and Africa: One Parasite, Two Opposite Population Structures.

PubMed

Galal, Lokman; Ajzenberg, Daniel; Hamidović, Azra; Durieux, Marie-Fleur; Dardé, Marie-Laure; Mercier, Aurélien

2018-02-01

Exploring the genetic diversity of Toxoplasma gondii is essential for an understanding of its worldwide distribution and the determinants of its evolution. Africa remains one of the least studied areas of the world regarding T. gondii genetic diversity. This review has compiled published data on T. gondii strains from Africa to generate a comprehensive map of their continent-wide geographical distribution. The emerging picture about T. gondii strain distribution in Africa suggests a geographical separation of the parasite populations across the continent. We discuss the potential role of a number of factors in shaping this structure. We finally suggest the next steps towards a better understanding of Toxoplasma epidemiology in Africa in light of the strains circulating on this continent. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Geographic location, network patterns and population distribution of rural settlements in Greece

NASA Astrophysics Data System (ADS)

Asimakopoulos, Avraam; Mogios, Emmanuel; Xenikos, Dimitrios G.

2016-10-01

Our work addresses the problem of how social networks are embedded in space, by studying the spread of human population over complex geomorphological terrain. We focus on villages or small cities up to a few thousand inhabitants located in mountainous areas in Greece. This terrain presents a familiar tree-like structure of valleys and land plateaus. Cities are found more often at lower altitudes and exhibit preference on south orientation. Furthermore, the population generally avoids flat land plateaus and river beds, preferring locations slightly uphill, away from the plateau edge. Despite the location diversity regarding geomorphological parameters, we find certain quantitative norms when we examine location and population distributions relative to the (man-made) transportation network. In particular, settlements at radial distance ℓ away from road network junctions have the same mean altitude, practically independent of ℓ ranging from a few meters to 10 km. Similarly, the distribution of the settlement population at any given ℓ is the same for all ℓ. Finally, the cumulative distribution of the number of rural cities n(ℓ) is fitted to the Weibull distribution, suggesting that human decisions for creating settlements could be paralleled to mechanisms typically attributed to this particular statistical distribution.

Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil.

PubMed

Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; Dos Santos, Flavio Antonio Maës

2015-05-01

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.

Most recent common ancestor probability distributions in gene genealogies under selection.

PubMed

Slade, P F

2000-12-01

A computational study is made of the conditional probability distribution for the allelic type of the most recent common ancestor in genealogies of samples of n genes drawn from a population under selection, given the initial sample configuration. Comparisons with the corresponding unconditional cases are presented. Such unconditional distributions differ from samples drawn from the unique stationary distribution of population allelic frequencies, known as Wright's formula, and are quantified. Biallelic haploid and diploid models are considered. A simplified structure for the ancestral selection graph of S. M. Krone and C. Neuhauser (1997, Theor. Popul. Biol. 51, 210-237) is enhanced further, reducing the effective branching rate in the graph. This improves efficiency of such a nonneutral analogue of the coalescent for use with computational likelihood-inference techniques.

Desert salt flats as oases for the spider Saltonia incerta Banks (Araneae: Dictynidae).

PubMed

Crews, Sarah C; Gillespie, Rosemary G

2014-10-01

The deserts of southwestern North America have undergone dramatic changes over their recent geological history including large changes in size and connectivity during the Pleistocene glaciopluvial cycles. This study examines the population history of the rare spider Saltonia incerta, once thought to be extinct, to determine the role of past climatological events in shaping the structure of the species. This species is restricted to salt crusts of intermittent or dry lakes, streams or rivers in the desert southwest, a region that was much wetter during glacial periods. We examine the distribution and genetic variability of populations to test whether there is recent dispersal throughout the range of the species. Analyses of mitochondrial and nuclear DNA indicate significant population structure, with one major clade comprising New Mexico localities and one comprising California-northern Baja California localities. Finer-scale structure is evident within the California clade, although not all of the subclades are reciprocally monophyletic. However, isolation with migration analysis suggests that migration is very low to non-existent. These results extend the known distribution of Saltonia, provide genetic evidence of strong isolation among localities within drainage basins and between drainage basins and provide a mechanistic understanding of population connectivity after the aridification of the American southwest. The implication is that although the species' distribution has been fragmented, populations have persisted throughout this area, suggesting that desert salt flats may have served as refugia for at least some terrestrial species.

Desert salt flats as oases for the spider Saltonia incerta Banks (Araneae: Dictynidae)

PubMed Central

Crews, Sarah C; Gillespie, Rosemary G

2014-01-01

The deserts of southwestern North America have undergone dramatic changes over their recent geological history including large changes in size and connectivity during the Pleistocene glaciopluvial cycles. This study examines the population history of the rare spider Saltonia incerta, once thought to be extinct, to determine the role of past climatological events in shaping the structure of the species. This species is restricted to salt crusts of intermittent or dry lakes, streams or rivers in the desert southwest, a region that was much wetter during glacial periods. We examine the distribution and genetic variability of populations to test whether there is recent dispersal throughout the range of the species. Analyses of mitochondrial and nuclear DNA indicate significant population structure, with one major clade comprising New Mexico localities and one comprising California-northern Baja California localities. Finer-scale structure is evident within the California clade, although not all of the subclades are reciprocally monophyletic. However, isolation with migration analysis suggests that migration is very low to non-existent. These results extend the known distribution of Saltonia, provide genetic evidence of strong isolation among localities within drainage basins and between drainage basins and provide a mechanistic understanding of population connectivity after the aridification of the American southwest. The implication is that although the species' distribution has been fragmented, populations have persisted throughout this area, suggesting that desert salt flats may have served as refugia for at least some terrestrial species. PMID:25614800

Integrating Paleodistribution Models and Phylogeography in the Grass-Cutting Ant Acromyrmex striatus (Hymenoptera: Formicidae) in Southern Lowlands of South America

PubMed Central

Cristiano, Maykon Passos; Clemes Cardoso, Danon; Fernandes-Salomão, Tânia Maria; Heinze, Jürgen

2016-01-01

Past climate changes often have influenced the present distribution and intraspecific genetic diversity of organisms. The objective of this study was to investigate the phylogeography and historical demography of populations of Acromyrmex striatus (Roger, 1863), a leaf-cutting ant species restricted to the open plains of South America. Additionally, we modeled the distribution of this species to predict its contemporary and historic habitat. From the partial sequences of the mitochondrial gene cytochrome oxidase I of 128 A. striatus workers from 38 locations we estimated genetic diversity and inferred historical demography, divergence time, and population structure. The potential distribution areas of A. striatus for current and quaternary weather conditions were modeled using the maximum entropy algorithm. We identified a total of 58 haplotypes, divided into five main haplogroups. The analysis of molecular variance (AMOVA) revealed that the largest proportion of genetic variation is found among the groups of populations. Paleodistribution models suggest that the potential habitat of A. striatus may have decreased during the Last Interglacial Period (LIG) and expanded during the Last Maximum Glacial (LGM). Overall, the past potential distribution recovered by the model comprises the current potential distribution of the species. The general structuring pattern observed was consistent with isolation by distance, suggesting a balance between gene flow and drift. Analysis of historical demography showed that populations of A. striatus had remained constant throughout its evolutionary history. Although fluctuations in the area of their potential historic habitat occurred during quaternary climate changes, populations of A. striatus are strongly structured geographically. However, explicit barriers to gene flow have not been identified. These findings closely match those in Mycetophylax simplex, another ant species that in some areas occurs in sympatry with A. striatus. Ecophysiological traits of this species and isolation by distance may together have shaped the phylogeographic pattern. PMID:26734939

Spatial Pattern and Population Structure of Artemisia ordosica Shrub in a Desert Grassland under Enclosure, Northwest China.

PubMed

Liu, Jiankang; Zhang, Kebin

2018-05-09

Enclosure is an effective practice for restoring and rehabilitating the degraded grassland ecosystem caused by overgrazing. Shrub species, which are dominant in most desert grasslands in arid and semiarid regions, have some beneficial ecological functions for grassland restoration. However, how the population structure and spatial pattern of the Artemisia ordosica shrub changes in a grassland ecosystem under enclosed practice is not well understood. This study, conducted in the Mu Us desert in northwest China, was designed to measure the A. ordosica population according to the chronosequence of enclosure (enclosure periods ranged from 5 years, 10 years, 15 years, and 25 years), contrasting this with an adjacent continuously grazed grassland. The results showed that the enclosed grasslands had a higher number of individuals of different age classes (seedling, adult, aging, and dead group) and greater population coverage, but shrubs had significant lower ( p < 0.05) crown diameter and height in comparison with those in continuously grazed grassland. Further, enclosed grasslands had a significantly higher ( p < 0.05) Shannon-Wiener index (H) and Evenness index (E), but a significantly lower ( p < 0.05) Richness index (R) than continuously grazed grassland. The crown of A. ordosica showed a significant linear positive correlation with height in all plots across succession, indicating that it was feasible to analyze the age structure by crown. The crown-class distribution structure of the A. ordosica population approximated a Gaussian distribution model in all survey plots. Within the population, seedling and adult groups exhibited aggregated spatial distribution at small scales, while aging and dead A. ordosica groups showed random distribution at almost all scales in different plots. The seedling A. ordosica group showed a positive correlation with adults at small scales in all plots except in 10 years of enclosure. However, it showed independent correlation with aging and dead groups at almost all scales. In long-term enclosed plots, the mortality rate of the A. ordosica population increased, therefore assistance management practices, such as fertilization, mowing, interval grazing, and seasonal grazing, must be employed to maintain population stability after long-term enclosure. This study can improve understanding and clarify the effects of enclosures in the desert grasslands of northwest China.

On the proportional abundance of species: Integrating population genetics and community ecology.

PubMed

Marquet, Pablo A; Espinoza, Guillermo; Abades, Sebastian R; Ganz, Angela; Rebolledo, Rolando

2017-12-01

The frequency of genes in interconnected populations and of species in interconnected communities are affected by similar processes, such as birth, death and immigration. The equilibrium distribution of gene frequencies in structured populations is known since the 1930s, under Wright's metapopulation model known as the island model. The equivalent distribution for the species frequency (i.e. the species proportional abundance distribution (SPAD)), at the metacommunity level, however, is unknown. In this contribution, we develop a stochastic model to analytically account for this distribution (SPAD). We show that the same as for genes SPAD follows a beta distribution, which provides a good description of empirical data and applies across a continuum of scales. This stochastic model, based upon a diffusion approximation, provides an alternative to neutral models for the species abundance distribution (SAD), which focus on number of individuals instead of proportions, and demonstrate that the relative frequency of genes in local populations and of species within communities follow the same probability law. We hope our contribution will help stimulate the mathematical and conceptual integration of theories in genetics and ecology.

The influence of hydrology and waterway distance on population structure of Chinook salmon Oncorhynchus tshawytscha in a large river.

PubMed

Olsen, J B; Beacham, T D; Wetklo, M; Seeb, L W; Smith, C T; Flannery, B G; Wenburg, J K

2010-04-01

Adult Chinook salmon Oncorhynchus tshawytscha navigate in river systems using olfactory cues that may be influenced by hydrologic factors such as flow and the number, size and spatial distribution of tributaries. Thus, river hydrology may influence both homing success and the level of straying (gene flow), which in turn influences population structure. In this study, two methods of multivariate analysis were used to examine the extent to which four indicators of hydrology and waterway distance explained population structure of O. tshawytscha in the Yukon River. A partial Mantel test showed that the indicators of hydrology were positively associated with broad-scale (Yukon basin) population structure, when controlling for the influence of waterway distance. Multivariate multiple regression showed that waterway distance, supplemented with the number and flow of major drainage basins, explained more variation in broad-scale population structure than any single indicator. At an intermediate spatial scale, indicators of hydrology did not appear to influence population structure after accounting for waterway distance. These results suggest that habitat changes in the Yukon River, which alter hydrology, may influence the basin-wide pattern of population structure in O. tshawytscha. Further research is warranted on the role of hydrology in concert with waterway distance in influencing population structure in Pacific salmon.

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico

PubMed Central

Ceballos-Vázquez, Bertha P.; Arellano-Martínez, Marcial; García-Rodríguez, Francisco J.; Culver, Melanie; Reyes-Bonilla, Hector

2018-01-01

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures. PMID:29472993

Spatial and temporal aspects of the genetic structure of Juniperus communis populations.

PubMed

Merwe, M V; Winfield, M O; Arnold, G M; Parker, J S

2000-04-01

Juniperus communis is a dioecious, wind pollinated shrub or small tree that produces 'berries' (female cones) containing a small number of seeds that are thought to be dispersed by birds. The expectation, therefore, would be that populations of Juniper are genetically diverse with little structuring between them. In Britain, the species has two main centres of distribution: a highland zone in the north and west, in which populations are still large and sexually reproducing, and a southern zone on chalk downlands in which populations are small and fragmented and individuals suffer from a decline in fertility. Thus, one would expect the large sexually viable populations in the north to exhibit high levels of within-population genetic variation, while the declining southern populations would be genetically depauperate. The analysis of amplified fragment length polymorphisms (AFLPs) was used to test this hypothesis. Surprisingly, all populations studied showed high levels of genetic variation although there was clear structuring between populations. On the basis of the geographical structuring of the populations it was hypothesized that J. communis colonized Britain via three separate routes.

Phylogeography of the tree lizard, Urosaurus ornatus: responses of populations to past climate change.

PubMed

Haenel, G J

2007-10-01

Isolation due to both geological barriers and range contractions during the Pleistocene glacial maxima has been an important cause of diversification of arid-adapted species in the North American deserts. Tree lizards, Urosaurus ornatus, are distributed across much of the southwestern arid regions and can tolerate a wide range of environments. Thus, they may have avoided large-scale shifts in distribution caused by Pleistocene climate change and any subsequent evolutionary impacts. Cytochrome b sequences were sampled from U. ornatus across the northern part of their range to test if current structure of these populations resulted from post-Pleistocene range expansion and habitat fragmentation, or prior geological isolation. Phylogenetic analyses found geographical structuring of populations consistent with a model of long-term geographical isolation corresponding to each of the desert regions. The two post-Pleistocene hypotheses were not well supported as estimated times of divergence predated the retreat of the last continental ice sheet. Populations in different regions were impacted by different processes. Southern populations of U. ornatus appear to have remained largely independent of more derived northern and eastern populations during Pleistocene climate change, while populations in regions containing more derived populations showed evidence of more recent range expansion (Colorado Plateau). As populations of U. ornatus attest to, the complex and dynamic history of the southwestern USA has left a deep-rooted and multifaceted imprint on genetic and phylogeographical structure of the species living there.

Fine-scale population structure and the era of next-generation sequencing.

PubMed

Henn, Brenna M; Gravel, Simon; Moreno-Estrada, Andres; Acevedo-Acevedo, Suehelay; Bustamante, Carlos D

2010-10-15

Fine-scale population structure characterizes most continents and is especially pronounced in non-cosmopolitan populations. Roughly half of the world's population remains non-cosmopolitan and even populations within cities often assort along ethnic and linguistic categories. Barriers to random mating can be ecologically extreme, such as the Sahara Desert, or cultural, such as the Indian caste system. In either case, subpopulations accumulate genetic differences if the barrier is maintained over multiple generations. Genome-wide polymorphism data, initially with only a few hundred autosomal microsatellites, have clearly established differences in allele frequency not only among continental regions, but also within continents and within countries. We review recent evidence from the analysis of genome-wide polymorphism data for genetic boundaries delineating human population structure and the main demographic and genomic processes shaping variation, and discuss the implications of population structure for the distribution and discovery of disease-causing genetic variants, in the light of the imminent availability of sequencing data for a multitude of diverse human genomes.

Predicting the distribution and ecological niche of unexploited snow crab (Chionoecetes opilio) populations in Alaskan waters: a first open-access ensemble model.

PubMed

Hardy, Sarah M; Lindgren, Michael; Konakanchi, Hanumantharao; Huettmann, Falk

2011-10-01

Populations of the snow crab (Chionoecetes opilio) are widely distributed on high-latitude continental shelves of the North Pacific and North Atlantic, and represent a valuable resource in both the United States and Canada. In US waters, snow crabs are found throughout the Arctic and sub-Arctic seas surrounding Alaska, north of the Aleutian Islands, yet commercial harvest currently focuses on the more southerly population in the Bering Sea. Population dynamics are well-monitored in exploited areas, but few data exist for populations further north where climate trends in the Arctic appear to be affecting species' distributions and community structure on multiple trophic levels. Moreover, increased shipping traffic, as well as fisheries and petroleum resource development, may add additional pressures in northern portions of the range as seasonal ice cover continues to decline. In the face of these pressures, we examined the ecological niche and population distribution of snow crabs in Alaskan waters using a GIS-based spatial modeling approach. We present the first quantitative open-access model predictions of snow-crab distribution, abundance, and biomass in the Chukchi and Beaufort Seas. Multi-variate analysis of environmental drivers of species' distribution and community structure commonly rely on multiple linear regression methods. The spatial modeling approach employed here improves upon linear regression methods in allowing for exploration of nonlinear relationships and interactions between variables. Three machine-learning algorithms were used to evaluate relationships between snow-crab distribution and environmental parameters, including TreeNet, Random Forests, and MARS. An ensemble model was then generated by combining output from these three models to generate consensus predictions for presence-absence, abundance, and biomass of snow crabs. Each algorithm identified a suite of variables most important in predicting snow-crab distribution, including nutrient and chlorophyll-a concentrations in overlying waters, temperature, salinity, and annual sea-ice cover; this information may be used to develop and test hypotheses regarding the ecology of this species. This is the first such quantitative model for snow crabs, and all GIS-data layers compiled for this project are freely available from the authors, upon request, for public use and improvement.

A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations.

PubMed

Rosenberg, Noah A; Nordborg, Magnus

2006-07-01

In linkage disequilibrium mapping of genetic variants causally associated with phenotypes, spurious associations can potentially be generated by any of a variety of types of population structure. However, mathematical theory of the production of spurious associations has largely been restricted to population structure models that involve the sampling of individuals from a collection of discrete subpopulations. Here, we introduce a general model of spurious association in structured populations, appropriate whether the population structure involves discrete groups, admixture among such groups, or continuous variation across space. Under the assumptions of the model, we find that a single common principle--applicable to both the discrete and admixed settings as well as to spatial populations--gives a necessary and sufficient condition for the occurrence of spurious associations. Using a mathematical connection between the discrete and admixed cases, we show that in admixed populations, spurious associations are less severe than in corresponding mixtures of discrete subpopulations, especially when the variance of admixture across individuals is small. This observation, together with the results of simulations that examine the relative influences of various model parameters, has important implications for the design and analysis of genetic association studies in structured populations.

An agent-based computational model for tuberculosis spreading on age-structured populations

NASA Astrophysics Data System (ADS)

Graciani Rodrigues, C. C.; Espíndola, Aquino L.; Penna, T. J. P.

2015-06-01

In this work we present an agent-based computational model to study the spreading of the tuberculosis (TB) disease on age-structured populations. The model proposed is a merge of two previous models: an agent-based computational model for the spreading of tuberculosis and a bit-string model for biological aging. The combination of TB with the population aging, reproduces the coexistence of health states, as seen in real populations. In addition, the universal exponential behavior of mortalities curves is still preserved. Finally, the population distribution as function of age shows the prevalence of TB mostly in elders, for high efficacy treatments.

Phylogeographic patterns of Lygus pratensis (Hemiptera: Miridae): Evidence for weak genetic structure and recent expansion in northwest China.

PubMed

Zhang, Li-Juan; Cai, Wan-Zhi; Luo, Jun-Yu; Zhang, Shuai; Wang, Chun-Yi; Lv, Li-Min; Zhu, Xiang-Zhen; Wang, Li; Cui, Jin-Jie

2017-01-01

Lygus pratensis (L.) is an important cotton pest in China, especially in the northwest region. Nymphs and adults cause serious quality and yield losses. However, the genetic structure and geographic distribution of L. pratensis is not well known. We analyzed genetic diversity, geographical structure, gene flow, and population dynamics of L. pratensis in northwest China using mitochondrial and nuclear sequence datasets to study phylogeographical patterns and demographic history. L. pratensis (n = 286) were collected at sites across an area spanning 2,180,000 km2, including the Xinjiang and Gansu-Ningxia regions. Populations in the two regions could be distinguished based on mitochondrial criteria but the overall genetic structure was weak. The nuclear dataset revealed a lack of diagnostic genetic structure across sample areas. Phylogenetic analysis indicated a lack of population level monophyly that may have been caused by incomplete lineage sorting. The Mantel test showed a significant correlation between genetic and geographic distances among the populations based on the mtDNA data. However the nuclear dataset did not show significant correlation. A high level of gene flow among populations was indicated by migration analysis; human activities may have also facilitated insect movement. The availability of irrigation water and ample cotton hosts makes the Xinjiang region well suited for L. pratensis reproduction. Bayesian skyline plot analysis, star-shaped network, and neutrality tests all indicated that L. pratensis has experienced recent population expansion. Climatic changes and extensive areas occupied by host plants have led to population expansion of L. pratensis. In conclusion, the present distribution and phylogeographic pattern of L. pratensis was influenced by climate, human activities, and availability of plant hosts.

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

PubMed

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

2011-12-01

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

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

Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China.

PubMed

Zhao, Wei; Shi, Xiaozheng; Li, Jiangnan; Guo, Wei; Liu, Chengbai; Chen, Xia

2014-01-01

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = -0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

Genetic, Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain, China

PubMed Central

Zhao, Wei; Shi, Xiaozheng; Li, Jiangnan; Guo, Wei; Liu, Chengbai; Chen, Xia

2014-01-01

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = –0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis. PMID:25386983

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

PubMed

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

2017-01-01

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

[Spatial point pattern analysis of main trees and flowering Fargesia qinlingensis in Abies fargesii forests in Mt Taibai of the Qinling Mountains, China].

PubMed

Li, Guo Chun; Song, Hua Dong; Li, Qi; Bu, Shu Hai

2017-11-01

In Abies fargesii forests of the giant panda's habitats in Mt. Taibai, the spatial distribution patterns and interspecific associations of main tree species and their spatial associations with the understory flowering Fargesia qinlingensis were analyzed at multiple scales by univariate and bivaria-te O-ring function in point pattern analysis. The results showed that in the A. fargesii forest, the number of A. fargesii was largest but its population structure was in decline. The population of Betula platyphylla was relatively young, with a stable population structure, while the population of B. albo-sinensis declined. The three populations showed aggregated distributions at small scales and gradually showed random distributions with increasing spatial scales. Spatial associations among tree species were mainly showed at small scales and gradually became not spatially associated with increasing scale. A. fargesii and B. platyphylla were positively associated with flowering F. qinlingensis at large and medium scales, whereas B. albo-sinensis showed negatively associated with flowering F. qinlingensis at large and medium scales. The interaction between trees and F. qinlingensis in the habitats of giant panda promoted the dynamic succession and development of forests, which changed the environment of giant panda's habitats in Qinling.

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

PubMed Central

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

2017-01-01

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

Investigation of Nuclear Structure and Quasi-Discrete Features in 150,152Sm via the (p,t) Reaction

NASA Astrophysics Data System (ADS)

Humby, Peter James Charnall

The (p,t) reaction was used to identify new levels and gamma-ray transitions in 150,152Sm utilising the particle-gamma and particle-gamma-gamma coincidence techniques. The experiment was performed using the STARLiTeR array located at the Cyclotron Institute of Texas A&M University. The relative partial cross sections for the observed levels, angle averaged between 34 and 58 degrees, were measured. A narrow peak-like structure was observed between 2.3-3.0 MeV excitation energy, in between the region of strongly populated discrete states at low energy and the high energy continuum region. In 150Sm, 39(4)% of the strength of the peak-like structure could be accounted for by the observed discrete states, which compares to a value of 93(15)% for 152Sm. The orbital angular-momentum transfer was probed by comparison of the experimental angular distributions to those calculated using the DWBA theory. The experimental angular distributions for the population of the peak-like structures are very similar in the two reactions, and significantly different to both the angular distribution of the background under the structures, and to the distribution obtained from the nearby continuum region at higher excitation energy. Post irradiation, the half-lives of isomeric states in 152Eu, populated in the 154Sm(p,3n) reaction, were obtained by measuring the decrease in intensity of the gamma rays emitted in the decay of these long lived levels. The half-life of the Jpi = 8- isomer 152m2Eu was measured to be 95.8(4) min, which is a factor of 2.5 reduction in uncertainty compared to the previous literature value of 96(1) min.

Molecular polymorphisms of the ABO locus as informative markers of ancestry in Central Argentina.

PubMed

Tavella, María Pía; García, Angelina; Pauro, Maia; Demarchi, Darío A; Nores, Rodrigo

2017-07-08

The aim of this study was to investigate the distribution of molecular polymorphisms of the ABO gene in four population samples from the province of Córdoba, in Central Argentina, and to compare them with other worldwide populations. A total of 110 buccal swab samples from autochthonous individuals of Córdoba were typified. Molecular characterization of the allelic variants was performed by the analysis of exons 6 and 7 of the ABO gene using PCR-RFLP analysis. Additionally, the Native American AIM O1v542 was characterized by direct sequencing. The four Córdoba populations did not show significant geographic structure, although the frequency of the O1v542 haplotype, detected in all the populations studied, ranged from 0.019 to 0.222. The principal component analysis based on O allele distribution showed that the populations from Córdoba clustered close to the admixed populations of Santiago and Mexico City, and at intermediate distances between European and Native American populations, while being distant from the African population. The results demonstrate that the analysis of the ABO system constitutes a useful tool for the study of the genetic structure and evolutionary history of human populations, reflecting accurately the relative contribution of parental continental contribution to the gene pool of admixed populations. © 2017 Wiley Periodicals, Inc.

Size and age structure of anadromous and landlocked populations of Rainbow Smelt

USGS Publications Warehouse

O'Malley, Andrew; Enterline, Claire; Zydlewski, Joseph D.

2017-01-01

Rainbow Smelt Osmerus mordax are widely distributed in both anadromous and landlocked populations throughout northeastern North America; abundance, size at age, and maximum size vary widely among populations and life histories. In the present study, size at age, von Bertalanffy growth parameters, population age distributions, and precision and bias in age assessment based on scales and sectioned otoliths were compared between ecotypes and among populations of Rainbow Smelt. To compare the ecotypes, we collected spawning adults from four anadromous and three landlocked populations in Maine during spring 2014. A significant bias was identified in only one of four scale comparisons but in four of seven otolith comparisons; however, a comparable level of precision was indicated. Anadromous populations had larger and more variable size at age and von Bertalanffy growth parameters than landlocked fish. Populations were composed of ages 1–4; six populations were dominated by age-2 or age-3 individuals, and one population was dominated by age-1 fish. These data suggest the presence of considerable plasticity among populations. A latitudinal gradient was observed in the anadromous Rainbow Smelt, which may show signs of population stress at the southern extent of their distribution.

Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk.

PubMed

Naveda-Rodríguez, Adrián; Vargas, Félix Hernán; Kohn, Sebastián; Zapata-Ríos, Galo

2016-01-01

The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km2. During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation.

Andean Condor (Vultur gryphus) in Ecuador: Geographic Distribution, Population Size and Extinction Risk

PubMed Central

Naveda-Rodríguez, Adrián; Vargas, Félix Hernán; Kohn, Sebastián; Zapata-Ríos, Galo

2016-01-01

The Andean Condor (Vultur gryphus) in Ecuador is classified as Critically Endangered. Before 2015, standardized and systematic estimates of geographic distribution, population size and structure were not available for this species, hampering the assessment of its current status and hindering the design and implementation of effective conservation actions. In this study, we performed the first quantitative assessment of geographic distribution, population size and population viability of Andean Condor in Ecuador. We used a methodological approach that included an ecological niche model to study geographic distribution, a simultaneous survey of 70 roosting sites to estimate population size and a population viability analysis (PVA) for the next 100 years. Geographic distribution in the form of extent of occurrence was 49 725 km2. During a two-day census, 93 Andean Condors were recorded and a population of 94 to 102 individuals was estimated. In this population, adult-to-immature ratio was 1:0.5. In the modeled PVA scenarios, the probability of extinction, mean time to extinction and minimum population size varied from zero to 100%, 63 years and 193 individuals, respectively. Habitat loss is the greatest threat to the conservation of Andean Condor populations in Ecuador. Population size reduction in scenarios that included habitat loss began within the first 15 years of this threat. Population reinforcement had no effects on the recovery of Andean Condor populations given the current status of the species in Ecuador. The population size estimate presented in this study is the lower than those reported previously in other countries where the species occur. The inferences derived from the population viability analysis have implications for Condor management in Ecuador. This study highlights the need to redirect efforts from captive breeding and population reinforcement to habitat conservation. PMID:26986004

A multiscale investigation of habitat use and within-river distribution of sympatric sand darter species

USGS Publications Warehouse

Thompson, Patricia A.; Welsh, Stuart A.; Strager, Michael P.; Rizzo, Austin A.

2018-01-01

The western sand darter Ammocrypta clara, and eastern sand darter Ammocrypta pellucida, are sand-dwelling fishes of conservation concern. Past research has emphasized the importance of studying individual populations of conservation concern, while recent research has revealed the importance of incorporating landscape scale processes that structure habitat mosaics and local populations. We examined habitat use and distributions of western and eastern sand darters in the lower Elk River of West Virginia. At the sandbar habitat use scale, western sand darters were detected in sandbars with greater area, higher proportions of coarse grain sand and faster bottom current velocity, while the eastern sand darter used a wider range of sandbar habitats. The landscape scale analysis revealed that contributing drainage area was an important predictor for both species, while sinuosity, which presumably represents valley type, also contributed to the western sand darter’s habitat suitability. Sandbar quality (area, grain size, and velocity) and fluvial geomorphic variables (drainage area and valley type) are likely key driving factors structuring sand darter distributions in the Elk River. This multiscale study of within-river species distribution and habitat use is unique, given that only a few sympatric populations are known of western and eastern sand darters.

Y Chromosome Haplogroup Distribution in Indo-European Speaking Tribes of Gujarat, Western India

PubMed Central

Aggarwal, Aastha; Mitra, Siuli; Italia, Yazdi M.; Saraswathy, Kallur N.; Chandrasekar, Adimoolam

2014-01-01

The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution. PMID:24614885

Y chromosome haplogroup distribution in Indo-European speaking tribes of Gujarat, western India.

PubMed

Khurana, Priyanka; Aggarwal, Aastha; Mitra, Siuli; Italia, Yazdi M; Saraswathy, Kallur N; Chandrasekar, Adimoolam; Kshatriya, Gautam K

2014-01-01

The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution.

Population-wide distributions of neural activity during perceptual decision-making

PubMed Central

Machens, Christian

2018-01-01

Cortical activity involves large populations of neurons, even when it is limited to functionally coherent areas. Electrophysiological recordings, on the other hand, involve comparatively small neural ensembles, even when modern-day techniques are used. Here we review results which have started to fill the gap between these two scales of inquiry, by shedding light on the statistical distributions of activity in large populations of cells. We put our main focus on data recorded in awake animals that perform simple decision-making tasks and consider statistical distributions of activity throughout cortex, across sensory, associative, and motor areas. We transversally review the complexity of these distributions, from distributions of firing rates and metrics of spike-train structure, through distributions of tuning to stimuli or actions and of choice signals, and finally the dynamical evolution of neural population activity and the distributions of (pairwise) neural interactions. This approach reveals shared patterns of statistical organization across cortex, including: (i) long-tailed distributions of activity, where quasi-silence seems to be the rule for a majority of neurons; that are barely distinguishable between spontaneous and active states; (ii) distributions of tuning parameters for sensory (and motor) variables, which show an extensive extrapolation and fragmentation of their representations in the periphery; and (iii) population-wide dynamics that reveal rotations of internal representations over time, whose traces can be found both in stimulus-driven and internally generated activity. We discuss how these insights are leading us away from the notion of discrete classes of cells, and are acting as powerful constraints on theories and models of cortical organization and population coding. PMID:23123501

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.

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.

Population-wide changes in pinyon-juniper woodlands caused by drought in the American Southwest: Effects on structure, composition, and distribution

Treesearch

John D. Shaw

2006-01-01

A complex of drought, insects, and disease caused widespread mortality in the pinyon-juniper forest types of the American Southwest in recent years. Data from 14,929 plots spanning 25 years and representing over 25 million hectares were analyzed to characterize effects of drought-related mortality on the structure, composition, and distribution of pinyon and juniper...

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

Conservation genetics of the endangered Iberian steppe plant Ferula loscosii (Apiaceae).

PubMed

Pérez-Collazos, E; Catalán, P

2008-07-01

Ferula loscosii (Lange) Willk (Apiaceae) is a threatened endemic species native to the Iberian Peninsula. The plant has a narrow and disjunct distribution in three regions, NE, C and SE Spain. Genetic variability within and among 11 populations from its natural distribution was assessed using allozymes. Intermediate levels of genetic diversity were detected in F. loscosii (P(99%) = 36.83; H(E) = 0.125; H(T) = 0.152). However, the highest genetic diversity (58%) corresponded to the threatened populations from SE and C Spain (H(T) = 0.169) rather than the more abundant and larger populations from NE Spain (Ebro valley) (H(T) = 0.122). Low to moderate levels of genetic structure were found among regional ranges (G(ST) = 0.134), and several statistical spatial correlation analyses corroborated substantial genetic differentiation among the three main regional ranges. However, no significant genetic differentiation was found among the NE Spain populations, except for a northernmost population that is geographically isolated. Outcrossing mating and other biological traits of the species could account for the maintenance of the present values of genetic diversity within populations. The existence of an ancestral late Tertiary wider distribution of the species in SE and C Spain, followed by the maintenance of different Quaternary refugia in these warmer areas, together with a more recent and rapid post-glacial expansion towards NE Spain, are arguments that could explain the low genetic variability and structure found in the Ebro valley and the higher levels of diversity in the southern Iberian populations.

Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple (Acer saccharum Marshall).

PubMed

Graignic, Noémie; Tremblay, Francine; Bergeron, Yves

2018-03-01

Due to climate change, the ranges of many North American tree species are expected to shift northward. Sugar maple ( Acer saccharum Marshall) reaches its northern continuous distributional limit in northeastern North America at the transition between boreal mixed-wood and temperate deciduous forests. We hypothesized that marginal fragmented northern populations from the boreal mixed wood would have a distinct pattern of genetic structure and diversity. We analyzed variation at 18 microsatellite loci from 23 populations distributed along three latitudinal transects (west, central, and east) that encompass the continuous-discontinuous species range. Each transect was divided into two zones, continuous (temperate deciduous) and discontinuous (boreal mixed wood), based on sugar maple stand abundance. Respective positive and negative relationships were found between the distance of each population to the northern limit (D_north), and allelic richness ( A R ) and population differentiation ( F ST ). These relations were tested for each transect separately; the pattern (discontinuous-continuous) remained significant only for the western transect. structure analysis revealed the presence of four clusters. The most northern populations of each transect were assigned to a distinct group. Asymmetrical gene flow occurred from the southern into the four northernmost populations. Southern populations in Québec may have originated from two different postglacial migration routes. No evidence was found to validate the hypothesis that northern populations were remnants of a larger population that had migrated further north of the species range after the retreat of the ice sheet. The northernmost sugar maple populations possibly originated from long-distance dispersal.

Fine scale population genetic structure and within tree distribution of mating types of Venturia effusa, cause of pecan scab in the USA

USDA-ARS?s Scientific Manuscript database

Scab (caused by Venturia effusa) is the major disease of pecan in the southeastern USA. There is no information available on the fine scale population genetic diversity. Four cv. Wichita trees (populations) were sampled hierarchically. Within each tree canopy, 4 approximately evenly spaced terminals...

CFD-PBM coupled simulation of a nanobubble generator with honeycomb structure

NASA Astrophysics Data System (ADS)

Ren, F.; Noda, N. A.; Ueda, T.; Sano, Y.; Takase, Y.; Umekage, T.; Yonezawa, Y.; Tanaka, H.

2018-06-01

In recent years, nanobubble technologies have drawn great attention due to their wide applications in many fields of science and technology. The nitrogen nanobubble water circulation can be used to slow the progressions of oxidation and spoilage for the seafood long- term storage. From previous studies, a kind of honeycomb structure for high-efficiency nanobubble generation has been proposed. In this paper, the bubbly flow in the honeycomb structure was studied. The numerical simulations of honeycomb structure were performed by using a computational fluid dynamics–population balance model (CFD-PBM) coupled model. The numerical model was based on the Eulerian multiphase model and the population balance model (PBM) was used to calculate the gas bubble size distribution. The bubble coalescence and breakage were included. Considering the effect of bubble diameter on the fluid flow, the phase interactions were coupled with the PBM. The bubble size distributions in the honeycomb structure under different work conditions were predicted. The experimental results were compared with the simulation predictions.

The Evolution of Galaxies Through the Spatial Distribution of Their Globular Clusters: the Brightest Galaxies in Fornax

NASA Astrophysics Data System (ADS)

Zegeye, David W.

2018-01-01

We present a study of the evolution of the 10 brightest galaxies in the Fornax Cluster, as reconstructed through their Globular Cluster (GC) populations. GCs can be characterized by their projected two-dimensional (2D) spatial distribution. Over- or under-densities in the GC distribution, can be linked to events in the host galaxy assembly history, and used to constrain the properties of their progenitors. With HST/ACS imaging, we identified significant structures in the GC distribution of the 10 galaxies investigated, with some of the galaxies possessing structures with >10-sigma significance. GC over-densities have been found within the galaxies, with significant differences between the red and blue GC population. For elongated galaxies, structures are preferentially to be aligned along the major axis. Fornax Cluster galaxies appear to be more dynamically relaxed than the Virgo Cluster galaxies previously investigated with the same methodology by D'Abrusco et al. (2016). However, from these observations, the evident imprints left in the spatial distribution of GCs in these galaxies suggest a similarly intense history of interactions.The SAO REU program is funded by the National Science Foundation REU and Department of Defense ASSURE programs under NSF Grant AST-1659473, and by the Smithsonian Institution.

Volcanisme, activité anthropique et circulation des masses océaniques : leur influence respective sur la distribution des populations d'ostracodes dans la baie de Kagoshima (île de Kyushu, Japon)Impact of volcanism, human activities, and water mass circulation on the distribution of ostracod populations in Kagoshima Bay (Kyushu Island, southern Japan)

NASA Astrophysics Data System (ADS)

Bodergat, Anne-Marie; Oki, Kimihiko; Ishizaki, Kunihiro; Rio, Michel

2002-11-01

The distribution of ostracod populations in Kagoshima Bay (Japan) is analysed with reference to different environmental parameters. The bay is an area of volcanic activity of Sakurajima volcano under the influence of the Kuroshio Current. Most of the Head environment is occupied by an acidic water mass. Numbers of individual and species decrease from the Mouth of the bay towards the Basin and Head environments. In this latter, acidic water mass has a drastic effect on ostracod populations, whereas volcanic ashes and domestic inputs are not hostile. Ostracod distribution is influenced by the quality and structure of water masses. To cite this article: A.-M. Bodergat et al., C. R. Geoscience 334 (2002) 1053-1059.

Country Profiles, Malaysia.

ERIC Educational Resources Information Center

Marzuki, Ariffin Bin; Peng, J. Y.

A profile of Malaysia is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population (size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition, migration,…

Country Profiles, Jamaica.

ERIC Educational Resources Information Center

Population Council, New York, NY.

A profile of Jamaica is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the island; population - size, growth patterns, age structure, rural/urban distribution, ethnic and religious composition, literacy, future…

Country Profiles, Indonesia.

ERIC Educational Resources Information Center

Population Council, New York, NY.

A profile of Indonesia is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population - size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition, migration,…

Country Profiles, Taiwan.

ERIC Educational Resources Information Center

Keeny, S. M.; And Others

A profile of Taiwan is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population (size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition, migration,…

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

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.

Population structure, spatial distribution and life-history traits of blacktip reef sharks Carcharhinus melanopterus.

PubMed

Mourier, J; Mills, S C; Planes, S

2013-03-01

During a survey of the population of blacktip reef shark Carcharhinus melanopterus in Moorea (French Polynesia) between 2007 and 2011, population structural characteristics were estimated from 268 individuals. Total length (LT ) ranged from 48 to 139 cm and 48 to 157 cm for males and females, respectively, demonstrating that the average LT of females was larger than that of males. The C. melanopterus population at Moorea showed an apparent spatial sexual segregation with females preferentially frequenting lagoons and males the fore-reefs. Mean growth rate was c. 6 cm year(-1) . Males reached sexual maturity at 111 cm LT . This study reports on the population characteristics of this widespread carcharhinid shark species and makes comparisons with other locations, confirming high geographic variability in the population structure of the species. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

Development of population structure and spatial distribution patterns of a restored forest during 17-year succession (1993-2010) in Pingshuo opencast mine spoil, China.

PubMed

Zhao, Zhongqiu; Wang, Lianhua; Bai, Zhongke; Pan, Ziguan; Wang, Yun

2015-07-01

Afforestation of native tree species is often recommended for ecological restoration in mining areas, but the understanding of the ecological processes of restored vegetation is quite limited. In order to provide insight of the ecological processes of restored vegetation, in this study, we investigate the development of the population structure and spatial distribution patterns of restored Robinia pseudoacacia (ROPS) and Pinus tabuliformis (PITA) mixed forests during the 17 years of the mine spoil period of the Pingshuo opencast mine, Shanxi Province, China. After a 17-year succession, apart from the two planted species, Ulmus pumila (ULPU), as an invasive species, settled in the plot along with a large number of small diameter at breast height (DBH) size. In total, there are 10,062 living individual plants, much more than that at the plantation (5105), and ROPS had become the dominant species with a section area with a breast height of 9.40 m(2) hm(-2) and a mean DBH of 6.72 cm, much higher than both PITA and ULPU. The DBH size classes of all the total species showed inverted J-shaped distributions, which may have been a result of the large number of small regenerated ULPU trees. The DBH size classes of both ROPS and PITA showed peak-type structures with individuals mainly gathering in the moderate DBH size class, indicating a relatively healthy DBH size class structure. Meanwhile, invasive ULPU were distributed in a clear L shape, concentrating on the small DBH size class, indicating a relatively low survival rate for adult trees. Both ROPS and PITA species survival in the plantation showed uniform and aggregated distribution at small scales and random with scales increasing. ULPU showed a strong aggregation at small scales as well as random with scales increasing. Both the population structure and spatial distribution indicated that ROPS dominates and will continue to dominate the community in the future succession, which should be continuously monitored.

Population structure and demographic history of a tropical lowland rainforest tree species Shorea parvifolia (Dipterocarpaceae) from Southeastern Asia.

PubMed

Iwanaga, Hiroko; Teshima, Kosuke M; Khatab, Ismael A; Inomata, Nobuyuki; Finkeldey, Reiner; Siregar, Iskandar Z; Siregar, Ulfah J; Szmidt, Alfred E

2012-07-01

Distribution of tropical rainforests in Southeastern Asia has changed over geo-logical time scale, due to movement of tectonic plates and/or global climatic changes. Shorea parvifolia is one of the most common tropical lowland rainforest tree species in Southeastern Asia. To infer population structure and demographic history of S. parvifolia, as indicators of temporal changes in the distribution and extent of tropical rainforest in this region, we studied levels and patterns of nucleotide polymorphism in the following five nuclear gene regions: GapC, GBSSI, PgiC, SBE2, and SODH. Seven populations from peninsular Malaysia, Sumatra, and eastern Borneo were included in the analyses. STRUCTURE analysis revealed that the investigated populations are divided into two groups: Sumatra-Malay and Borneo. Furthermore, each group contained one admixed population. Under isolation with migration model, divergence of the two groups was estimated to occur between late Pliocene (2.6 MYA) and middle Pleistocene (0.7 MYA). The log-likelihood ratio tests of several demographic models strongly supported model with population expansion and low level of migration after divergence of the Sumatra-Malay and Borneo groups. The inferred demographic history of S. parvifolia suggested the presence of a scarcely forested land bridge on the Sunda Shelf during glacial periods in the Pleistocene and predominance of tropical lowland rainforest at least in Sumatra and eastern Borneo.

[The use of RAPD and ITE molecular markers to study genetical structure of the Crimean population of Triticum boeoticum Boiss].

PubMed

Mallabaeva, D Sh; Ignatov, A N; Sheĭko, I A; Isikov, V P; Geliuta, V P; Boĭko, N G; Seriapin, A A; Dorokhov, D B

2007-01-01

Wild wheat Triticum boeoticum Boiss. is the rare species are included in the Red Book of Ukraine. This species are reducing the magnitude of population and the area of distribution under anthropogenic activity. We studied genetic structure of two populations of T. boeoticum, located on Sapun Mountain and in Baidar Valley in Crimea. According RAPD and ITE molecular analysis we have estimated that the population of T. boeoticum on Sapun Mountain is genetically more impoverished than a population from the Baidar Valley. For preservation of maximal natural genetic polymorphism of the rare species it is recommended to direct efforts to preservations of a population of T. boeoticum from the Baidar Valley.

The Structure of the Distant Kuiper Belt in a Nice Model Scenario

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

Pike, R. E.; Shankman, C. J.; Kavelaars, J. J.

2017-03-01

This work explores the orbital distribution of minor bodies in the outer Solar System emplaced as a result of a Nice model migration from the simulations of Brasser and Morbidelli. This planetary migration scatters a planetesimal disk from between 29 and 34 au and emplaces a population of objects into the Kuiper Belt region. From the 2:1 Neptune resonance and outward, the test particles analyzed populate the outer resonances with orbital distributions consistent with trans-Neptunian object (TNO) detections in semimajor axis, inclination, and eccentricity, while capture into the closest resonances is too efficient. The relative populations of the simulated scatteringmore » objects and resonant objects in the 3:1 and 4:1 resonances are also consistent with observed populations based on debiased TNO surveys, but the 5:1 resonance is severely underpopulated compared to population estimates from survey results. Scattering emplacement results in the expected orbital distribution for the majority of the TNO populations; however, the origin of the large observed population in the 5:1 resonance remains unexplained.« less

Genetic structure of Zymoseptoria tritici in northern France at region, field, plant and leaf layer scales.

PubMed

Siah, Ali; Bomble, Myriam; Tisserant, Benoit; Cadalen, Thierry; Holvoet, Maxime; Hilbert, Jean-Louis; Halama, Patrice; Reignault, Philippe Lucien

2018-04-16

Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values ≥ 0.44 and haplotype frequencies ≥ 94 %) were found at all the examined scales. Such rates of diversity are likely due to an active sexual recombination in the investigated areas, as revealed by equal proportions of the two mating types scored in all sampled populations. Interestingly, a rare occurrence of clones among lesions from a same leaf, as well as among leaves from different plant leaf layers (e.g. upper vs lower leaves), was highlighted, indicating that ascospores contribute much more than expected to Z. tritci epidemics, compared to pycnidiospores. Population structure and AMOVA analyses revealed significant genetic differentiation at the regional scale (GST = 0.23) and, as expected, not at the other more local scales (GST ≤ 0.01). Further analyses using Bayesian and unweighted neighbor-joining statistical methods detected six genetic clusters within the regional population, overall distributed according to the locations from which the isolates were sampled. Neither clear directional relative migration linked to the geographical distribution of the locations, nor isolation by distance, were observed. Separate evolutionary trajectories caused by selection and adaptations to habitat heterogeneity could be the main forces shaping such structuration. This study provides new insights into the epidemiology and the genetic structure of Z. tritici at small local and, for the first time, at single plant and leaf layer scales. Such findings would be helpful in implementing effective control strategies.

Rank Regressions, Wage Distributions, and the Gender Gap.

ERIC Educational Resources Information Center

Fortin, Nicole M.; Lemieux, Thomas

1998-01-01

Current Population Survey data from 1979 and 1991 were used to decompose changes in the gender wage gap into three components: skill distribution, wage structure, and improvements in women's position. Relative wage gains by women may have been a source of increasing wage inequality among men. (SK)

Spatial Description of Drinking Water Bacterial Community Structures in Bulk Water Samples Collected in a Metropolitan Distribution System

EPA Science Inventory

The description of microorganisms inhabiting drinking water distribution systems has commonly been performed using techniques that are biased towards easy to culture bacterial populations. As most environmental microorganisms cannot be grown on artificial media, our understanding...

[The economically active population in Verviers during the industrial revolution. Part 2. The employed: economic distribution and demographic structures].

PubMed

Desama, C

1979-01-01

A study of the active population in Verviers during the 1st 1/2 of the 19th century shows that the distribution of immigrants into workers and nonworkers and among the different lines of activity takes place more in line with demographic factors than in line with the real needs of the economy. For instance, the changes in the demographic structure of the working population (younger people and larger numbers of women) removed any rigidity from the employment market. Each element of the production apparatus, including the service industries, was able to count on the human resources necessary for optimum functioning. The available surplus manpower, resulting from immigration, thus made it possible to reach the most profitable production level at the lowest salary costs at the work and technology conditions imposed by the company head. (author's)

Life in a rock pool: Radiation and population genetics of myxozoan parasites in hosts inhabiting restricted spaces.

PubMed

Bartošová-Sojková, Pavla; Lövy, Alena; Reed, Cecile C; Lisnerová, Martina; Tomková, Tereza; Holzer, Astrid S; Fiala, Ivan

2018-01-01

Intertidal rock pools where fish and invertebrates are in constant close contact due to limited space and water level fluctuations represent ideal conditions to promote life cycles in parasites using these two alternate hosts and to study speciation processes that could contribute to understanding the roles of parasitic species in such ecosystems. Gall bladder and liver samples from five clinid fish species (Blenniiformes: Clinidae) were morphologically and molecularly examined to determine the diversity, prevalence, distribution and host specificity of Ceratomyxa parasites (Cnidaria: Myxozoa) in intertidal habitats along the coast of South Africa. Phylogenetic relationships of clinid ceratomyxids based on the SSU rDNA, LSU rDNA and ITS regions were assessed additionally to the investigation of population genetic structure of Ceratomyxa cottoidii and subsequent comparison with the data known from type fish host Clinus cottoides. Seven Ceratomyxa species including previously described Ceratomyxa dehoopi and C. cottoidii were recognized in clinids. They represent a diverse group of rapidly evolving, closely related species with a remarkably high prevalence in their hosts, little host specificity and frequent concurrent infections, most probably as a result of parasite radiation after multiple speciation events triggered by limited host dispersal within restricted spaces. C. cottoidii represents the most common clinid parasite with a population structure characterized by young expanding populations in the south west and south east coast and by older populations in equilibrium on the west coast of its distribution. Parasite and fish host population structures show overlapping patterns and are very likely affected by similar oceanographic barriers possibly due to reduced host dispersal enhancing parasite community differentiation. While fish host specificity had little impact on parasite population structure, the habitat preference of the alternate invertebrate host as well as tidal water exchange may be additional crucial variables affecting the dispersal and associated population structure of C. cottoidii.

Life in a rock pool: Radiation and population genetics of myxozoan parasites in hosts inhabiting restricted spaces

PubMed Central

Reed, Cecile C.; Lisnerová, Martina; Tomková, Tereza; Holzer, Astrid S.; Fiala, Ivan

2018-01-01

Introduction Intertidal rock pools where fish and invertebrates are in constant close contact due to limited space and water level fluctuations represent ideal conditions to promote life cycles in parasites using these two alternate hosts and to study speciation processes that could contribute to understanding the roles of parasitic species in such ecosystems. Material and methods Gall bladder and liver samples from five clinid fish species (Blenniiformes: Clinidae) were morphologically and molecularly examined to determine the diversity, prevalence, distribution and host specificity of Ceratomyxa parasites (Cnidaria: Myxozoa) in intertidal habitats along the coast of South Africa. Phylogenetic relationships of clinid ceratomyxids based on the SSU rDNA, LSU rDNA and ITS regions were assessed additionally to the investigation of population genetic structure of Ceratomyxa cottoidii and subsequent comparison with the data known from type fish host Clinus cottoides. Results and discussion Seven Ceratomyxa species including previously described Ceratomyxa dehoopi and C. cottoidii were recognized in clinids. They represent a diverse group of rapidly evolving, closely related species with a remarkably high prevalence in their hosts, little host specificity and frequent concurrent infections, most probably as a result of parasite radiation after multiple speciation events triggered by limited host dispersal within restricted spaces. C. cottoidii represents the most common clinid parasite with a population structure characterized by young expanding populations in the south west and south east coast and by older populations in equilibrium on the west coast of its distribution. Parasite and fish host population structures show overlapping patterns and are very likely affected by similar oceanographic barriers possibly due to reduced host dispersal enhancing parasite community differentiation. While fish host specificity had little impact on parasite population structure, the habitat preference of the alternate invertebrate host as well as tidal water exchange may be additional crucial variables affecting the dispersal and associated population structure of C. cottoidii. PMID:29561884

Evidence for a population bottleneck in an Apicomplexan parasite of caribou and reindeer, Besnoitia tarandi

USDA-ARS?s Scientific Manuscript database

The evolutionary history and epidemiology of parasites may be reflected in the extent and geographic distribution of their genetic variation. Among coccidian parasites, the population structure of only Toxoplasma gondii has been extensively examined. Intraspecific variation in other coccidia, for ...

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.

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

PubMed Central

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

2016-01-01

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

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

PubMed Central

Vergara, María; Basto, Mafalda P.; Madeira, María José; Gómez-Moliner, Benjamín J.; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species. PMID:26222680

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study.

PubMed

Vergara, María; Basto, Mafalda P; Madeira, María José; Gómez-Moliner, Benjamín J; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

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.

Social and Population Structure in the Ant Cataglyphis emmae

PubMed Central

Jowers, Michael J.; Leniaud, Laurianne; Cerdá, Xim; Alasaad, Samer; Caut, Stephane; Amor, Fernando; Aron, Serge; Boulay, Raphaël R.

2013-01-01

Dispersal has consequences not only for individual fitness, but also for population dynamics, population genetics and species distribution. Social Hymenoptera show two contrasting colony reproductive strategies, dependent and independent colony foundation modes, and these are often associated to the population structures derived from inter and intra-population gene flow processes conditioned by alternative dispersal strategies. Here we employ microsatellite and mitochondrial markers to investigate the population and social genetic structure and dispersal patterns in the ant Cataglyphis emmae at both, local and regional scales. We find that C. emmae is monogynous and polyandrous. Lack of detection of any population viscosity and population structure with nuclear markers at the local scale suggests efficient dispersal, in agreement with a lack of inbreeding. Contrasting demographic differences before and during the mating seasons suggest that C. emmae workers raise sexuals in peripheric nest chambers to reduce intracolonial conflicts. The high genetic differentiation recovered from the mtDNA haplotypes, together with the significant correlation of such to geographic distance, and presence of new nuclear alleles between areas (valleys) suggest long-term historical isolation between these regions, indicative of limited dispersal at the regional scale. Our findings on the ecological, social and population structure of this species increases our understanding of the patterns and processes involved under independent colony foundation. PMID:24039827

Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation

PubMed Central

Zhang, Jinju; Li, Zuozhou; Fritsch, Peter W.; Tian, Hua; Yang, Aihong; Yao, Xiaohong

2015-01-01

Background and Aims The phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management. Methods Samples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM). Key Results A low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests. Conclusions Climatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for this endangered species. PMID:26187222

Phylogeography and genetic structure of a Tertiary relict tree species, Tapiscia sinensis (Tapisciaceae): implications for conservation.

PubMed

Zhang, Jinju; Li, Zuozhou; Fritsch, Peter W; Tian, Hua; Yang, Aihong; Yao, Xiaohong

2015-10-01

The phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management. Samples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM). A low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests. Climatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for this endangered species. © 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.

Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

USDA-ARS?s Scientific Manuscript database

The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To decipher the cosmopolitan distribution of this fungus, the population genetic structure of 17 geographic samples was investigated from four continental regions (Australia, California, Europ...

77 FR 19645 - Marine Mammals; File No. 16111

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-02

... abundance, distribution, population structure, habitat use, social structure, movement patterns, diving behavior, and diet. The proposed project would also assess the impact of human activities such as ship strikes, noise exposure, contaminants, and fishery interactions on marine mammals. Focal species are blue...

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

PubMed

Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

2017-01-01

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.

[Characteristics of the genetic structure of parasite and host populations by the example of helminthes from moor frog Rana arvalis Nilsson].

PubMed

Zhigalev, O N

2010-01-01

The genetic structure of populations of four helminth species from moor frog Rana arvalis, in comparison with the population-genetic structure of the host, has been studied with the gel-electrophoresis method. As compared with the host, parasites are characterized by more distinct deviation from the balance of genotypic frequencies and higher level of interpopulation genetic differences. The genetic variability indices in the three of four frog helminthes examined are lower than those in the host. Moreover, these indices are lower than the average indices typical of free-living invertebrates; this fact contradicts the opinion on polyhostality of these helminthes and their wide distribution.

Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor

PubMed Central

Naydenov, Krassimir; Senneville, Sauphie; Beaulieu, Jean; Tremblay, Francine; Bousquet, Jean

2007-01-01

Background At the last glacial maximum, Fennoscandia was covered by an ice sheet while the tundra occupied most of the rest of northern Eurasia. More or less disjunct refugial populations of plants were dispersed in southern Europe, often trapped between mountain ranges and seas. Genetic and paleobotanical evidences indicate that these populations have contributed much to Holocene recolonization of more northern latitudes. Less supportive evidence has been found for the existence of glacial populations located closer to the ice margin. Scots pine (Pinus sylvestris L.) is a nordic conifer with a wide natural range covering much of Eurasia. Fractures in its extant genetic structure might be indicative of glacial vicariance and how different refugia contributed to the current distribution at the continental level. The population structure of Scots pine was investigated on much of its Eurasian natural range using maternally inherited mitochondrial DNA polymorphisms. Results A novel polymorphic region of the Scots pine mitochondrial genome has been identified, the intron 1 of nad7, with three variants caused by insertions-deletions. From 986 trees distributed among 54 populations, four distinct multi-locus mitochondrial haplotypes (mitotypes) were detected based on the three nad7 intron 1 haplotypes and two previously reported size variants for nad1 intron B/C. Population differentiation was high (GST = 0.657) and the distribution of the mitotypes was geographically highly structured, suggesting at least four genetically distinct ancestral lineages. A cosmopolitan lineage was widely distributed in much of Europe throughout eastern Asia. A previously reported lineage limited to the Iberian Peninsula was confirmed. A new geographically restricted lineage was found confined to Asia Minor. A new lineage was restricted to more northern latitudes in northeastern Europe and the Baltic region. Conclusion The contribution of the various ancestral lineages to the current distribution of Scots pine was asymmetric and extant endemism reflected the presence of large geographic barriers to migration. The results suggest a complex biogeographical history with glacial refugia shared with temperate plant species in southern European Peninsulas and Asia Minor, and a genetically distinct glacial population located more North. These results confirm recent observations for cold tolerant species about the possible existence of refugial populations at mid-northern latitudes contributing significantly to the recolonization of northern Europe. Thus, Eurasian populations of nordic plant species might not be as genetically homogenous as assumed by simply considering them as offsets of glacial populations located in southern peninsulas. As such, they might have evolved distinctive genetic adaptations during glacial vicariance, worth evaluating and considering for conservation. PMID:18034901

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

PubMed

Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

Genetic diversity and structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China.

PubMed

Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

2014-01-01

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation.

Genetic Diversity and Structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China

PubMed Central

Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

2014-01-01

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation. PMID:25333788

Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa

PubMed Central

Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania

2016-01-01

Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica. PMID:27077002

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

PubMed Central

Shringarpure, Suyash; Xing, Eric P.

2014-01-01

Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

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...

Anthropogenics: Human influence on global and genetic homogenization of parasite populations

USDA-ARS?s Scientific Manuscript database

The distribution, abundance, and diversity of life on Earth have been greatly shaped by human activities. This is no truer than in the geographic expansion of parasites; however, measuring the extent to which humans have influenced the dissemination and population structure of parasites has been cha...

REGION-WIDE GENETIC STRUCTURE OF THE CENTRAL STONEROLLER (CAMPOSTOMA ANOMALUM) AND THE RELATIONSHIP OF GENETIC DIVERSITY TO ENVIRONMENTAL QUALITY

EPA Science Inventory

Anthropogenic stressors that reduce population size, alter migration corridors or modify mutational and selective forces on populations are expected to leave a lasting genetic footprint on the distribution of intraspecific genetic variation. Thus, the pattern of intraspecific gen...

Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India.

PubMed

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; Navya, R; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-10-29

Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F(ST) of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.

Ecology Driving Genetic Variation: A Comparative Phylogeography of Jungle Cat (Felis chaus) and Leopard Cat (Prionailurus bengalensis) in India

PubMed Central

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; R, Navya; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-01-01

Background Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. Methodology/Principal Findings We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Conclusions/Significance Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention. PMID:21060831

Peanut-shaped metallicity distributions in bulges of edge-on galaxies: the case of NGC 4710

NASA Astrophysics Data System (ADS)

Gonzalez, Oscar A.; Debattista, Victor P.; Ness, Melissa; Erwin, Peter; Gadotti, Dimitri A.

2017-03-01

Bulges of edge-on galaxies are often boxy/peanut-shaped (B/PS), and unsharp masks reveal the presence of an X shape. Simulations show that these shapes can be produced by dynamical processes driven by a bar which vertically thickens the centre. In the Milky Way, which contains such a B/PS bulge, the X-shaped structure is traced by the metal-rich stars but not by the metal-poor ones. Recently, Debattista et al. interpreted this property as a result of the varying effect of the bar on stellar populations with different starting kinematics. This kinematic fractionation model predicts that cooler populations at the time of bar formation go on to trace the X shape, whereas hotter populations are more uniformly distributed. As this prediction is not specific to the Milky Way, we test it with Multi Unit Spectroscopic Explorer (MUSE) observations of the B/PS bulge in the nearby galaxy NGC 4710. We show that the metallicity map is more peanut-shaped than the density distribution itself, in good agreement with the prediction. This result indicates that the X-shaped structure in B/PS bulges is formed of relatively metal-rich stars that have been vertically redistributed by the bar, whereas the metal-poor stars have a more uniform, box-shaped distribution.

Two distinct mtDNA lineages of the blue crab reveal large-scale population structure in its native Atlantic distribution

NASA Astrophysics Data System (ADS)

Alaniz Rodrigues, Marcos; Dumont, Luiz Felipe Cestari; dos Santos, Cléverson Rannieri Meira; D'Incao, Fernando; Weiss, Steven; Froufe, Elsa

2017-10-01

For the first time, a molecular approach was used to evaluate the phylogenetic structure of the disjunct native American distribution of the blue crab Callinectes sapidus. Population structure was investigated by sequencing 648bp of the Cytochrome oxidase subunit 1 (COI), in a total of 138 sequences stemming from individual samples from both the northern and southern hemispheres of the Western Atlantic distribution of the species. A Bayesian approach was used to construct a phylogenetic tree for all samples, and a 95% confidence parsimony network was created to depict the relationship among haplotypes. Results revealed two highly distinct lineages, one containing all samples from the United States and some from Brazil (lineage 1) and the second restricted to Brazil (lineage 2). In addition, gene flow (at least for females) was detected among estuaries at local scales and there is evidence for shared haplotypes in the south. Furthermore, the findings of this investigation support the contemporary introduction of haplotypes that have apparently spread from the south to the north Atlantic.

Reliability and validity analysis of modified Nursing Stress Scale for Indian population.

PubMed

Pathak, Vasundhara; Chakraborty, Tania; Mukhopadhyay, Suman

2013-01-01

The original Nursing Stress Scale (NSS) was structurally modified according to results of factorial analysis and a new scale was named as modified nursing stress scale (MNSS). This is the first study to modify and validate NSS for Indian nursing population. Factorial analysis showed different factor loading for two subscales and items were shifted according to their loading to provide a more meaningful structure. After relocation of Items 13, 14, and 15 into first factor, this factor was renamed as "emotional and painful conditions of patients" to provide a more appropriate name to the first factor. Items 24, 25, 26, 27, 28, and 29 were found to be distributed under two different factors; one of these two was renamed as "unpredictable changes" and another retained its original name (i.e., workload). This distribution was also supported by rational analysis. All other items were distributed under factors as in the original scale. Rest of the validity assessment was done with the modified scale. Thus, with minor changes in structure, the scale was found to have better content validity.

Analysis of B3LYP and MP2 conformational population distributions in trans-nicotine, acetylcholine, and ABT-594

NASA Astrophysics Data System (ADS)

Mora, M.; Castro, M. E.; Niño, A.; Melendez, F. J.; Muñoz-Caro, C.

This work presents an analysis of the equivalence of MP2 and DFT (B3LYP functional) conformational populations. As a test case, we select three cholinergic agents (trans-nicotine, acetylcholine, and the nicotinic analgesic ABT-594), where the minima on the conformational energy hypersurfaces expand a large range of energies (˜0-30 kJ mol-1). From energetic and structural data obtained in vacuo at the MP2 and B3LYP/cc-pVDZ levels, we build conformational partition functions, including the effect of the conformational kinetic energy and the rotovibrational coupling. Our results at a physiological temperature (37°C) show qualitative agreement in all cases. Quantitative agreement, however, is only found for trans-nicotine and ABT-594. In the first case, energy minima differ by <0.2 kJ mol-1. Therefore, the equivalence of structural results translates in the equivalence of the conformational distribution. For ABT-594, the minima are separated by as much as 8.0 kJ mol-1, and the conformational energy determines the conformational distribution. In this case, the slight relative variation of conformational energy, between B3LYP and MP2, does not affect the population, since the secondary minima are high in energy and very low in population.

Spatial distribution of Illex argentinus in San Matias Gulf (Northern Patagonia, Argentina) in relation to environmental variables: A contribution to the new interpretation of the population structuring

NASA Astrophysics Data System (ADS)

Crespi-Abril, Augusto C.; Morsan, Enrique M.; Williams, Gabriela N.; Gagliardini, Domingo A.

2013-03-01

Traditionally, it was assumed that major spawning activity of Illex argentinus occurs in discrete pulses along the outer-shelf/slope off Argentina/southern Brazil during late-fall/winter and that early life stages develop near the Brazil-Malvinas Confluence (BMC). However, a novel hypothesis of the population structuring of the species was proposed that states that coastal waters may be important as spawning and feeding grounds. Here, we analyzed the spatial distribution of Illex argentinus inside San Matias Gulf based on the position of the CPUE of jiggers in order to improve the knowledge of the population structuring in coastal regions. Squids were mainly concentrated on the northern region of the gulf where favorable oceanographic conditions (e.g. water stratification, chlorophyll-a concentration peaks) to feeding and spawning are present. These results provided empirical evidences that individuals of I. argentinus use Argentinean coastal waters, particularly San Matias Gulf, as permanent feeding and spawning grounds which supports the new hypothesis.

Geographic Population Structure in Epstein-Barr Virus Revealed by Comparative Genomics

PubMed Central

Chiara, Matteo; Manzari, Caterina; Lionetti, Claudia; Mechelli, Rosella; Anastasiadou, Eleni; Chiara Buscarinu, Maria; Ristori, Giovanni; Salvetti, Marco; Picardi, Ernesto; D’Erchia, Anna Maria; Pesole, Graziano; Horner, David S.

2016-01-01

Epstein-Barr virus (EBV) latently infects the majority of the human population and is implicated as a causal or contributory factor in numerous diseases. We sequenced 27 complete EBV genomes from a cohort of Multiple Sclerosis (MS) patients and healthy controls from Italy, although no variants showed a statistically significant association with MS. Taking advantage of the availability of ∼130 EBV genomes with known geographical origins, we reveal a striking geographic distribution of EBV sub-populations with distinct allele frequency distributions. We discuss mechanisms that potentially explain these observations, and their implications for understanding the association of EBV with human disease. PMID:27635051

Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country.

PubMed

Pumpaibool, Tepanata; Arnathau, Céline; Durand, Patrick; Kanchanakhan, Naowarat; Siripoon, Napaporn; Suegorn, Aree; Sitthi-Amorn, Chitr; Renaud, François; Harnyuttanakorn, Pongchai

2009-07-14

The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites). Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 +/- 0.17), where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai populations during this study. Comparison of the genetic structure of P. falciparum populations in Thailand with those in the French Guyana, Congo and Cameroon revealed a significant genetic differentiation between all of them, except the two African countries, whilst the genetic variability of P. falciparum amongst countries showed overlapping distributions. Plasmodium falciparum shows genetically structured populations across local areas of Thailand. Although Thailand is considered to be a low transmission area, a relatively high level of genetic diversity and no linkage disequilibrium was found in five of the studied areas, the exception being the Yala province (Southern peninsular Thailand), where a clonal population structure was revealed and in Kanchanaburi province (Western Thailand). This finding is particularly relevant in the context of malaria control, because it could help in understanding the special dynamics of parasite populations in areas with different histories of, and exposure to, drug regimens.

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.

Population genetic structure of a California endemic Branchiopod, Branchinecta sandiegonensis

USGS Publications Warehouse

Davies, Cathleen P.; Simovich, Marie A.; Hathaway, Stacie A.

1997-01-01

Branchinecta sandiegonensis (Crustacea: Anostraca) is a narrow range endemic fairy shrimp discontinuously distributed in ephemeral pools on coastal mesas in San Diego County, USA. Ten populations across the range of the species were subjected to allozyme analysis for eleven loci. The species exhibits low variability (P95 =9.1–45.5) and one third of the loci tested did not conform to Hardy-Weinberg equilibrium expectations. The species also exhibited a high degree of genetic differentiation between populations. F ST values (fixation index) for most pairs of populations were above 0.25 (0.036–0.889).Low genetic variability and high genetic structure may result from low gene flow and founder effects due to habitat fragmentation and the lack of potential vectors for cyst dispersal. The unpredictable rainfall of the region also creates potential for variable population sizes which could affect structure and variability.

Spatial and temporal distribution of the vibrionaceae in coastal waters of Hawaii, Australia, and France.

PubMed

Jones, B W; Maruyama, A; Ouverney, C C; Nishiguchi, M K

2007-08-01

Relatively little is known about large-scale spatial and temporal fluctuations in bacterioplankton, especially within the bacterial families. In general, however, a number of abiotic factors (namely, nutrients and temperature) appear to influence distribution. Community dynamics within the Vibrionaceae are of particular interest to biologists because this family contains a number of important pathogenic, commensal, and mutualist species. Of special interest to this study is the mutualism between sepiolid squids and Vibrio fischeri and Vibrio logei, where host squids seed surrounding waters daily with their bacterial partners. This study seeks to examine the spatial and temporal distribution of the Vibrionaceae with respect to V. fischeri and V. logei in Hawaii, southeastern Australia, and southern France sampling sites. In particular, we examine how the presence of sepiolid squid hosts influences community population structure within the Vibrionaceae. We found that abiotic (temperature) and biotic (host distribution) factors both influence population dynamics. In Hawaii, three sites within squid host habitat contained communities of Vibrionaceae with higher proportions of V. fischeri. In Australia, V. fischeri numbers at host collection sites were greater than other populations; however, there were no spatial or temporal patterns seen at other sample sites. In France, host presence did not appear to influence Vibrio communities, although sampled populations were significantly greater in the winter than summer sampling periods. Results of this study demonstrate the importance of understanding how both abiotic and biotic factors interact to influence bacterial community structure within the Vibrionaceae.

Cell population modelling of yeast glycolytic oscillations.

PubMed Central

Henson, Michael A; Müller, Dirk; Reuss, Matthias

2002-01-01

We investigated a cell-population modelling technique in which the population is constructed from an ensemble of individual cell models. The average value or the number distribution of any intracellular property captured by the individual cell model can be calculated by simulation of a sufficient number of individual cells. The proposed method is applied to a simple model of yeast glycolytic oscillations where synchronization of the cell population is mediated by the action of an excreted metabolite. We show that smooth one-dimensional distributions can be obtained with ensembles comprising 1000 individual cells. Random variations in the state and/or structure of individual cells are shown to produce complex dynamic behaviours which cannot be adequately captured by small ensembles. PMID:12206713

Establishing conservation baselines with dynamic distribution models for bat populations facing imminent decline

USGS Publications Warehouse

Rodhouse, Thomas J.; Ormsbee, Patricia C.; Irvine, Kathryn M.; Vierling, Lee A.; Szewczak, Joseph M.; Vierling, Kerri T.

2015-01-01

Landscape keystone structures associated with roosting habitat emerged as regionally important predictors of bat distributions. The challenges of bat monitoring have constrained previous species distribution modelling efforts to temporally static presence-only approaches. Our approach extends to broader spatial and temporal scales than has been possible in the past for bats, making a substantial increase in capacity for bat conservation.

Changes in Urban-Rural Social Structure and Distribution of High School Educational Opportunities--An Analysis Based on Middle School Graduation Education Tracking in Q County, Gansu

ERIC Educational Resources Information Center

Baoyan, Yang; Minggang, Wan

2015-01-01

To a certain extent, the distribution of high school education opportunities among the population determines the stratification of high school education opportunities. The researchers examined the distribution of high school education opportunities within the county region based on survey data on middle school graduation education tracking in Q…

Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares).

PubMed

Pecoraro, Carlo; Babbucci, Massimiliano; Villamor, Adriana; Franch, Rafaella; Papetti, Chiara; Leroy, Bruno; Ortega-Garcia, Sofia; Muir, Jeff; Rooker, Jay; Arocha, Freddy; Murua, Hilario; Zudaire, Iker; Chassot, Emmanuel; Bodin, Nathalie; Tinti, Fausto; Bargelloni, Luca; Cariani, Alessia

2016-02-01

Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated genetic structuring at a much smaller geographic scales than previously considered, pointing out that YFT population genetic structure has not been properly assessed so far. In this study, we demonstrated for the first time, the utility of 2b-RAD genotyping technique for investigating population genetic diversity and differentiation in high gene-flow species. Running de novo pipeline in Stacks, a total of 6772 high-quality genome-wide SNPs were identified across Atlantic, Indian and Pacific population samples representing all major distribution areas. Preliminary analyses showed shallow but significant population structure among oceans (FST=0.0273; P-value<0.01). Discriminant Analysis of Principal Components endorsed the presence of genetically discrete yellowfin tuna populations among three oceanic pools. Although such evidence needs to be corroborated by increasing sample size, these results showed the efficiency of this genotyping technique in assessing genetic divergence in a marine fish with high dispersal potential. Copyright © 2015 Elsevier B.V. All rights reserved.

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens).

PubMed

Oliveira, Larissa Rosa de; Gehara, Marcelo C M; Fraga, Lúcia D; Lopes, Fernando; Túnez, Juan Ignacio; Cassini, Marcelo H; Majluf, Patricia; Cárdenas-Alayza, Susana; Pavés, Héctor J; Crespo, Enrique Alberto; García, Nestor; Loizaga de Castro, Rocío; Hoelzel, A Rus; Sepúlveda, Maritza; Olavarría, Carlos; Valiati, Victor Hugo; Quiñones, Renato; Pérez-Alvarez, Maria Jose; Ott, Paulo Henrique; Bonatto, Sandro L

2017-01-01

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean.

Using particle dispersal models to assist in the conservation and recovery of the overexploited native oyster (Ostrea edulis) in an enclosed sea lough

NASA Astrophysics Data System (ADS)

Smyth, David; Kregting, Louise; Elsäßer, Björn; Kennedy, Richard; Roberts, Dai

2016-02-01

Oyster populations around the world have seen catastrophic decline which has been largely attributed to overexploitation, disease and pollution. While considerable effort and resources have been implemented into restoring these important environmental engineers, the success of oyster populations is often limited by poor understanding of site-specific dispersal patterns of propagules. Water-borne transport is a key factor controlling or regulating the dispersal of the larval stage of benthic marine invertebrates which have limited mobility. The distribution of the native oyster Ostrea edulis in Strangford Lough, Northern Ireland, together with their densities and population structure at subtidal and intertidal sites has been documented at irregular intervals between 1997 and 2013. This paper revisits this historical data and considers whether different prevailing environmental conditions can be used to explain the distribution, densities and population structure of O. edulis in Strangford Lough. The approach adopted involved comparing predictive 2D hydrodynamic models coupled with particle tracking to simulate the dispersal of oyster larvae with historical and recent field records of the distribution of both subtidal and intertidal, populations since 1995. Results from the models support the hypothesis that commercial stocks of O. edulis introduced into Strangford Lough in the 1990s resulted in the re-establishment of wild populations of oysters in the Northern Basin which in turn provided a potential source of propagules for subtidal populations. These results highlight that strategic site selection (while inadvertent in the case of the introduced population in 1995) for the re-introduction of important shellfish species can significantly accelerate their recovery and restoration.

Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens)

PubMed Central

Gehara, Marcelo C. M.; Fraga, Lúcia D.; Lopes, Fernando; Túnez, Juan Ignacio; Cassini, Marcelo H.; Majluf, Patricia; Cárdenas-Alayza, Susana; Pavés, Héctor J.; Crespo, Enrique Alberto; García, Nestor; Loizaga de Castro, Rocío; Hoelzel, A. Rus; Sepúlveda, Maritza; Olavarría, Carlos; Valiati, Victor Hugo; Quiñones, Renato; Pérez-Alvarez, Maria Jose; Ott, Paulo Henrique

2017-01-01

The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean. PMID:28654647

The demographic consequences of growing older and bigger in oyster populations.

PubMed

Moore, Jacob L; Lipcius, Romuald N; Puckett, Brandon; Schreiber, Sebastian J

2016-10-01

Structured population models, particularly size- or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age- and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age- and size-structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean. We analyzed sensitivity of model results across values of local retention that give populations decreasing in size to populations increasing in size. We found that age- and size-structured models yielded the best fit to the demographic data and provided more reliable results about long-term demography. Elasticity analysis showed that population growth rate was most sensitive to changes in the survival of both large (>175 mm shell length) and small (<75 mm shell length) oysters, indicating that a maximum size limit, in addition to a minimum size limit, could be an effective strategy for maintaining a sustainable population. In contrast, the purely size-structured model did not detect the importance of large individuals. Finally, patterns in stable age and stable size distributions differed between populations decreasing in size due to limited local retention and populations increasing in size due to high local retention. These patterns can be used to determine population status and restoration success. The methodology described here provides general insight into the necessity of including both age- and size-structure into modeling frameworks when using population models to inform restoration and management decisions. © 2016 by the Ecological Society of America.

Population structure of the hydrocoral Millepora platyphylla in habitats experiencing different flow regimes in Moorea, French Polynesia

PubMed Central

Mercière, Alexandre; Vermeij, Mark J. A.; Planes, Serge

2017-01-01

While the fire coral Millepora platyphylla is an important component of Indo-Pacific reefs, where it thrives in a wide range of environments, the ecological and biological processes driving its distribution and population structure are not well understood. Here, we quantified this species’ population structure in five habitats with contrasting hydrodynamic regimes in Moorea, French Polynesia; two in the fore reef: mid and upper slopes, and three in the lagoon: back, fringing and patch reefs. A total of 3651 colonies of fire corals were mapped and measured over 45,000 m2 of surveyed reef. Due to the species’ sensitivity to fragmentation in response to strong water movement, hydrodynamic conditions (e.g. waves, pass and lagoonal circulation) corresponded to marked differences in colony size distributions, morphology and recruitment dynamics among habitats. The size structure varied among reef habitats with higher proportions of larger colonies in calm nearshore reefs (fringing and patch reefs), while populations were dominated by smaller colonies in the exposed fore reefs. The highest densities of fire corals were recorded in fore reef habitats (0.12–0.20 n.m-2) where the proportion of recruits and juveniles was higher at mid slope populations (49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, most colonies grew as vertical sheets on encrusting bases making them more vulnerable to colony fragmentation, whereas fire corals were encrusting or massive in all other habitats. The lowest densities of M. platyphylla occurred in lagoonal habitats (0.02–0.04 n.m-2) characterized by a combination of low water movement and other physical and biological stressors. This study reports the first evidence of population structure of fire corals in two common reef environments and illustrates the importance of water flow in driving population dynamic processes of these reef-building species. PMID:28273119

Population structure of the hydrocoral Millepora platyphylla in habitats experiencing different flow regimes in Moorea, French Polynesia.

PubMed

Dubé, Caroline E; Mercière, Alexandre; Vermeij, Mark J A; Planes, Serge

2017-01-01

While the fire coral Millepora platyphylla is an important component of Indo-Pacific reefs, where it thrives in a wide range of environments, the ecological and biological processes driving its distribution and population structure are not well understood. Here, we quantified this species' population structure in five habitats with contrasting hydrodynamic regimes in Moorea, French Polynesia; two in the fore reef: mid and upper slopes, and three in the lagoon: back, fringing and patch reefs. A total of 3651 colonies of fire corals were mapped and measured over 45,000 m2 of surveyed reef. Due to the species' sensitivity to fragmentation in response to strong water movement, hydrodynamic conditions (e.g. waves, pass and lagoonal circulation) corresponded to marked differences in colony size distributions, morphology and recruitment dynamics among habitats. The size structure varied among reef habitats with higher proportions of larger colonies in calm nearshore reefs (fringing and patch reefs), while populations were dominated by smaller colonies in the exposed fore reefs. The highest densities of fire corals were recorded in fore reef habitats (0.12-0.20 n.m-2) where the proportion of recruits and juveniles was higher at mid slope populations (49.3%) than on the upper slope near where waves break (29.0%). In the latter habitat, most colonies grew as vertical sheets on encrusting bases making them more vulnerable to colony fragmentation, whereas fire corals were encrusting or massive in all other habitats. The lowest densities of M. platyphylla occurred in lagoonal habitats (0.02-0.04 n.m-2) characterized by a combination of low water movement and other physical and biological stressors. This study reports the first evidence of population structure of fire corals in two common reef environments and illustrates the importance of water flow in driving population dynamic processes of these reef-building species.

Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

PubMed

Peacock, Mary M; Gustin, Mae S; Kirchoff, Veronica S; Robinson, Morgan L; Hekkala, Evon; Pizzarro-Barraza, Claudia; Loux, Tim

2016-09-01

In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2018-01-01

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

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

PubMed Central

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

2018-01-01

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

Nucleotide variation in the mitochondrial genome provides evidence for dual routes of postglacial recolonization and genetic recombination in the northeastern brook trout (Salvelinus fontinalis).

PubMed

Pilgrim, B L; Perry, R C; Barron, J L; Marshall, H D

2012-09-26

Levels and patterns of mitochondrial DNA (mtDNA) variation were examined to investigate the population structure and possible routes of postglacial recolonization of the world's northernmost native populations of brook trout (Salvelinus fontinalis), which are found in Labrador, Canada. We analyzed the sequence diversity of a 1960-bp portion of the mitochondrial genome (NADH dehydrogenase 1 gene and part of cytochrome oxidase 1) of 126 fish from 32 lakes distributed throughout seven regions of northeastern Canada. These populations were found to have low levels of mtDNA diversity, a characteristic trait of populations at northern extremes, with significant structuring at the level of the watershed. Upon comparison of northeastern brook trout sequences to the publicly available brook trout whole mitochondrial genome (GenBank AF154850), we infer that the GenBank sequence is from a fish whose mtDNA has recombined with that of Arctic charr (S. alpinus). The haplotype distribution provides evidence of two different postglacial founding groups contributing to present-day brook trout populations in the northernmost part of their range; the evolution of the majority of the haplotypes coincides with the timing of glacier retreat from Labrador. Our results exemplify the strong influence that historical processes such as glaciations have had on shaping the current genetic structure of northern species such as the brook trout.

Population estimates of extended family structure and size.

PubMed

Garceau, Anne; Wideroff, Louise; McNeel, Timothy; Dunn, Marsha; Graubard, Barry I

2008-01-01

Population-based estimates of biological family size can be useful for planning genetic studies, assessing how distributions of relatives affect disease associations with family history and estimating prevalence of potential family support. Mean family size per person is estimated from a population-based telephone survey (n = 1,019). After multivariate adjustment for demographic variables, older and non-White respondents reported greater mean numbers of total, first- and second-degree relatives. Females reported more total and first-degree relatives, while less educated respondents reported more second-degree relatives. Demographic differences in family size have implications for genetic research. Therefore, periodic collection of family structure data in representative populations would be useful. Copyright 2008 S. Karger AG, Basel.

Population structure of Angiostrongylus cantonensis (Nematoda: Metastrongylidae) in Thailand based on PCR-RAPD markers.

PubMed

Thaenkham, Urusa; Pakdee, Wallop; Nuamtanong, Supaporn; Maipanich, Wanna; Pubampen, Somchit; Sa-Nguankiat, Surapol; Komalamisra, Chalit

2012-05-01

Angiostrongylus cantonensis is the causative agent of angiostrongyliasis, which is widely distributed throughout the world. It can specifically infect many species of intermediate and definitive hosts. This study examined the genetic differentiation and population structure using the RAPD-PCR method of parasites obtained from 8 different geographical areas of Thailand. Based on 8 primers, high levels of genetic diversity and low levels of gene flow among populations were found. Using genetic distance and neighbor-joining dendrogram methods, A. cantonensis in Thailand could be divided into two groups with statistically significant genetic differentiation of the two populations. However, genotypic variations and haplotype relationships need to be further elucidated using other markers.

On the effects of suprathermal populations in dusty plasmas: The case of dust-ion-acoustic waves

NASA Astrophysics Data System (ADS)

Lazar, M.; Kourakis, I.; Poedts, S.; Fichtner, H.

2018-07-01

Suprathermal populations with energetic distributions deviating from a standard Maxwellian are ubiquitous in dusty plasmas from space environments, as a proof that these systems are out of thermal equilibrium. The excess of free energy may have important implications in the relaxation processes by the plasma waves and fluctuations, as well as in their dissipation. In order to emphasize the effects of suprathermal populations a new realistic interpretation is proposed on the basis of an advanced Kappa modeling in accord with the observations. This article is focused on the kinetic description of dust-modified ion acoustic (DIA) waves in the presence of Kappa-distributed (suprathermal) particles. Our methodology follows closely recent considerations on the structural characteristics of Kappa distributions, contrasting the high-energy tails enhanced by the suprathermal populations with the Maxwellian (thermal) core of the distribution. The effects on DIA waves are found to be highly dependent on the nature of suprathermal particles: both the wave-frequency and Landau damping rate are inhibited by the suprathermal electrons, while the suprathermal ions have an opposite influence.

Marketing and population problems.

PubMed

Farley, J U; Leavitt, H J

1971-07-01

There are many elements in population programs that are more familiar to marketing men than to some population experts. Advertising is essential to reach the target population, and advertising evaluation techniques (e.g., surrogate indexes or audience measures) might be useful for evaluating both population information activities and the import of the entire program. Fundamental research on basid demand for fertility control is needed and a marketer's experience with planning and evaluating test markets can be useful in assessing potential selling targets and evaluating alternative promotional and distributional strategies. Special family planning clinics have certain disadvantages: expensive and scarce personnel are needed; red tape may be present; the network is based on the assumption that the client is willing to travel relatively great distances repeatedly; and clinics lack anonymity which may scare potential acceptors away. Most developing cultures have an intensively functioning distribution structure which delivers basic commodities to the most remote areas, providing relatively anonymous outlets that are physically close to the customs. Materials requiring a prescription might be distributed in exchange for script issued at and ultimately redeemed by clinics, this requiring only an occasional visit to a clinic. Mail-order service can be used to supplement a clinic's distribution of some contraceptives. It should be remembered that population administrators often have an antipathetic view toward business and marketing and "suspect" the profit motive.

Conformation Types of Ubiquitin [M+8H]8+ Ions from Water:Methanol Solutions: Evidence for the N and A States in Aqueous Solution

PubMed Central

Shi, Huilin; Pierson, Nicholas A.; Valentine, Stephen J.; Clemmer, David E.

2012-01-01

Ion mobility and mass spectrometry measurements are used to examine the gas-phase populations of [M+8H]8+ ubiquitin ions formed upon electrospraying 20 different solutions: from 100:0 to 5:95 water:methanol that are maintained at pH = 2.0. Over this range of solution conditions, mobility distributions for the +8 charge state show substantial variations. Here we develop a model that treats the combined measurements as one data set. By varying the relative abundances of a discrete set of conformation types, it is possible to represent distributions obtained from any solution. For solutions that favor the well-known A-state ubiquitin, it is possible to represent the gas-phase distributions with seven conformation types. Aqueous conditions that favor the native structure require four more structural types to represent the distribution. This analysis provides the first direct evidence for trace amounts of the A state under native conditions. The method of analysis presented here should help illuminate how solution populations evolve into new gas-phase structures as solvent is removed. Evidence for trace quantities of previously unknown states under native solution conditions may provide insight about the relationship of dynamics to protein function as well as misfolding and aggregation phenomena. PMID:22315998

Population declines lead to replicate patterns of internal range structure at the tips of the distribution of the California red-legged frog (Rana draytonii)

USGS Publications Warehouse

Richmond, Jonathan Q.; Backlin, Adam R.; Tatarian, Patricia J.; Solvesky, Ben G.; Fisher, Robert N.

2014-01-01

Demographic declines and increased isolation of peripheral populations of the threatened California red-legged frog (Rana draytonii) have led to the formation of internal range boundaries at opposite ends of the species’ distribution. While the population genetics of the southern internal boundary has been studied in some detail, similar information is lacking for the northern part of the range. In this study, we used microsatellite and mtDNA data to examine the genetic structuring and diversity of some of the last remaining R. draytonii populations in the northern Sierra Nevada, which collectively form the northern external range boundary. We compared these data to coastal populations in the San Francisco Bay Area, where the species is notably more abundant and still exists throughout much of its historic range. We show that ‘external’ Sierra Nevada populations have lower genetic diversity and are more differentiated from one another than their ‘internal’ Bay Area counterparts. This same pattern was mirrored across the distribution in California, where Sierra Nevada and Bay Area populations had lower allelic variability compared to those previously studied in coastal southern California. This genetic signature of northward range expansion was mirrored in the phylogeography of mtDNA haplotypes; northern Sierra Nevada haplotypes showed greater similarity to haplotypes from the south Coast Ranges than to the more geographically proximate populations in the Bay Area. These data cast new light on the geographic origins of Sierra Nevada R. draytonii populations and highlight the importance of distinguishing the genetic effects of contemporary demographic declines from underlying signatures of historic range expansion when addressing the most immediate threats to population persistence. Because there is no evidence of contemporary gene flow between any of the Sierra Nevada R. draytonii populations, we suggest that management activities should focus on maintaining and creating additional ponds to support breeding within typical dispersal distances of occupied habitat.

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

PubMed Central

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

2012-01-01

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

Tetraploid Wheat Landraces in the Mediterranean Basin: Taxonomy, Evolution and Genetic Diversity

PubMed Central

Oliveira, Hugo R.; Campana, Michael G.; Jones, Huw; Hunt, Harriet V.; Leigh, Fiona; Redhouse, David I.; Lister, Diane L.; Jones, Martin K.

2012-01-01

The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields. PMID:22615891

Krill population dynamics in the Scotia Sea: variability in growth and mortality within a single population

NASA Astrophysics Data System (ADS)

Reid, K.; Murphy, E. J.; Loeb, V.; Hewitt, R. P.

2002-07-01

Understanding the demographics of Antarctic krill over large scales may be complicated by regional differences in the processes that govern population structure. The influence of regional differences in growth and mortality on population size structure was examined using data on the length-frequency distribution of krill in the Scotia Sea using samples from the South Shetland Islands and South Georgia collected annually from 1991 to 2000. A correction function, which took account of the higher growth rate at South Georgia, produced a consistent similarity in the position of the modal size classes that was not present in the raw data. Optimising the mortality rate, to minimise the differences in the growth corrected length-frequency distribution, suggested a higher mortality rate at South Georgia that the South Shetlands. The intra-specific variations in growth and mortality rates are consistent with published values and with other Euphausiids species. Having accounted for the demographic plasticity, it is apparent that strong recruitment of the smallest size class of krill is represented in both populations simultaneously. It appears that first-year krill are advected into different regions of the Scotia Sea where the resultant population size structure is determined by regional differences in growth and mortality. The majority of the commercial harvest of krill in the Antarctic occurs in a relatively small number of regional fisheries within the Scotia Sea and is managed using population models based on a single set of demographic parameters. Where substantial differences in these parameters exist between fishing areas, the calculation of catch limits should take these differences into account.

Beyond topology: coevolution of structure and flux in metabolic networks.

PubMed

Morrison, E S; Badyaev, A V

2017-10-01

Interactions between the structure of a metabolic network and its functional properties underlie its evolutionary diversification, but the mechanism by which such interactions arise remains elusive. Particularly unclear is whether metabolic fluxes that determine the concentrations of compounds produced by a metabolic network, are causally linked to a network's structure or emerge independently of it. A direct empirical study of populations where both structural and functional properties vary among individuals' metabolic networks is required to establish whether changes in structure affect the distribution of metabolic flux. In a population of house finches (Haemorhous mexicanus), we reconstructed full carotenoid metabolic networks for 442 individuals and uncovered 11 structural variants of this network with different compounds and reactions. We examined the consequences of this structural diversity for the concentrations of plumage-bound carotenoids produced by flux in these networks. We found that concentrations of metabolically derived, but not dietary carotenoids, depended on network structure. Flux was partitioned similarly among compounds in individuals of the same network structure: within each network, compound concentrations were closely correlated. The highest among-individual variation in flux occurred in networks with the strongest among-compound correlations, suggesting that changes in the magnitude, but not the distribution of flux, underlie individual differences in compound concentrations on a static network structure. These findings indicate that the distribution of flux in carotenoid metabolism closely follows network structure. Thus, evolutionary diversification and local adaptations in carotenoid metabolism may depend more on the gain or loss of enzymatic reactions than on changes in flux within a network structure. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Ecological associations, dispersal ability, and landscape connectivity in the northern Rocky Mountains

Treesearch

Samuel A. Cushman; Erin L. Landguth

2012-01-01

Population connectivity is a function of the dispersal ability of the species, influences of different landscape elements on its movement behavior, density and distribution of the population, and structure of the landscape. Often, researchers have not carefully considered each of these factors when evaluating connectivity and making conservation recommendations. We...

Prevalance of aflatoxin contamination in maize and groundnut in Ghana: Population structure, distribution, and toxigenicity of the causal agents

USDA-ARS?s Scientific Manuscript database

Aflatoxin contamination in maize and groundnut is perennial in Ghana with substantial health and economic burden on the population. The present study examined for the first time the prevalence of aflatoxin contamination in maize and groundnut in major producing regions across three agroecological zo...

Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

PubMed

Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

2016-09-01

Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetic Variability and Population Structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae) Based on AFLP Analysis

PubMed Central

Yu, Yi; Fan, Qiang; Shen, Rujiang; Guo, Wei; Jin, Jianhua; Cui, Dafang; Liao, Wenbo

2014-01-01

Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP) fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and “excess flowers production, but little fruit set”. It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible. PMID:25250583

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

PubMed Central

Damerau, Malte; Matschiner, Michael; Jentoft, Sissel

2017-01-01

Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic. PMID:28419285

Population genetics of the malaria vector Anopheles aconitus in China and Southeast Asia

PubMed Central

Chen, Bin; Harbach, Ralph E.; Walton, Catherine; He, Zhengbo; Zhong, Daibin; Yan, Guiyun; Butlin, Roger K.

2012-01-01

Anopheles aconitus is a well-known vector of malaria and is broadly distributed in the Oriental Region, yet there is no information on its population genetic characteristics. In this study, the genetic differentiation among populations was examined using 140 mtDNA COII sequences from 21 sites throughout southern China, Myanmar, Vietnam, Thailand, Laos and Sri Lanka. The population in Sri Lanka has characteristic rDNA D3 and ITS2, mtDNA COII and ND5 haplotypes, and may be considered a distinct subspecies. Clear genetic structure was observed with highly significant genetic variation present among population groups in Southeast Asia. The greatest genetic diversity exists in Yunnan and Myanmar population groups. All population groups are significantly different from one another in pairwise Fst values, except northern Thailand with central Thailand. Mismatch distributions and extremely significant Fs values suggest that the populations passed through a recent demographic expansion. These patterns are discussed in relation to the likely biogeographic history of the region and compared to other Anopheles species. PMID:22982161

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.

Population Genetic Structure of the Magnificent Frigatebird Fregata magnificens (Aves, Suliformes) Breeding Colonies in the Western Atlantic Ocean

PubMed Central

Nuss, Andressa; Carlos, Caio J.; Moreno, Ignacio B.; Fagundes, Nelson J. R.

2016-01-01

The Magnificent Frigatebird Fregata magnificens has a pantropical distribution, nesting on islands along the Atlantic and Pacific coasts. In the Caribbean, there is little genetic structure among colonies; however, the genetic structure among the colonies off Brazil and its relationship with those in the Caribbean are unknown. In this study, we used mtDNA and microsatellite markers to infer population structure and evolutionary history in a sample of F. magnificens individuals collected in Brazil, Grand Connétable (French Guyana), and Barbuda. Virtually all Brazilian individuals had the same mtDNA haplotype. There was no haplotype sharing between Brazil and the Caribbean, though Grand Connétable shared haplotypes with both regions. A Bayesian clustering analysis using microsatellite data found two genetic clusters: one associated with Barbuda and the other with the Brazilian populations. Grand Connétable was more similar to Barbuda but had ancestry from both clusters, corroborating its “intermediate” position. The Caribbean and Grand Connétable populations showed higher genetic diversity and effective population size compared to the Brazilian population. Overall, our results are in good agreement with an effect of marine winds in isolating the Brazilian meta-population. PMID:26901878

Phylogeographic pattern suggests a general northeastward dispersal in the distribution of Machilus pauhoi in South China

PubMed Central

Zhu, Qin; Liao, Bo-Yong; Li, Pei; Li, Jun-Cheng; Deng, Xiao-Mei; Chen, Xiao-Yang

2017-01-01

Machilus pauhoi Kanehira is an important timber species in China. A provenance trial was recently set up to evaluate the growth performance of trees from different localities, with the aim of designing seed transfer guidelines. Here, we tested twelve nuclear microsatellite markers derived from other species of the Lauraceae family and investigated population genetic structure in M. pauhoi. Both the number of observed alleles per locus (Na) and the polymorphic information content (PIC) significantly decreased against the latitude, but showed an insignificant decrease against the longitude. Heterozygosity (Ho) and gene diversity (h) exhibited a weak correlation with geographic location. Private alleles were present in multiple populations, and a moderate level of population genetic differentiation was detected (Gst = 0.1691). The joint pattern of genetic diversity (Na, PIC, Ho, and h) suggests that general northeastward dispersal led to the current distribution of M. pauhoi. Significant but weak effects of isolation-by-distance (IBD) occurred, implicating the mountain ranges as the major barrier to gene flow. Both STRUCTURE and hierarchical clustering analyses showed three distinct groups of populations related to the physical connectivity among mountain ranges. A priority in designing genetic conservation should be given to the populations at the southwest side of the species’ distribution. This conservation strategy can also be combined with the pattern of adaptive genetic variation from the provenance trial for comprehensive genetic resource management of native M. pauhoi. PMID:28886133

Wired: impacts of increasing power line use by a growing bird population

NASA Astrophysics Data System (ADS)

Moreira, Francisco; Encarnação, Vitor; Rosa, Gonçalo; Gilbert, Nathalie; Infante, Samuel; Costa, Julieta; D'Amico, Marcello; Martins, Ricardo C.; Catry, Inês

2017-02-01

Power lines are increasingly widespread across many regions of the planet. Although these linear infrastructures are known for their negative impacts on bird populations, through collision and electrocution, some species take advantage of electricity pylons for nesting. In this case, estimation of the net impact of these infrastructures at the population level requires an assessment of trade-offs between positive and negative impacts. We compiled historical information (1958-2014) of the Portuguese white stork Ciconia ciconia population to analyze long-term changes in numbers, distribution range and use of nesting structures. White stork population size increased 660% up to 12000 breeding pairs between 1984 and 2014. In the same period, the proportion of nests on electricity pylons increased from 1% to 25%, likely facilitated by the 60% increase in the length of the very high tension power line grid (holding the majority of the nests) in the stork’s distribution range. No differences in breeding success were registered for storks nesting on electricity pylons versus other structures, but a high risk of mortality by collision and electrocution with power lines was estimated. We discuss the implications of this behavioral change, and of the management responses by power line companies, both for stork populations and for managers.

Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub species.

PubMed

Collevatti, Rosane Garcia; Rabelo, Suelen Gonçalves; Vieira, Roberto F

2009-09-01

Lychnophora ericoides (Asteraceae) presents disjunct geographical distribution in cerrado rupestre in the south-east and central Brazil. The phylogeography of the species was investigated to understand the origin of the disjunct geographical distribution. Populations in the south and centre of Serra do Espinhaço, south-east Brazil and on ten other localities in Federal District and Goiás in central Brazil were sampled. Analyses were based on the polymorphisms at chloroplast (trnL intron and psbA-trnH intergenic spacer) and nuclear (ITS nrDNA) genomes. From 12 populations, 192 individuals were sequenced. Network analysis, AMOVA and the Mantel test were performed to understand the relationships among haplotypes and population genetic structure. To understand better the origin of disjunct distribution, demographic parameters and time to most recent common ancestor (T(MRCA)) were estimated using coalescent analyses. A remarkable differentiation between populations from the south-east and central Brazil was found and no haplotype was shared between these two regions. No significant effect of isolation by distance was detected. Coalescent analyses showed that some populations are shrinking and others are expanding and that gene flow between populations from the south-east and central Brazil was probably negligible. The results strongly support that the disjunct distribution of L. ericoides may represent a climatic relict and that long-distance gene flow is unlikely. With an estimated time to most recent common ancestor (T(MRCA)) dated from approx. 790,655 +/- 36,551 years bp (chloroplast) and approx. 623,555 +/- 55,769 years bp (ITS), it was hypothesized that the disjunct distribution may be a consequence of an expansion of the geographical distribution favoured by the drier and colder conditions that prevailed in much of Brazil during the Kansan glaciation, followed by the retraction of the distribution due to the extinction of populations in some areas as climate became warmer and moister.

Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub species

PubMed Central

Collevatti, Rosane Garcia; Rabelo, Suelen Gonçalves; Vieira, Roberto F.

2009-01-01

Background and Aims Lychnophora ericoides (Asteraceae) presents disjunct geographical distribution in cerrado rupestre in the south-east and central Brazil. The phylogeography of the species was investigated to understand the origin of the disjunct geographical distribution. Methods Populations in the south and centre of Serra do Espinhaço, south-east Brazil and on ten other localities in Federal District and Goiás in central Brazil were sampled. Analyses were based on the polymorphisms at chloroplast (trnL intron and psbA-trnH intergenic spacer) and nuclear (ITS nrDNA) genomes. From 12 populations, 192 individuals were sequenced. Network analysis, AMOVA and the Mantel test were performed to understand the relationships among haplotypes and population genetic structure. To understand better the origin of disjunct distribution, demographic parameters and time to most recent common ancestor (TMRCA) were estimated using coalescent analyses. Key Results A remarkable differentiation between populations from the south-east and central Brazil was found and no haplotype was shared between these two regions. No significant effect of isolation by distance was detected. Coalescent analyses showed that some populations are shrinking and others are expanding and that gene flow between populations from the south-east and central Brazil was probably negligible. Conclusions The results strongly support that the disjunct distribution of L. ericoides may represent a climatic relict and that long-distance gene flow is unlikely. With an estimated time to most recent common ancestor (TMRCA) dated from approx. 790 655 ± 36 551 years bp (chloroplast) and approx. 623 555 ± 55 769 years bp (ITS), it was hypothesized that the disjunct distribution may be a consequence of an expansion of the geographical distribution favoured by the drier and colder conditions that prevailed in much of Brazil during the Kansan glaciation, followed by the retraction of the distribution due to the extinction of populations in some areas as climate became warmer and moister. PMID:19656805

Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus)

PubMed Central

Carr, Steven M.; Duggan, Ana T.; Stenson, Garry B.; Marshall, H. Dawn

2015-01-01

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on “fast ice” attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40 ~ 60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed. PMID:26301872

Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus).

PubMed

Carr, Steven M; Duggan, Ana T; Stenson, Garry B; Marshall, H Dawn

2015-01-01

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on "fast ice" attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40~60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed.

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

2013-01-01

Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

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

PubMed Central

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

2009-01-01

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

Breeding system and demography shape population genetic structure across ecological and climatic zones in the African freshwater snail, Bulinus forskalii (Gastropoda, Pulmonata), intermediate host for schistosomes.

PubMed

Gow, J L; Noble, L R; Rollinson, D; Mimpfoundi, R; Jones, C S

2004-11-01

The role of breeding system and population bottlenecks in shaping the distribution of neutral genetic variation among populations inhabiting patchily distributed, ephemeral water bodies was examined for the hermaphroditic freshwater snail Bulinus forskalii, intermediate host for the medically important trematode Schistosoma guineensis. Levels of genetic variation at 11 microsatellite loci were assessed for 600 individuals sampled from 19 populations that span three ecological and climatic zones (ecozones) in Cameroon, West Africa. Significant heterozygote deficiencies and linkage disequilibria indicated very high selfing rates in these populations. Despite this and the large genetic differentiation detected between populations, high levels of genetic variation were harboured within these populations. The high level of gene flow inferred from assignment tests may be responsible for this pattern. Indeed, metapopulation dynamics, including high levels of gene flow as well as extinction/contraction and recolonization events, are invoked to account for the observed population structuring, which was not a consequence of isolation-by-distance. Because B. forskalii populations inhabiting the northern, Sahelian area are subject to more pronounced annual cycles of drought and flood than the southern equatorial ones, they were expected to be subject to population bottlenecks of increased frequency and severity and, therefore, show reduced genetic variability and elevated population differentiation. Contrary to predictions, the populations inhabiting the most northerly ecozone exhibited higher genetic diversity and lower genetic differentiation than those in the most southerly one, suggesting that elevated gene flow in this region is counteracting genetic drift.

On spatial coalescents with multiple mergers in two dimensions.

PubMed

Heuer, Benjamin; Sturm, Anja

2013-08-01

We consider the genealogy of a sample of individuals taken from a spatially structured population when the variance of the offspring distribution is relatively large. The space is structured into discrete sites of a graph G. If the population size at each site is large, spatial coalescents with multiple mergers, so called spatial Λ-coalescents, for which ancestral lines migrate in space and coalesce according to some Λ-coalescent mechanism, are shown to be appropriate approximations to the genealogy of a sample of individuals. We then consider as the graph G the two dimensional torus with side length 2L+1 and show that as L tends to infinity, and time is rescaled appropriately, the partition structure of spatial Λ-coalescents of individuals sampled far enough apart converges to the partition structure of a non-spatial Kingman coalescent. From a biological point of view this means that in certain circumstances both the spatial structure as well as larger variances of the underlying offspring distribution are harder to detect from the sample. However, supplemental simulations show that for moderately large L the different structure is still evident. Copyright © 2012 Elsevier Inc. All rights reserved.

Visualizing the geography of genetic variants.

PubMed

Marcus, Joseph H; Novembre, John

2017-02-15

One of the key characteristics of any genetic variant is its geographic distribution. The geographic distribution can shed light on where an allele first arose, what populations it has spread to, and in turn on how migration, genetic drift, and natural selection have acted. The geographic distribution of a genetic variant can also be of great utility for medical/clinical geneticists and collectively many genetic variants can reveal population structure. Here we develop an interactive visualization tool for rapidly displaying the geographic distribution of genetic variants. Through a REST API and dynamic front-end, the Geography of Genetic Variants (GGV) browser ( http://popgen.uchicago.edu/ggv/ ) provides maps of allele frequencies in populations distributed across the globe. GGV is implemented as a website ( http://popgen.uchicago.edu/ggv/ ) which employs an API to access frequency data ( http://popgen.uchicago.edu/freq_api/ ). Python and javascript source code for the website and the API are available at: http://github.com/NovembreLab/ggv/ and http://github.com/NovembreLab/ggv-api/ . jnovembre@uchicago.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Galactic dual population models of gamma-ray bursts

NASA Technical Reports Server (NTRS)

Higdon, J. C.; Lingenfelter, R. E.

1994-01-01

We investigate in more detail the properties of two-population models for gamma-ray bursts in the galactic disk and halo. We calculate the gamma-ray burst statistical properties, mean value of (V/V(sub max)), mean value of cos Theta, and mean value of (sin(exp 2) b), as functions of the detection flux threshold for bursts coming from both Galactic disk and massive halo populations. We consider halo models inferred from the observational constraints on the large-scale Galactic structure and we compare the expected values of mean value of (V/V(sub max)), mean value of cos Theta, and mean value of (sin(exp 2) b), with those measured by Burst and Transient Source Experiment (BATSE) and other detectors. We find that the measured values are consistent with solely Galactic populations having a range of halo distributions, mixed with local disk distributions, which can account for as much as approximately 25% of the observed BATSE bursts. M31 does not contribute to these modeled bursts. We also demonstrate, contrary to recent arguments, that the size-frequency distributions of dual population models are quite consistent with the BATSE observations.

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.

Genetic structure of Rajaka caste and affinities with other caste populations of Andhra Pradesh, India.

PubMed

Parvatheesam, C; Babu, B V; Babu, M C

1997-01-01

The present study gives an account of the genetic structure in terms of distribution of a few genetic markers, viz., A1A2B0, Rh(D), G6PD deficiency and haemoglobin among the Rajaka caste population of Andhra Pradesh, India. The genetic relationships of the Rajaka caste with other Andhra caste populations were investigated in terms of genetic distance, i.e., Sq B (mn) of Balakrishnan and Sanghvi. Relatively lesser distance was established between the Rajaka and two Panchama castes. Also, the pattern of genetic distance corroborates the hierarchical order of the Hindu varna system.

Building up a QSAR model for toxicity toward Tetrahymena pyriformis by the Monte Carlo method: A case of benzene derivatives.

PubMed

Toropova, Alla P; Schultz, Terry W; Toropov, Andrey A

2016-03-01

Data on toxicity toward Tetrahymena pyriformis is indicator of applicability of a substance in ecologic and pharmaceutical aspects. Quantitative structure-activity relationships (QSARs) between the molecular structure of benzene derivatives and toxicity toward T. pyriformis (expressed as the negative logarithms of the population growth inhibition dose, mmol/L) are established. The available data were randomly distributed three times into the visible training and calibration sets, and invisible validation sets. The statistical characteristics for the validation set are the following: r(2)=0.8179 and s=0.338 (first distribution); r(2)=0.8682 and s=0.341 (second distribution); r(2)=0.8435 and s=0.323 (third distribution). These models are built up using only information on the molecular structure: no data on physicochemical parameters, 3D features of the molecular structure and quantum mechanics descriptors are involved in the modeling process. Copyright © 2016 Elsevier B.V. All rights reserved.

A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds

PubMed Central

Zeldovich, Konstantin B; Chen, Peiqiu; Shakhnovich, Boris E; Shakhnovich, Eugene I

2007-01-01

In this work we develop a microscopic physical model of early evolution where phenotype—organism life expectancy—is directly related to genotype—the stability of its proteins in their native conformations—which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the “Big Bang” scenario whereby exponential population growth ensues as soon as favorable sequence–structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species—subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution. PMID:17630830

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

PubMed

Zeldovich, Konstantin B; Chen, Peiqiu; Shakhnovich, Boris E; Shakhnovich, Eugene I

2007-07-01

In this work we develop a microscopic physical model of early evolution where phenotype--organism life expectancy--is directly related to genotype--the stability of its proteins in their native conformations-which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species--subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.

Comparative population structure of cavity-nesting sea ducks

USGS Publications Warehouse

Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

2014-01-01

A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

Quantifying Adventitious Error in a Covariance Structure as a Random Effect

PubMed Central

Wu, Hao; Browne, Michael W.

2017-01-01

We present an approach to quantifying errors in covariance structures in which adventitious error, identified as the process underlying the discrepancy between the population and the structured model, is explicitly modeled as a random effect with a distribution, and the dispersion parameter of this distribution to be estimated gives a measure of misspecification. Analytical properties of the resultant procedure are investigated and the measure of misspecification is found to be related to the RMSEA. An algorithm is developed for numerical implementation of the procedure. The consistency and asymptotic sampling distributions of the estimators are established under a new asymptotic paradigm and an assumption weaker than the standard Pitman drift assumption. Simulations validate the asymptotic sampling distributions and demonstrate the importance of accounting for the variations in the parameter estimates due to adventitious error. Two examples are also given as illustrations. PMID:25813463

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.

Population genetic structure of Monimopetalum chinense (Celastraceae), an endangered endemic species of eastern China.

PubMed

Xie, Guo-Wen; Wang, De-Lian; Yuan, Yong-Ming; Ge, Xue-Jun

2005-04-01

Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp=0.183) and at the population level (Ipop=0.083). High clonal diversity (D = 0.997) was found, and strong genetic differentiation among populations was detected (49.06 %). Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species.

[Genetic aspects of species structure of the compost worm Eisenia foetida (Sav.) (Oligochaeta, Lumbricidae)].

PubMed

Bolotetskiĭ, N M; Kodolova, O P

2002-01-01

Distribution of frequencies alleles of polymorphous loci of peroxidase (Pox), leucineaminopeptidase (Lap), phosphoglucomutase (Pgm) and octanoldehydrogenase (Odh) were studied by electrophoresis in polyacrylamide gel in 22 local samples of Esenia foetida in Russia (European part), Ukraine, Kazakhstan and Kirghizia. The samples form two spatial groups--"northern" and "southern", distinguished by set of alleles in every studied locus. The "northern" groups is formed by local populations of European Russia from Murmansk region on the north to Smolensk region on the south, and also by cultivated population of selection line "red California hybrid". The "southern" group is formed by local populations on the territory of Russia from middle Volga to the North Caucasus, Ukraine, Kazakhstan, Kirghizia, cultivated populations from Kirghizia and Portugal. High degree of genetic difference between samples and independence of alleles frequencies distribution from geographical location and habitat allows to consider almost all studied groups as separate populations. Statistical processing of Nei genetic distances (Nei, 1972) revealed reliable differences between averages of within- and intergroup distances. Besides, discrete differences between intervals of significance of genetic distances were revealed. The results indicate that on the studied territory E. foetida has hierarchical two level structure. The first level is formed by local populations differed by frequency of the same alleles. The second level is formed by local populations, united into spatial groups, that are qualitatively distinguished by the set of alleles in the same loci.

Population genetic diversity and genetic structure of Spodoptera exigua around the Bohai Gulf area of China based on mitochondrial DNA signatures.

PubMed

Zhou, L-H; Wang, X-Y; Lei, J-J

2016-09-30

The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae), is an economically important pest that causes major losses in some main crop-producing areas of China. To control this pest effectively, it is necessary to investigate its population genetic diversity and genetic structure around the Bohai Gulf area of China. In this study, we used two mitochondrial genes, COI (578 bp) and Cytb (724 bp), to investigate its genetic diversity. We obtained 622 COI sequences and 462 Cytb sequences from 23 populations, and 28 and 73 haplotypes, respectively, were identified. Low to moderate levels of genetic diversity (COI: Hd = 0.267 ± 0.023, Pi = 0.00082 ± 0.00010; Cytb: Hd = 0.689 ± 0.018, Pi = 0.00255 ± 0.00029) for the total populations were observed. Phylogenetic and median-joining network analyses indicated no distinct geographical distribution pattern among the haplotypes. Overall, this study revealed that there was significant differentiation among the populations (COI: F ST = 0.158, P < 0.001; Cytb: F ST = 0.148, P < 0.001). F ST values for Shenyang, Baoding, and Funing were significantly different to those for most of the other populations. Finally, unimodal mismatch distribution analysis, combined with negative neutrality test results, showed a recent population expansion of the beet armyworm around the Bohai Gulf area of China.

Consanguinity and Its Sociodemographic Differentials in Bhimber District, Azad Jammu and Kashmir, Pakistan

PubMed Central

Jabeen, Nazish

2014-01-01

ABSTRACT Kashmiri population in the northeast of Pakistan has strong historical, cultural and linguistic affinities with the neighbouring populations of upper Punjab and Potohar region of Pakistan. However, the study of consanguineous unions, which are customarily practised in many populations of Pakistan, revealed marked differences between the Kashmiris and other populations of northern Pakistan with respect to the distribution of marriage types and inbreeding coefficient (F). The current descriptive epidemiological study carried out in Bhimber district of Mirpur division, Azad Jammu and Kashmir, Pakistan, demonstrated that consanguineous marriages were 62% of the total marriages (F=0.0348). First-cousin unions were the predominant type of marriages and constituted 50.13% of total marital unions. The estimates of inbreeding coefficient were higher in the literate subjects, and consanguinity was witnessed to be rising with increasing literacy level. Additionally, consanguinity was observed to be associated with ethnicity, family structure, language, and marriage arrangements. Based upon these data, a distinct sociobiological structure, with increased stratification and higher genomic homozygosity, is expected for this Kashmiri population. In this communication, we present detailed distribution of the types of marital unions and the incidences of consanguinity and inbreeding coefficient (F) across various sociodemographic strata of Bhimber/Mirpuri population. The results of this study would have implication not only for other endogamous populations of Pakistan but also for the sizeable Kashmiri community immigrated to Europe. PMID:25076667

Population structuring of the ubiquitous stingless bee Tetragonisca angustula in southern Brazil as revealed by microsatellite and mitochondrial markers.

PubMed

Francisco, Flávio O; Santiago, Leandro R; Mizusawa, Yuri M; Oldroyd, Benjamin P; Arias, Maria C

2017-10-01

Tetragonisca angustula is one of the most widespread stingless bees in the Neotropics. This species swarms frequently and is extremely successful in urban environments. In addition, it is one of the most popular stingless bee species for beekeeping in Latin America, so nest transportation and trading is common. Nest transportation can change the genetic structure of the host population, reducing inbreeding and increasing homogenization. Here, we evaluate the genetic structure of 17 geographic populations of T. angustula in southern Brazil to quantify the level of genetic differentiation between populations. Analyses were conducted on partially sequenced mitochondrial genes and 11 microsatellite loci of 1002 workers from 457 sites distributed on the mainland and on 3 islands. Our results show that T. angustula populations are highly differentiated as demonstrated by mitochondrial DNA (mtDNA) and microsatellite markers. Of 73 haplotypes, 67 were population-specific. MtDNA diversity was low in 9 populations but microsatellite diversity was moderate to high in all populations. Microsatellite data suggest 10 genetic clusters and low level of gene flow throughout the studied area. However, physical barriers, such as rivers and mountain ranges, or the presence or absence of forest appear to be unrelated to population clusters. Factors such as low dispersal, different ecological conditions, and isolation by distance are most likely shaping the population structure of this species. Thus far, nest transportation has not influenced the general population structure in the studied area. However, due to the genetic structure we found, we recommend that nest transportation should only occur within and between populations that are genetically similar. © 2016 Institute of Zoology, Chinese Academy of Sciences.

The Black Urban Population of the Pre-civil War South

ERIC Educational Resources Information Center

Wilkie, Jane Riblett

1976-01-01

Examines the urbanization of blacks in the slave states from 1790 to 1860. Changes in the geographic distribution and demographic structure of the black urban population provide new evidence to evaluate the causes of the decline of urban blacks and reveal the likelihood of a disproportionate incidence of incomplete families for both slave and free…

Population genetic structure of Diaphorina citri Kuwayama (Hemiptera: Liviidae): host-driven genetic differentiation in China.

PubMed

Meng, Lixue; Wang, Yongmo; Wei, Wen-Hua; Zhang, Hongyu

2018-01-24

The Asian citrus psyllid Diaphorina citri Kuwayama is a major pest in citrus production, transmitting Candidatus Liberibacter asiaticus. It has spread widely across eastern and southern China. Unfortunately, little is known about the genetic diversity and population structure of D. citri, making pest control difficult. In this study, nine specifically developed SSR markers and three known mitochondrial DNA were used for population genetics study of D. citri using 225 samples collected from all 7 distribution regions in China. Based on the SSR data, D. citri was found highly diverse with a mean observed heterozygosity of 0.50, and three subgroups were structured by host plant: (i) Shatangju, NF mandarin and Ponkan; (ii) Murraya paniculata and Lemon; (iii) Citrus unshiu, Bingtangcheng, Summer orange and Navel. No significant genetic differences were found with mtDNA data. We suggested the host-associated divergence is likely to have occurred very recently. A unimodal distribution of paired differences, the negative and significant Tajima's D and Fu's F S parameters among mtDNA suggested a recent demographic expansion. The extensive citrus cultivation and increased suitable living habitat was recommended as a key for this expansion event.

Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island.

PubMed

Gifford, Matthew E; Powell, Robert; Larson, Allan; Gutberlet, Ronald L

2004-09-01

Ameiva chrysolaema is distributed across the island of Hispaniola in the West Indies. The species is restricted to dry lowlands between major mountain ranges and along the southern and eastern coasts. Phylogenetic and phylogeographic analyses of mtDNA sequence variation from 14 sampling localities identify at least three independent evolutionary lineages, separated from one another by major mountain ranges. Nested clade phylogeographic analysis (NCPA) suggests a complex history of population fragmentation, consistent with geological evidence of seawater incursions into the Azua and Enriquillo basins during the Pliocene/Pleistocene (approximately 1.6 mya). Significantly negative Fu's F(S) values and parameters of mismatch distributions suggest that formerly fragmented populations have recently expanded their ranges. Significantly large average population clade distances (APCD) for two sampling localities in the Azua basin suggest secondary contact at these localities of previously separated populations. The distribution of haplotypes among polymorphic populations of A. chrysolaema suggests that variation in dorsal pattern represents a polymorphism within evolutionary lineages. Ameiva leberi is ecologically indistinguishable from and syntopic with A. chrysolaema. Genetic data suggest that A. leberi is a junior synonym of A. chrysolaema.

Evolutionary and ecological forces influencing population diversification in Bornean montane passerines.

PubMed

Chua, Vivien L; Smith, Brian Tilston; Burner, Ryan C; Rahman, Mustafa Abdul; Lakim, Maklarin; Prawiradilaga, Dewi M; Moyle, Robert G; Sheldon, Frederick H

2017-08-01

The mountains of Borneo are well known for their high endemicity and historical role in preserving Southeast Asian rainforest biodiversity, but the diversification of populations inhabiting these mountains is poorly studied. Here we examine the genetic structure of 12 Bornean montane passerines by comparing complete mtDNA ND2 gene sequences of populations spanning the island. Maximum likelihood and Bayesian phylogenetic trees and haplotype networks are examined for common patterns that might signal important historical events or boundaries to dispersal. Morphological and ecological characteristics of each species are also examined using phylogenetic generalized least-squares (PGLS) for correlation with population structure. Populations in only four of the 12 species are subdivided into distinct clades or haplotype groups. Although this subdivision occurred at about the same time in each species (ca. 0.6-0.7Ma), the spatial positioning of the genetic break differs among the species. In two species, northeastern populations are genetically divergent from populations elsewhere on the island. In the other two species, populations in the main Bornean mountain chain, including the northeast, are distinct from those on two isolated peaks in northwestern Borneo. We suggest different historical forces played a role in shaping these two distributions, despite commonality in timing. PGLS analysis showed that only a single characteristic-hand-wing index-is correlated with population structure. Birds with longer wings, and hence potentially more dispersal power, have less population structure. To understand historical forces influencing montane population structure on Borneo, future studies must compare populations across the entirety of Sundaland. Copyright © 2017 Elsevier Inc. All rights reserved.

A novel method of estimating cost of therapy by using patient population characteristics: analysis of fluoroquinolones in various populations with different distributions of renal function.

PubMed

Enzweiler, Kevin A; Bosso, John A; White, Roger L

2003-07-01

Formulary decisions regarding a given drug class are often made in the absence of patient outcome and/or sophisticated pharmacoeconomic data. Analyses that consider factors beyond simple acquisition costs may be useful in such situations. For example, the cost implications of using manufacturers' recommendations for dosing in patients with renal dysfunction may be important, depending on the distribution of various levels of renal function within a patient population. Using four 1000-patient populations representing different renal function distributions and a fifth population of our medical center's distribution, we determined the costs of therapy for intravenous and oral levofloxacin, gatifloxacin, and moxifloxacin for a 10-day course of therapy for community-acquired pneumonia. Costs considered were average wholesale prices (AWPs), 50% of AWP, or same daily price, plus intravenous dose preparation and administration costs when applicable. Costs for each renal function distribution were examined for significant differences with an analysis-of-variance test. Also, costs of failing to adjust dosing regimens for decreased renal function were determined. Differences in fluoroquinolone costs (AWP, 50% AWP, or when matched as the same daily price) among the populations were found. When considering same daily prices, differences among populations ranged from about 35,000 dollars with intravenous gatifloxacin to more than 51,000 dollars for intravenous levofloxacin (all fluoroquinolones, p>0.05). Within a population, differences in costs among the intravenous fluoroquinolones ranged from 47,000-99,000 dollars. Rank orders of the drugs and population costs of therapy were affected by the pricing structure used and varied by the specific population and drug. Differences among the fluoroquinolones or populations were much smaller (<2100 dollars) when considering oral regimens. Costs potentially incurred by failing to adjust dosing for renal function were substantial. Formulary decisions can be facilitated by considering factors such as patient characteristics and related dosing in addition to simple acquisition costs. In our example, consideration of the distribution of renal function within a given patient population and related dosing for these fluoroquinolones revealed potentially important differences within the class.

Genetic structuring among silverside fish (Atherinella brasiliensis) populations from different Brazilian regions

NASA Astrophysics Data System (ADS)

da Silva Cortinhas, Maria Cristina; Kersanach, Ralf; Proietti, Maíra; Dumont, Luiz Felipe Cestari; D'Incao, Fernando; Lacerda, Ana Luzia F.; Prata, Pedro Sanmartin; Matoso, Daniele Aparecida; Noleto, Rafael Bueno; Ramsdorf, Wanessa; Boni, Talge Aiex; Prioli, Alberto José; Cestari, Marta Margarete

2016-09-01

Estuaries are dynamic environments, key for the survival of innumerous ecologically or economically important fish species. Among these species are Neotropical silversides (Atherinella brasiliensis), which are resident and abundant in Brazilian estuaries and used as a complementary source of income and food for local communities. To better understand silverside populations in Brazil, we evaluated the genetic diversity, structure and demography of fish sampled at six estuaries from the northeastern to the southern coast, using Random Amplified Polymorphic DNA and mitochondrial DNA (D-loop) markers. High haplotype diversities (h ranging from 0.75 to 0.99) were found in all populations except Carapebus, located in Southeast Brazil (h = 0.54). A total of 69 mtDNA haplotypes were found, with Itaparica (Northeast Brazil) and Carapebus presenting only exclusive haplotypes, while some were shared among populations in the South. Strong regional structure was observed, with very high differentiation between Itaparica and Carapebus, as well as among these two populations and the ones from the Southern region (Paranaguá, Conceição, Camacho and Patos). Among southern areas, low/moderate structure was detected. Most populations showed unimodal mismatch distributions indicating recent demographic expansion, while Carapebus presented a multimodal distribution characteristic of a stable or bottlenecked population. Times since possible population expansion were highest in Itaparica (32,500 ya) and Carapebus (29,540 ya), while in the Southern region longest time was observed at Conceição (25,540 ya) and shortest at Patos (9720 ya). In a general manner, haplotype diversities were directly related to times since population expansions; again, Carapebus was the exception, displaying long time since expansion but low diversity, possibly due to a recent bottleneck caused by the isolation and human impacts this lagoon is subject to. Isolation by Distance was significant for Itaparica and Carapebus, and considering the extremely high differentiation of these populations, we suggest that they could be undergoing speciation. To adequately manage and maintain the genetic variability of silversides in Brazilian estuaries, we propose three distinct management units for this species: 1) Itaparica; 2) Carapebus; and 3) Southern Brazil.

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

PubMed

Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

2007-07-01

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure

PubMed Central

De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J.; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E. Richard; Soriani, Marco; Donati, Claudio

2014-01-01

One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen. PMID:24706866

Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.

PubMed

De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E Richard; Soriani, Marco; Donati, Claudio

2014-04-08

One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen.

Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

PubMed

Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

2011-02-01

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

77 FR 55456 - Marine Mammals; File No. 17410

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-10

... proposed research are to obtain information on population status and distribution, stock structure, age... occur world-wide. No live animal takes are being requested under this permit. The requested duration of...

Neither biased sex ratio nor spatial segregation of the sexes in the subtropical dioecious tree Eurycorymbus cavaleriei (Sapindaceae).

PubMed

Gao, Puxin; Kang, Ming; Wang, Jing; Ye, Qigang; Huang, Hongwen

2009-06-01

Knowledge of sex ratio and spatial distribution of males and females of dioecious species is both of evolutionary interest and of crucial importance for biological conservation. Eurycorymbus cavaleriei, the only species in the genus Eurycorymbus (Sapindaceae), is a dioecious tree endemic to subtropical montane forest in South China. Sex ratios were investigated in 15 natural populations for the two defined ages (young and old). Spatial distribution of males and females was further studied in six large populations occurring in different habitats (fragmented and continuous). The study revealed a slight trend of male-biased sex ratio in both ages of E. cavaleriei, but sex ratio of most populations (13 out of 15) did not display statistically significant deviation from equality. All of the four significantly male-biased populations in the young class shifted to equality or even female-biased. The Ripley's K analysis of the distribution of males with respect to females suggested that individuals of the opposite sexes were more randomly distributed rather than spatially structured. These results suggest that the male-biased sex ratio in E. cavaleriei may result from the precocity of males and habitat heterogeneity. The sex ratio and the sex spatial distribution pattern are unlikely to constitute a serious threat to the survival of the species.

Population Genetic Analysis of Streptomyces albidoflavus Reveals Habitat Barriers to Homologous Recombination in the Diversification of Streptomycetes

PubMed Central

Cheng, Kun; Rong, Xiaoying; Pinto-Tomás, Adrián A.; Fernández-Villalobos, Marcela; Murillo-Cruz, Catalina

2014-01-01

Examining the population structure and the influence of recombination and ecology on microbial populations makes great sense for understanding microbial evolution and speciation. Streptomycetes are a diverse group of bacteria that are widely distributed in nature and a rich source of useful bioactive compounds; however, they are rarely subjected to population genetic investigations. In this study, we applied a five-gene-based multilocus sequence analysis (MLSA) scheme to 41 strains of Streptomyces albidoflavus derived from diverse sources, mainly insects, sea, and soil. Frequent recombination was detected in S. albidoflavus, supported by multiple lines of evidence from the pairwise homoplasy index (Φw) test, phylogenetic discordance, the Shimodaira-Hasegawa (SH) test, and network analysis, underpinning the predominance of homologous recombination within Streptomyces species. A strong habitat signal was also observed in both phylogenetic and Structure 2.3.3 analyses, indicating the importance of ecological difference in shaping the population structure. Moreover, all three habitat-associated groups, particularly the entomic group, demonstrated significantly reduced levels of gene flow with one another, generally revealing habitat barriers to recombination. Therefore, a combined effect of homologous recombination and ecology is inferred for S. albidoflavus, where dynamic evolution is at least partly balanced by the extent that differential distributions of strains among habitats limit genetic exchange. Our study stresses the significance of ecology in microbial speciation and reveals the coexistence of homologous recombination and ecological divergence in the evolution of streptomycetes. PMID:25416769

Population genetic structure of serotine bats (Eptesicus serotinus) across Europe and implications for the potential spread of bat rabies (European bat lyssavirus EBLV-1).

PubMed

Moussy, C; Atterby, H; Griffiths, A G F; Allnutt, T R; Mathews, F; Smith, G C; Aegerter, J N; Bearhop, S; Hosken, D J

2015-07-01

Understanding of the movements of species at multiple scales is essential to appreciate patterns of population connectivity and in some cases, the potential for pathogen transmission. The serotine bat (Eptesicus serotinus) is a common and widely distributed species in Europe where it frequently harbours European bat lyssavirus type 1 (EBLV-1), a virus causing rabies and transmissible to humans. In the United Kingdom, it is rare, with a distribution restricted to south of the country and so far the virus has never been found there. We investigated the genetic structure and gene flow of E. serotinus across the England and continental Europe. Greater genetic structuring was found in England compared with continental Europe. Nuclear data suggest a single population on the continent, although further work with more intensive sampling is required to confirm this, while mitochondrial sequences indicate an east-west substructure. In contrast, three distinct populations were found in England using microsatellite markers, and mitochondrial diversity was very low. Evidence of nuclear admixture indicated strong male-mediated gene flow among populations. Differences in connectivity could contribute to the high viral prevalence on the continent in contrast with the United Kingdom. Although the English Channel was previously thought to restrict gene flow, our data indicate relatively frequent movement from the continent to England highlighting the potential for movement of EBLV-1 into the United Kingdom.

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

PubMed Central

Ball, R. Martin; Freeman, Scott; James, Frances C.; Bermingham, Eldredge; Avise, John C.

1988-01-01

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P ≈ 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow. PMID:16593914

Estimating survival rates with time series of standing age‐structure data

USGS Publications Warehouse

Udevitz, Mark S.; Gogan, Peter J.

2012-01-01

It has long been recognized that age‐structure data contain useful information for assessing the status and dynamics of wildlife populations. For example, age‐specific survival rates can be estimated with just a single sample from the age distribution of a stable, stationary population. For a population that is not stable, age‐specific survival rates can be estimated using techniques such as inverse methods that combine time series of age‐structure data with other demographic data. However, estimation of survival rates using these methods typically requires numerical optimization, a relatively long time series of data, and smoothing or other constraints to provide useful estimates. We developed general models for possibly unstable populations that combine time series of age‐structure data with other demographic data to provide explicit maximum likelihood estimators of age‐specific survival rates with as few as two years of data. As an example, we applied these methods to estimate survival rates for female bison (Bison bison) in Yellowstone National Park, USA. This approach provides a simple tool for monitoring survival rates based on age‐structure data.

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers.

PubMed

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.

Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China.

PubMed

Zhu, Chaoying; Chen, Peng; Han, Yuqing; Ruan, Luzhang

2018-05-12

The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.

Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792) in a Fragmented Landscape: Implications for Conservation Management

PubMed Central

Takács, Péter; Erős, Tibor; Specziár, András; Sály, Péter; Vitál, Zoltán; Ferincz, Árpád; Molnár, Tamás; Szabolcsi, Zoltán; Bíró, Péter; Csoma, Eszter

2015-01-01

The European mudminnow (Umbra krameri) is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs) and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80–90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed. PMID:26393510

Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida

PubMed Central

Fedrizzi, Nathan; Stiassny, Melanie L. J.; Boehm, J. T.; Dougherty, Eric R.; Amato, George; Mendez, Martin

2015-01-01

The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as indicated by significant fixation indices. Despite an overall significant population structure, we observed evidence of interbreeding between individuals from geographically distant sites, supporting the hypothesis that rafting serves to maintain a degree of population connectivity. All individuals collected from Pensacola belong to a single distinct subpopulation, which is highly differentiated from the rest of Floridian dwarf seahorses sampled. Our findings highlight the utility of mtDNA markers in evaluating barriers to gene flow and identifying genetically distinct populations, which are vital to the development of comprehensive conservation strategies for exploited taxa. PMID:26200110

Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida.

PubMed

Fedrizzi, Nathan; Stiassny, Melanie L J; Boehm, J T; Dougherty, Eric R; Amato, George; Mendez, Martin

2015-01-01

The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as indicated by significant fixation indices. Despite an overall significant population structure, we observed evidence of interbreeding between individuals from geographically distant sites, supporting the hypothesis that rafting serves to maintain a degree of population connectivity. All individuals collected from Pensacola belong to a single distinct subpopulation, which is highly differentiated from the rest of Floridian dwarf seahorses sampled. Our findings highlight the utility of mtDNA markers in evaluating barriers to gene flow and identifying genetically distinct populations, which are vital to the development of comprehensive conservation strategies for exploited taxa.

Ecological patterns, distribution and population structure of Prionace glauca (Chondrichthyes: Carcharhinidae) in the tropical-subtropical transition zone of the north-eastern Pacific.

PubMed

Vögler, Rodolfo; Beier, Emilio; Ortega-García, Sofía; Santana-Hernández, Heriberto; Valdez-Flores, J Javier

2012-02-01

Regional ecological patterns, distribution and population structure of Prionace glauca were analyzed based on samples collected on-board two long-line fleets operating in oceanic waters (1994-96/2000-02) and in coastal oceanic waters (2003-2009) of the eastern tropical Pacific off México. Generalized additive models were applied to catch per unit of effort data to evaluate the effect of spatial, temporal and environmental factors on the horizontal distribution of the life stages (juvenile, adult) and the sexes at the estimated depth of catch. The presence of breeding areas was explored. The population structure was characterized by the presence of juveniles' aggregations and pregnant females towards coastal waters and the presence of adult males' aggregations towards oceanic waters. The species exhibited horizontal segregation by sex-size and vertical segregation by sex. Distribution of the sex-size groups at oceanic waters was seasonally affected by the latitude; however, at coastal oceanic waters mainly females were influenced by the longitude. Latitudinal changes on the horizontal distribution were coupled to the seasonal forward and backward of water masses through the study area. Adult males showed positive relationship with high temperatures and high-salinities waters (17.0°-20.0 °C; 34.2-34.4) although they were also detected in low-salinities waters. The distribution of juvenile males mainly occurred beyond low temperatures and low-salinities waters (14.0°-15.0 °C; 33.6-34.1), suggesting a wide tolerance of adult males to explore subartic and subtropical waters. At oceanic areas, adult females were aggregated towards latitudes <25.0°N, mainly associated to subtropical waters during summer. The distribution of juvenile females indicated its preference by lower temperatures and more saline waters. Presence of pregnant females suggests that the eastern tropical Pacific off México represents an ecological key region to the reproductive cycle of P. glauca. Copyright © 2011 Elsevier Ltd. All rights reserved.

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

PubMed

Manrubia, Susanna; Cuesta, José A

2017-04-01

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

Fifty years after Welles and Welles: Distribution and genetic structure of Desert Bighorn Sheep in Death Valley National Park

USGS Publications Warehouse

Epps, Clinton W.; Wehausen, John D.; Sloan, William B.; Holt, Stacy; Creech, Tyler G.; Crowhurst, Rachel S.; Jaeger, Jef R.; Longshore, Kathleen M.; Monello, Ryan J.

2013-01-01

Where possible, we revisited many of the water sources and other locations originally investigated by Welles and Welles (1961) and earlier researchers. We extracted DNA from fecal pellets, carcass tissue samples, and blood samples archived from earlier captures and genotyped them using highly variable genetic markers (15 microsatellite loci) with sufficient power to distinguish individuals and characterize gene flow and genetic structure. We also analyzed DNA samples collected from other bighorn sheep populations extending north to the White Mountains, west to the Inyo Mountains, south to the Avawatz Mountains, and southeast to the Clark Mountain Range, Kingston Range, and Spring Mountains of Nevada. We estimated genetic structure and recent gene flow among nearly all known populations of bighorn sheep in and around Death Valley National Park (DEVA), and used assignment tests to evaluate individual and population-level genetic structure to infer connectivity across the region. We found that bighorn sheep are still widely distributed in mountain ranges throughout DEVA, including many of the areas described by Welles and Welles (1961), although some use patterns appear to have changed and other areas still require resurvey. Gene flow was relatively high through some sections of fairly continuous habitat, such as the Grapevine and Funeral Mountains along the eastern side of Death Valley, but other populations were more isolated. Genetic diversity was relatively high throughout the park. Although southern Death Valley populations were genetically distinct from populations to the southeast, population assignment tests and recent gene flow estimates suggested that individuals occasionally migrate between those regions, indicating the potential for the recent outbreak of respiratory disease in the southern Mojave Desert to spread into the Death Valley system. We recommend careful monitoring of bighorn sheep using remote cameras to check for signs of respiratory disease in southeastern DEVA and ground surveys in the still-understudied southwestern part of DEVA.

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

PubMed Central

Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Singh, N. K.; Singh, Rakesh

2013-01-01

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis. PMID:24367635

Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

PubMed

Vickruck, J L; Richards, M H

2017-05-01

While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

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

MODELING PHYSICAL HABITAT PARAMETERS

EPA Science Inventory

Salmonid populations can be affected by alterations in stream physical habitat. Fish productivity is determined by the stream's physical habitat structure ( channel form, substrate distribution, riparian vegetation), water quality, flow regime and inputs from the watershed (sedim...

Temporal analysis of genetic structure to assess population dynamics of reintroduced swift foxes.

PubMed

Cullingham, Catherine I; Moehrenschlager, Axel

2013-12-01

Reintroductions are increasingly used to reestablish species, but a paucity of long-term postrelease monitoring has limited understanding of whether and when viable populations subsequently persist. We conducted temporal genetic analyses of reintroduced populations of swift foxes (Vulpes velox) in Canada (Alberta and Saskatchewan) and the United States (Montana). We used samples collected 4 years apart, 17 years from the initiation of the reintroduction, and 3 years after the conclusion of releases. To assess program success, we genotyped 304 hair samples, subsampled from the known range in 2000 and 2001, and 2005 and 2006, at 7 microsatellite loci. We compared diversity, effective population size, and genetic connectivity over time in each population. Diversity remained stable over time and there was evidence of increasing effective population size. We determined population structure in both periods after correcting for differences in sample sizes. The geographic distribution of these populations roughly corresponded with the original release locations, which suggests the release sites had residual effects on the population structure. However, given that both reintroduction sites had similar source populations, habitat fragmentation, due to cropland, may be associated with the population structure we found. Although our results indicate growing, stable populations, future connectivity analyses are warranted to ensure both populations are not subject to negative small-population effects. Our results demonstrate the importance of multiple sampling years to fully capture population dynamics of reintroduced populations. Análisis Temporal de la Estructura Genética para Evaluar la Dinámica Poblacional de Zorros (Vulpes velox) Reintroducidos. © 2013 Society for Conservation Biology.

Opinion formation and distribution in a bounded-confidence model on various networks

NASA Astrophysics Data System (ADS)

Meng, X. Flora; Van Gorder, Robert A.; Porter, Mason A.

2018-02-01

In the social, behavioral, and economic sciences, it is important to predict which individual opinions eventually dominate in a large population, whether there will be a consensus, and how long it takes for a consensus to form. Such ideas have been studied heavily both in physics and in other disciplines, and the answers depend strongly both on how one models opinions and on the network structure on which opinions evolve. One model that was created to study consensus formation quantitatively is the Deffuant model, in which the opinion distribution of a population evolves via sequential random pairwise encounters. To consider heterogeneity of interactions in a population along with social influence, we study the Deffuant model on various network structures (deterministic synthetic networks, random synthetic networks, and social networks constructed from Facebook data). We numerically simulate the Deffuant model and conduct regression analyses to investigate the dependence of the time to reach steady states on various model parameters, including a confidence bound for opinion updates, the number of participating entities, and their willingness to compromise. We find that network structure and parameter values both have important effects on the convergence time and the number of steady-state opinion groups. For some network architectures, we observe that the relationship between the convergence time and model parameters undergoes a transition at a critical value of the confidence bound. For some networks, the steady-state opinion distribution also changes from consensus to multiple opinion groups at this critical value.

Finding optimal vaccination strategies for pandemic influenza using genetic algorithms.

PubMed

Patel, Rajan; Longini, Ira M; Halloran, M Elizabeth

2005-05-21

In the event of pandemic influenza, only limited supplies of vaccine may be available. We use stochastic epidemic simulations, genetic algorithms (GA), and random mutation hill climbing (RMHC) to find optimal vaccine distributions to minimize the number of illnesses or deaths in the population, given limited quantities of vaccine. Due to the non-linearity, complexity and stochasticity of the epidemic process, it is not possible to solve for optimal vaccine distributions mathematically. However, we use GA and RMHC to find near optimal vaccine distributions. We model an influenza pandemic that has age-specific illness attack rates similar to the Asian pandemic in 1957-1958 caused by influenza A(H2N2), as well as a distribution similar to the Hong Kong pandemic in 1968-1969 caused by influenza A(H3N2). We find the optimal vaccine distributions given that the number of doses is limited over the range of 10-90% of the population. While GA and RMHC work well in finding optimal vaccine distributions, GA is significantly more efficient than RMHC. We show that the optimal vaccine distribution found by GA and RMHC is up to 84% more effective than random mass vaccination in the mid range of vaccine availability. GA is generalizable to the optimization of stochastic model parameters for other infectious diseases and population structures.

Inference and Analysis of Population Structure Using Genetic Data and Network Theory

PubMed Central

Greenbaum, Gili; Templeton, Alan R.; Bar-David, Shirli

2016-01-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition’s modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). PMID:26888080

Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

PubMed

Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

2016-04-01

Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). Copyright © 2016 by the Genetics Society of America.

M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm.

PubMed

Onyśk, Agnieszka; Boczkowska, Maja

2017-01-01

Simple Sequence Repeat (SSR) markers are one of the most frequently used molecular markers in studies of crop diversity and population structure. This is due to their uniform distribution in the genome, the high polymorphism, reproducibility, and codominant character. Additional advantages are the possibility of automatic analysis and simple interpretation of the results. The M13 tagged PCR reaction significantly reduces the costs of analysis by the automatic genetic analyzers. Here, we also disclose a short protocol of SSR data analysis.

Population genetic structure of Patagonian toothfish (Dissostichus eleginoides) in the Southeast Pacific and Southwest Atlantic Ocean

PubMed Central

Canales-Aguirre, Cristian B.; Galleguillos, Ricardo; Oyarzun, Fernanda X.; Hernández, Cristián E.

2018-01-01

Previous studies of population genetic structure in Dissostichus eleginoides have shown that oceanographic and geographic discontinuities drive in this species population differentiation. Studies have focused on the genetics of D. eleginoides in the Southern Ocean; however, there is little knowledge of their genetic variation along the South American continental shelf. In this study, we used a panel of six microsatellites to test whether D. eleginoides shows population genetic structuring in this region. We hypothesized that this species would show zero or very limited genetic structuring due to the habitat continuity along the South American shelf from Peru in the Pacific Ocean to the Falkland Islands in the Atlantic Ocean. We used Bayesian and traditional analyses to evaluate population genetic structure, and we estimated the number of putative migrants and effective population size. Consistent with our predictions, our results showed no significant genetic structuring among populations of the South American continental shelf but supported two significant and well-defined genetic clusters of D. eleginoides between regions (South American continental shelf and South Georgia clusters). Genetic connectivity between these two clusters was 11.3% of putative migrants from the South American cluster to the South Georgia Island and 0.7% in the opposite direction. Effective population size was higher in locations from the South American continental shelf as compared with the South Georgia Island. Overall, our results support that the continuity of the deep-sea habitat along the continental shelf and the biological features of the study species are plausible drivers of intraspecific population genetic structuring across the distribution of D. eleginoides on the South American continental shelf. PMID:29362690

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.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

PubMed

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics

PubMed Central

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Background Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. Results We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Conclusions Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant. PMID:27711241

Evolutionary dynamics of social dilemmas in structured heterogeneous populations.

PubMed

Santos, F C; Pacheco, J M; Lenaerts, Tom

2006-02-28

Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations.

Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region.

PubMed

Amzati, Gaston S; Pelle, Roger; Muhigwa, Jean-Berckmans B; Kanduma, Esther G; Djikeng, Appolinaire; Madder, Maxime; Kirschvink, Nathalie; Marcotty, Tanguy

2018-05-31

The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa. Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution. Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa. Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes.

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.

Ecophysiology of phototrophic sulfur bacteria in lakes: Vertical distribution of planktonic populations

NASA Technical Reports Server (NTRS)

Guerrero, R.

1985-01-01

The study of purple and green sulfur bacterial populations in nature is of interest for the following reasons: (1) high quantities of biomass, with low species diversity can be collected; (2) study of planktonic life permits one to understand the mechanisms, structural as well as physiological, used to maintain their vertical position without sinking; and (3) they are capable of sulfur oxidations and reductions that act as important intermediates in the global sulfur cycle. Purple and green photosynthetic bacteria, moreover, may be responsible for certain geological deposits. Planktonic phototrophic sulfur bacteria were analyzed in relation to their vertical distribution in the water column. Factors, including competition for light, that determine their sedimentation rates and the numerical changes in species and populations were assessed.

Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh.

PubMed

Sultana, Nasrin; Igawa, Takeshi; Islam, Mohammed Mafizul; Hasan, Mahmudul; Alam, Mohammad Shafiqul; Komaki, Shohei; Kawamura, Kensuke; Khan, Md Mukhlesur Rahman; Sumida, Masayuki

2017-03-17

The five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers. The resultant phylogenetic tree revealed monophyly in each species, notwithstanding the involvement of cryptic species in H. chinensis and H. tigerinus, which are evident from the higher genetic divergence between populations. Bayesian inference of population structure revealed genetic divergence between western and eastern H. tigerinus populations in Bangladesh, suggesting restricted gene flow caused by barriers posed by major rivers. However, genetic distances among populations were generally low. A discrete population is located in the low riverine delta region, which likely reflects long-distance dispersal. These results strongly suggest that the environment specific to this river system has maintained the population structure of H. tigerinus in this region.

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

PubMed

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

2006-01-01

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

Generating a Dynamic Synthetic Population – Using an Age-Structured Two-Sex Model for Household Dynamics

PubMed Central

Namazi-Rad, Mohammad-Reza; Mokhtarian, Payam; Perez, Pascal

2014-01-01

Generating a reliable computer-simulated synthetic population is necessary for knowledge processing and decision-making analysis in agent-based systems in order to measure, interpret and describe each target area and the human activity patterns within it. In this paper, both synthetic reconstruction (SR) and combinatorial optimisation (CO) techniques are discussed for generating a reliable synthetic population for a certain geographic region (in Australia) using aggregated- and disaggregated-level information available for such an area. A CO algorithm using the quadratic function of population estimators is presented in this paper in order to generate a synthetic population while considering a two-fold nested structure for the individuals and households within the target areas. The baseline population in this study is generated from the confidentialised unit record files (CURFs) and 2006 Australian census tables. The dynamics of the created population is then projected over five years using a dynamic micro-simulation model for individual- and household-level demographic transitions. This projection is then compared with the 2011 Australian census. A prediction interval is provided for the population estimates obtained by the bootstrapping method, by which the variability structure of a predictor can be replicated in a bootstrap distribution. PMID:24733522

Calls reveal population structure of blue whales across the southeast Indian Ocean and the southwest Pacific Ocean.

PubMed

Balcazar, Naysa E; Tripovich, Joy S; Klinck, Holger; Nieukirk, Sharon L; Mellinger, David K; Dziak, Robert P; Rogers, Tracey L

2015-11-24

For effective species management, understanding population structure and distribution is critical. However, quantifying population structure is not always straightforward. Within the Southern Hemisphere, the blue whale ( Balaenoptera musculus ) complex is extremely diverse but difficult to study. Using automated detector methods, we identified "acoustic populations" of whales producing region-specific call types. We examined blue whale call types in passive acoustic data at sites spanning over 7,370 km across the southeast Indian Ocean and southwest Pacific Ocean (SWPO) from 2009 to 2012. In the absence of genetic resolution, these acoustic populations offer unique information about the blue whale population complex. We found that the Australian continent acts as a geographic boundary, separating Australia and New Zealand blue whale acoustic populations at the junction of the Indian and Pacific Ocean basins. We located blue whales in previously undocumented locations, including the far SWPO, in the Tasman Sea off the east coast of Australia, and along the Lau Basin near Tonga. Our understanding of population dynamics across this broad scale has significant implications to recovery and conservation management for this endangered species, at a regional and global scale.

Genetic structure of Culex erraticus populations across the Americas.

PubMed

Mendenhall, Ian H; Bahl, Justin; Blum, Michael J; Wesson, Dawn M

2012-05-01

Culex erraticus (Dyar & Knab) is a potential competent vector for several arboviruses such as Eastern and Venezuelan equine encephalitis viruses and West Nile virus. It therefore may play a role in the maintenance and spread of viral populations in areas of concern, including the United States where it occurs in >33 states. However, little information is available on potential barriers to movement across the species' distribution. Here, we analyze genetic variation among Cx. erraticus collected from Colombia, Guatemala, and nine locations in the United States to better understand population structure and connectivity. Comparative sequence analysis of the second internal transcribed spacer and mitochondrial NADH dehydrogenase genes identified two major lineages of sampled populations. One lineage represented the central and eastern United States, whereas the other corresponded to Central America, South America, and the western United States. Hierarchical analysis of genetic variation provided further evidence of regional population structure, although the majority of genetic variation was found to reside within populations, suggestive of large population sizes. Although significant physical barriers such as the Chihuahuan Desert probably constrain the spread of Cx. erraticus, large population sizes and connectivity within regions remain important risk factors that probably contribute to the movement of arboviruses within and between these regions.

Diet shifts and population dynamics of estuarine foraminifera during ecosystem recovery after experimentally induced hypoxia crises

NASA Astrophysics Data System (ADS)

Brouwer, G. M.; Duijnstee, I. A. P.; Hazeleger, J. H.; Rossi, F.; Lourens, L. J.; Middelburg, J. J.; Wolthers, M.

2016-03-01

This study shows foraminiferal dynamics after experimentally induced hypoxia within the wider context of ecosystem recovery. 13C-labeled bicarbonate and glucose were added to the sediments to examine foraminiferal diet shifts during ecosystem recovery and test-size measurements were used to deduce population dynamics. Hypoxia-treated and undisturbed patches were compared to distinguish natural (seasonal) fluctuations from hypoxia-induced responses. The effect of timing of disturbance and duration of recovery were investigated. The foraminiferal diets and population dynamics showed higher fluctuations in the recovering patches compared to the controls. The foraminiferal diet and population structure of Haynesina germanica and Ammonia beccarii responded differentially and generally inversely to progressive stages of ecosystem recovery. Tracer inferred diet estimates in April and June and the two distinctly visible cohorts in the test-size distribution, discussed to reflect reproduction in June, strongly suggest that the ample availability of diatoms during the first month of ecosystem recovery after the winter hypoxia was likely profitable to A. beccarii. Enhanced reproduction itself was strongly linked to the subsequent dietary shift to bacteria. The distribution of the test dimensions of H. germanica indicated that this species had less fluctuation in population structure during ecosystem recovery but possibly reproduced in response to the induced winter hypoxia. Bacteria seemed to consistently contribute more to the diet of H. germanica than diatoms. For the diet and test-size distribution of both species, the timing of disturbance seemed to have a higher impact than the duration of the subsequent recovery period.

Living in the Past: Phylogeography and Population Histories of Indo-Pacific Wrasses (Genus Halichoeres) in Shallow Lagoons versus Outer Reef Slopes

PubMed Central

Ludt, William B.; Bernal, Moisés A.; Bowen, Brian W.; Rocha, Luiz A.

2012-01-01

Sea level fluctuations during glacial cycles affect the distribution of shallow marine biota, exposing the continental shelf on a global scale, and displacing coral reef habitat to steep slopes on oceanic islands. In these circumstances we expect that species inhabiting lagoons should show shallow genetic architecture relative to species inhabiting more stable outer reefs. Here we test this expectation on an ocean-basin scale with four wrasses (genus Halichoeres): H. claudia (N = 194, with ocean-wide distribution) and H. ornatissimus (N = 346, a Hawaiian endemic) inhabit seaward reef slopes, whereas H. trimaculatus (N = 239) and H. margaritaceus (N = 118) inhabit lagoons and shallow habitats throughout the Pacific. Two mitochondrial markers (cytochrome oxidase I and control region) were sequenced to resolve population structure and history of each species. Haplotype and nucleotide diversity were similar among all four species. The outer reef species showed significantly less population structure, consistent with longer pelagic larval durations. Mismatch distributions and significant negative Fu’s F values indicate Pleistocene population expansion for all species, and (contrary to expectations) shallower histories in the outer slope species. We conclude that lagoonal wrasses may persist through glacial habitat disruptions, but are restricted to refugia during lower sea level stands. In contrast, outer reef slope species have homogeneous and well-connected populations through their entire ranges regardless of sea level fluctuations. These findings contradict the hypothesis that shallow species are less genetically diverse as a consequence of glacial cycles. PMID:22701597

Spatial and seasonal dynamics of brook trout populations inhabiting a central Appalachian watershed

USGS Publications Warehouse

Petty, J.T.; Lamothe, P.J.; Mazik, P.M.

2005-01-01

We quantified the watershed-scale spatial population dynamics of brook trout Salvelinus fontinalis in the Second Fork, a third-order tributary of Shavers Fork in eastern West Virginia. We used visual surveys, electrofishing, and mark-recapture techniques to quantify brook trout spawning intensity, population density, size structure, and demographic rates (apparent survival and immigration) throughout the watershed. Our analyses produced the following results. Spawning by brook trout was concentrated in streams with small basin areas (i.e., segments draining less than 3 km2), relatively high alkalinity (>10 mg CaCO3/L), and high amounts of instream cover. The spatial distribution of juvenile and small-adult brook trout within the watershed was relatively stable and was significantly correlated with spawning intensity. However, no such relationship was observed for large adults, which exhibited highly variable distribution patterns related to seasonally important habitat features, including instream cover, stream depth and width, and riparian canopy cover. Brook trout survival and immigration rates varied seasonally, spatially, and among size-classes. Differential survival and immigration tended to concentrate juveniles and small adults in small, alkaline streams, whereas dispersal tended to redistribute large adults at the watershed scale. Our results suggest that spatial and temporal variations in spawning, survival, and movement interact to determine the distribution, abundance, and size structure of brook trout populations at a watershed scale. These results underscore the importance of small tributaries for the persistence of brook trout in this watershed and the need to consider watershed-scale processes when designing management plans for Appalachian brook trout populations. ?? Copyright by the American Fisheries Society 2005.

Quantitative Aspects of Communicative Impairment Ascertained in a Large National Survey of Japanese Children

ERIC Educational Resources Information Center

Oi, Manabu; Fujino, Hiroshi; Tsukidate, Naotake; Kamio, Yoko; Yoshimura, Yuko; Kikuchi, Mitsuru; Hasegawa, Chiaki; Gondou, Keiko; Matsui, Tomoko

2017-01-01

The Japanese version of the Children's Communication Checklist-2 (CCC-2) was rated by caregivers in a large national population sample of 22,871 children aged 3-15 years. The General Communication Composite (GCC) of the CCC-2 exhibited a distribution with a single-factor structure. The GCC distribution between autism spectrum disorders (ASD) and…

Degrees of Isolation: The Impact of Climate Change on the Dispersal and Population Genetic Structure of Two Antarctic Fish Species

NASA Astrophysics Data System (ADS)

Young, E. F.; Belchier, M.; Meredith, M. P.; Tysklind, N.; Carvalho, G. R.

2016-02-01

Understanding the key drivers of larval dispersal and population connectivity in the marine environment is essential for estimating the potential impacts of climate change on the genetic structure and resilience of populations. Small, isolated and fragmented communities will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant, and with a frequent exchange of members. Using a `seascape genetics' approach, combining oceanographic modelling and genetic analyses, we have elucidated the fundamental roles of oceanographic transport and planktonic duration on the connectivity and population genetic structure of two Antarctic fish species with contrasting early life histories, Champsocephalus gunnari and Notothenia rossii. Here, we extend these analyses to consider the impact of rising sea temperatures due to climate change on planktonic dispersal and population connectivity. Using a theoretical approach, the effect of increased water temperatures on mortality rates and species-specific egg and larval phase durations has been incorporated into the models, and the relative impact of these climate-related influences on connectivity and population genetic structure has been investigated. Here we present the key findings of our research and consider the roles of early life history and oceanography in the response of fragmented fish populations to climate change.

Genomic differentiation and demographic histories of Atlantic and Indo-Pacific yellowfin tuna (Thunnus albacares) populations.

PubMed

Barth, J M I; Damerau, M; Matschiner, M; Jentoft, S; Hanel, R

2017-04-13

Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Development and assessment of 30-meter pine density maps for landscape-level modeling of mountain pine beetle dynamics

Treesearch

Benjamin A. Crabb; James A. Powell; Barbara J. Bentz

2012-01-01

Forecasting spatial patterns of mountain pine beetle (MPB) population success requires spatially explicit information on host pine distribution. We developed a means of producing spatially explicit datasets of pine density at 30-m resolution using existing geospatial datasets of vegetation composition and structure. Because our ultimate goal is to model MPB population...

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...

Models of GexSe1-x

NASA Astrophysics Data System (ADS)

Malouin, Marc-André.; Mousseau, Normand

2008-03-01

We present numerical models of chalcogenide glasses constructed using the effective two and three body interaction potential developed by Mauro and Varshneya [1] combined with the activation-relaxation technique (ART nouveau) [2]. Structures are prepared starting from a random distribution, avoiding biases and crystalline remnants. Structural properties are studied mainly via characteristic system measurements including partial and total radial distribution functions, bond angle distributions, mean coordinations and bonds population. Results are shown for GexSe1-x for various x concentrations and compared to both experimental measurements and ab initio simulation results. [1] J.C. Mauro and A.K. Varshneya, J. Am. Ceram. Soc., 89 [7] 2323-6 (2006). [2] R. Malek and N. Mousseau, Phys. Rev. E 62, 7723 (2000).

Genetic structure of winter populations of the endangered Indiana bat (Myotis sodalis) prior to the white nose syndrome epidemic: implications for the risk of disease spread

Treesearch

Maarten J. Vonhof; Sybill K. Amelon; Robert R. Currie; Gary F. McCracken

2016-01-01

The spread of white nose syndrome raises serious concerns about the long-term viability of affected bat species. Here we examine the geographic distribution of genetic variation, levels of population connectivity that may influence the spatial spread of WNS, and the likelihood that recent population declines in regions affected by WNS have led to the loss of unique...

Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

NASA Astrophysics Data System (ADS)

Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

2008-02-01

The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).

PubMed

Palop-Esteban, M; Segarra-Moragues, J G; González-Candelas, F

2007-09-01

Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed.

Habitat suitability of patch types: a case study of the Yosemite toad

USGS Publications Warehouse

Liang, Christina T.; Stohlgren, Thomas J.

2011-01-01

Understanding patch variability is crucial in understanding the spatial population structure of wildlife species, especially for rare or threatened species. We used a well-tested maximum entropy species distribution model (Maxent) to map the Yosemite toad (Anaxyrus (= Bufo) canorus) in the Sierra Nevada mountains of California. Twenty-six environmental variables were included in the model representing climate, topography, land cover type, and disturbance factors (e.g., distances to agricultural lands, fire perimeters, and timber harvest areas) throughout the historic range of the toad. We then took a novel approach to the study of spatially structured populations by applying the species-environmental matching model separately for 49 consistently occupied sites of the Yosemite toad compared to 27 intermittently occupied sites. We found that the distribution of the entire population was highly predictable (AUC = 0.95±0.03 SD), and associated with low slopes, specific vegetation types (wet meadow, alpine-dwarf shrub, montane chaparral, red fir, and subalpine conifer), and warm temperatures. The consistently occupied sites were also associated with these same factors, and they were also highly predictable (AUC = 0.95±0.05 SD). However, the intermittently occupied sites were associated with distance to fire perimeter, a slightly different response to vegetation types, distance to timber harvests, and a much broader set of aspect classes (AUC = 0.90±0.11 SD). We conclude that many studies of species distributions may benefit by modeling spatially structured populations separately. Modeling and monitoring consistently-occupied sites may provide a realistic snapshot of current species-environment relationships, important climatic and topographic patterns associated with species persistence patterns, and an understanding of the plasticity of the species to respond to varying climate regimes across its range. Meanwhile, modeling and monitoring of widely dispersing individuals and intermittently occupied sites may uncover environmental thresholds and human-related threats to population persistence.

Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation.

PubMed

Zhang, Q; Chiang, T Y; George, M; Liu, J Q; Abbott, R J

2005-10-01

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N(ST) = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N(ST) > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.

Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

PubMed Central

Nicola, Marcela V; Sede, Silvana M; Pozner, Raúl; Johnson, Leigh A

2014-01-01

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central-western and south-eastern Patagonia, consistent with long-term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range. PMID:25540689

Isolation, characterization, and cross-species amplification of polymorphic microsatellite markers for Pilosocereus machrisii (Cactaceae).

PubMed

Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Moraes, Evandro M

2011-08-01

Microsatellite primers were developed in Pilosocereus machrisii, a columnar cactus with a patchy distribution in eastern tropical South America, to assess its genetic diversity and population structure. Eleven microsatellite markers were developed, of which one was monomorphic among 51 individuals from two populations. The number of alleles per polymorphic locus ranged from two to eight, and the total number of alleles was 57. From the 11 isolated loci, nine were successfully amplified in the other four Pilosocereus species. The results showed that these markers will be useful for studies of genetic diversity, patterns of gene flow, and population genetic structure in P. machrisii, as well as across other congeneric species.

Limits to gene flow in a cosmopolitan marine planktonic diatom.

PubMed

Casteleyn, Griet; Leliaert, Frederik; Backeljau, Thierry; Debeer, Ann-Eline; Kotaki, Yuichi; Rhodes, Lesley; Lundholm, Nina; Sabbe, Koen; Vyverman, Wim

2010-07-20

The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.

Enteroaggregative Escherichia coli have evolved independently as distinct complexes within the E. coli population with varying ability to cause disease.

PubMed

Chattaway, Marie Anne; Jenkins, Claire; Rajendram, Dunstan; Cravioto, Alejandro; Talukder, Kaisar Ali; Dallman, Tim; Underwood, Anthony; Platt, Steve; Okeke, Iruka N; Wain, John

2014-01-01

Enteroaggregative E. coli (EAEC) is an established diarrhoeagenic pathotype. The association with virulence gene content and ability to cause disease has been studied but little is known about the population structure of EAEC and how this pathotype evolved. Analysis by Multi Locus Sequence Typing of 564 EAEC isolates from cases and controls in Bangladesh, Nigeria and the UK spanning the past 29 years, revealed multiple successful lineages of EAEC. The population structure of EAEC indicates some clusters are statistically associated with disease or carriage, further highlighting the heterogeneous nature of this group of organisms. Different clusters have evolved independently as a result of both mutational and recombination events; the EAEC phenotype is distributed throughout the population of E. coli.

Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers.

PubMed

Pazmiño, Diana A; Maes, Gregory E; Green, Madeline E; Simpfendorfer, Colin A; Hoyos-Padilla, E Mauricio; Duffy, Clinton J A; Meyer, Carl G; Kerwath, Sven E; Salinas-de-León, Pelayo; van Herwerden, Lynne

2018-05-01

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise Φ ST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F ST  = 0.023-0.035), mtDNA exhibited more divergence (Φ ST  = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.

Spatial structure and distribution of small pelagic fish in the northwestern Mediterranean Sea.

PubMed

Saraux, Claire; Fromentin, Jean-Marc; Bigot, Jean-Louis; Bourdeix, Jean-Hervé; Morfin, Marie; Roos, David; Van Beveren, Elisabeth; Bez, Nicolas

2014-01-01

Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall's basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.

Extensive population structure in San, Khoe, and mixed ancestry populations from southern Africa revealed by 44 short 5-SNP haplotypes.

PubMed

Schlebusch, Carina M; Soodyall, Himlya

2012-12-01

The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Genetic studies [mitochondrial deoxyribonucleic acid (DNA) and Y-chromosome] conducted on San and Khoe groups revealed that they harbor some of the most divergent lineages found in living peoples throughout the world. Recently, high-density, autosomal, single-nucleotide polymorphism (SNP)-array studies confirmed the early divergence of Khoe-San population groups from all other human populations. The present study made use of 220 autosomal SNP markers (in the format of both haplotypes and genotypes) to examine the population structure of various San and Khoe groups and their relationship to other neighboring groups. Whereas analyses based on the genotypic SNP data only supported the division of the included populations into three main groups-Khoe-San, Bantu-speakers, and non-African populations-haplotype analyses revealed finer structure within Khoe-San populations. By the use of only 44 short SNP haplotypes (compiled from a total of 220 SNPs), most of the Khoe-San groups could be resolved as separate groups by applying STRUCTURE analyses. Therefore, by carefully selecting a few SNPs and combining them into haplotypes, we were able to achieve the same level of population distinction that was achieved previously in high-density SNP studies on the same population groups. Using haplotypes proved to be a very efficient and cost-effective way to study population structure. Copyright © 2013 Wayne State University Press, Detroit, Michigan 48201-1309.

From diagnostics to metagenomics: Applications of DNA-based tools in forest pathology

Treesearch

Amy L. Ross-Davis; Mee-Sook Kim; Jane E. Stewart; John W. Hanna; John D. Shaw; Ned B. Klopfenstein

2013-01-01

Advances in molecular technology provide an accessible set of tools to 1) help forest pathologists detect, identify, and monitor forest pathogens, 2) examine the evolutionary relationships and global distributions of forest pathogens and their hosts, 3) assess the diversity and structure of host and pathogen populations, and 4) evaluate the structure and function of...

Maternity roosts of bats at the Bosque Del Apache National Wildlife Refuge: A preliminary report

Treesearch

Alice Chung-MacCoubrey

1999-01-01

Historic and recent changes in the structure, composition, and distribution of riparian forests have likely influenced populations of bats through their effects on habitat quality for reproductive females. This project seeks to identify natural structures used by maternity colonies, determine criteria used in the selection of these roosts, and interpret how historic...

Fine-scale genetic structure of bull trout at the southern limit of their distribution

Treesearch

A. Whiteley; P. Spruell; B. Rieman; F. Allendorf

2006-01-01

We used six polymorphic microsatellite loci to analyze the population genetic structure of bull trout Salvelinus confluentus in the Boise River, Idaho, and we compared our results with previous data from similarly sized river systems in western North America. Within the Boise River, we found low genetic variation within and significant...

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

PubMed

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

2018-01-01

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

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

PubMed Central

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

2018-01-01

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

Genetic admixture and lineage separation in a southern Andean plant

PubMed Central

Morello, Santiago; Sede, Silvana M.

2016-01-01

Mountain uplifts have generated new ecologic opportunities for plants, and triggered evolutionary processes, favouring an increase on the speciation rate in all continents. Moreover, mountain ranges may act as corridors or barriers for plant lineages and populations. In South America a high rate of diversification has been linked to Andean orogeny during Pliocene/Miocene. More recently, Pleistocene glacial cycles have also shaped species distribution and demography. The endemic genus Escallonia is known to have diversified in the Andes. Species with similar morphology obscure species delimitation and plants with intermediate characters occur naturally. The aim of this study is to characterize genetic variation and structure of two widespread species of Escallonia: E. alpina and E. rubra. We analyzed the genetic variation of populations of the entire distribution range of the species and we also included those with intermediate morphological characters; a total of 94 accessions from 14 populations were used for the Amplified Fragment Length Polymorphism (AFLP) analysis. Plastid DNA sequences (trnS-trnG, 3′trnV-ndhC intergenic spacers and the ndhF gene) from sixteen accessions of Escallonia species were used to construct a Statistical Parsimony network. Additionally, we performed a geometric morphometrics analysis on 88 leaves from 35 individuals of the two E. alpina varieties to further study their differences. Wright’s Fst and analysis of molecular variance tests performed on AFLP data showed a significant level of genetic structure at the species and population levels. Intermediate morphology populations showed a mixed genetic contribution from E. alpina var. alpina and E. rubra both in the Principal Coordinates Analysis (PCoA) and STRUCTURE. On the other hand, E. rubra and the two varieties of E. alpina are well differentiated and assigned to different genetic clusters. Moreover, the Statistical Parsimony network showed a high degree of divergence between the varieties of E. alpina: var. alpina is more closely related to E. rubra and other species than to its own counterpart E. alpina var. carmelitana. Geometric morphometrics analysis (Elliptic Fourier descriptors) revealed significant differences in leaf shape between varieties. We found that diversity in Escallonia species analyzed here is geographically structured and deep divergence between varieties of E. alpina could be associated to ancient evolutionary events like orogeny. Admixture in southern populations could be the result of hybridization at the margins of the parental species’ distribution range. PMID:27179539

Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude.

PubMed

Hasselman, Daniel J; Ricard, Daniel; Bentzen, Paul

2013-03-01

Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure. © 2013 Blackwell Publishing Ltd.

The genetic structure of a relict population of wood frogs

USGS Publications Warehouse

Scherer, Rick; Muths, Erin; Noon, Barry; Oyler-McCance, Sara

2012-01-01

Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulations), and this result was further supported by factorial component analysis. In addition, an estimate of FST (FST = 0.0675, P value \\0.0001) supported the genetic differentiation of the two clusters. Estimates of migration rates among the two subpopulations were low, as were estimates of genetic variability. Conservation of the population of wood frogs may be improved by increasing the spatial distribution of the population and improving gene flow between the subpopulations. Construction or restoration of wetlands in the landscape between the clusters has the potential to address each of these objectives.

Population Genetic Structure of Monimopetalum chinense (Celastraceae), an Endangered Endemic Species of Eastern China

PubMed Central

XIE, GUO-WEN; WANG, DE-LIAN; YUAN, YONG-MING; GE, XUE-JUN

2005-01-01

• Background and Aims Monimopetalum chinense (Celastraceae) standing for the monotypic genus is endemic to eastern China. Its conservation status is vulnerable as most populations are small and isolated. Monimopetalum chinense is capable of reproducing both sexually and asexually. The aim of this study was to understand the genetic structure of M. chinense and to suggest conservation strategies. • Methods One hundred and ninety individuals from ten populations sampled from the entire distribution area of M. chinense were investigated by using inter-simple sequence repeats (ISSR). • Key Results A total of 110 different ISSR bands were generated using ten primers. Low levels of genetic variation were revealed both at the species level (Isp = 0·183) and at the population level (Ipop = 0·083). High clonal diversity (D = 0·997) was found, and strong genetic differentiation among populations was detected (49·06 %). • Conclusions Small population size, possible inbreeding, limited gene flow due to short distances of seed dispersal, fragmentation of the once continuous range and subsequent genetic drift, may have contributed to shaping the population genetic structure of the species. PMID:15710646

No population genetic structure in a widespread aquatic songbird from the Neotropics

USGS Publications Warehouse

Cadena, Carlos Daniel; Gutierrez-Pinto, Natalia; Davila, Nicolas; Chesser, R. Terry

2011-01-01

Neotropical lowland organisms often show marked population genetic structure, suggesting restricted migration among populations. However, most phylogeographic studies have focused on species inhabiting humid forest interior. Little attention has been devoted to the study of species with ecologies conducive to dispersal, such as those of more open and variable environments associated with watercourses. Using mtDNA sequences, we examined patterns of genetic variation in a widely distributed Neotropical songbird of aquatic environments, the Yellow-hooded Blackbird (Icteridae, Chrysomus icterocephalus). In contrast to many forest species, Yellow-hooded Blackbirds showed no detectable genetic structure across their range, which includes lowland populations on both sides of the Andes, much of northeastern South America, Amazonia, as well as a phenotypically distinct highland population in Colombia. A coalescent-based analysis of the species indicated that its effective population size has increased considerably, suggesting a range expansion. Our results support the hypothesis that species occurring in open habitats and tracking temporally dynamic environments should show increased dispersal propensities (hence gene flow) relative to species from closed and more stable environments. The phenotypic and behavioral variation among populations of our study species appears to have arisen recently and perhaps in the face of gene flow.

Making sense of snapshot data: ergodic principle for clonal cell populations

PubMed Central

2017-01-01

Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. PMID:29187636

Making sense of snapshot data: ergodic principle for clonal cell populations.

PubMed

Thomas, Philipp

2017-11-01

Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. © 2017 The Author(s).

What can otolith shape analysis tell us about population structure of the European sardine, Sardina pilchardus, from Atlantic and Mediterranean waters?

NASA Astrophysics Data System (ADS)

Jemaa, Sharif; Bacha, Mahmoud; Khalaf, Gaby; Dessailly, David; Rabhi, Khalef; Amara, Rachid

2015-02-01

The European sardine, Sardina pilchardus, exhibits a complex population structure, which has produced conflicting results in previous genetic studies. Despite its importance in the fisheries industry, stock delineation for management and conservation purposes is still a matter of debate throughout the distribution range of the species. This study examines whether otolith shapes are more efficient than genetic markers to detect population structure in pelagic species with large population sizes. Sardines were analyzed from 15 sampling localities in the Northeast Atlantic and Mediterranean Sea covering almost the whole distribution range of the species. A combination of otolith shape indices and elliptic Fourier descriptors was investigated by multivariate statistical procedures. Within the studied area, three distinct groups were identified with an overall correct classification of 77%. Group A: northern Mediterranean Sea and Gulf of Gabès; group B: Atlantic Morocco-south Alboran-Algero-provençal coasts; and group C: European Atlantic coast. The Almeria-Oran front and the Gibraltar strait are not an efficient barrier for sardine population separation as there seems to be exchanges between populations of the south-western Mediterranean Sea and those of the Moroccan Atlantic Ocean coast or Gulf of Cadiz. The results are discussed in relation to environmental conditions, oceanographic features, and physical barriers to dispersal in the study area, and compared with those obtained by previous genetic, morphometric, and meristic data. For pelagic species with high gene flow, present results highlighted the need to take into account the identification of phenotypic stocks to ensure sustainable fishery benefits and efficient conservation as they may have unique demographic properties and responses to exploitation.

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations.

PubMed

Wang, Yuchen; Lu, Dongsheng; Chung, Yeun-Jun; Xu, Shuhua

2018-01-01

Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied. We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant. These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

Comparison of mitochondrial DNA control region sequence and microsatellite DNA analyses in estimating population structure and gene flow rates in Atlantic sturgeon Acipenser oxyrinchus

USGS Publications Warehouse

Wirgin, I.; Waldman, J.; Stabile, J.; Lubinski, B.; King, T.

2002-01-01

Atlantic sturgeon Acipenser oxyrinchus is large, long-lived, and anadromous with subspecies distributed along the Atlantic (A. oxyrinchus oxyrinchus) and Gulf of Mexico (A. o. desotoi) coasts of North America. Although it is not certain if extirpation of some population units has occurred, because of anthropogenic influences abundances of all populations are low compared with historical levels. Informed management of A. oxyrinchus demands a detailed knowledge of its population structure, levels of genetic diversity, and likelihood to home to natal rivers. We compared the use of mitochondrial DNA (mtDNA) control region sequence and microsatellite nuclear DNA (nDNA) analyses in identifying the stock structure and homing fidelity of Atlantic and Gulf coast populations of A. oxyrinchus. The approaches were concordant in that they revealed moderate to high levels of genetic diversity and suggested that populations of Atlantic sturgeon are highly structured. At least six genetically distinct management units were detected using the two approaches among the rivers surveyed. Mitochondrial DNA sequences revealed a significant cline in haplotype diversity along the Atlantic coast with monomorphism observed in Canadian populations. High levels of nDNA diversity were also observed among populations along the Atlantic coast, including the two Canadian populations, probably resulting from the more rapid rate of mutational and evolutionary change at microsatellite loci. Estimates of gene flow among populations were similar between both approaches with the exception that because of mtDNA monomorphism in Canadian populations, gene flow estimates between them were unobtainable. Analyses of both genomes provided high resolution and confidence in characterizing the population structure of Atlantic sturgeon. Microsatellite analysis was particularly informative in delineating population structure in rivers that were recently glaciated and may prove diagnostic in rivers that are geographically proximal along the south Atlantic coast of the US.

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

Evolutionary dynamics of incubation periods

PubMed Central

Ottino-Loffler, Bertrand; Scott, Jacob G

2017-01-01

The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease. PMID:29266000

Evolutionary dynamics of incubation periods.

PubMed

Ottino-Loffler, Bertrand; Scott, Jacob G; Strogatz, Steven H

2017-12-21

The incubation period for typhoid, polio, measles, leukemia and many other diseases follows a right-skewed, approximately lognormal distribution. Although this pattern was discovered more than sixty years ago, it remains an open question to explain its ubiquity. Here, we propose an explanation based on evolutionary dynamics on graphs. For simple models of a mutant or pathogen invading a network-structured population of healthy cells, we show that skewed distributions of incubation periods emerge for a wide range of assumptions about invader fitness, competition dynamics, and network structure. The skewness stems from stochastic mechanisms associated with two classic problems in probability theory: the coupon collector and the random walk. Unlike previous explanations that rely crucially on heterogeneity, our results hold even for homogeneous populations. Thus, we predict that two equally healthy individuals subjected to equal doses of equally pathogenic agents may, by chance alone, show remarkably different time courses of disease.

Lithotype characterizations by Nuclear Magnetic Resonance (NMR): A case study on limestone and associated rocks from the eastern Dahomey Basin, Nigeria

NASA Astrophysics Data System (ADS)

Olatinsu, O. B.; Olorode, D. O.; Clennell, B.; Esteban, L.; Josh, M.

2017-05-01

Three representative rock types (limestone, sandstone, and shale) and glauconite samples collected from Ewekoro Quarry, eastern Dahomey Basin in Nigeria were characterized using low field 2 MHz and 20 MHz Nuclear Magnetic Resonance (NMR) techniques. NMR T2 relaxation time decay measurement was conducted on disc samples under partial water-saturation and full water-saturation conditions using CPMG spin-echo routine. The T2 relaxation decay was converted into T2 distribution in the time domain to assess and evaluate the pore size distribution of the samples. Good agreement exists between water content from T2 NMR distributions and water imbibition porosity (WIP) technique. Results show that the most useful characteristics to discriminate the different facies come from full saturation NMR 2 MHz pore size distribution (PSD). Shale facies depict a quasi-unimodal distribution with greater than 90% contribution from clay bound water component (T2s) coupled to capillary bound water component (T2i) centred on 2 ms. The other facies with well connected pore structure show either bimodal or trimodal T2 distribution composed of the similar clay bound water component centred on 0.3 ms and quasi-capillary bound water component centred on 10 ms. But their difference depends on the movable water T2 component (T2l) that does not exist in the glauconite facies (bimodal distribution) while it exists in both the sandstone and limestone facies. The basic difference between the limestone and sandstone facies is related to the longer T2 coupling: T2i and T2l populations are coupled in sandstone generating a single population which convolves both populations (bimodal distribution). Limestone with a trimodal distribution attests to the fact that carbonate rocks have more complex pore system than siliclastic rocks. The degree of pore connectivity is highest in sandstone, followed by limestone and least in glauconite. Therefore a basic/quick NMR log run on samples along a geological formation can provide precise lithofacies characterization with quantitative information on pore size, structure and distributions.

On the Improvement of Convergence Performance for Integrated Design of Wind Turbine Blade Using a Vector Dominating Multi-objective Evolution Algorithm

NASA Astrophysics Data System (ADS)

Wang, L.; Wang, T. G.; Wu, J. H.; Cheng, G. P.

2016-09-01

A novel multi-objective optimization algorithm incorporating evolution strategies and vector mechanisms, referred as VD-MOEA, is proposed and applied in aerodynamic- structural integrated design of wind turbine blade. In the algorithm, a set of uniformly distributed vectors is constructed to guide population in moving forward to the Pareto front rapidly and maintain population diversity with high efficiency. For example, two- and three- objective designs of 1.5MW wind turbine blade are subsequently carried out for the optimization objectives of maximum annual energy production, minimum blade mass, and minimum extreme root thrust. The results show that the Pareto optimal solutions can be obtained in one single simulation run and uniformly distributed in the objective space, maximally maintaining the population diversity. In comparison to conventional evolution algorithms, VD-MOEA displays dramatic improvement of algorithm performance in both convergence and diversity preservation for handling complex problems of multi-variables, multi-objectives and multi-constraints. This provides a reliable high-performance optimization approach for the aerodynamic-structural integrated design of wind turbine blade.

Parameter estimation techniques based on optimizing goodness-of-fit statistics for structural reliability

NASA Technical Reports Server (NTRS)

Starlinger, Alois; Duffy, Stephen F.; Palko, Joseph L.

1993-01-01

New methods are presented that utilize the optimization of goodness-of-fit statistics in order to estimate Weibull parameters from failure data. It is assumed that the underlying population is characterized by a three-parameter Weibull distribution. Goodness-of-fit tests are based on the empirical distribution function (EDF). The EDF is a step function, calculated using failure data, and represents an approximation of the cumulative distribution function for the underlying population. Statistics (such as the Kolmogorov-Smirnov statistic and the Anderson-Darling statistic) measure the discrepancy between the EDF and the cumulative distribution function (CDF). These statistics are minimized with respect to the three Weibull parameters. Due to nonlinearities encountered in the minimization process, Powell's numerical optimization procedure is applied to obtain the optimum value of the EDF. Numerical examples show the applicability of these new estimation methods. The results are compared to the estimates obtained with Cooper's nonlinear regression algorithm.

Genetic structure of Mexican Mestizo women with breast cancer based on three STR loci.

PubMed

Calderón-Garcidueñas, Ana L; Rivera-Prieto, Roxana A; Ortíz-Lopez, Rocio; Rivas, Fernando; Barrera-Saldaña, Hugo A; Peñaloza-Espinosa, Rosenda I; Cerda-Flores, Ricardo M

2008-01-01

The aim of this population genetics study was to compare the genetic structure of Mexican women with breast cancer (BrCa) with previously reported data of four random populations (Nuevo León, Hispanics, Chihuahua, and Central Region of Mexico). A sample of 115 unrelated women with BrCa and whose four grandparents were born in five zones of Mexico were interviewed at a reference hospital in Northeastern Mexico. Noncodifying STRs D7S820, D13S317, and D16S39 were analyzed; genotype distribution was in agreement with Hardy-Weinberg expectations for all three markers. Similar allele frequencies among four random populations and this selected population were found. According with this and previous studies using molecular and nonmolecular nuclear DNA markers not associated with any disease, Mexican Mestizo population is genetically homogeneous and therefore, genetic causes of BrCa are less heterogeneous, simplifying genetic epidemiologic studies.

The roles of competition and habitat in the dynamics of populations and species distributions Ecology

Treesearch

Charles B. Yackulic; Janice Reid; James D. Nichols; James E. Hines; Raymond Davis; Eric Forsman

2014-01-01

The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition’s importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl,...

A Precise Description of the Hot Classical Belt from the High Lattitude Ecliptic Survey

NASA Astrophysics Data System (ADS)

Petit, Jean-Marc; Kavelaars, John J.; Gladman, Brett; Jones, Lynne; Parker, Joel

2014-11-01

The Canada-France Ecliptic Plane Survey (CFEPS) determined the orbital structure of the Cold classical belt, a component restricted to the semimajor-axis range between the 3:2 and 2:1 mean motion resonances with Neptune. It also showed that the high-inclination component of the inner, main and outer belt form a continuous population, but failed to constrain the inclination distribution itself.The High Latitude survey (HiLat) covered 600 sq.deg. from 15 to 90 deg. ecliptic latitude to address this question. We find that the Brown-like gaussian inclination distribution for each survey separately requires incompatible width of the distribution. Rather, it appears that a gaussian centered on a high (10 to 15 deg.) latitude, à la Gulbis et al. (2010) provides a better match to the observations. We also confirm that the resonant populations have an inclination distribution compatible with a common origin with the Hot component. The hot component itself comes from a constraint q range (35 < q < 41 AU) slightly larger than what some researchers associated with the scattered disk. This enlarged q range place contraints on the eccentricity reached by Neptune in its early history and the duration of this phase.With this more accurate orbital distribution and a refined modelling of the surveys, we present new population estimates of the various populations.

Population structure of the alligator snapping turtle, macrochelys temminckii, on the western edge of its distribution

USGS Publications Warehouse

Riedle, J.D.; Shipman, P.A.; Fox, S. F.; Hackler, J.C.; Lesie, D.M.

2008-01-01

A mark-recapture project on Macrochelys temminckii was conducted between 1997 and 2000 at Sequoyah National Wildlife Refuge, Muskogee and Sequoyah counties, in eastern Oklahoma. Turtles were captured in all streams and exhibited equal sex ratios, marked sexual-size dimorphism, and population densities between 28 and 34 animals per km stretch of stream. There was evidence of past population perturbations, with very few large adults captured, and a cohort of subadults highly underrepresented. ?? 2008 Chelonian Research Foundation.

The leverage of demographic dynamics on carbon dioxide emissions: does age structure matter?

PubMed

Zagheni, Emilio

2011-02-01

This article provides a methodological contribution to the study of the effect of changes in population age structure on carbon dioxide (CO(2)) emissions. First, I propose a generalization of the IPAT equation to a multisector economy with an age-structured population and discuss the insights that can be obtained in the context of stable population theory. Second, I suggest a statistical model of household consumption as a function of household size and age structure to quantitatively evaluate the extent of economies of scale in consumption of energy-intensive goods, and to estimate age-specific profiles of consumption of energy-intensive goods and of CO(2) emissions. Third, I offer an illustration of the methodologies using data for the United States. The analysis shows that per-capita CO(2) emissions increase with age until the individual is in his or her 60s, and then emissions tend to decrease. Holding everything else constant, the expected change in U.S. population age distribution during the next four decades is likely to have a small, but noticeable, positive impact on CO(2) emissions.

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

PubMed Central

Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

2015-01-01

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573

Effects of recruitment, growth, and exploitation on walleye population size structure in northern Wisconsin lakes

USGS Publications Warehouse

Hansen, Michael J.; Nate, Nancy A.

2014-01-01

We evaluated the dynamics of walleye Sander vitreus population size structure, as indexed by the proportional size distribution (PSD) of quality-length fish, in Escanaba Lake during 1967–2003 and in 204 other lakes in northern Wisconsin during 1990–2011. We estimated PSD from angler-caught walleyes in Escanaba Lake and from spring electrofishing in 204 other lakes, and then related PSD to annual estimates of recruitment to age-3, length at age 3, and annual angling exploitation rate. In Escanaba Lake during 1967–2003, annual estimates of PSD were highly dynamic, growth (positively) explained 35% of PSD variation, recruitment explained only 3% of PSD variation, and exploitation explained only 7% of PSD variation. In 204 other northern Wisconsin lakes during 1990–2011, PSD varied widely among lakes, recruitment (negatively) explained 29% of PSD variation, growth (positively) explained 21% of PSD variation, and exploitation explained only 4% of PSD variation. We conclude that population size structure was most strongly driven by recruitment and growth, rather than exploitation, in northern Wisconsin walleye populations. Studies of other species over wide spatial and temporal ranges of recruitment, growth, and mortality are needed to determine which dynamic rate most strongly influences population size structure of other species. Our findings indicate a need to be cautious about assuming exploitation is a strong driver of walleye population size structure.

Bacterioplankton communities of Crater Lake, OR: Dynamic changes with euphotic zone food web structure and stable deep water populations

USGS Publications Warehouse

Urbach, E.; Vergin, K.L.; Larson, G.L.; Giovannoni, S.J.

2007-01-01

The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by ??-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting. ?? 2007 Springer Science+Business Media B.V.

The Cuban Population of the United States: The Results of the 1980 U.S. Census of Population. Occasional Papers Series, Dialogues #40.

ERIC Educational Resources Information Center

Perez, Lisandro

The principal results of the 1980 United States Census regarding Cuban Americans are summarized and analyzed in this report. The presentation is divided into the following sections: (1) residence and geographic distribution; (2) age and sex composition; (3) fertility; (4) family structure and marital status; (5) educational characteristics; (6)…

Development of a site fidelity index based on population capture-recapture data

PubMed Central

Ferrari, Mariano A.; Crespo, Enrique A.; Coscarella, Mariano A.

2018-01-01

Background Site fidelity is considered as an animal’s tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal’s life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies. Methods This investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson’s dolphins (Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability (p). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case. Results Eight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index—SSFI). Discussion The SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons. PMID:29761064

Development of a site fidelity index based on population capture-recapture data.

PubMed

Tschopp, Ayelen; Ferrari, Mariano A; Crespo, Enrique A; Coscarella, Mariano A

2018-01-01

Site fidelity is considered as an animal's tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal's life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies. This investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson's dolphins ( Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability ( p ). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case. Eight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index-SSFI). The SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons.

Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen.

PubMed

Brar, Simren; Tsui, Clement K M; Dhillon, Braham; Bergeron, Marie-Josée; Joly, David L; Zambino, P J; El-Kassaby, Yousry A; Hamelin, Richard C

2015-01-01

White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.

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

Molecular Markers Reveal Limited Population Genetic Structure in a North American Corvid, Clark’s Nutcracker (Nucifraga columbiana)

PubMed Central

Dohms, Kimberly M.; Burg, Theresa M.

2013-01-01

The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark’s nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker’s encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark’s nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark’s nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark’s nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark’s nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets. PMID:24223982

Quantitative Aspects of Communicative Impairment Ascertained in a Large National Survey of Japanese Children.

PubMed

Oi, Manabu; Fujino, Hiroshi; Tsukidate, Naotake; Kamio, Yoko; Yoshimura, Yuko; Kikuchi, Mitsuru; Hasegawa, Chiaki; Gondou, Keiko; Matsui, Tomoko

2017-10-01

The Japanese version of the Children's Communication Checklist-2 (CCC-2) was rated by caregivers in a large national population sample of 22,871 children aged 3-15 years. The General Communication Composite (GCC) of the CCC-2 exhibited a distribution with a single-factor structure. The GCC distribution between autism spectrum disorders (ASD) and language impairment (LI) groups in the general population fit inside a bell curve with significant overlap with the general population, and a continuum was evident between groups. No evidence of a natural cutoff that would differentiate categorically affected from unaffected children was seen. The Social Interaction Deviance Composite (SIDC) supported the notion that ASD and LI are on the opposite endpoints of a SIDC continuum of communication impairment.

A Landscape Approach to Invasive Species Management.

PubMed

Lurgi, Miguel; Wells, Konstans; Kennedy, Malcolm; Campbell, Susan; Fordham, Damien A

2016-01-01

Biological invasions are not only a major threat to biodiversity, they also have major impacts on local economies and agricultural production systems. Once established, the connection of local populations into metapopulation networks facilitates dispersal at landscape scales, generating spatial dynamics that can impact the outcome of pest-management actions. Much planning goes into landscape-scale invasive species management. However, effective management requires knowledge on the interplay between metapopulation network topology and management actions. We address this knowledge gap using simulation models to explore the effectiveness of two common management strategies, applied across different extents and according to different rules for selecting target localities in metapopulations with different network topologies. These management actions are: (i) general population reduction, and (ii) reduction of an obligate resource. The reduction of an obligate resource was generally more efficient than population reduction for depleting populations at landscape scales. However, the way in which local populations are selected for management is important when the topology of the metapopulation is heterogeneous in terms of the distribution of connections among local populations. We tested these broad findings using real-world scenarios of European rabbits (Oryctolagus cuniculus) infesting agricultural landscapes in Western Australia. Although management strategies targeting central populations were more effective in simulated heterogeneous metapopulation structures, no difference was observed in real-world metapopulation structures that are highly homogeneous. In large metapopulations with high proximity and connectivity of neighbouring populations, different spatial management strategies yield similar outcomes. Directly considering spatial attributes in pest-management actions will be most important for metapopulation networks with heterogeneously distributed links. Our modelling framework provides a simple approach for identifying the best possible management strategy for invasive species based on metapopulation structure and control capacity. This information can be used by managers trying to devise efficient landscape-oriented management strategies for invasive species and can also generate insights for conservation purposes.

Microscale vicariance and diversification of Western Balkan caddisflies linked to karstification.

PubMed

Previšić, Ana; Schnitzler, Jan; Kučinić, Mladen; Graf, Wolfram; Ibrahimi, Halil; Kerovec, Mladen; Pauls, Steffen U

2014-03-01

The karst areas in the Dinaric region of the Western Balkan Peninsula are a hotspot of freshwater biodiversity. Many investigators have examined diversification of the subterranean freshwater fauna in these karst systems. However, diversification of surface-water fauna remains largely unexplored. We assessed local and regional diversification of surface-water species in karst systems and asked whether patterns of population differentiation could be explained by dispersal-diversification processes or allopatric diversification following karst-related microscale vicariance. We analyzed mitochondrial cytochrome c oxidase subunit I (mtCOI) sequence data of 4 caddisfly species (genus Drusus ) in a phylogeographic framework to assess local and regional population genetic structure and Pliocene/Pleistocene history. We used BEAST software to assess the timing of intraspecific diversification of the target species. We compared climate envelopes of the study species and projected climatically suitable areas during the last glacial maximum (LGM) to assess differences in the species climatic niches and infer potential LGM refugia. The haplotype distribution of the 4 species (324 individuals from 32 populations) was characterized by strong genetic differentiation with few haplotypes shared among populations (16%) and deep divergence among populations of the 3 endemic species, even at local scales. Divergence among local populations of endemics often exceeded divergence among regional and continental clades of the widespread D. discolor . Major divergences among regional populations dated to 2.0 to 0.5 Mya. Species distribution model projections and genetic structure suggest that the endemic species persisted in situ and diversified locally throughout multiple Pleistocene climate cycles. The pattern for D. discolor was different and consistent with multiple invasions into the region. Patterns of population genetic structure and diversification were similar for the 3 regional endemic Drusus species and consistent with microscale vicariance after the onset of intensified karstification in the Dinaric region. Karstification may induce microscale vicariance of running surface-water habitats and probably promotes allopatric fragmentation of stream insects at small spatial scales.

New record of Steinernema arenarium (Artyukhovsky) (Rhabditida: Steinernematidae) from Ukraine and a note on its distribution.

PubMed

Yakovlev, Yegor; Nermut, Jiří; Půža, Vladimír; Kharchenko, Vitaliy A; Mráček, Zdeněk

2017-06-01

During a survey of the biodiversity of entomopathogenic nematodes in Ukraine, a population of Steinernema arenarium, strain Ch, was recovered in the sensitive Chornobyl Exclusion Zone. In the present work, this strain was morphologically and molecularly characterised using light microscopy and the sequences of the ITS and D2-D3 region of the 28S rDNA. In addition, we sequenced the ITS and D2-D3 regions of four populations of S. arenarium from a laboratory collection. Phylogenetic analyses were performed and the phylogenetic structure and geographic distribution of S. arenarium are discussed.

Structured Modeling and Analysis of Stochastic Epidemics with Immigration and Demographic Effects

PubMed Central

Baumann, Hendrik; Sandmann, Werner

2016-01-01

Stochastic epidemics with open populations of variable population sizes are considered where due to immigration and demographic effects the epidemic does not eventually die out forever. The underlying stochastic processes are ergodic multi-dimensional continuous-time Markov chains that possess unique equilibrium probability distributions. Modeling these epidemics as level-dependent quasi-birth-and-death processes enables efficient computations of the equilibrium distributions by matrix-analytic methods. Numerical examples for specific parameter sets are provided, which demonstrates that this approach is particularly well-suited for studying the impact of varying rates for immigration, births, deaths, infection, recovery from infection, and loss of immunity. PMID:27010993

Structured Modeling and Analysis of Stochastic Epidemics with Immigration and Demographic Effects.

PubMed

Baumann, Hendrik; Sandmann, Werner

2016-01-01

Stochastic epidemics with open populations of variable population sizes are considered where due to immigration and demographic effects the epidemic does not eventually die out forever. The underlying stochastic processes are ergodic multi-dimensional continuous-time Markov chains that possess unique equilibrium probability distributions. Modeling these epidemics as level-dependent quasi-birth-and-death processes enables efficient computations of the equilibrium distributions by matrix-analytic methods. Numerical examples for specific parameter sets are provided, which demonstrates that this approach is particularly well-suited for studying the impact of varying rates for immigration, births, deaths, infection, recovery from infection, and loss of immunity.

Local Population Structure and Patterns of Western Hemisphere Dispersal for Coccidioides spp., the Fungal Cause of Valley Fever.

PubMed

Engelthaler, David M; Roe, Chandler C; Hepp, Crystal M; Teixeira, Marcus; Driebe, Elizabeth M; Schupp, James M; Gade, Lalitha; Waddell, Victor; Komatsu, Kenneth; Arathoon, Eduardo; Logemann, Heidi; Thompson, George R; Chiller, Tom; Barker, Bridget; Keim, Paul; Litvintseva, Anastasia P

2016-04-26

Coccidioidomycosis (or valley fever) is a fungal disease with high morbidity and mortality that affects tens of thousands of people each year. This infection is caused by two sibling species, Coccidioides immitis and C. posadasii, which are endemic to specific arid locales throughout the Western Hemisphere, particularly the desert southwest of the United States. Recent epidemiological and population genetic data suggest that the geographic range of coccidioidomycosis is expanding, as new endemic clusters have been identified in the state of Washington, well outside the established endemic range. The genetic mechanisms and epidemiological consequences of this expansion are unknown and require better understanding of the population structure and evolutionary history of these pathogens. Here we performed multiple phylogenetic inference and population genomics analyses of 68 new and 18 previously published genomes. The results provide evidence of substantial population structure in C. posadasii and demonstrate the presence of distinct geographic clades in central and southern Arizona as well as dispersed populations in Texas, Mexico, South America, and Central America. Although a smaller number of C. immitis strains were included in the analyses, some evidence of phylogeographic structure was also detected in this species, which has been historically limited to California and Baja, Mexico. Bayesian analyses indicated that C. posadasii is the more ancient of the two species and that Arizona contains the most diverse subpopulations. We propose a southern Arizona-northern Mexico origin for C. posadasii and describe a pathway for dispersal and distribution out of this region. Coccidioidomycosis, or valley fever, is caused by the pathogenic fungi Coccidioides posadasii and C. immitis The fungal species and disease are primarily found in the American desert southwest, with spotted distribution throughout the Western Hemisphere. Initial molecular studies suggested a likely anthropogenic movement of C. posadasii from North America to South America. Here we comparatively analyze eighty-six genomes of the two Coccidioides species and establish local and species-wide population structures to not only clarify the earlier dispersal hypothesis but also provide evidence of likely ancestral populations and patterns of dispersal for the known subpopulations of C. posadasii. Copyright © 2016 Engelthaler et al.

Galactic gamma-ray observations and galactic structure

NASA Technical Reports Server (NTRS)

Stecker, F. W.

1975-01-01

Recent observations of gamma-rays originating in the galactic disk together with radio observations, support an emerging picture of the overall structure of our galaxy with higher interstellar gas densities and star formation rates in a region which corresponds to that of the inner arms. The emerging picture is one where molecular clouds make up the dominant constituent of the interstellar gas in the inner galaxy and play a key role in accounting for the gamma-rays and phenomena associated with the production of young stars and other population 1 objects. In this picture, cosmic rays are associated with supernovae and are primarily of galactic origin. These newly observed phenomena can be understood as consequences of the density wave theories of spiral structure. Based on these new developments, the suggestion is made that a new galactic population class, Population O, be added to the standard Populations 1 and 2 in order to recognize important differences in dynamics and distribution between diffuse galactic H1 and interstellar molecular clouds.

Intercontinental gene flow among western arctic populations of Lesser Snow Geese

USGS Publications Warehouse

Shorey, Rainy I.; Scribner, Kim T.; Kanefsky, Jeannette; Samuel, Michael D.; Libants, Scot V.

2011-01-01

Quantifying the spatial genetic structure of highly vagile species of birds is important in predicting their degree of population demographic and genetic independence during changing environmental conditions, and in assessing their abundance and distribution. In the western Arctic, Lesser Snow Geese (Chen caerulescens caerulescens) provide an example useful for evaluating spatial population genetic structure and the relative contribution of male and female philopatry to breeding and wintering locales. We analyzed biparentally inherited microsatellite loci and maternally inherited mtDNA sequences from geese breeding at Wrangel Island (Russia) and Banks Island (Canada) to estimate gene flow among populations whose geographic overlap during breeding and winter differ. Significant differences in the frequencies of mtDNA haplotypes contrast with the homogeneity of allele frequencies for microsatellite loci. Coalescence simulations revealed high variability and asymmetry between males and females in rates and direction of gene flow between populations. Our results highlight the importance of wintering areas to demographic independence and spatial genetic structure of these populations. Male-mediated gene flow among the populations on northern Wrangel Island, southern Wrangel Island, and Banks Island has been substantial. A high rate of female-mediated gene flow from southern Wrangel Island to Banks Island suggests that population exchange can be achieved when populations winter in a common area. Conversely, when birds from different breeding populations do not share a common wintering area, the probability of population exchange is likely to be dramatically reduced.

Asymmetric competition causes multimodal size distributions in spatially structured populations

PubMed Central

Velázquez, Jorge; Allen, Robert B.; Coomes, David A.; Eichhorn, Markus P.

2016-01-01

Plant sizes within populations often exhibit multimodal distributions, even when all individuals are the same age and have experienced identical conditions. To establish the causes of this, we created an individual-based model simulating the growth of trees in a spatially explicit framework, which was parametrized using data from a long-term study of forest stands in New Zealand. First, we demonstrate that asymmetric resource competition is a necessary condition for the formation of multimodal size distributions within cohorts. By contrast, the legacy of small-scale clustering during recruitment is transient and quickly overwhelmed by density-dependent mortality. Complex multi-layered size distributions are generated when established individuals are restricted in the spatial domain within which they can capture resources. The number of modes reveals the effective number of direct competitors, while the separation and spread of modes are influenced by distances among established individuals. Asymmetric competition within local neighbourhoods can therefore generate a range of complex size distributions within even-aged cohorts. PMID:26817778

Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

NASA Astrophysics Data System (ADS)

Sun, Xinxu; Xu, Dongdong; Lou, Bao; Zhang, Tao; Xin, Jian; Guo, Yaoshi; Ma, Shilei

2013-11-01

Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 76 specimens were collected from three localities around the East (Qidong and Zhoushan) and South China Seas (Zhuhai). Among these individuals, nine polymorphic sites were detected and 11 distinct haplotypes were defined. High levels of haplotype diversity ( h =0.759±0.035) and low levels of nucleotide diversity ( π= 0.001 98±0.003 26) were observed in these populations. Hierarchical analysis of molecular variance (AMOVA) indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant ( φ st=0.032 85, P<0.01). These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

Standardization of PCR-RFLP analysis of nsSNP rs1468384 of NPC1L1 gene

PubMed Central

Balgir, Praveen P.; Khanna, Divya; Kaur, Gurlovleen

2008-01-01

Niemann-Pick C1-like 1 (NPC1L1) protein, a newly identified sterol influx transporter, located at the apical membrane of the enterocyte, which may actively facilitate the uptake of cholesterol by promoting the passage of sterols across the brush border membrane of the enterocyte. It effects intestinal cholesterol absorption and intracellular transport and as such is an integral part of complex process of cholesterol homeostasis. The study of population data for the distribution of these single nucleotide polymorphisms (SNP) of NPC1L1 has lead to the identification of six non-synonymous single nucleotide polymorphisms (nsSNP). The in vitro analysis using the software MuPro and StructureSNP shows that nsSNP M510I (rs1468384), which involves A→G base pair change leads to decrease in the stability of the protein. A reproducible and a cost-effective PCR-RFLP based assay was developed to screen for the SNP among population data. This SNP has been studied in Caucasian, Asian, and African American populations. Till date, no data is available on Indian population. The distribution of M510I NPC1L1 genotype was estimated in the North Western Indian Population as a test case. The allele distribution in Indian Population differs significantly from that of other populations. The methodology thus proved to be robust enough to bring out these differences. PMID:20300301

Exploring Population Admixture Dynamics via Empirical and Simulated Genome-wide Distribution of Ancestral Chromosomal Segments

PubMed Central

Jin, Wenfei; Wang, Sijia; Wang, Haifeng; Jin, Li; Xu, Shuhua

2012-01-01

The processes of genetic admixture determine the haplotype structure and linkage disequilibrium patterns of the admixed population, which is important for medical and evolutionary studies. However, most previous studies do not consider the inherent complexity of admixture processes. Here we proposed two approaches to explore population admixture dynamics, and we demonstrated, by analyzing genome-wide empirical and simulated data, that the approach based on the distribution of chromosomal segments of distinct ancestry (CSDAs) was more powerful than that based on the distribution of individual ancestry proportions. Analysis of 1,890 African Americans showed that a continuous gene flow model, in which the African American population continuously received gene flow from European populations over about 14 generations, best explained the admixture dynamics of African Americans among several putative models. Interestingly, we observed that some African Americans had much more European ancestry than the simulated samples, indicating substructures of local ancestries in African Americans that could have been caused by individuals from some particular lineages having repeatedly admixed with people of European ancestry. In contrast, the admixture dynamics of Mexicans could be explained by a gradual admixture model in which the Mexican population continuously received gene flow from both European and Amerindian populations over about 24 generations. Our results also indicated that recent gene flows from Sub-Saharan Africans have contributed to the gene pool of Middle Eastern populations such as Mozabite, Bedouin, and Palestinian. In summary, this study not only provides approaches to explore population admixture dynamics, but also advances our understanding on population history of African Americans, Mexicans, and Middle Eastern populations. PMID:23103229

Shear-flow driven dissipative instability and investigation of nonlinear drift-vortex modes in dusty plasmas with non-thermal ion population

NASA Astrophysics Data System (ADS)

Gul-e-Ali, Masood, W.; Mirza, Arshad M.

2017-12-01

The shear flow in dust dynamics driven waves in combination with the dust-neutral drag is studied in a plasma comprising of ions, electrons, and dust. Non-thermal population of ions is considered, which has been observed by many satellite missions. It is found that the dissipative instability produced by dust sheared flow and dust-neutral drag gets modified by the presence of nonthermal ions. It is found that the dissipative instability enhances for the Cairns distribution, whereas the kappa distribution arrests the growth of this instability. In the nonlinear regime, the formation of vortices in the system is studied. It is found that the nonthermal population of ions significantly alters these structures in comparison with their Maxwellian counterpart. The results obtained in this paper may have relevance in the planetary magnetospheres where the dust particles are present and non-Maxwellian distribution of particles have been observed by Freja and Viking satellites.

Asymmetric changes of growth and reproductive investment herald altitudinal and latitudinal range shifts of two woody species.

PubMed

Matías, Luis; Jump, Alistair S

2015-02-01

Ongoing changes in global climate are altering ecological conditions for many species. The consequences of such changes are typically most evident at the edge of the geographical distribution of a species, where range expansions or contractions may occur. Current demographical status at geographical range limits can help us to predict population trends and their implications for the future distribution of the species. Thus, understanding the comparability of demographical patterns occurring along both altitudinal and latitudinal gradients would be highly informative. In this study, we analyse the differences in the demography of two woody species through altitudinal gradients at their southernmost distribution limit and the consistency of demographical patterns at the treeline across a latitudinal gradient covering the complete distribution range. We focus on Pinus sylvestris and Juniperus communis, assessing their demographical structure (density, age and mortality rate), growth, reproduction investment and damage from herbivory on 53 populations covering the upper, central and lower altitudes as well as the treeline at central latitude and northernmost and southernmost latitudinal distribution limits. For both species, populations at the lowermost altitude presented older age structure, higher mortality, decreased growth and lower reproduction when compared to the upper limit, indicating higher fitness at the treeline. This trend at the treeline was generally maintained through the latitudinal gradient, but with a decreased growth at the northern edge for both species and lower reproduction for P. sylvestris. However, altitudinal and latitudinal transects are not directly comparable as factors other than climate, including herbivore pressure or human management, must be taken into account if we are to understand how to infer latitudinal processes from altitudinal data. © 2014 John Wiley & Sons Ltd.

Mountaintops phylogeography: A case study using small mammals from the Andes and the coast of central Chile

PubMed Central

González, Juan F.; Boric-Bargetto, Dusan; Torres-Pérez, Fernando

2017-01-01

We evaluated if two sigmodontine rodent taxa (Abrothrix olivacea and Phyllotis darwini) from the Andes and Coastal mountaintops of central Chile, experienced distributional shifts due to altitudinal movements of habitat and climate change during and after the Last Glacial Maximum (LGM). We tested the hypothesis that during LGM populations of both species experienced altitudinal shifts from the Andes to the lowlands and the coastal Cordillera, and then range retractions during interglacial towards higher elevations in the Andes. These distributional shifts may have left remnants populations on the mountaintops. We evaluated the occurrence of intraspecific lineages for each species, to construct distribution models at LGM and at present, as extreme climatic conditions for each lineage. Differences in distribution between extreme climatic conditions were interpreted as post-glacial distributional shifts. Abrothrix olivacea displayed a lineage with shared sequences between both mountain systems, whereas a second lineage was restricted to the Andes. A similar scenario of panmictic unit in the past was recovered for A. olivacea in the Andes, along with an additional unit that included localities from the rest of its distribution. For P. darwini, both lineages recovered were distributed in coastal and Andean mountain ranges at present as well, and structuring analyses for this species recovered coastal and Andean localities as panmictic units in the past. Niche modeling depicted differential postglacial expansions in the recovered lineages. Results suggest that historical events such as LGM triggered the descending of populations to Andean refuge areas (one of the A. olivacea’s lineages), to the lowlands, and to the coastal Cordillera. Backward movements of populations after glacial retreats may have left isolates on mountaintops of the coastal Cordillera, suggesting that current species distribution would be the outcome of climate change and habitat reconfiguration after LGM. PMID:28672032

Density, distribution, and genetic structure of grizzly bears in the Cabinet-Yaak Ecosystem

USGS Publications Warehouse

Macleod, Amy C.; Boyd, Kristina L.; Boulanger, John; Royle, J. Andrew; Kasworm, Wayne F.; Paetkau, David; Proctor, Michael F.; Annis, Kim; Graves, Tabitha A.

2016-01-01

The conservation status of the 2 threatened grizzly bear (Ursus arctos) populations in the Cabinet-Yaak Ecosystem (CYE) of northern Montana and Idaho had remained unchanged since designation in 1975; however, the current demographic status of these populations was uncertain. No rigorous data on population density and distribution or analysis of recent population genetic structure were available to measure the effectiveness of conservation efforts. We used genetic detection data from hair corral, bear rub, and opportunistic sampling in traditional and spatial capture–recapture models to generate estimates of abundance and density of grizzly bears in the CYE. We calculated mean bear residency on our sampling grid from telemetry data using Huggins and Pledger models to estimate the average number of bears present and to correct our superpopulation estimates for lack of geographic closure. Estimated grizzly bear abundance (all sex and age classes) in the CYE in 2012 was 48–50 bears, approximately half the population recovery goal. Grizzly bear density in the CYE (4.3–4.5 grizzly bears/1,000 km2) was among the lowest of interior North American populations. The sizes of the Cabinet (n = 22–24) and Yaak (n = 18–22) populations were similar. Spatial models produced similar estimates of abundance and density with comparable precision without requiring radio-telemetry data to address assumptions of geographic closure. The 2 populations in the CYE were demographically and reproductively isolated from each other and the Cabinet population was highly inbred. With parentage analysis, we documented natural migrants to the Cabinet and Yaak populations by bears born to parents in the Selkirk and Northern Continental Divide populations. These events supported data from other sources suggesting that the expansion of neighboring populations may eventually help sustain the CYE populations. However, the small size, isolation, and inbreeding documented by this study demonstrate the need for comprehensive management designed to support CYE population growth and increased connectivity and gene flow with other populations.

A map of copy number variations in Chinese populations.

PubMed

Lou, Haiyi; Li, Shilin; Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.

A Map of Copy Number Variations in Chinese Populations

PubMed Central

Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies. PMID:22087296

Variability and population genetic structure in Achyrocline flaccida (Weinm.) DC., a species with high value in folk medicine in South America.

PubMed

Rosa, Juliana da; Weber, Gabriela Gomes; Cardoso, Rafaela; Górski, Felipe; Da-Silva, Paulo Roberto

2017-01-01

Better knowledge of medicinal plant species and their conservation is an urgent need worldwide. Decision making for conservation strategies can be based on the knowledge of the variability and population genetic structure of the species and on the events that may influence these genetic parameters. Achyrocline flaccida (Weinm.) DC. is a native plant from the grassy fields of South America with high value in folk medicine. In spite of its importance, no genetic and conservation studies are available for the species. In this work, microsatellite and ISSR (inter-simple sequence repeat) markers were used to estimate the genetic variability and structure of seven populations of A. flaccida from southern Brazil. The microsatellite markers were inefficient in A. flaccida owing to a high number of null alleles. After the evaluation of 42 ISSR primers on one population, 10 were selected for further analysis of seven A. flaccida populations. The results of ISSR showed that the high number of exclusive absence of loci might contribute to the inter-population differentiation. Genetic variability of the species was high (Nei's diversity of 0.23 and Shannon diversity of 0.37). AMOVA indicated higher genetic variability within (64.7%) than among (33.96%) populations, and the variability was unevenly distributed (FST 0.33). Gene flow among populations ranged from 1.68 to 5.2 migrants per generation, with an average of 1.39. The results of PCoA and Bayesian analyses corroborated and indicated that the populations are structured. The observed genetic variability and population structure of A. flaccida are discussed in the context of the vegetation formation history in southern Brazil, as well as the possible anthropogenic effects. Additionally, we discuss the implications of the results in the conservation of the species.

Population Structure of Sclerotinia subarctica and Sclerotinia sclerotiorum in England, Scotland and Norway

PubMed Central

Clarkson, John P.; Warmington, Rachel J.; Walley, Peter G.; Denton-Giles, Matthew; Barbetti, Martin J.; Brodal, Guro; Nordskog, Berit

2017-01-01

Sclerotinia species are important fungal pathogens of a wide range of crops and wild host plants. While the biology and population structure of Sclerotinia sclerotiorum has been well-studied, little information is available for the related species S. subarctica. In this study, Sclerotinia isolates were collected from different crop plants and the wild host Ranuculus ficaria (meadow buttercup) in England, Scotland, and Norway to determine the incidence of Sclerotinia subarctica and examine the population structure of this pathogen for the first time. Incidence was very low in England, comprising only 4.3% of isolates while moderate and high incidence of S. subarctica was identified in Scotland and Norway, comprising 18.3 and 48.0% of isolates respectively. Characterization with eight microsatellite markers identified 75 haplotypes within a total of 157 isolates over the three countries with a few haplotypes in Scotland and Norway sampled at a higher frequency than the rest across multiple locations and host plants. In total, eight microsatellite haplotypes were shared between Scotland and Norway while none were shared with England. Bayesian and principal component analyses revealed common ancestry and clustering of Scottish and Norwegian S. subarctica isolates while English isolates were assigned to a separate population cluster and exhibited low diversity indicative of isolation. Population structure was also examined for S. sclerotiorum isolates from England, Scotland, Norway, and Australia using microsatellite data, including some from a previous study in England. In total, 484 haplotypes were identified within 800 S. sclerotiorum isolates with just 15 shared between England and Scotland and none shared between any other countries. Bayesian and principal component analyses revealed a common ancestry and clustering of the English and Scottish isolates while Norwegian and Australian isolates were assigned to separate clusters. Furthermore, sequencing part of the intergenic spacer (IGS) region of the rRNA gene resulted in 26 IGS haplotypes within 870 S. sclerotiorum isolates, nine of which had not been previously identified and two of which were also widely distributed across different countries. S. subarctica therefore has a multiclonal population structure similar to S. sclerotiorum, but has a different ancestry and distribution across England, Scotland, and Norway. PMID:28421039

Dental and phylogeographic patterns of variation in gorillas.

PubMed

Pilbrow, Varsha

2010-07-01

Gorilla patterns of variation have great relevance for studies of human evolution. In this study, molar morphometrics were used to evaluate patterns of geographic variation in gorillas. Dental specimens of 323 adult individuals, drawn from the current distribution of gorillas in equatorial Africa were divided into 14 populations. Discriminant analyses and Mahalanobis distances were used to study population structure. Results reveal that: 1) the West and East African gorillas form distinct clusters, 2) the Cross River gorillas are well separated from the rest of the western populations, 3) gorillas from the Virunga mountains and the Bwindi Forest can be differentiated from the lowland gorillas of Utu and Mwenga-Fizi, 4) the Tshiaberimu gorillas are distinct from other eastern gorillas, and the Kahuzi-Biega gorillas are affiliated with them. These findings provide support for a species distinction between Gorilla gorilla and Gorilla beringei, with subspecies G. g. diehli, G. g. gorilla, G. b. graueri, G. b. beringei, and possibly, G. b. rex-pygmaeorum. Clear correspondence between dental and other patterns of taxonomic diversity demonstrates that dental data reveal underlying genetic patterns of differentiation. Dental distances increased predictably with altitude but not with geographic distances, indicating that altitudinal segregation explains gorilla patterns of population divergence better than isolation-by-distance. The phylogeographic pattern of gorilla dental metric variation supports the idea that Plio-Pleistocene climatic fluctuations and local mountain building activity in Africa affected gorilla phylogeography. I propose that West Africa comprised the historic center of gorilla distribution and experienced drift-gene flow equilibrium, whereas Nigeria and East Africa were at the periphery, where climatic instability and altitudinal variation promoted drift and genetic differentiation. This understanding of gorilla population structure has implications for gorilla conservation, and for understanding the distribution of sympatric chimpanzees and Plio-Pleistocene hominins.

Influence of Pleistocene glacial/interglacial cycles on the genetic structure of the mistletoe cactus Rhipsalis baccifera (Cactaceae) in Mesoamerica.

PubMed

Ornelas, Juan Francisco; Rodríguez-Gómez, Flor

2015-01-01

Phylogeographical work on cloud forest-adapted species provides inconsistent evidence on cloud forest dynamics during glacial cycles. A study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic mistletoe cactus, was conducted to investigate genetic variation at sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the species range in Mesoamerica to determine if such patterns are consistent with the expansion/contraction model of cloud forest during glacial cycles. We conducted population and spatial genetic analyses as well as gene flow and divergence time estimates between 24 populations comprising the distribution of R. baccifera in Mexico and Guatemala to gain insight of the evolutionary history of these populations, and a complementary species distribution modeling approach to frame information derived from the genetic analyses into an explicit paleoecological context. The results revealed a phylogeographical break at the Isthmus of Tehuantepec, and high levels of genetic diversity among populations and cloud forest areas. Despite the genetic differentiation of some R. baccifera populations, the widespread ITS ribotypes suggest effective nuclear gene flow via pollen and population differentiation shown by the rpl32-trnL suggests more restricted seed flow. Predictions of species distribution models under past last glacial maximum (LGM) climatic conditions and a significant signal of demographic expansion suggest that R. baccifera populations experienced a range expansion tracking the conditions of the cloud forest distribution and shifted to the lowlands with population connectivity during the LGM. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Phylogeography and population structure of the Reevese's Butterfly Lizard (Leiolepis reevesii) inferred from mitochondrial DNA sequences.

PubMed

Lin, Long-Hui; Ji, Xiang; Diong, Cheong-Hoong; Du, Yu; Lin, Chi-Xian

2010-08-01

Butterfly lizards of the genus Leiolepis (Agamidae) are widely distributed in coastal regions of Southeast Asia and South China, with the Reevese's Butterfly Lizard Leiolepis reevesii having a most northerly distribution that ranges from Vietnam to South China. To assess the genetic diversity within L. reevesii, and its population structure and evolutionary history, we sequenced 1004 bp of cytochrome b for 448 individuals collected from 28 localities covering almost the whole range of the lizard. One hundred and forty variable sites were observed, and 93 haplotypes were defined. We identified three genetically distinct clades, of which Clade A includes haplotypes mainly from southeastern Hainan, Clade B from Guangdong and northern Hainan, and Clade C from Vietnam and the other localities of China. Clade A was well distinguished and divergent from the other two. The Wuzhishan and Yinggeling mountain ranges were important barriers limiting gene exchange between populations on the both sides of the mountain series, whereas the Gulf of Tonkin and the Qiongzhou Strait were not. One plausible scenario to explain our genetic data is a historical dispersion of L. reevesii as proceeding from Vietnam to Hainan, followed by a second wave of dispersal from Hainan to Guangdong and Guangxi. Another equally plausible scenario is a historically widespread population that has been structured by vicariant factors such as the mountains in Hainan and sea level fluctuations. Copyright 2010 Elsevier Inc. All rights reserved.

Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics.

PubMed

Larmuseau, Maarten H D; Ottoni, Claudio; Raeymaekers, Joost A M; Vanderheyden, Nancy; Larmuseau, Hendrik F M; Decorte, Ronny

2012-04-01

The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and the Netherlands (Northwest Europe). Genealogical data of 881 individuals from Northwest Europe were collected, from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chr genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chr distribution was detected through a north-south gradient in the frequencies distribution of sub-haplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-U152). The gradient on R-U106 faded in time and even became totally invisible during the Industrial Revolution in the first half of the nineteenth century. Therefore, genealogical data for at least 200 years are required to study small-scale 'autochthonous' population structure in Western Europe.

Phylogeography, phylogeny and hybridization in trichechid sirenians: Implications for manatee conservation

USGS Publications Warehouse

Vianna, J.A.; Bonde, R.K.; Caballero, S.; Giraldo, J.P.; Lima, R.P.; Clark, A.; Marmontel, M.; Morales-Vela, B.; De Souza, M. J.; Parr, L.; Rodriguez-Lopez, M.A.; Mignucci-Giannoni, A. A.; Powell, J.A.; Santos, F.R.

2006-01-01

The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization. ?? 2006 Blackwell Publishing Ltd.

Global population structure of the spiny dogfish Squalus acanthias, a temperate shark with an antitropical distribution.

PubMed

Veríssimo, A; McDowell, J R; Graves, J E

2010-04-01

The spiny dogfish (Squalus acanthias) is a temperate, coastal squaloid shark with an antitropical distribution in the Atlantic and Pacific oceans. The global population structure of this species is poorly understood, although individuals are known to undergo extensive migrations within coastal waters and across ocean basins. In this study, an analysis of the global population structure of the spiny dogfish was conducted using eight polymorphic nuclear microsatellite markers and a 566-bp fragment of the mitochondrial ND2 gene region. A low level of genetic divergence was found among collections from the Atlantic and South Pacific basins, whereas a high level of genetic divergence was found among Pacific Ocean collections. Two genetically distinct groups were recovered by both marker classes: one exclusive to North Pacific collections, and one including collections from the South Pacific and Atlantic locations. The strong genetic break across the equatorial Pacific coincides with major regional differences in the life-history characters of spiny dogfish, suggesting that spiny dogfish in areas on either side of the Pacific equator have been evolving independently for a considerable time. Phylogeographic analyses indicate that spiny dogfish populations had a Pacific origin, and that the North Atlantic was colonized as a result of a recent range expansion from the South American coast. Finally, the available data strongly argue for the taxonomic separation of the North Pacific spiny dogfish from S. acanthias and a re-evaluation of the specific status of S. acanthias is warranted.

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

PubMed

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

2018-06-15

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

Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species.

PubMed

Choupina, A B; Martins, I M

2014-08-01

Freshwater mussel species are in global decline. Anthropogenic changes of river channels and the decrease of autochthonous fish population, the natural hosts of mussels larval stages (glochidia), are the main causes. Therefore, the conservation of mussel species depends not only on habitat conservation, but also on the availability of the fish host. In Portugal, information concerning most of the mussel species is remarkably scarce. One of the most known species, Unio pictorum is also in decline however, in the basins of the rivers Tua and Sabor (Northeast of Portugal), there is some indication of relatively large populations. The aforementioned rivers can be extremely important for this species conservation not only in Portugal, but also in the remaining Iberian Peninsula. Thus, it is important to obtain data concerning Unio pictorum bioecology (distribution, habitat requirements, population structure, genetic variability, reproductive cycle and recruitment rates), as well as the genetic variability and structure of the population. Concomitantly, information concerning fish population structure, the importance of the different fish species as "glochidia" hosts and their appropriate density to allow effective mussel recruitment, will also be assessed. The achieved data is crucial to obtain information to develop effective management measures in order to promote the conservation of this bivalve species, the conservation of autochthonous fish populations, and consequently the integrity of the river habitats.

Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicate potential for spread of herbicide resistance via gene flow.

PubMed

Karn, Elizabeth; Jasieniuk, Marie

2017-07-01

Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggest the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne .

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

PubMed

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

2015-05-01

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

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

PubMed Central

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

2015-01-01

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

Investigation of discrete states and quasidiscrete structures observed in 150Sm and 152Sm using the ( p,tγ) reaction

DOE PAGES

Peter, Humby; Simon, Anna; Beausang, C. W.; ...

2016-01-01

New levels and γ-ray transitions were identified in 150,152Sm utilizing the (p,t) reaction and particle-γ coincidence data. A large, peak-like structure observed between 2.3–3.0 MeV in excitation energy in the triton energy spectra was also investigated. The orbital angular-momentum transfer was probed by comparing the experimental angular distributions of the outgoing tritons to calculated distorted wave Born approximation curves. The angular distributions of the outgoing tritons populating the peak-like structure are remarkably similar in the two reactions and are significantly different from the angular distributions associated with the nearby continuum region. Relative partial cross sections for the observed levels, anglemore » averaged between 34 and 58 degrees, were measured. In 150Sm, 39(4)% of the strength of the peak-like structure could be accounted for by the observed discrete states. This compares with a value of 93(15)% for 152Sm« less

Investigation of discrete states and quasidiscrete structures observed in 150Sm and 152Sm using the ( p,tγ) reaction

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

Peter, Humby; Simon, Anna; Beausang, C. W.

New levels and γ-ray transitions were identified in 150,152Sm utilizing the (p,t) reaction and particle-γ coincidence data. A large, peak-like structure observed between 2.3–3.0 MeV in excitation energy in the triton energy spectra was also investigated. The orbital angular-momentum transfer was probed by comparing the experimental angular distributions of the outgoing tritons to calculated distorted wave Born approximation curves. The angular distributions of the outgoing tritons populating the peak-like structure are remarkably similar in the two reactions and are significantly different from the angular distributions associated with the nearby continuum region. Relative partial cross sections for the observed levels, anglemore » averaged between 34 and 58 degrees, were measured. In 150Sm, 39(4)% of the strength of the peak-like structure could be accounted for by the observed discrete states. This compares with a value of 93(15)% for 152Sm« less

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

PubMed

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

2015-07-01

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

Comparative Genetic Structure and Demographic History in Endemic Galápagos Weevils

PubMed Central

Stepien, Courtney C.; Sijapati, Manisha; Roque Albelo, Lázaro

2012-01-01

The challenge of maintaining genetic diversity within populations can be exacerbated for island endemics if they display population dynamics and behavioral attributes that expose them to genetic drift without the benefits of gene flow. We assess patterns of the genetic structure and demographic history in 27 populations of 9 species of flightless endemic Galápagos weevils from 9 of the islands and 1 winged introduced close relative. Analysis of mitochondrial DNA reveals a significant population structure and moderately variable, though demographically stable, populations for lowland endemics (FST = 0.094–0.541; π: 0.014–0.042; Mismatch P = 0.003–0.026; and D(Tajima) = −0.601 to 1.203), in contrast to signals of past contractions and expansions in highland specialists on 2 islands (Mismatch P = 0.003–0.026 and D(Tajima) = −0.601 to 1.203). We interpret this series of variable and highly structured population groups as a system of long-established, independently founded island units, where structuring could be a signal of microallopatric differentiation due to patchy host plant distribution and poor dispersal abilities. We suggest that the severe reduction and subsequent increase of a suitably moist habitat that accompanied past climatic variation could have contributed to the observed population fluctuations in highland specialists. We propose the future exploration of hybridization between the introduced and highland endemic species on Santa Cruz, especially given the expansion of the introduced species into the highlands, the sensitivity to past climatic variation detected in highland populations, and the potentially threatened state of single-island endemics. PMID:22174444

Population dynamics, structure and behavior of Anopheles darlingi in a rural settlement in the Amazon rainforest of Acre, Brazil.

PubMed

Moutinho, Paulo Rufalco; Gil, Luis Herman Soares; Cruz, Rafael Bastos; Ribolla, Paulo Eduardo Martins

2011-06-24

Anopheles darlingi is the major vector of malaria in South America, and its behavior and distribution has epidemiological importance to biomedical research. In Brazil, An. darlingi is found in the northern area of the Amazon basin, where 99.5% of the disease is reported. The study area, known as Ramal do Granada, is a rural settlement inside the Amazon basin in the state of Acre. Population variations and density have been analysed by species behaviour, and molecular analysis has been measured by ND4 mitochondrial gene sequencing. The results show higher density in collections near a recent settlement, suggesting that a high level of colonization decreases the vector presence. The biting activity showed higher activity at twilight and major numbers of mosquitos in the remaining hours of the night in months of high density. From a sample of 110 individual mosquitoes, 18 different haplotypes were presented with a diversity index of 0.895, which is higher than that found in other Anopheles studies. An. darlingi depends on forested regions for their larval and adult survival. In months with higher population density, the presence of mosquitoes persisted in the second part of the night, increasing the vector capacity of the species. Despite the intra-population variation in the transition to rainy season, the seasonal distribution of haplotypes shows no change in the structure population of An. darlingi.

Assessing the drivers shaping global patterns of urban vegetation landscape structure.

PubMed

Dobbs, C; Nitschke, C; Kendal, D

2017-08-15

Vegetation is one of the main resources involve in ecosystem functioning and providing ecosystem services in urban areas. Little is known on the landscape structure patterns of vegetation existing in urban areas at the global scale and the drivers of these patterns. We studied the landscape structure of one hundred cities around the globe, and their relation to demography (population), socioeconomic factors (GDP, Gini Index), climate factors (temperature and rain) and topographic characteristics (altitude, variation in altitude). The data revealed that the best descriptors of landscape structure were amount, fragmentation and spatial distribution of vegetation. Populated cities tend to have less, more fragmented, less connected vegetation with a centre of the city with low vegetation cover. Results also provided insights on the influence of socioeconomics at a global scale, as landscape structure was more fragmented in areas that are economically unequal and coming from emergent economies. This study shows the effects of the social system and climate on urban landscape patterns that gives useful insights for the distribution in the provision of ecosystem services in urban areas and therefore the maintenance of human well-being. This information can support local and global policy and planning which is committing our cities to provide accessible and inclusive green space for all urban inhabitants. Copyright © 2017 Elsevier B.V. All rights reserved.

Conservation biology of the Cross River gorilla (Gorilla gorilla diehli)

NASA Astrophysics Data System (ADS)

Bergl, Richard Alexander

The Cross River gorilla (Gorilla gorilla diehli), a recently revived fourth subspecies of gorilla, is the most endangered and poorly studied ape taxon. Only about 300 Cross River gorillas remain and these gorillas occur in at least eleven different localities. This dissertation presents a population-wide assessment of threats to this population based on molecular genetic data, satellite imagery and demographic modeling. I used DNA extracted from non-invasively collected fecal samples to amplify eleven microsatellite loci for population genetic analysis. Microsatellite data suggested that a complex population structure is present in the Cross River gorilla, with three genetically identifiable subpopulations present. Though levels of gene flow between certain subpopulations were low, there is evidence that reproductive contact persists between many of the subpopulations. The genetic data also demonstrate that levels of diversity in the Cross River population are not evenly distributed across subpopulations, and that one subpopulation has higher levels of variability than the others. In a genus-wide comparison, levels of genetic diversity in the Cross River gorilla were comparable to those of the similarly small populations of the mountain gorilla ( Gorilla beringei beringei) in Bwindi and the Virunga volcanoes, but showed lower levels of diversity than a sample from a large, continuous population of Gorilla gorilla gorilla at Mondika, Central African Republic. Genetic data also showed strong evidence of a population bottleneck in the Cross River gorilla, but not in the other three gorilla populations examined. I used analysis of remotely-sensed data from the Landsat satellite to assess the extent and pattern of land cover distribution across the Cross River gorilla's range. Considerable potential gorilla habitat remains within the range of the Cross River gorilla and each gorilla locality is at least tenuously connected by forest. Finally, I developed a model-based population viability analysis for the Cross River gorilla. Demographic modeling suggested that both population structure and variables associated with female reproductive output most influence population growth in the Cross River gorilla. Taken together, the results of my study are encouraging for the conservation of the Cross River gorilla population, and highlight the resilience of these animals in the face of human activities. Conservation efforts should promote connectivity between gorilla localities and foster the growth of their population. The methods I applied could provide useful insights into patterns of population structure and migration for a wide range of animal taxa.

Population genetic structure of critically endangered salamander (Hynobius amjiensis) in China: recommendations for conservation.

PubMed

Yang, J; Chen, C S; Chen, S H; Ding, P; Fan, Z Y; Lu, Y W; Yu, L P; Lin, H D

2016-06-10

Amji's salamander (Hynobius amjiensis) is a critically endangered species (IUCN Red List), which is endemic to mainland China. In the present study, five haplotypes were genotyped for the mtDNA cyt b gene in 45 specimens from three populations. Relatively low levels of haplotype diversity (h = 0.524) and nucleotide diversity (π = 0.00532) were detected. Analyses of the phylogenic structure of H. amjiensis showed no evidence of major geographic partitions or substantial barriers to historical gene flow throughout the species' range. Two major phylogenetic haplotype groups were revealed, and were estimated to have diverged about 1.262 million years ago. Mismatch distribution analysis, neutrality tests, and Bayesian skyline plots revealed no evidence of dramatic changes in the effective population size. According to the SAMOVA and STRUCTURE analyses, H. amjiensis should be regarded as two different management units.

A structured population model with diffusion in structure space.

PubMed

Pugliese, Andrea; Milner, Fabio

2018-05-09

A structured population model is described and analyzed, in which individual dynamics is stochastic. The model consists of a PDE of advection-diffusion type in the structure variable. The population may represent, for example, the density of infected individuals structured by pathogen density x, [Formula: see text]. The individuals with density [Formula: see text] are not infected, but rather susceptible or recovered. Their dynamics is described by an ODE with a source term that is the exact flux from the diffusion and advection as [Formula: see text]. Infection/reinfection is then modeled moving a fraction of these individuals into the infected class by distributing them in the structure variable through a probability density function. Existence of a global-in-time solution is proven, as well as a classical bifurcation result about equilibrium solutions: a net reproduction number [Formula: see text] is defined that separates the case of only the trivial equilibrium existing when [Formula: see text] from the existence of another-nontrivial-equilibrium when [Formula: see text]. Numerical simulation results are provided to show the stabilization towards the positive equilibrium when [Formula: see text] and towards the trivial one when [Formula: see text], result that is not proven analytically. Simulations are also provided to show the Allee effect that helps boost population sizes at low densities.

Genetic variation and structure in remnant population of critically endangered Melicope zahlbruckneri

USGS Publications Warehouse

Raji, J. A.; Atkinson, Carter T.

2016-01-01

The distribution and amount of genetic variation within and between populations of plant species are important for their adaptability to future habitat changes and also critical for their restoration and overall management. This study was initiated to assess the genetic status of the remnant population of Melicope zahlbruckneri–a critically endangered species in Hawaii, and determine the extent of genetic variation and diversity in order to propose valuable conservation approaches. Estimated genetic structure of individuals based on molecular marker allele frequencies identified genetic groups with low overall differentiation but identified the most genetically diverse individuals within the population. Analysis of Amplified Fragment Length Polymorphic (AFLP) marker loci in the population based on Bayesian model and multivariate statistics classified the population into four subgroups. We inferred a mixed species population structure based on Bayesian clustering and frequency of unique alleles. The percentage of Polymorphic Fragment (PPF) ranged from 18.8 to 64.6% for all marker loci with an average of 54.9% within the population. Inclusion of all surviving M. zahlbruckneri trees in future restorative planting at new sites are suggested, and approaches for longer term maintenance of genetic variability are discussed. To our knowledge, this study represents the first report of molecular genetic analysis of the remaining population of M. zahlbruckneri and also illustrates the importance of genetic variability for conservation of a small endangered population.

Effects of sample size on estimates of population growth rates calculated with matrix models.

PubMed

Fiske, Ian J; Bruna, Emilio M; Bolker, Benjamin M

2008-08-28

Matrix models are widely used to study the dynamics and demography of populations. An important but overlooked issue is how the number of individuals sampled influences estimates of the population growth rate (lambda) calculated with matrix models. Even unbiased estimates of vital rates do not ensure unbiased estimates of lambda-Jensen's Inequality implies that even when the estimates of the vital rates are accurate, small sample sizes lead to biased estimates of lambda due to increased sampling variance. We investigated if sampling variability and the distribution of sampling effort among size classes lead to biases in estimates of lambda. Using data from a long-term field study of plant demography, we simulated the effects of sampling variance by drawing vital rates and calculating lambda for increasingly larger populations drawn from a total population of 3842 plants. We then compared these estimates of lambda with those based on the entire population and calculated the resulting bias. Finally, we conducted a review of the literature to determine the sample sizes typically used when parameterizing matrix models used to study plant demography. We found significant bias at small sample sizes when survival was low (survival = 0.5), and that sampling with a more-realistic inverse J-shaped population structure exacerbated this bias. However our simulations also demonstrate that these biases rapidly become negligible with increasing sample sizes or as survival increases. For many of the sample sizes used in demographic studies, matrix models are probably robust to the biases resulting from sampling variance of vital rates. However, this conclusion may depend on the structure of populations or the distribution of sampling effort in ways that are unexplored. We suggest more intensive sampling of populations when individual survival is low and greater sampling of stages with high elasticities.

The Not So Simple Globular Cluster ω Cen. I. Spatial Distribution of the Multiple Stellar Populations

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

Calamida, A.; Saha, A.; Strampelli, G.

2017-04-01

We present a multi-band photometric catalog of ≈1.7 million cluster members for a field of view of ≈2° × 2° across ω Cen. Photometry is based on images collected with the Dark Energy Camera on the 4 m Blanco telescope and the Advanced Camera for Surveys on the Hubble Space Telescope . The unprecedented photometric accuracy and field coverage allowed us, for the first time, to investigate the spatial distribution of ω Cen multiple populations from the core to the tidal radius, confirming its very complex structure. We found that the frequency of blue main-sequence stars is increasing compared to red main-sequencemore » stars starting from a distance of ≈25′ from the cluster center. Blue main-sequence stars also show a clumpy spatial distribution, with an excess in the northeast quadrant of the cluster pointing toward the direction of the Galactic center. Stars belonging to the reddest and faintest red-giant branch also show a more extended spatial distribution in the outskirts of ω Cen, a region never explored before. Both these stellar sub-populations, according to spectroscopic measurements, are more metal-rich compared to the cluster main stellar population. These findings, once confirmed, make ω Cen the only stellar system currently known where metal-rich stars have a more extended spatial distribution compared to metal-poor stars. Kinematic and chemical abundance measurements are now needed for stars in the external regions of ω Cen to better characterize the properties of these sub-populations.« less

Phylogeography of the sand dune ant Mycetophylax simplex along the Brazilian Atlantic Forest coast: remarkably low mtDNA diversity and shallow population structure.

PubMed

Cardoso, Danon Clemes; Cristiano, Maykon Passos; Tavares, Mara Garcia; Schubart, Christoph D; Heinze, Jürgen

2015-06-10

During past glacial periods, many species of forest-dwelling animals experienced range contractions. In contrast, species living outside such moist habitats appear to have reacted to Quaternary changes in different ways. The Atlantic Forest represents an excellent opportunity to test phylogeographic hypotheses, because it has a wide range of vegetation types, including unforested habitats covered predominantly by herbaceous and shrubby plants, which are strongly influenced by the harsh environment with strong wind and high insolation. Here, we investigated the distribution of genetic diversity in the endemic sand dune ant Mycetophylax simplex across its known range along the Brazilian coast, with the aim of contributing to the understanding of alternative phylogeographic patterns. We used partial sequences of the mitochondrial gene cytochrome oxidase I and nuclear gene wingless from 108 specimens and 51 specimens, respectively, to assess the phylogeography and demographic history of this species. To achieve this we performed different methods of phylogenetic and standard population genetic analyses. The observed genetic diversity distribution and historical demographic profile suggests that the history of M. simplex does not match the scenario suggested for other Atlantic Forest species. Instead, it underwent demographic changes and range expansions during glacial periods. Our results show that M. simplex presents a shallow phylogeographic structure with isolation by distance among the studied populations, living in an almost panmictic population. Our coalescence approach indicates that the species maintained a stable population size until roughly 75,000 years ago, when it underwent a gradual demographic expansion that were coincident with the low sea-level during the Quaternary. Such demographic events were likely triggered by the expansion of the shorelines during the lowering of the sea level. Our data suggest that over evolutionary time M. simplex did not undergo dramatic range fragmentation, but rather it likely persisted in largely interconnected populations. Furthermore, we add an important framework about how both glacial and interglacial events could positively affect the distribution and diversification of species. The growing number of contrasting phylogeographic patterns within and among species and regions have shown that Quaternary events influenced the distribution of species in more ways than first supposed.

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

PubMed

Wereszczuk, Anna; Leblois, Raphaël; Zalewski, Andrzej

2017-12-22

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

Extreme Genetic Structure in a Small-Bodied Freshwater Fish, the Purple Spotted Gudgeon, Mogurnda adspersa (Eleotridae)

PubMed Central

Hughes, Jane M.; Real, Kathryn M.; Marshall, Jonathan C.; Schmidt, Daniel J.

2012-01-01

Freshwater fish are a group that is especially susceptible to biodiversity loss as they often exist naturally in small, fragmented populations that are vulnerable to habitat degradation, pollution and introduction of exotic species. Relatively little is known about spatial dynamics of unperturbed populations of small-bodied freshwater fish species. This study examined population genetic structure of the purple spotted gudgeon (Mogurnda adspersa, Eleotridae), a small-bodied freshwater fish that is widely distributed in eastern Australia. The species is threatened in parts of its range but is common in coastal streams of central Queensland where this study took place. Microsatellite (msat) and mitochondrial DNA (mtDNA) variation was assessed for nine sites from four stream sections in two drainage basins. Very high levels of among population structure were observed (msat F ST = 0.18; mtDNA ΦST = 0.85) and evidence for contemporary migration among populations was rare and limited to sites within the same section of stream. Hierarchical structuring of variation was best explained by stream section rather than by drainage basin. Estimates of contemporary effective population size for each site was low (range 28 – 63, Sibship method), but compared favorably with similar estimates for other freshwater fish species, and there was no genetic evidence for inbreeding or recent population bottlenecks. In conclusion, within a stable part of its range, M adspersa exists as a series of small, demographically stable populations that are highly isolated from one another. Complimentary patterns in microsatellites and mtDNA indicate this structuring is the result of long-term processes that have developed over a remarkably small spatial scale. High population structure and limited dispersal mean that recolonisation of locally extinct populations is only likely to occur from closely situated populations within stream sections. Limited potential for recolonisation should be considered as an important factor in conservation and management of this species. PMID:22808190

Dimensions of global population projections: what do we know about future population trends and structures?

PubMed Central

Lutz, Wolfgang; KC, Samir

2010-01-01

The total size of the world population is likely to increase from its current 7 billion to 8–10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA. PMID:20713384

Past and future demographic dynamics of alpine species: limited genetic consequences despite dramatic range contraction in a plant from the Spanish Sierra Nevada.

PubMed

Blanco-Pastor, J L; Fernández-Mazuecos, M; Vargas, P

2013-08-01

Anthropogenic global climate change is expected to cause severe range contractions among alpine plants. Alpine areas in the Mediterranean region are of special concern because of the high abundance of endemic species with narrow ranges. This study combined species distribution models, population structure analyses and Bayesian skyline plots to trace the past and future distribution and diversity of Linaria glacialis, an endangered narrow endemic species that inhabits summits of Sierra Nevada (Spain). The results showed that: (i) the habitat of this alpine-Mediterranean species in Sierra Nevada suffered little changes during glacial and interglacial stages of late Quaternary; (ii) climatic oscillations in the last millennium (Medieval Warm Period and Little Ice Age) moderately affected the demographic trends of L. glacialis; (iii) future warming conditions will cause severe range contractions; and (iv) genetic diversity will not diminish at the same pace as the distribution range. As a consequence of the low population structure of this species, genetic impoverishment in the alpine zones of Sierra Nevada should be limited during range contraction. We conclude that maintenance of large effective population sizes via high mutation rates and high levels of gene flow may promote the resilience of alpine plant species when confronted with global warming. © 2013 John Wiley & Sons Ltd.

Latitudinal variation in population structure of wintering Pacific Black Brant

USGS Publications Warehouse

Schamber, J.L.; Sedinger, J.S.; Ward, D.H.; Hagmeier, K.R.

2007-01-01

Latitudinal variation in population structure during the winter has been reported in many migratory birds, but has been documented in few species of waterfowl. Variation in environmental and social conditions at wintering sites can potentially influence the population dynamics of differential migrants. We examined latitudinal variation in sex and age classes of wintering Pacific Black Brant (Branta bernicla nigricans). Brant are distributed along a wide latitudinal gradient from Alaska to Mexico during the winter. Accordingly, migration distances for brant using different wintering locations are highly variable and winter settlement patterns are likely associated with a spatially variable food resource. We used resightings of brant banded in southwestern Alaska to examine sex and age ratios of birds wintering at Boundary Bay in British Columbia, and at San Quintin Bay, Ojo de Liebre Lagoon, and San Ignacio Lagoon in Baja California from 1998 to 2000. Sex ratios were similar among wintering locations for adults and were consistent with the mating strategy of geese. The distribution of juveniles varied among wintering areas, with greater proportions of juveniles observed at northern (San Quintin Bay and Ojo de Liebre Lagoon) than at southern (San Ignacio Lagoon) locations in Baja California. We suggest that age-related variation in the winter distribution of Pacific Black Brant is mediated by variation in productivity among individuals at different wintering locations and by social interactions among wintering family groups.

Population at risk: using areal interpolation and Twitter messages to create population models for burglaries and robberies

PubMed Central

2018-01-01

ABSTRACT Population at risk of crime varies due to the characteristics of a population as well as the crime generator and attractor places where crime is located. This establishes different crime opportunities for different crimes. However, there are very few efforts of modeling structures that derive spatiotemporal population models to allow accurate assessment of population exposure to crime. This study develops population models to depict the spatial distribution of people who have a heightened crime risk for burglaries and robberies. The data used in the study include: Census data as source data for the existing population, Twitter geo-located data, and locations of schools as ancillary data to redistribute the source data more accurately in the space, and finally gridded population and crime data to evaluate the derived population models. To create the models, a density-weighted areal interpolation technique was used that disaggregates the source data in smaller spatial units considering the spatial distribution of the ancillary data. The models were evaluated with validation data that assess the interpolation error and spatial statistics that examine their relationship with the crime types. Our approach derived population models of a finer resolution that can assist in more precise spatial crime analyses and also provide accurate information about crime rates to the public. PMID:29887766

The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant-centre hypothesis.

PubMed

Pérez-Collazos, E; Sanchez-Gómez, P; Jiménez, F; Catalán, P

2009-03-01

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.

The increasing importance of small-scale forestry: evidence from family forest ownership patterns in the United States

Treesearch

Y. Zhang; X. Liao; B.J. Butler; J. Schelhas

2009-01-01

The state-level distribution of the size of family forest holdings in the contiguous United States was examined using data collected by the USDA Forest Service in 1993 and 2003. Regressions models were used to analyze the factors influencing the mean size and structural variation among states and between the two periods. Population density, percent of the population at...

Emerging Ecosystems Change the Spatial Distribution of Top Carnivores Even in Poorly Populated Areas

PubMed Central

Barbar, Facundo; Werenkraut, Victoria; Morales, Juan Manuel; Lambertucci, Sergio Agustín

2015-01-01

Humans affect biological diversity and species distribution patterns by modifying resource availability and generating novel environments where generalist species benefit and specialist species are rare. In particular, cities create local homogenization while roads fragment habitat, although both processes can increase food availability for some species that may be able to take advantage of this new source. We studied space use by birds of prey in relation to human construction, hypothesizing that these birds would be affected even in poorly populated areas. We worked in Northwestern Patagonia, Argentina, which is experiencing a high population growth, but still having very large unpopulated areas. We related the presence of raptors with different sources of human disturbance and found that both the abundance and richness of these birds were positively associated with anthropogenic environments. These results are driven mostly by a strong association between the medium-sized generalist species and these novel environments (mainly roads and cities). This may create an imbalance in intra-guild competitive abilities, modifying the normal structures of top carnivore hierarchies. Indeed, the structure of raptor communities seems to be changing, even in poorly populated areas, with anthropogenic constructions seemingly producing changes in wild areas more promptly than thought, a cause for concern in ecosystems conservation issues. PMID:25799547

Lack of spatial genetic structure among nesting and wintering King Eiders

USGS Publications Warehouse

Pearce, J.M.; Talbot, S.L.; Pierson, Barbara J.; Petersen, M.R.; Scribner, K.T.; Dickson, D.L.; Mosbech, A.

2004-01-01

The King Eider (Somateria spectabilis) has been delineated into two broadly distributed breeding populations in North America (the western and eastern Arctic) on the basis of banding data and their use of widely separated Pacific and Atlantic wintering areas. Little is known about the level of gene flow between these two populations. Also unknown is whether behavioral patterns common among migratory waterfowl, such as site fidelity to wintering areas and pair formation at these sites, have existed for sufficient time to create a population structure defined by philopatry to wintering rather than to nesting locations. We used six nuclear microsatellite DNA loci and cytochrome b mitochondrial DNA sequence data to estimate the extent of spatial genetic differentiation among nesting and wintering areas of King Eiders across North America and adjacent regions. Estimates of interpopulation variance in microsatellite allele and mtDNA haplotype frequency were both low and nonsignificant based on samples from three wintering and four nesting areas. Results from nested clade analysis, mismatch distributions, and coalescent-based analyses suggest historical population growth and gene flow that collectively may have homogenized gene frequencies. The presence of several unique mtDNA haplotypes among birds wintering near Greenland suggests that gene flow may now be more limited between the western and eastern Arctic, which is consistent with banding data.

Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars.

PubMed

Bertagnolli, Anthony D; Meinhardt, Kelley A; Pannu, Manmeet; Brown, Sally; Strand, Stuart; Fransen, Steven C; Stahl, David A

2015-04-01

Ammonia-oxidizing thaumarcheota (AOA) and ammonia-oxidizing bacteria (AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene (amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass (Panicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. Nitrosotalea-like and Nitrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with Nitrososphaera and Nitrosospira cluster 3A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Genetic diversity of Morato's Digger Toad, Proceratophrys moratoi: spatial structure, gene flow, effective size and the need for differential management strategies of populations.

PubMed

Arruda, Mauricio P; Costa, William P; Recco-Pimentel, Shirlei M

2017-01-01

The Morato's Digger Toad, Proceratophrys moratoi, is a critically endangered toad species with a marked population decline in southern Brazilian Cerrado. Despite this, new populations are being discovered, primarily in the northern part of the distribution range, which raises a number of questions with regard to the conservation status of the species. The present study analyzed the genetic diversity of the species based on microsatellite markers. Our findings permitted the identification of two distinct management units. We found profound genetic structuring between the southern populations, on the left margin of the Tietê River, and all other populations. A marked reduction was observed in the contemporary gene flow among the central populations that are most affected by anthropogenic impacts, such as extensive sugar cane plantations, which presumably decreases habitat connectivity. The results indicated reduced diversity in the southern populations which, combined with a smaller effective population size, may make these populations more susceptible to extinction. We recommend the reclassification of P. moratoi as vulnerable and the establishment of a special protection program for the southern populations. Our results provide important insights about the local extinction of southern populations of this toad.

Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae) Endemic to Southwest China by Multiple Molecular Markers

PubMed Central

Feng, Xiuyan; Liu, Jian; Chiang, Yu-Chung; Gong, Xun

2017-01-01

Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs), three nuclear genes (nDNAs) and 12 nuclear microsatellites (SSRs), we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD) in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida. PMID:28580005

Shaping Policy Change in Population Health: Policy Entrepreneurs, Ideas, and Institutions.

PubMed

Béland, Daniel; Katapally, Tarun R

2018-01-14

Political realities and institutional structures are often ignored when gathering evidence to influence population health policies. If these policies are to be successful, social science literature on policy change should be integrated into the population health approach. In this contribution, drawing on the work of John W. Kingdon and related scholarship, we set out to examine how key components of the policy change literature could contribute towards the effective development of population health policies. Shaping policy change would require a realignment of the existing school of thought, where the contribution of population health seems to end at knowledge translation. Through our critical analysis of selected literature, we extend recommendations to advance a burgeoning discussion in adopting new approaches to successfully implement evidence-informed population health policies. © 2018 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

PubMed Central

Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Ahmad, Altaf; Singh, N. K.; Singh, Rakesh

2014-01-01

The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies. PMID:25412256

Genetic consequences of polygyny and social structure in an Indian fruit bat, Cynopterus sphinx. II. Variance in male mating success and effective population size.

PubMed

Storz, J F; Bhat, H R; Kunz, T H

2001-06-01

Variance in reproductive success is a primary determinant of genetically effective population size (Ne), and thus has important implications for the role of genetic drift in the evolutionary dynamics of animal taxa characterized by polygynous mating systems. Here we report the results of a study designed to test the hypothesis that polygynous mating results in significantly reduced Ne in an age-structured population. This hypothesis was tested in a natural population of a harem-forming fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae), in western India. The influence of the mating system on the ratio of variance Ne to adult census number (N) was assessed using a mathematical model designed for age-structured populations that incorporated demographic and genetic data. Male mating success was assessed by means of direct and indirect paternity analysis using 10-locus microsatellite genotypes of adults and progeny from two consecutive breeding periods (n = 431 individually marked bats). Combined results from both analyses were used to infer the effective number of male parents in each breeding period. The relative proportion of successfully reproducing males and the size distribution of paternal sibships comprising each offspring cohort revealed an extremely high within-season variance in male mating success (up to 9.2 times higher than Poisson expectation). The resultant estimate of Ne/N for the C. sphinx study population was 0.42. As a result of polygynous mating, the predicted rate of drift (1/2Ne per generation) was 17.6% higher than expected from a Poisson distribution of male mating success. However, the estimated Ne/N was well within the 0.25-0.75 range expected for age-structured populations under normal demographic conditions. The life-history schedule of C. sphinx is characterized by a disproportionately short sexual maturation period scaled to adult life span. Consequently, the influence of polygynous mating on Ne/N is mitigated by the extensive overlap of generations. In C. sphinx, turnover of breeding males between seasons ensures a broader sampling of the adult male gamete pool than expected from the variance in mating success within a single breeding period.

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

Geographic structure of genetic variation in the widespread woodland grass Milium effusum L. A comparison between two regions with contrasting history and geomorphology.

PubMed

Tyler, Torbjörn

2002-12-01

Allozyme variation in the forest grass Milium effusum L. was studied in 21-23 populations within each of two equally sized densely sampled areas in northern and southern Sweden. In addition, 25 populations from other parts of Eurasia were studied for comparison. The structure of variation was analysed with both diversity statistics and measures based on allelic richness at a standardised sample size. The species was found to be highly variable, but no clear geographic patterns in the distribution of alleles or in overall genetic differentiation were found, either within the two regions or within the whole sample. Thus, no inferences about the direction of postglacial migration could be made. Obviously, migration and gene flow must have taken place in a manner capable of randomising the distribution of alleles. However, there were clear differences in levels and structuring of the variation between the two regions. Levels of variation, both in terms of genetic diversity and allelic richness, were lower in northern Sweden as compared with southern Sweden. In contrast, different measures of geographic structure all showed higher levels of population differentiation in the northern region. This is interpreted as due to different geomorphological conditions in the two regions, creating a relatively continuous habitat and gene flow in the southern region as compared with the northern region where the species, although common, is confined to narrow and mutually isolated corridors in the landscape.

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

PubMed

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

2014-11-01

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

Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

PubMed

Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

2016-06-17

In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

Continuous and Discrete Structured Population Models with Applications to Epidemiology and Marine Mammals

NASA Astrophysics Data System (ADS)

Tang, Tingting

In this dissertation, we develop structured population models to examine how changes in the environmental affect population processes. In Chapter 2, we develop a general continuous time size structured model describing a susceptible-infected (SI) population coupled with the environment. This model applies to problems arising in ecology, epidemiology, and cell biology. The model consists of a system of quasilinear hyperbolic partial differential equations coupled with a system of nonlinear ordinary differential equations that represent the environment. We develop a second-order high resolution finite difference scheme to numerically solve the model. Convergence of this scheme to a weak solution with bounded total variation is proved. We numerically compare the second order high resolution scheme with a first order finite difference scheme. Higher order of convergence and high resolution property are observed in the second order finite difference scheme. In addition, we apply our model to a multi-host wildlife disease problem, questions regarding the impact of the initial population structure and transition rate within each host are numerically explored. In Chapter 3, we use a stage structured matrix model for wildlife population to study the recovery process of the population given an environmental disturbance. We focus on the time it takes for the population to recover to its pre-event level and develop general formulas to calculate the sensitivity or elasticity of the recovery time to changes in the initial population distribution, vital rates and event severity. Our results suggest that the recovery time is independent of the initial population size, but is sensitive to the initial population structure. Moreover, it is more sensitive to the reduction proportion to the vital rates of the population caused by the catastrophe event relative to the duration of impact of the event. We present the potential application of our model to the amphibian population dynamic and the recovery of a certain plant population. In addition, we explore, in details, the application of the model to the sperm whale population in Gulf of Mexico after the Deepwater Horizon oil spill. In Chapter 4, we summarize the results from Chapter 2 and Chapter 3 and explore some further avenues of our research.

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti.

PubMed

Franco, Fernando Faria; Jojima, Cecília Leiko; Perez, Manolo Fernandez; Zappi, Daniela Cristina; Taylor, Nigel; Moraes, Evandro Marsola

2017-11-01

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis , C. fernambucensis subsp. sericifer , and C. insularis . These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis , northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis , southern distribution of C. fernambucensis subsp. sericifer , and northern distribution of C. fernambucensis subsp. sericifer . Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.

Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa

PubMed Central

Allal, F; Sanou, H; Millet, L; Vaillant, A; Camus-Kulandaivelu, L; Logossa, Z A; Lefèvre, F; Bouvet, J-M

2011-01-01

The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (FST=0.21; RST=0.28; RST>RST (permuted)) and chloroplast simple sequence repeats (SSRs) (GST=0.81; NST=0.90; NST>NST (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa. PMID:21407253

Are There Different Populations of Flux Ropes in the Solar Wind?

NASA Astrophysics Data System (ADS)

Janvier, M.; Démoulin, P.; Dasso, S.

2014-07-01

Flux ropes are twisted magnetic structures that can be detected by in-situ measurements in the solar wind. However, different properties of detected flux ropes suggest different types of flux-rope populations. As such, are there different populations of flux ropes? The answer is positive and is the result of the analysis of four lists of flux ropes, including magnetic clouds (MCs), observed at 1 AU. The in-situ data for the four lists were fitted with the same cylindrical force-free field model, which provides an estimate of the local flux-rope parameters such as its radius and orientation. Since the flux-rope distributions have a broad dynamic range, we went beyond a simple histogram analysis by developing a partition technique that uniformly distributes the statistical fluctuations across the radius range. By doing so, we found that small flux ropes with radius R<0.1 AU have a steep power-law distribution in contrast to the larger flux ropes (identified as MCs), which have a Gaussian-like distribution. Next, from four CME catalogs, we estimated the expected flux-rope frequency per year at 1 AU. We found that the predicted numbers are similar to the frequencies of MCs observed in-situ. However, we also found that small flux ropes are at least ten times too abundant to correspond to CMEs, even to narrow ones. Investigating the different possible scenarios for the origin of these small flux ropes, we conclude that these twisted structures can be formed by blowout jets in the low corona or in coronal streamers.

High-Level Genetic Diversity and Complex Population Structure of Siberian Apricot (Prunus sibirica L.) in China as Revealed by Nuclear SSR Markers

PubMed Central

Wang, Zhe; Kang, Ming; Liu, Huabo; Gao, Jiao; Zhang, Zhengdong; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

2014-01-01

Siberian apricot (Prunus sibirica L.), an ecologically and economically important tree species with a high degree of tolerance to a variety of extreme environmental conditions, is widely distributed across the mountains of northeastern and northern China, eastern and southeastern regions of Mongolia, Eastern Siberia, and the Maritime Territory of Russia. However, few studies have examined the genetic diversity and population structure of this species. Using 31 nuclear microsatellites, we investigated the level of genetic diversity and population structure of Siberian apricot sampled from 22 populations across China. The number of alleles per locus ranged from 5 to 33, with an average of 19.323 alleles. The observed heterozygosity and expected heterozygosity ranged from 0.037 to 0.874 and 0.040 to 0.924 with average values of 0.639 and 0.774, respectively. A STRUCTURE-based analysis clustered all of the populations into four genetic clusters. Significant genetic differentiation was observed between all population pairs. A hierarchical analysis of molecular variance attributed about 94% of the variation to within populations. No significant difference was detected between the wild and semi-wild groups, indicating that recent cultivation practices have had little impact on the genetic diversity of Siberian apricot. The Mantel test showed that the genetic distance among the populations was not significantly correlated with geographic distance (r = 0.4651, p = 0.9940). Our study represents the most comprehensive investigation of the genetic diversity and population structure of Siberian apricot in China to date, and it provides valuable information for the collection of genetic resources for the breeding of Siberian apricot and related species. PMID:24516551

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

PubMed

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

2011-07-01

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

Population Genomics of the Euryhaline Teleost Poecilia latipinna

PubMed Central

Hoover, D.; Travis, J.; Oleksiak, M. F.; Crawford, D. L.

2015-01-01

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence. PMID:26335684

Population Genomics of the Euryhaline Teleost Poecilia latipinna.

PubMed

Nunez, J C B; Seale, T P; Fraser, M A; Burton, T L; Fortson, T N; Hoover, D; Travis, J; Oleksiak, M F; Crawford, D L

2015-01-01

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.

The structure of the distant Kuiper belt in a Nice model scenario

NASA Astrophysics Data System (ADS)

Pike, Rosemary E.; Lawler, Samantha; Brasser, Ramon; Shankman, Cory; Alexandersen, Mike; Kavelaars, J. J.

2016-10-01

By utilizing a well-sampled migration model and characterized survey detections, we demonstrate that the Nice-model scenario results in consistent populations of scattering trans-Neptunian objects (TNOs) and several resonant TNO populations, but fails to reproduce the large population of 5:1 resonators discovered in surveys. We examine in detail the TNO populations implanted by the Nice model simulation from Brasser and Morbidelli (2013, B&M). This analysis focuses on the region from 25-155 AU, probing the classical, scattering, detached, and major resonant populations. Additional integrations were necessary to classify the test particles and determine population sizes and characteristics. The classified simulation objects are compared to the real TNOs from the Canada-France Ecliptic Plane Survey (CFEPS), CFEPS high latitude fields, and the Alexandersen (2016) survey. These surveys all include a detailed characterization of survey depth, pointing, and tracking efficiency, which allows detailed testing of this independently produced model of TNO populations. In the B&M model, the regions of the outer Solar System populated via capture of scattering objects are consistent with survey constraints. The scattering TNOs and most n:1 resonant populations have consistent orbital distributions and population sizes with the real detections, as well as a starting disk mass consistent with expectations. The B&M 5:1 resonators have a consistent orbital distribution with the real detections and previous models. However, the B&M 5:1 Neptune resonance is underpopulated by a factor of ~100 and would require a starting proto-planetesimal disk with a mass of ~100 Earth masses. The large population in the 5:1 Neptune resonance is unexplained by scattering capture in a Nice-model scenario, however this model accurately produces the TNO subpopulations that result from scattering object capture and provides additional insight into sub-population orbital distributions.

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

Flow cytometry, microsatellites and niche models reveal the origins and geographical structure of Alnus glutinosa populations in Europe

PubMed Central

Mandák, Bohumil; Vít, Petr; Krak, Karol; Trávníček, Pavel; Havrdová, Alena; Hadincová, Věroslava; Zákravský, Petr; Jarolímová, Vlasta; Bacles, Cecile Fanny Emilie; Douda, Jan

2016-01-01

Background and Aims Polyploidy in plants has been studied extensively. In many groups, two or more cytotypes represent separate biological entities with distinct distributions, histories and ecology. This study examines the distribution and origins of cytotypes of Alnus glutinosa in Europe, North Africa and western Asia. Methods A combined approach was used involving flow cytometry and microsatellite analysis of 12 loci in 2200 plants from 209 populations combined with species distribution modelling using MIROC and CCSM climatic models, in order to analyse (1) ploidy and genetic variation, (2) the origin of tetraploid A. glutinosa, considering A. incana as a putative parent, and (3) past distributions of the species. Key Results The occurrence of tetraploid populations of A. glutinosa in Europe is determined for the first time. The distribution of tetraploids is far from random, forming two geographically well-delimited clusters located in the Iberian Peninsula and the Dinaric Alps. Based on microsatellite analysis, both tetraploid clusters are probably of autopolyploid origin, with no indication that A. incana was involved in their evolutionary history. A projection of the MIROC distribution model into the Last Glacial Maximum (LGM) showed that (1) populations occurring in the Iberian Peninsula and North Africa were probably interconnected during the LGM and (2) populations occurring in the Dinaric Alps did not exist throughout the last glacial periods, having retreated southwards into lowland areas of the Balkan Peninsula. Conclusions Newly discovered tetraploid populations are situated in the putative main glacial refugia, and neither of them was likely to have been involved in the colonization of central and northern Europe after glacial withdrawal. This could mean that neither the Iberian Peninsula nor the western part of the Balkan Peninsula served as effective refugial areas for northward post-glacial expansion of A. glutinosa. PMID:26467247

Phylogeography of Tibouchina papyrus (Pohl) Toledo (Melastomataceae), an endangered tree species from rocky savannas, suggests bidirectional expansion due to climate cooling in the Pleistocene

PubMed Central

Collevatti, Rosane Garcia; de Castro, Thaís Guimarães; de Souza Lima, Jacqueline; de Campos Telles, Mariana Pires

2012-01-01

Many endemic species present disjunct geographical distribution; therefore, they are suitable models to test hypotheses about the ecological and evolutionary mechanisms involved in the origin of disjunct distributions in these habitats. We studied the genetic structure and phylogeography of Tibouchina papyrus (Melastomataceae), endemic to rocky savannas in Central Brazil, to test hypothesis of vicariance and dispersal in the origin of the disjunct geographical distribution. We sampled 474 individuals from the three localities where the species is reported: Serra dos Pirineus, Serra Dourada, and Serra de Natividade. Analyses were based on the polymorphisms at cpDNA and on nuclear microsatellite loci. To test for vicariance and dispersal we constructed a median-joining network and performed an analysis of molecular variance (AMOVA). We also tested population bottleneck and estimated demographic parameters and time to most recent common ancestor (TMRCA) using coalescent analyses. A remarkable differentiation among populations was found. No significant effect of population expansion was detected and coalescent analyses showed a negligible gene flow among populations and an ancient coalescence time for chloroplast genome. Our results support that the disjunct distribution of T. papyrus may represent a climatic relict. With an estimated TMRCA dated from ∼836.491 ± 107.515 kyr BP (before present), we hypothesized that the disjunct distribution may be the outcome of bidirectional expansion of the geographical distribution favored by the drier and colder conditions that prevailed in much of Brazil during the Pre-Illinoian glaciation, followed by the retraction as the climate became warmer and moister. PMID:22837846

Stock structure of sea otters (Enhydra lutris kenyoni) in Alaska

USGS Publications Warehouse

Gorbics, C.S.; Bodkin, James L.

2001-01-01

Sea otters in Alaska are recognized as a single subspecies (Enhydra lutris kenyoni) and currently managed as a single, interbreeding population. However, geographic and behavioral mechanisms undoubtably constrain sea otter movements on much smaller scales. This paper applies the phylogeographic method (Dizon et al. 1992) and considers distribution, population response, phenotype and genotype data to identify stocks of sea otters within Alaska. The evidence for separate stock identity is genotypic (all stocks), phenotypic (Southcentral and Southwest stocks), and geographic distribution (Southeast stock), whereas population response data are equivocal (all stocks). Differences in genotype frequencies and the presence of unique genotypes among areas indicate restricted gene flow. Genetic exchange may be limited by little or no movement across proposed stock boundaries and discontinuities in distribution at proposed stock boundaries. Skull size differences (phenotypic) between Southwest and Southcentral Alaska populations further support stock separation. Population response information was equivocal in either supporting or refuting stock identity. On the basis of this review, we suggest the following: (1) a Southeast stock extending from Dixon Entrance to Cape Yakataga; (2) a Southcentral stock extending from Cape Yakataga to Cape Douglas including Prince William Sound and Kenai peninsula coast; and (3) a Southwest stock including Alaska Peninsula coast, the Aleutians to Attu Island, Barren, Kodiak, Pribilof Islands, and Bristol Bay.

WHITE DWARFS IN LOCAL STAR STREAMS

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

Fuchs, Burkhard; Dettbarn, Christian

2011-01-15

We have studied the fine structure of the phase space distribution of white dwarfs in the solar neighborhood. White dwarfs have kinematics that are typical for the stellar population of the old thin disk of the Milky Way. Using a projection of the space velocities of stars onto vertical angular momentum components and eccentricities of the stellar orbits we demonstrate that stellar streams can be identified in the phase space distribution of the white dwarfs. These correspond to the well-known Sirius, Pleiades, and Hercules star streams. Membership of white dwarfs, which represent the oldest population in the Galaxy, in thesemore » streams lends support to the interpretation that the streams owe their existence to dynamical resonance effects of the stars with Galactic spiral arms or the Galactic bar, because these indiscriminately affect all stellar populations.« less

Genetic differences among Haplorchis taichui populations in Indochina revealed by mitochondrial COX1 sequences.

PubMed

Thaenkham, U; Phuphisut, O; Nuamtanong, S; Yoonuan, T; Sa-Nguankiat, S; Vonghachack, Y; Belizario, V Y; Dung, D T; Dekumyoy, P; Waikagul, J

2017-09-01

Haplorchis taichui is an intestinal heterophyid fluke that is pathogenic to humans. It is widely distributed in Asia, with a particularly high prevalence in Indochina. Previous work revealed that the lack of gene flow between three distinct populations of Vietnamese H. taichui can be attributed to their geographic isolation with no interconnected river basins. To test the hypothesis that interconnected river basins allow gene flow between otherwise isolated populations of H. taichui, as previously demonstrated for another trematode, Opisthorchis viverrini, we compared the genetic structures of seven populations of H. taichui from various localities in the lower Mekong Basin, in Thailand and Laos, with those in Vietnam, using the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. To determine the gene flow between these H. taichui populations, we calculated their phylogenetic relationships, genetic distances and haplotype diversity. Each population showed very low nucleotide diversity at this locus. However, high levels of genetic differentiation between the populations indicated very little gene flow. A phylogenetic analysis divided the populations into four clusters that correlated with the country of origin. The negligible gene flow between the Thai and Laos populations, despite sharing the Mekong Basin, caused us to reject our hypothesis. Our data suggest that the distribution of H. taichui populations was incidentally associated with national borders.

Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

USGS Publications Warehouse

Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

2013-01-01

In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard, Ctenophorus ornatus.

PubMed

Levy, Esther; Tomkins, Joseph L; Lebas, Natasha R; Kennington, W Jason

2013-08-01

Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine-scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (FST  = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure. © 2013 John Wiley & Sons Ltd.

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

On the probabilistic structure of water age

NASA Astrophysics Data System (ADS)

Porporato, Amilcare; Calabrese, Salvatore

2015-05-01

The age distribution of water in hydrologic systems has received renewed interest recently, especially in relation to watershed response to rainfall inputs. The purpose of this contribution is first to draw attention to existing theories of age distributions in population dynamics, fluid mechanics and stochastic groundwater, and in particular to the McKendrick-von Foerster equation and its generalizations and solutions. A second and more important goal is to clarify that, when hydrologic fluxes are modeled by means of time-varying stochastic processes, the age distributions must themselves be treated as random functions. Once their probabilistic structure is obtained, it can be used to characterize the variability of age distributions in real systems and thus help quantify the inherent uncertainty in the field determination of water age. We illustrate these concepts with reference to a stochastic storage model, which has been used as a minimalist model of soil moisture and streamflow dynamics.

Population sub-structuring among Trypanosoma evansi stocks.

PubMed

Njiru, Z K; Constantine, C C

2007-10-01

To investigate the population genetic structure of Trypanosoma evansi from domesticated animals, we have analysed 112 stocks from camels, buffaloes, cattle and horses using the tandemly repeated coding sequence (MORF2) and minisatellite markers 292 and cysteine-rich acidic integral membrane protein (CRAM). We recorded a total of six alleles at the MORF2 locus, seven at 292 and 12 at the CRAM loci. Nei's genetic distance showed reduced allelic diversity between buffaloes and cattle stocks (1.2) as compared to the diversity between camels and buffaloes (3.75) and camels and cattle stock (1.69). The mean index of association (IA=0.92) significantly deviated from zero, and the average number of multilocus genotypes (G/N ratio) was 0.21. Twenty-four multilocus genotypes were defined from the combination of alleles at the three loci. The Kenyan sub-populations showed Fst=0.28 and analysis of molecular variance showed significant divergence (22.7%) between the Laikipia, Kulal and Galana regions. The regional and host distribution of multi-locus genotypes significant population differentiation and high Nei's genetic distances suggest existence of genetic sub-structuring within T. evansi stocks while the few multi-locus genotypes and deviation of association index from zero indicate the lack of recombination. In conclusion, this study reveals that some genetic sub-structuring does occur within T. evansi, which has a clonal population structure.

SimBA: simulation algorithm to fit extant-population distributions.

PubMed

Parida, Laxmi; Haiminen, Niina

2015-03-14

Simulation of populations with specified characteristics such as allele frequencies, linkage disequilibrium etc., is an integral component of many studies, including in-silico breeding optimization. Since the accuracy and sensitivity of population simulation is critical to the quality of the output of the applications that use them, accurate algorithms are required to provide a strong foundation to the methods in these studies. In this paper we present SimBA (Simulation using Best-fit Algorithm) a non-generative approach, based on a combination of stochastic techniques and discrete methods. We optimize a hill climbing algorithm and extend the framework to include multiple subpopulation structures. Additionally, we show that SimBA is very sensitive to the input specifications, i.e., very similar but distinct input characteristics result in distinct outputs with high fidelity to the specified distributions. This property of the simulation is not explicitly modeled or studied by previous methods. We show that SimBA outperforms the existing population simulation methods, both in terms of accuracy as well as time-efficiency. Not only does it construct populations that meet the input specifications more stringently than other published methods, SimBA is also easy to use. It does not require explicit parameter adaptations or calibrations. Also, it can work with input specified as distributions, without an exemplar matrix or population as required by some methods. SimBA is available at http://researcher.ibm.com/project/5669 .

Genetic diversity and distribution patterns of host insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau.

PubMed

Quan, Qing-Mei; Chen, Ling-Ling; Wang, Xi; Li, Shan; Yang, Xiao-Ling; Zhu, Yun-Guo; Wang, Mu; Cheng, Zhou

2014-01-01

The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05) was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host insects as well as O. sinensis.

Selected Demographic Characteristics of the U.S. Hispanic Population and of Hispanic Subgroups. A Report Prepared by the Congressional Research Service for the Subcommittee on Census and Population of the Committee on Post Office and Civil Service, U.S. House of Representatives. 99th Congress, 2d Session.

ERIC Educational Resources Information Center

Library of Congress, Washington, DC. Congressional Research Service.

The report compares U.S. Hispanic subgroups with regard to five demographic statistics: (1) Geographic Distribution: the greatest number of Hispanics are found in Texas, California, New York and Florida. (2) Age Structure and Fertility: Hispanics are generally younger than the U.S. population, except for Cubans who are usually older. Mexicans have…

[Fertility of the Yanomami population of Sierra Parima (Amazonas Federal Territory, Venezuela)].

PubMed

Schkolnik, S

1983-08-01

This article presents information on the age structure and level of female fertility obtained on the basis of a sample of the Yanomami population (653 individuals) residing in the Venezuelan margin of Sierra Parima. The population observed is very young, over 50% are less than age 15, and the mean age is 18. The total fertility rate reaches 7.76 children/woman while the age distribution of rates show that fertility begins at a very early age and begins to decrease only after age 30. (author's modified)

On the Structure of a Best Possible Crossover Selection Strategy in Genetic Algorithms

NASA Astrophysics Data System (ADS)

Lässig, Jörg; Hoffmann, Karl Heinz

The paper considers the problem of selecting individuals in the current population in genetic algorithms for crossover to find a solution with high fitness for a given optimization problem. Many different schemes have been described in the literature as possible strategies for this task but so far comparisons have been predominantly empirical. It is shown that if one wishes to maximize any linear function of the final state probabilities, e.g. the fitness of the best individual in the final population of the algorithm, then a best probability distribution for selecting an individual in each generation is a rectangular distribution over the individuals sorted in descending sequence by their fitness values. This means uniform probabilities have to be assigned to a group of the best individuals of the population but probabilities equal to zero to individuals with lower fitness, assuming that the probability distribution to choose individuals from the current population can be chosen independently for each iteration and each individual. This result is then generalized also to typical practically applied performance measures, such as maximizing the expected fitness value of the best individual seen in any generation.

Pleiotropic Effects of Immune Responses Explain Variation in the Prevalence of Fibroproliferative Diseases

PubMed Central

Russell, Shirley B.; Smith, Joan C.; Huang, Minjun; Trupin, Joel S.; Williams, Scott M.

2015-01-01

Many diseases are differentially distributed among human populations. Differential selection on genetic variants in ancestral environments that coincidentally predispose to disease can be an underlying cause of these unequal prevalence patterns. Selected genes may be pleiotropic, affecting multiple phenotypes and resulting in more than one disease or trait. Patterns of pleiotropy may be helpful in understanding the underlying causes of an array of conditions in a population. For example, several fibroproliferative diseases are more prevalent and severe in populations of sub-Saharan ancestry. We propose that this disparity is due to selection for an enhanced Th2 response that confers resistance to helminthic infections, and concurrently increases susceptibility to fibrosis due to the profibrotic action of Th2 cytokines. Many studies on selection of Th2-related genes for host resistance to helminths have been reported, but the pleiotropic impact of this selection on the distribution of fibrotic disorders has not been explicitly investigated. We discuss the disproportionate occurrence of fibroproliferative diseases in individuals of African ancestry and provide evidence that adaptation of the immune system has shaped the genetic structure of these human populations in ways that alter the distribution of multiple fibroproliferative diseases. PMID:26540410

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

PubMed

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

2014-08-01

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

Genetic 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.

Genetic characterization of an X-STR decaplex system in the State of Mato Grosso, Brazil: distribution, forensic efficiency and population structure.

PubMed

Martins, Joyce A; Martins, Denise P; Oliveira-Brancati, Camila I F; Martinez, Juliana; Cicarelli, Regina M B; Souza, Dorotéia R S

2017-11-01

Studies with X-STR loci show population genetic substructure, which makes necessary the characterization of such markers in the different geographical and/or ethnic populations. Therefore, this study assessed the distribution and forensic efficiency of an X-STR decaplex system in the population of the State of Mato Grosso, as well as analysed the population structure of this State based on the aforementioned system. All X-STR markers were in Hardy-Weinberg equilibrium and linkage equilibrium, and the DXS6809 was the most informative marker. The power of discrimination value in females and males was 0.99999999995 and 0.9999994, respectively. Analysis of molecular variance indicated 1.10% (p < 0.00001) of heterogeneity among Europeans, Africans, Brazilians and other Latin Americans, and in relation to such groups, the population of the State of Mato Grosso showed lower genetic variation when compared with the Brazilian group (-0.10%, p = 0.67327). The genetic distance analysis showed lower values of F ST (0.0004 ≤ F ST  ≤ 0.00331), with non-significant p value (p > 0.00024), between the populations of Mato Grosso and Mato Grosso do Sul, Paraná and the Southeast region of Brazil (except for one sample of Rio de Janeiro). F ST values with significant p values (p ≤ 0.00024) were obtained between the population of Mato Grosso and Iberian, African and some Latin American populations. The X-STR decaplex system proved to be extremely useful in the population of the State of Mato Grosso, and the data obtained does not show the need for a specific forensic database for this State in relation to the Brazilian populations compared in this study, except for population of Rio de Janeiro.

Food

ERIC Educational Resources Information Center

Science, 1975

1975-01-01

This entire issue is devoted to the problem of producing enough food for the world population and of distributing it equitably. Areas covered include reports on the latest agricultural research, biological research concerned with more efficient photosynthesis, nutrition, and the world social structure, politics, and economics of food. (MA)

Sewage reflects the microbiomes of human populations.

PubMed

Newton, Ryan J; McLellan, Sandra L; Dila, Deborah K; Vineis, Joseph H; Morrison, Hilary G; Eren, A Murat; Sogin, Mitchell L

2015-02-24

Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics. Copyright © 2015 Newton et al.

South American Plasmodium falciparum after the Malaria Eradication Era: Clonal Population Expansion and Survival of the Fittest Hybrids

PubMed Central

Griffing, Sean M.; Mixson-Hayden, Tonya; Sridaran, Sankar; Alam, Md Tauqeer; McCollum, Andrea M.; Cabezas, César; Marquiño Quezada, Wilmer; Barnwell, John W.; Macedo De Oliveira, Alexandre; Lucas, Carmen; Arrospide, Nancy; Escalante, Ananias A.; Bacon, David J.; Udhayakumar, Venkatachalam

2011-01-01

Malaria has reemerged in many regions where once it was nearly eliminated. Yet the source of these parasites, the process of repopulation, their population structure, and dynamics are ill defined. Peru was one of malaria eradication's successes, where Plasmodium falciparum was nearly eliminated for two decades. It reemerged in the 1990s. In the new era of malaria elimination, Peruvian P. falciparum is a model of malaria reinvasion. We investigated its population structure and drug resistance profiles. We hypothesized that only populations adapted to local ecological niches could expand and repopulate and originated as vestigial populations or recent introductions. We investigated the genetic structure (using microsatellites) and drug resistant genotypes of 220 parasites collected from patients immediately after peak epidemic expansion (1999–2000) from seven sites across the country. The majority of parasites could be grouped into five clonal lineages by networks and AMOVA. The distribution of clonal lineages and their drug sensitivity profiles suggested geographic structure. In 2001, artesunate combination therapy was introduced in Peru. We tested 62 parasites collected in 2006–2007 for changes in genetic structure. Clonal lineages had recombined under selection for the fittest parasites. Our findings illustrate that local adaptations in the post-eradication era have contributed to clonal lineage expansion. Within the shifting confluence of drug policy and malaria incidence, populations continue to evolve through genetic outcrossing influenced by antimalarial selection pressure. Understanding the population substructure of P. falciparum has implications for vaccine, drug, and epidemiologic studies, including monitoring malaria during and after the elimination phase. PMID:21949680

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

USGS Publications Warehouse

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

2017-01-01

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

Genetic diversity and population structure of Anastrepha striata (Diptera: Tephritidae) in three natural regions of southwestern Colombia using mitochondrial sequences.

PubMed

Gallo-Franco, Jenny Johana; Velasco-Cuervo, Sandra Marcela; Aguirre-Ramirez, Elkin; González Obando, Ranulfo; Carrejo, Nancy Soraya; Toro-Perea, Nelson

2017-02-01

Anastrepha striata is widely distributed across the Americas and is a pest of economically important crops, especially crops of the Myrtaceae family. Insect population structures can be influenced by the presence of physical barriers or characteristics associated with habitat differences. This study evaluated the effect of the Western Andes on the population structure of A. striata. Individuals were collected from Psidium guajava fruits from three natural regions of southwestern Colombia (Pacific Coast, mountainous region and the inter-Andean valley of the Cauca River). Based on a 1318 bp concatenated of the genes Cytochrome Oxidase subunit I (COI) and NADH dehydrogenase subunit 6 (ND6), 14 haplotypes with few changes among them (between 1 and 3) were found. There was only one dominant haplotype in all three regions. No genetic structure associated with the three eco-geographical regions of the study was found. Moreover, the Western Andes are not an effective barrier for the genetic isolation of the populations from the Pacific Coast compared with the inter-Andean valley populations. This genetic homogeneity could be partially due to anthropogenic intervention, which acts as a dispersal agent of infested fruits. Another hypothesis to explain the lack of structure would be the relatively recent arrival of A. striata to the region, as indicated by an analysis of the demographic history, which reveals a process of population expansion. This study represents the first attempt to understand the population genetics of A. striata in Colombia and could contribute to the integral management of this pest.

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.

Population genetic structure of the melon fly, Bactrocera cucurbitae (Diptera: Tephritidae), from China and Southeast Asia.

PubMed

Hu, Jian; Zhang, Jun L; Nardi, Francesco; Zhang, Run J

2008-11-01

The melon fly, Bactrocera cucurbitae Coquillett, is a species of fruit flies of significant agricultural interest. Of supposed Indian origin, the melon fly is now widely distributed throughout South East Asia up to China, while it has been recently eradicated from Japan. The population structure of seven geographic populations from coastal China, as well as samples from other regions of South East Asia and Japan, including lab colonies, have been studied using a 782 bp fragment of mitochondrial cytochrome oxidase I (COI) gene sequence. The observed genetic diversity was exceedingly low, considering the geographic scale of the sampling, and one single haplotype was found to be predominant from Sri Lanka to China. We confirm that Bactrocera cucurbitae exists in South East Asia as a single phyletic lineage, that Chinese populations are genetically uniform, and that no apparent genetic differentiation exists between these and three available Japanese melon fly sequences.

Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene.

PubMed

Kumar, Ravindra; Pandey, Brijesh Kumar; Sarkar, Uttam Kumar; Nagpure, Naresh Sahebrao; Baisvar, Vishwamitra Singh; Agnihotri, Praveen; Awasthi, Abhishek; Mishra, Abha; Kumar, Narendra

2017-05-01

Documentation of genetic differentiation among the populations of a species can provide useful information that has roles in conservation, breeding, and management plans. In the present study, we examined the genetic structure and phylogenetic relationships among the 149 individuals of Ompok bimaculatus belonging to 24 populations, collected from Indian waters, using cytochrome b gene. The combined analyses of data suggested that the Indian O. bimaculatus consist of three distinct mtDNA lineages with star-like haplotypes network, which exhibited high genetic variation and haplotypic diversity. Analysis of molecular variance indicated that most of the observed genetic variation was found among the populations suggesting restricted gene flow. Long-term interruption of gene flow was also evidenced by high overall Fst values (0.82367) that could be favored by the discontinuous distributions of the lineages.

The effects of plague on the distribution of property: Ivrea, Northern Italy 1630.

PubMed

Alfani, Guido

2010-03-01

The demographic effects of the epidemics of plague in Early Modern Europe and their economic consequences illuminate the evolution of property structures and of wealth distribution during and after a mortality crisis. An analysis of the high-quality data available for the Italian city of Ivrea at the time of the 1630 plague shows the exceptional resilience of property structures. Like the social structures of the period, property structures were able to recover quickly, informed as they were by the lessons learnt by trial and error by the patrician families of the late Middle Ages, whose patrimonies had been badly damaged by the Black Death. In a period of recurrent catastrophes that struck European populations during the Old Demographic Regime, apparently 'inegalitarian' institutions seem to have had long-term 'egalitarian' effects.

Microsatellite variation suggests a recent fine-scale population structure of Drosophila sechellia, a species endemic of the Seychelles archipelago.

PubMed

Legrand, Delphine; Vautrin, Dominique; Lachaise, Daniel; Cariou, Marie-Louise

2011-07-01

Drosophila sechellia is closely related to the cosmopolitan and widespread model species, D. simulans. This species, endemic to the Seychelles archipelago, is specialized on the fruits of Morinda citrifolia, and harbours the lowest overall genetic diversity compared to other species of Drosophila. This low diversity is associated with a small population size. In addition, no obvious population structure has been evidenced so far across islands of the Seychelles archipelago. Here, a microsatellite panel of 17 loci in ten populations from nine islands of the Seychelles was used to assess the effect of the D. sechellia's fragmented distribution on the fine-scale population genetic structure, the migration pattern, as well as on the demography of the species. Contrary to previous results, also based on microsatellites, no evidence for population contraction in D. sechellia was found. The results confirm previous studies based on gene sequence polymorphism that showed a long-term stable population size for this species. Interestingly, a pattern of Isolation By Distance which had not been described yet in D. sechellia was found, with evidence of first-generation migrants between some neighbouring islands. Bayesian structuring algorithm results were consistent with a split of D. sechellia into two main groups of populations: Silhouette/Mahé versus all the other islands. Thus, microsatellites suggest that variability in D. sechellia is most likely explained by local genetic exchanges between neighbouring islands that have recently resulted in slight differentiation of the two largest island populations from all the others.

Inequality measures perform differently in global and local assessments: An exploratory computational experiment

NASA Astrophysics Data System (ADS)

Chiang, Yen-Sheng

2015-11-01

Inequality measures are widely used in both the academia and public media to help us understand how incomes and wealth are distributed. They can be used to assess the distribution of a whole society-global inequality-as well as inequality of actors' referent networks-local inequality. How different is local inequality from global inequality? Formalizing the structure of reference groups as a network, the paper conducted a computational experiment to see how the structure of complex networks influences the difference between global and local inequality assessed by a selection of inequality measures. It was found that local inequality tends to be higher than global inequality when population size is large; network is dense and heterophilously assorted, and income distribution is less dispersed. The implications of the simulation findings are discussed.

Intercontinental gene flow among western arctic populations of lesser snow geese

USGS Publications Warehouse

Shorey, Rainy I.; Scribner, K.T.; Kanefsky, Jeannette; Samuel, M.D.; Libants, S.V.

2011-01-01

Quantifying the spatial genetic structure of highly vagile species of birds is important in predicting their degree of population demographic and genetic independence during changing environmental conditions, and in assessing their abundance and distribution. In the western Arctic, Lesser Snow Geese (Chen caerulescens caerulescens) provide an example useful for evaluating spatial population genetic structure and the relative contribution of male and female philopatry to breeding and wintering locales. We analyzed biparentally inherited microsatellite loci and maternally inherited mtDNA sequences from geese breeding at Wrangel Island (Russia) and Banks Island (Canada) to estimate gene flow among populations whose geographic overlap during breeding and winter differ. Significant differences in the frequencies of mtDNA haplotypes contrast with the homogeneity of allele frequencies for microsatellite loci. Coalescence simulations revealed high variability and asymmetry between males and females in rates and direction of gene flow between populations. Our results highlight the importance of wintering areas to demographic independence and spatial genetic structure of these populations. Male-mediated gene flow among the populations on northern Wrangel Island, southern Wrangel Island, and Banks Island has been substantial. A high rate of female-mediated gene flow from southern Wrangel Island to Banks Island suggests that population exchange can be achieved when populations winter in a common area. Conversely, when birds from different breeding populations do not share a common wintering area, the probability of population exchange is likely to be dramatically reduced. ?? The Cooper Ornithological Society 2011.

Integration of genetic and demographic data to assess population risk in a continuously distributed species

USGS Publications Warehouse

Fedy, Bradley C.; Row, Jeffery R.; Oyler-McCance, Sara J.

2017-01-01

The identification and demographic assessment of biologically meaningful populations is fundamental to species’ ecology and management. Although genetic tools are used frequently to identify populations, studies often do not incorporate demographic data to understand their respective population trends. We used genetic data to define subpopulations in a continuously distributed species. We assessed demographic independence and variation in population trends across the distribution. Additionally, we identified potential barriers to gene flow among subpopulations. We sampled greater sage-grouse (Centrocercus urophasianus) leks from across their range (≈175,000 Km2) in Wyoming and amplified DNA at 14 microsatellite loci for 1761 samples. Subsequently, we assessed population structure in unrelated individuals (n = 872) by integrating results from multiple Bayesian clustering approaches and used the boundaries to inform our assessment of long-term population trends and lek activity over the period of 1995–2013. We identified four genetic clusters of which two northern ones showed demographic independence from the others. Trends in population size for the northwest subpopulation were statistically different from the other three genetic clusters and the northeast and southwest subpopulations demonstrated a general trend of increasing proportion of inactive leks over time. Population change from 1996 to 2012 suggested population growth in the southern subpopulations and decline, or neutral, change in the northern subpopulations. We suggest that sage-grouse subpopulations in northern Wyoming are at greater risk of extirpation than the southern subpopulations due to smaller census and effective population sizes and higher variability within subpopulations. Our research is an example of incorporating genetic and demographic data and provides guidance on the identification of subpopulations of conservation concern.

Harbor porpoise Phocoena phocoena strandings on the Dutch coast: No genetic structure, but evidence of inbreeding

NASA Astrophysics Data System (ADS)

van der Plas-Duivesteijn, Suzanne J.; Smit, Femmie J. L.; van Alphen, Jacques J. M.; Kraaijeveld, Ken

2015-03-01

Conservation management in the North Sea is often motivated by the population size of marine mammals, like harbor porpoises Phocoena phocoena. In the Dutch part of the North Sea, sighting and stranding data are used to estimate population sizes, but these data give little insight into genetic structuring of the population. In this study we investigated genetic structure among animals stranded at different locations and times of year. We also tested whether there is a link between stranding and necropsy data, and genetic diversity. We made use of both mitochondrial (mtDNA) and microsatellite DNA analysis of samples from dead stranded porpoises along the Dutch coast during 2007. mtDNA analysis showed 6 variable positions in the control region, defining 3 different haplotypes. mtDNA haplotypes were not randomly distributed along the Dutch coastline. However, microsatellite analysis showed that these mtDNA haplotypes did not represent separate groups on a nuclear level. Furthermore, microsatellite analysis revealed no genotypic differences between seasons, locations or genders. The results of this study indicate that the Dutch population is panmictic. In contrast, heterozygosity levels were low, indicating some level of inbreeding in this population. However, this was not corroborated by other indices of inbreeding. This research provided insight into genetic structuring of stranded porpoises in 2007, but data from multiple years should be included to be able to help estimate population sizes.

Elevated genetic structure in the coastal tailed frog (Ascaphus truei) in managed redwood forests.

PubMed

Aguilar, Andres; Douglas, Robert B; Gordon, Eric; Baumsteiger, Jason; Goldsworthy, Matthew O

2013-03-01

Landscape alterations have dramatic impacts on the distribution of genetic variation within and among populations and understanding these effects can guide contemporary and future conservation strategies. We initiated a landscape-scale genetic study of the coastal tailed frog (Ascaphus truei) on commercial timberlands within the southern range of the species in Mendocino County (CA, USA). In total, 294 individuals from 13 populations were analyzed at 9 microsatellite loci. None of the sampled populations departed from mutation-drift equilibrium, indicating recent population bottlenecks were not detected in contemporary samples. Fine-scale analysis indicated sampled populations were structured at the watershed level (mean F (ST) = 0.077 and mean G'(ST) = 0.425). Landscape analyses suggested wet and moist areas may serve as significant corridors for gene flow within watersheds in this region (r (2) = 0.32-0.54 for moisture-related features). Results indicate populations of frogs may have persisted at this scale through intense periods of timber harvest, making southern range edge populations of coastal tailed frogs resilient to past land use practices.

Transferability of electronic structure of four energetic materials by using single crystal and high resolution X-ray diffraction experiments

NASA Astrophysics Data System (ADS)

Chen, Yu-Sheng

The electronic structures of four energetic materials, trinitrodiazapentalene (C6H3N5O6, TNDAP), beta-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (C4H8N8O8, beta-HMX), 1,3,3-trinitroazetidine (C3H4N4O6, TNAZ), and hexahydro-1,3,5-trinitro-1,3,5-s-triazine (C3H6N6O6, RDX), have been analyzed using Hansen-Coppens multipole refinements, using high resolution X-ray diffraction data collected at low temperature, as well as from theoretical calculated structure factors from the solid state phase using density functional theory (DFT), plus B3LYP level theory, and the 6-31G* basis set. However, when comparing both the deformation density and the electrostatic potentials from the theoretical results in TNDAP and TNAZ, they disagree with the experimental results. Therefore, those results have been deposited in appendices A4 and A6, for future reference. In HMX and RDX the theoretical results are in good agreement with experimental results. The physical properties derived from the electronic structure in these four energetic materials, such as multipole populations, the values of the electron density and its Laplacian of the electron density at the bond critical points, have also been calculated using "Atoms in Molecules" (AIM) theory both from the solid state phase calculation, and the experiment, as well as directly calculated from the free molecule in the gas phase. The electron density and the magnitude of its Laplacian from the gas phase are always larger than for the solid state phase calculation and the experiment. This may be due to the packing effect. The transferability of the experimental electronic structure of the NO 2 groups from HMX to TNDAP, TNAZ and RDX are also presented here. Even though the major populated multipoles are robust (small e.s.d.'s), these are few in number, compared with other lower populated multipoles for which the populations span a larger range. Since the deformation electron density distributions are reconstructed using linear combinations of the multipoles, it is necessary to give more degrees of freedom in the refinements. Therefore, those electron density distributions which have a wider range of the multipole populations should not be fixed in the refinements. Utilizing the same coordinate system setup in the multipole refinements of the functional groups, this system can be used as a starting point for solving the charge distribution of a larger system.

Is the nestedness of metazoan parasite assemblages of marine fishes from the southeastern Pacific coast a pattern associated with the geographical distributional range of the host?

PubMed

González, M T; Oliva, M E

2009-04-01

Nested structure is a pattern originally described in island biogeography to characterize how a set of species is distributed among a set of islands. In parasite communities, nestedness has been intensively studied among individual fish from a locality. However, nested patterns among parasite assemblages from different host populations (localities) have scarcely been investigated. We recorded the occurrence of parasites in 9 fish species widely distributed along the southeastern Pacific coast to determine whether the ecto- and endoparasite assemblages of marine fishes show a nested structure associated with host distributional range. Nestedness was tested using Brualdi-Sanderson index of discrepancy (BR); and 5 null models incorporated in a 'Nestedness' programme (Ulrich, 2006). The ecto- and endoparasite richness do not show similar patterns of latitudinal gradients among fish hosts, with 33-66% of analysed ectoparasite assemblages, and 25-75% of endoparasite assemblages showing nested structures through the host distributional range. For ectoparasites, species richness gradients and nested structure (when present) might be associated with decreased host densities or could reflect negative environmental conditions in the distributional border of the host species, whereas for endoparasites might be caused by geographical breaks of prey or changes in prey availability (intermediate hosts). The sampled extension of the distributional range of the host species, as well as the lack of specificity of some parasites, could influence the detection of nestedness.

Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus) (Chiroptera: Phyllostomidae) of Mexico.

PubMed

Romero-Nava, Claudia; León-Paniagua, Livia; Ortega, Jorge

2014-06-01

A limited number of studies have focused on the population genetic structure of vampire bats (Desmous rotundus) in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting) and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North) to Quintana Roo (Southeast). Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise (ST) and R(ST) detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site.

The early bird gets the shrimp: Confronting assumptions of isotopic equilibrium and homogeneity in a wild bird population

USGS Publications Warehouse

Wunder, Michael B.; Jehl, Joseph R.; Stricker, Craig A.

2012-01-01

1. Because stable isotope distributions in organic material vary systematically across energy gradients that exist in ecosystems, community and population structures, and in individual physiological systems, isotope values in animal tissues have helped address a broad range of questions in animal ecology. It follows that every tissue sample provides an isotopic profile that can be used to study dietary or movement histories of individual animals. Interpretations of these profiles depend on the assumption that metabolic pools are isotopically well mixed and in equilibrium with dietary resources prior to tissue synthesis, and they extend to the population level by assuming isotope profiles are identically distributed for animals using the same proximal dietary resource. As these assumptions are never fully met, studying structure in the variance of tissue isotope values from wild populations is informative. 2. We studied variation in δ13C, δ15N, δ2H and δ18O data for feathers from a population of eared grebes (Podiceps nigricollis) that migrate to Great Salt Lake each fall to moult feathers. During this time, they cannot fly and feed almost exclusively on superabundant brine shrimp (Artemia franciscana). The ecological simplicity of this situation minimized the usual spatial and trophic complexities often present in natural studies of feather isotope values. 3. Ranges and variances of isotope values for the feathers were larger than those from previously published studies that report feather isotopic variance, but they were bimodally distributed in all isotope dimensions. Isotope values for proximal dietary resources and local surface water show that some of the feathers we assumed to have been grown locally must have been grown before birds reached isotopic equilibrium with local diet or immediately prior to arrival at Great Salt Lake. 4. Our study provides novel insights about resource use strategies in eared grebes during migration. More generally, it demonstrates the utility of studying variance structures and questioning assumptions implicit in the interpretation of stable isotope data from wild animals.

Bamboo thickets alter the demographic structure of Euterpe edulis population: A keystone, threatened palm species of the Atlantic forest

NASA Astrophysics Data System (ADS)

Rother, Débora Cristina; Rodrigues, Ricardo Ribeiro; Pizo, Marco Aurélio

2016-01-01

The rapid spread of bamboos can strongly affect forest structure by interfering plant regeneration and reducing local biodiversity. Considering that bamboos exert a negative influence on the plant community, our main goal was to investigate how this influence manifests at the population level. We compared the demographic structure of the threatened palm Euterpe edulis between bamboo and non-bamboo dominated patches within the Atlantic forest. In the study site, the native bamboo Guadua tagoara has created a marked patchiness and heterogeneity in the vegetation. Plots were set up randomly in bamboo and non-bamboo patches and the heights of all E. edulis individuals were measured. Data from canopy openness and litter depth were collected for both patches. Greater number of E. edulis was recorded in bamboo patches. However, frequency distribution of the height classes differed between patches revealing a predominance of seedling and sapling I classes in bamboo patches, in comparison to a more evenly distribution of height classes in non-bamboo patches. The canopy in bamboo patches was more open and the litter depth was thicker. Our analyses evidenced G. tagoara is functioning as a demographic bottleneck of natural population of E. edulis by arresting its later stages of regeneration and in high densities that bamboos may limit recruitment of this palm species.

Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity

PubMed Central

Solomon, Scott E.; Bacci, Mauricio; Martins, Joaquim; Vinha, Giovanna Gonçalves; Mueller, Ulrich G.

2008-01-01

The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene—or both—have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area. PMID:18648512

Interindividual registration and dose mapping for voxelwise population analysis of rectal toxicity in prostate cancer radiotherapy

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

Dréan, Gaël; Acosta, Oscar, E-mail: Oscar.Acosta@univ-rennes1.fr; Simon, Antoine

2016-06-15

Purpose: Recent studies revealed a trend toward voxelwise population analysis in order to understand the local dose/toxicity relationships in prostate cancer radiotherapy. Such approaches require, however, an accurate interindividual mapping of the anatomies and 3D dose distributions toward a common coordinate system. This step is challenging due to the high interindividual variability. In this paper, the authors propose a method designed for interindividual nonrigid registration of the rectum and dose mapping for population analysis. Methods: The method is based on the computation of a normalized structural description of the rectum using a Laplacian-based model. This description takes advantage of themore » tubular structure of the rectum and its centerline to be embedded in a nonrigid registration-based scheme. The performances of the method were evaluated on 30 individuals treated for prostate cancer in a leave-one-out cross validation. Results: Performance was measured using classical metrics (Dice score and Hausdorff distance), along with new metrics devised to better assess dose mapping in relation with structural deformation (dose-organ overlap). Considering these scores, the proposed method outperforms intensity-based and distance maps-based registration methods. Conclusions: The proposed method allows for accurately mapping interindividual 3D dose distributions toward a single anatomical template, opening the way for further voxelwise statistical analysis.« less

Restoration over time and sustainability of Schinus terebinthifolius Raddi.

PubMed

Álvares-Carvalho, S V; Silva-Mann, R; Gois, I B; Melo, M F V; Oliveira, A S; Ferreira, R A; Gomes, L J

2017-05-31

The success of recovery programs on degraded areas is dependent on the genetic material to be used, which should present heterozygosity and genetic diversity in native and recovered populations. This study was carried out to evaluate the model efficiency to enable the recovery of a degraded area of the Lower São Francisco, Sergipe, Brazil. The target species for this study was Schinus terebinthifolius Raddi. Three populations were analyzed, the recovered area, seed-tree source population, and native tree population border established to the recovered area. The random amplified polymorphic DNA (RAPD) markers were used for diversity analysis. Genetic structure was estimated to evaluate the level of genetic variability existent in each population. There was no correlation between the spatial distribution and the genetic distances for all trees of the recovered area. The heterozygosity present in the recovered population was higher than the native tree population. The seed-tree source population presents genetic bottlenecks. Three clusters were suggested (ΔK = 3) with non-genetic structure. High intra-population genetic variability and inter-population differentiation are present. However, gene flow may also introduce potentially adaptive alleles in the populations of the recovered area, and the native population is necessary to ensure the sustainability and maintenance of the populations by allelic exchange.

ON A POSSIBLE SIZE/COLOR RELATIONSHIP IN THE KUIPER BELT

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

Pike, R. E.; Kavelaars, J. J., E-mail: repike@uvic.ca

2013-10-01

Color measurements and albedo distributions introduce non-intuitive observational biases in size-color relationships among Kuiper Belt Objects (KBOs) that cannot be disentangled without a well characterized sample population with systematic photometry. Peixinho et al. report that the form of the KBO color distribution varies with absolute magnitude, H. However, Tegler et al. find that KBO color distributions are a property of object classification. We construct synthetic models of observed KBO colors based on two B-R color distribution scenarios: color distribution dependent on H magnitude (H-Model) and color distribution based on object classification (Class-Model). These synthetic B-R color distributions were modified tomore » account for observational flux biases. We compare our synthetic B-R distributions to the observed ''Hot'' and ''Cold'' detected objects from the Canada-France Ecliptic Plane Survey and the Meudon Multicolor Survey. For both surveys, the Hot population color distribution rejects the H-Model, but is well described by the Class-Model. The Cold objects reject the H-Model, but the Class-Model (while not statistically rejected) also does not provide a compelling match for data. Although we formally reject models where the structure of the color distribution is a strong function of H magnitude, we also do not find that a simple dependence of color distribution on orbit classification is sufficient to describe the color distribution of classical KBOs.« less

DFT Study of Small Gold Clusters, Au n (2≤ n ≤ 6): Stability and Charge Distribution Using M08-SO Functional

NASA Astrophysics Data System (ADS)

Carvalho, F. S.; Braga, J. P.

2018-05-01

We have investigated the more stable structures for small gold clusters, Aun (2≤ n ≤ 6), using the density functional theory method. Two functionals used in the literature, the well-known B3LYP and M06-L, were compared with the one that has not been used for this system yet, M08-SO, and the results for dimer were compared with experimental data. It was found that M08-SO gives the best results for the effective core potential and basis set tested. Therefore, the functional M08-SO was used for other structures. The planar geometries were found to have the lowest energies. After the geometry optimization, Mulliken populational analysis (MPA) and natural populational analysis (NPA) were carried out and the results for charge distribution in gold trimer and tetramer were compared with data found in literature. The MPA calculation does not give results in agreement with the literature. On the other hand, the NPA calculation gives coherent data. The results showed that the charge distribution will not always predict the more favorable site of interaction.

Extinction rate, historical population structure and ecological role of the Caribbean monk seal.

PubMed

McClenachan, Loren; Cooper, Andrew B

2008-06-22

The productivity and biomass of pristine coral reef ecosystems is poorly understood, particularly in the Caribbean where communities have been impacted by overfishing and multiple other stressors over centuries. Using historical data on the spatial distribution and abundance of the extinct Caribbean monk seal (Monachus tropicalis), this study reconstructs the population size, structure and ecological role of this once common predator within coral reef communities, and provides evidence that historical reefs supported biomasses of fishes and invertebrates up to six times greater than those found on typical modern Caribbean reefs. An estimated 233,000-338,000 monk seals were distributed among 13 colonies across the Caribbean. The biomass of reef fishes and invertebrates required to support historical seal populations was 732-1018 gm(-2) of reefs, which exceeds that found on any Caribbean reef today and is comparable with those measured in remote Pacific reefs. Quantitative estimates of historically dense monk seal colonies and their consumption rates on pristine reefs provide concrete data on the magnitude of decline in animal biomass on Caribbean coral reefs. Realistic reconstruction of these past ecosystems is critical to understanding the profound and long-lasting effect of human hunting on the functioning of coral reef ecosystems.