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Sample records for explain population genetic

  1. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

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    Martina Temunović

    Full Text Available Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM. We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

  2. Biophysical connectivity explains population genetic structure in a highly dispersive marine species

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    Truelove, Nathan K.; Kough, Andrew S.; Behringer, Donald C.; Paris, Claire B.; Box, Stephen J.; Preziosi, Richard F.; Butler, Mark J.

    2017-03-01

    Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster ( Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F ST of 0.0016 ( P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus ( P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation ( P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

  3. Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models

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    Drozd Pavel

    2011-03-01

    Full Text Available Abstract Background Quest for understanding the nature of mechanisms governing the life span of clonal organisms lasts for several decades. Phylogenetic evidence for recent origins of most clones is usually interpreted as proof that clones suffer from gradual age-dependent fitness decay (e.g. Muller's ratchet. However, we have shown that a neutral drift can also qualitatively explain the observed distribution of clonal ages. This finding was followed by several attempts to distinguish the effects of neutral and non-neutral processes. Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200. reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data. Moreover, the authors inferred that similar types of mechanisms determine maximum asexual lineage ages in all asexual taxa. In this paper we review recent methods for distinguishing the effects of neutral and non-neutral processes and point at methodological problems related with them. Results and Discussion We found that contemporary analyses based on phylogenetic data are inadequate to provide any clear-cut answer about the nature and generality of processes affecting evolution of clones. As an alternative approach, we demonstrate that sequence variability in asexual populations is suitable to detect age-dependent selection against clonal lineages. We found that asexual taxa with relatively old clonal lineages are characterised by progressively stronger deviations from neutrality. Conclusions Our results demonstrate that some type of age-dependent selection against clones is generally operational in asexual animals, which cover a wide taxonomic range spanning from flatworms to vertebrates. However, we also found a notable difference between the data distribution predicted by available models of sequence evolution and those observed in empirical data. These findings point at the

  4. Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models

    National Research Council Canada - National Science Library

    Janko, Karel; Drozd, Pavel; Eisner, Jan

    2011-01-01

    .... Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200.) reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data...

  5. Molecular Population Genetics

    OpenAIRE

    Casillas, S?nia; Barbadilla, Antonio

    2017-01-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theo...

  6. Explaining spatial heterogeneity in population dynamics and genetics from spatial variation in resources for a large herbivore.

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    Contasti, Adrienne L; Tissier, Emily J; Johnstone, Jill F; McLoughlin, Philip D

    2012-01-01

    Fine-scale spatial variation in genetic relatedness and inbreeding occur across continuous distributions of several populations of vertebrates; however, the basis of observed variation is often left untested. Here we test the hypothesis that prior observations of spatial patterns in genetics for an island population of feral horses (Sable Island, Canada) were the result of spatial variation in population dynamics, itself based in spatial heterogeneity in underlying habitat quality. In order to assess how genetic and population structuring related to habitat, we used hierarchical cluster analysis of water sources and an indicator analysis of the availability of important forage species to identify a longitudinal gradient in habitat quality along the length of Sable Island. We quantify a west-east gradient in access to fresh water and availability of two important food species to horses: sandwort, Honckenya peploides, and beach pea, Lathyrus japonicas. Accordingly, the population clusters into three groups that occupy different island segments (west, central, and east) that vary markedly in their local dynamics. Density, body condition, and survival and reproduction of adult females were highest in the west, followed by central and east areas. These results mirror a previous analysis of genetics, which showed that inbreeding levels are highest in the west (with outbreeding in the east), and that there are significant differences in fixation indices among groups of horses along the length of Sable Island. Our results suggest that inbreeding depression is not an important limiting factor to the horse population. We conclude that where habitat gradients exist, we can anticipate fine-scale heterogeneity in population dynamics and hence genetics.

  7. Genetic variants in LEP, LEPR, and MC4R explain 30% of severe obesity in children from a consanguineous population.

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    Saeed, Sadia; Bonnefond, Amélie; Manzoor, Jaida; Shabir, Faiza; Ayesha, Hina; Philippe, Julien; Durand, Emmanuelle; Crouch, Hutokshi; Sand, Olivier; Ali, Muhammad; Butt, Taeed; Rathore, Ahsan W; Falchi, Mario; Arslan, Muhammad; Froguel, Philippe

    2015-08-01

    Single gene mutations leading to severe obesity have so far been identified in 3-5% cases in European populations. However, prevalence of these pathogenic mutations has not systematically been examined in specific consanguineous populations. Here we describe the incidence of obesity-associated mutations through a step-wise sequence analysis, in a cohort of 73 Pakistani children with severe obesity from consanguineous families. Initially, all subjects were screened for mutations in coding regions of leptin (LEP) and melanocortin 4 receptor (MC4R) genes by direct sequencing. Subjects negative for mutation in these genes were screened using microdroplet PCR enrichment and NGS. Genomic structural variation was assessed by genotyping. Serum leptin, insulin, and cortisol were determined by ELISA. Among 73 children with severe obesity (BMI SDS > 3.0), we identified 22 probands and 5 relatives, carrying 10 different loss-of-function homozygous mutations in LEP, leptin receptor (LEPR), and MC4R genes, including 4 novel variants. Hypercortisolemia was significantly emphasized in LEP mutation carriers. The prevalence of pathogenic mutations in genes known to directly influence leptin-melanocortin signaling is 30% in our cohort. The results of this study emphasize the desirability of undertaking systematic and in-depth genetic analysis of cases with severe obesity in specific consanguineous populations. © 2015 The Obesity Society.

  8. Molecular Population Genetics.

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    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  9. Explaining stasis: microevolutionary studies in natural populations.

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    Merilä, J; Sheldon, B C; Kruuk, L E

    2001-01-01

    Microevolution, defined as a change in the genetic constitution of a population over time, is considered to be of commonplace occurrence in nature. Its ubiquity can be inferred from the observation that quantitative genetic divergence among populations usually exceeds that to be expected due to genetic drift alone, and from numerous observations and experiments consistent with local adaptation. Experimental manipulations in natural populations have provided evidence that rapid evolutionary responses may occur in the wild. However, there are remarkably few cases where direct observations of natural populations have revealed microevolutionary changes occurring, despite the frequent demonstration of additive genetic variation and strong directional selection for particular traits. Those few cases where responses congruent with expectation have been demonstrated are restricted to changes over one generation. In this article we focus on possible explanations as to why heritable traits under apparently strong directional selection often fail to show the expected evolutionary response. To date, few of these explanations for apparent stasis have been amenable to empirical testing. We describe new methods, derived from procedures developed by animal breeding scientists, which can be used to address these explanations, and illustrate the approach with examples from long-term studies of collared flycatchers (Ficedula albicollis) and red deer (Cervus elaphus). Understanding why most intensively studied natural populations do not appear to be evolving is an important challenge for evolutionary biology.

  10. Population genetic analysis of cat populations from Mexico ...

    Indian Academy of Sciences (India)

    Unknown

    view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration ... Bolivia, and the Dominican Republic: identification of different gene pools in Latin America. J. Genet. ...... 77, 460-462. Klein K. K. 1993 Population genetics and gene geography. In.

  11. Population genetics and evolution

    Energy Technology Data Exchange (ETDEWEB)

    De Jong, G.

    1988-01-01

    This volume reevaluates the position of population genetics in evolutionary biology by using population genetics as the tool to study the role of development and adaptation in evolution. The emphasis is on the organismic process of selection, and on how the study of selection means connecting variation at the molecular, biochemical, and phenotypic levels of organization with the resulting variation in fitness. This book illustrates that the tendency to view single locus differences in isolation as the building blocks of evolution is disappearing.

  12. Population genetics and pharmacogenetics

    OpenAIRE

    Heude, Barbara; Ong, Ken

    2006-01-01

    The highlight for 2005/6 in population genetics was undoubtedly the publication of HapMap, a freely available public resource nearly of all common (>5% minor allele frequency) genetic differences in humans. Compared to the estimated 10 million single nucleotide polymorphisms (SNP) that we all share, at the launch of HapMap in 2002 there were fewer than 1.7 million SNPs on the public database dbSNP. Today, largely due to HapMap and related efforts, that number is around 9.2 million. Furthermor...

  13. Genetic structure of Algerian populations.

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    Lefevre-Witier, Philippe; Aireche, Hadi; Benabadji, Mohamed; Darlu, Pierre; Melvin, Kristin; Sevin, Andre; Crawford, Michael H

    2006-01-01

    Blood samples were collected in Algeria from 4,444 army recruits and tested for 10 genetic polymorphic systems. These samples were collected from territorial Wilayas (administrative units of Algeria) from which the young soldiers had originated. Based on similar geography and economic and political history, these Wilayas were clustered into 10 regions. These regions, not part of the governmental administrative units, were characterized by allelic frequencies, and analyzed using R-matrix principal components, Wright's F(ST), spatial autocorrelation, and Mantel tests. Hierarchical relationships between the culturally defined regions were examined using two different analytical methods of phylogenetic tree constructions: neighbor-joining, and unweighted pair group average arithmetic (UPGMA). These results indicated the predominance of genetic homogeneity due to the gene flow between regions, but with some migration emanating from sub-Saharan Africa and Mediterranean Europe. Wright's F(ST) value of 0.0063, based on 16 alleles, suggested a relatively small genetic microdifferentiation of the regions. In Algeria, gene flow apparently swamped most of the effects of stochastic processes and disrupted the relationship between geography and genetics, as characterized by the isolation-by-distance model. Some genetic differences and similarities were observed between regions or clusters of regions. The resulting genetic structure of the Algerian populations is best explained by a combination of gene flow, ecology, and history.

  14. Population genetics without intraspecific data

    DEFF Research Database (Denmark)

    Thorne, Jeffrey L; Choi, Sang Chul; Yu, Jiaye

    2007-01-01

    populations, and parameters of interspecific models should have population genetic interpretations. We show, with two examples, how population genetic interpretations can be assigned to evolutionary models. The first example considers the impact of RNA secondary structure on sequence change, and the second...... genetic interpretation. Udgivelsesdato: 2007-Aug...

  15. Population Genetics with Fluctuating Population Sizes

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    Chotibut, Thiparat; Nelson, David R.

    2017-05-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuation-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  16. Explaining consumer attitudes to genetic modification in food production

    DEFF Research Database (Denmark)

    Bredahl, Lone

    Consumers have not had many possibilities yet for seeking out, buying and consuming genetically modified food products. However, for various reasons consumer attitude formation with regard to these products is likely to be complex and closely related to personal values. The paper presents a model...... for explaining consumer attitudes to genetic modification in food production which builds on modern cognitive psychology and multi-attribute attitude theory. In addition, the paper introduces the empirical research which is undertaken at present to validate and estimate the parameters of the model by means...

  17. History matters more when explaining genetic diversity within the context of the core-periphery hypothesis.

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    Duncan, Sarah I; Crespi, Erica J; Mattheus, Nichole M; Rissler, Leslie J

    2015-08-01

    The core-periphery hypothesis (CPH) predicts that populations located at the periphery of a species' range should have lower levels of genetic variation than those at the centre of the range. However, most of the research on the CPH focuses on geographic distance and not on ecological distance, or uses categorical definitions of core and periphery to explain the distribution of genetic diversity. We use current climate data and historical climate data from the last glacial maxima to develop quantitative estimates of contemporary and historical ecological suitability using ecological niche models. We analysed genetic diversity using 12 polymorphic microsatellites to estimate changes in heterozygosity, allelic richness and population differentiation in 31 populations of the wood frog (Lithobates sylvaticus) spanning the species' entire eastern clade (33(o) to 45(o) latitude) from Alabama, USA, to Nova Scotia, Canada. Our data support predictions based on the CPH. Populations showed significant differences in genetic diversity across the range, with lower levels of genetic variation at the geographic range edge and in areas with lower levels of historical and contemporary ecological suitability. However, history and geography (not current ecological suitability) best explain the patterns. This study highlights the importance of examining more than just geography when assessing the CPH, and the importance of historical ecological suitability in the maintenance of genetic diversity and population differentiation. © 2015 John Wiley & Sons Ltd.

  18. CDPOP: A spatially explicit cost distance population genetics program

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    Erin L. Landguth; S. A. Cushman

    2010-01-01

    Spatially explicit simulation of gene flow in complex landscapes is essential to explain observed population responses and provide a foundation for landscape genetics. To address this need, we wrote a spatially explicit, individual-based population genetics model (CDPOP). The model implements individual-based population modelling with Mendelian inheritance and k-allele...

  19. The DNA revolution in population genetics.

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    Cavalli-Sforza, L L

    1998-02-01

    Unprecedental clarity has come to our understanding of genetic variation by the analysis of DNA sequences. It is not surprising that the new DNA technologies are leading to a resurgence of interest in population genetics. In this review, I discuss recent progress and future directions towards reconstructing the history of human populations. There is increasing consensus on a recent 'Out of Africa' origin of modern humans, which explains why the greatest fraction of genetic diversity is found within populations, rather than between them. The comparison of Y chromosome and mitochondrial DNA data shows remarkable sex differences in geographic variation. The analysis of Neanderthal DNA has been a major breakthrough in the study of fossil DNA. Among major hopes for the future are application to polygenic diseases.

  20. Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species.

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    Stapley, Jessica; Santure, Anna W; Dennis, Stuart R

    2015-05-01

    Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies. © 2015 John Wiley & Sons Ltd.

  1. Strong selection barriers explain microgeographic adaptation in wild salamander populations.

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    Richardson, Jonathan L; Urban, Mark C

    2013-06-01

    Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow, and the spatial arrangement of populations in shaping patterns of adaptive divergence in natural populations of the spotted salamander (Ambystoma maculatum). Within the study region, A. maculatum co-occur with the predatory marbled salamander (Ambystoma opacum) in some ponds, and past studies have established a link between predation risk and adaptive trait variation in A. maculatum. Using 14 microsatellite loci, we found a significant pattern of genetic divergence among A. maculatum populations corresponding to levels of A. opacum predation risk. Additionally, A. maculatum foraging rate was strongly associated with predation risk, genetic divergence, and the spatial relationship of ponds on the landscape. Our results indicate the sorting of adaptive genotypes by selection regime and strongly suggest that substantial selective barriers operate against gene flow. This outcome suggests that microgeographic adaptation in A. maculatum is possible because strong antagonistic selection quickly eliminates maladapted phenotypes despite ongoing and substantial immigration. Increasing evidence for microgeographic adaptation suggests a strong role for selective barriers in counteracting the homogenizing influence of gene flow. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  2. Genetic aspects of population policy.

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    Morton, N E

    1999-08-01

    Every science begins in folklore and matures as it reacts against dogma and myth. Astronomy developed in the Neolithic, but it did not outgrow astrology until the sixteenth century. Chemistry discarded alchemy at about the same time. On the contrary, the short history of genetics has been concurrent with the pseudo-science of eugenics, which, at times, has been widely accepted and incorporated in population policy and directive genetic counselling, with rare opposition by geneticists. Societal pressures are likely to increase with the power of genetic technology, the fear it generates and the perception that population growth threatens human welfare. Without a pertinent ethical code, geneticists are vulnerable to both temptation and opprobrium. The intrusion of eugenics into genetic counselling has been a recent source of concern to societies and congresses of genetics. This review traces the causes of this concern and the manner of its expression in the absence of an international voice for genetics that could address ethical and other common interests.

  3. Mantel test in population genetics

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    José Alexandre F. Diniz-Filho

    2013-01-01

    Full Text Available The comparison of genetic divergence or genetic distances, estimated by pairwise F ST and related statistics, with geographical distances by Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure. There have been, however, recent criticisms and discussions on the statistical performance of the Mantel test. Simultaneously, alternative frameworks for data analyses are being proposed. Here, we review the Mantel test and its variations, including Mantel correlograms and partial correlations and regressions. For illustrative purposes, we studied spatial genetic divergence among 25 populations of Dipteryx alata ("Baru", a tree species endemic to the Cerrado, the Brazilian savannas, based on 8 microsatellite loci. We also applied alternative methods to analyze spatial patterns in this dataset, especially a multivariate generalization of Spatial Eigenfunction Analysis based on redundancy analysis. The different approaches resulted in similar estimates of the magnitude of spatial structure in the genetic data. Furthermore, the results were expected based on previous knowledge of the ecological and evolutionary processes underlying genetic variation in this species. Our review shows that a careful application and interpretation of Mantel tests, especially Mantel correlograms, can overcome some potential statistical problems and provide a simple and useful tool for multivariate analysis of spatial patterns of genetic divergence.

  4. Fisher population and landscape genetics

    Science.gov (United States)

    Michael Schwartz; Joel Saunder; Kristine L. Pilgrim; Ray Vinkey; Michael K. Lucid; Sean Parks; Nathan Albrecht

    2013-01-01

    This talk provides a population and landscape genetic overview of fishers in Idaho and Montana. We start by discussing some of our initial findings using mitochondrial DNA (Vinkey et al. 2006, Schwartz 2007, Knaus et al. 2011). On balance these results demonstrate the uniqueness of a native haplotype that persisted in the Bitterroot-Selway Ecosystem. They also show the...

  5. Genetic structure of chimpanzee populations.

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    Celine Becquet

    2007-04-01

    Full Text Available Little is known about the history and population structure of our closest living relatives, the chimpanzees, in part because of an extremely poor fossil record. To address this, we report the largest genetic study of the chimpanzees to date, examining 310 microsatellites in 84 common chimpanzees and bonobos. We infer three common chimpanzee populations, which correspond to the previously defined labels of "western," "central," and "eastern," and find little evidence of gene flow between them. There is tentative evidence for structure within western chimpanzees, but we do not detect distinct additional populations. The data also provide historical insights, demonstrating that the western chimpanzee population diverged first, and that the eastern and central populations are more closely related in time.

  6. Leveraging population admixture to explain missing heritability of complex traits

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    Zaitlen, Noah; Pasaniuc, Bogdan; Sankararaman, Sriram; Bhatia, Gaurav; Zhang, Jianqi; Gusev, Alexander; Young, Taylor; Tandon, Arti; Pollack, Samuela; Vilhjálmsson, Bjarni J.; Assimes, Themistocles L.; Berndt, Sonja I.; Blot, William J.; Chanock, Stephen; Franceschini, Nora; Goodman, Phyllis G.; He, Jing; Hennis, Anselm JM; Hsing, Ann; Ingles, Sue A.; Isaacs, William; Kittles, Rick A.; Klein, Eric A.; Lange, Leslie A.; Nemesure, Barbara; Patterson, Nick; Reich, David; Rybicki, Benjamin A.; Stanford, Janet L.; Stevens, Victoria L; Strom, Sara S.; Whitsel, Eric A; Witte, John S.; Xu, Jianfeng; Haiman, Christopher; Wilson, James G.; Kooperberg, Charles; Stram, Daniel; Reiner, Alex P.; Tang, Hua; Price, Alkes L.

    2014-01-01

    Despite recent progress on estimating the heritability explained by genotyped SNPs (hg2), a large gap between hg2 and estimates of total narrow-sense heritability (h2) remains. Explanations for this gap include rare variants, or upward bias in family-based estimates of h2 due to shared environment or epistasis. We estimate h2 from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (hγ2). We show that hγ2 = 2FSTCθ(1−θ)h2, where FSTC measures frequency differences between populations at causal loci and θ is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We examined 21,497 African Americans from three cohorts, analyzing 13 phenotypes. For height and BMI, we obtained h2 estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of hg2 in these and other data, but smaller than family-based estimates of h2. PMID:25383972

  7. Stochastic problems in population genetics

    CERN Document Server

    Maruyama, Takeo

    1977-01-01

    These are" notes based on courses in Theoretical Population Genetics given at the University of Texas at Houston during the winter quarter, 1974, and at the University of Wisconsin during the fall semester, 1976. These notes explore problems of population genetics and evolution involving stochastic processes. Biological models and various mathematical techniques are discussed. Special emphasis is given to the diffusion method and an attempt is made to emphasize the underlying unity of various problems based on the Kolmogorov backward equation. A particular effort was made to make the subject accessible to biology students who are not familiar with stochastic processes. The references are not exhaustive but were chosen to provide a starting point for the reader interested in pursuing the subject further. Acknowledgement I would like to use this opportunity to express my thanks to Drs. J. F. Crow, M. Nei and W. J. Schull for their hospitality during my stays at their universities. I am indebted to Dr. M. Kimura...

  8. How Ebola impacts genetics of Western lowland gorilla populations.

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    Pascaline J Le Gouar

    Full Text Available BACKGROUND: Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species' extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. METHODOLOGY/PRINCIPAL FINDINGS: We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi's periphery not affected. Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. CONCLUSIONS/SIGNIFICANCE: Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

  9. Explaining the Linguistic Diversity of Sahul Using Population Models

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    Reesink, Ger; Singer, Ruth; Dunn, Michael

    2009-01-01

    The region of the ancient Sahul continent (present day Australia and New Guinea, and surrounding islands) is home to extreme linguistic diversity. Even apart from the huge Austronesian language family, which spread into the area after the breakup of the Sahul continent in the Holocene, there are hundreds of languages from many apparently unrelated families. On each of the subcontinents, the generally accepted classification recognizes one large, widespread family and a number of unrelatable smaller families. If these language families are related to each other, it is at a depth which is inaccessible to standard linguistic methods. We have inferred the history of structural characteristics of these languages under an admixture model, using a Bayesian algorithm originally developed to discover populations on the basis of recombining genetic markers. This analysis identifies 10 ancestral language populations, some of which can be identified with clearly defined phylogenetic groups. The results also show traces of early dispersals, including hints at ancient connections between Australian languages and some Papuan groups (long hypothesized, never before demonstrated). Systematic language contact effects between members of big phylogenetic groups are also detected, which can in some cases be identified with a diffusional or substrate signal. Most interestingly, however, there remains striking evidence of a phylogenetic signal, with many languages showing negligible amounts of admixture. PMID:19918360

  10. Explaining the linguistic diversity of Sahul using population models.

    Directory of Open Access Journals (Sweden)

    Ger Reesink

    2009-11-01

    Full Text Available The region of the ancient Sahul continent (present day Australia and New Guinea, and surrounding islands is home to extreme linguistic diversity. Even apart from the huge Austronesian language family, which spread into the area after the breakup of the Sahul continent in the Holocene, there are hundreds of languages from many apparently unrelated families. On each of the subcontinents, the generally accepted classification recognizes one large, widespread family and a number of unrelatable smaller families. If these language families are related to each other, it is at a depth which is inaccessible to standard linguistic methods. We have inferred the history of structural characteristics of these languages under an admixture model, using a Bayesian algorithm originally developed to discover populations on the basis of recombining genetic markers. This analysis identifies 10 ancestral language populations, some of which can be identified with clearly defined phylogenetic groups. The results also show traces of early dispersals, including hints at ancient connections between Australian languages and some Papuan groups (long hypothesized, never before demonstrated. Systematic language contact effects between members of big phylogenetic groups are also detected, which can in some cases be identified with a diffusional or substrate signal. Most interestingly, however, there remains striking evidence of a phylogenetic signal, with many languages showing negligible amounts of admixture.

  11. [Recent progress in plant molecular population genetics].

    Science.gov (United States)

    Wang, Yun-Sheng; Huang, Hong-Wen; Wang, Ying

    2007-10-01

    Molecular population genetics is not only one of the most important subjects of evolutionary biology, but also the basics subject of breeding, association mapping, and linkage analysis. Molecular population genetics has been developed from the classical population genetics aiming at studying population genetic structure and the factors that affect the population genetic structure by investigating the variation of DNA sequences. Therefore, population evolving history can be deduced accurately and quantitatively for evaluating the former conclusions about long-term evolution and the stability of genetic systems. Thus, molecular population genetics can avoid the shortcomings of classical population genetics, i.e. limiting to deduce the short evolving history of a population. Moreover, understanding of molecular variation patterns leads to further evaluation of the evolution theory, which is based on "Natural Selection" and introduced by Darwin. Molecular population genetics has made great progress and revealed many important scientific issues, such as the pattern of DNA polymorphism, the level of linkage disequilibrium, demographical history, and the genetic forces affecting gene evolvement. Furthermore, new research areas have been developed from molecular population genetics and become the hot fields, such as molecular phylogeography. In this review, we summarized studies and progresses of plant molecular population genetics.

  12. Review Synthetic Article: Sardinian Population (Italy): a Genetic ...

    African Journals Online (AJOL)

    Researches on genetic structure of Sardinian population, performed with of both classical and DNA markers, revealed an extremely complex picture of the relationships between Sardinian and other Italian and Mediterranean populations, that can be explained by Sardinian's historical and demographic past. A high degree ...

  13. Movement behavior explains genetic differentiation in American black bears

    Science.gov (United States)

    Samuel A Cushman; Jesse S. Lewis

    2010-01-01

    Individual-based landscape genetic analyses provide empirically based models of gene flow. It would be valuable to verify the predictions of these models using independent data of a different type. Analyses using different data sources that produce consistent results provide strong support for the generality of the findings. Mating and dispersal movements are the...

  14. The Growth of Older Inmate Populations: How Population Aging Explains Rising Age at Admission.

    Science.gov (United States)

    Luallen, Jeremy; Cutler, Christopher

    2017-09-01

    Older inmates are the fastest growing segment of the prison population; however, the reasons for this are not well understood. One explanation is that the general population is aging, driving prison age distributions to change. For this article, we study the role of population aging in prison growth by investigating how the baby boom phenomenon of post-World War II has contributed to the growth of older inmate populations. We identify the impact of population aging using simulation methods that explain prison growth as the combination of criminal justice processes. Overall, we find evidence that population aging has played a significant role in explaining the growth of older inmate populations, in particular among inmates aged between 50 and 64 years, contributing to as much as half of the observed increase in these groups since 2000. This finding stands in contrast to the notion that population aging has little explanatory power in describing the growth of prison populations and implies that older inmate groups are more sensitive to compositional changes in the general population. We argue that prediction-based modeling of prison growth should more seriously consider the impacts and consequences of demographic shifts among older prisoner populations.

  15. Explaining individual differences in alcohol intake in adults: evidence for genetic and cultural transmission?

    Science.gov (United States)

    van Beek, Jenny H D A; de Moor, Marleen H M; Geels, Lot M; Willemsen, Gonneke; Boomsma, Dorret I

    2014-03-01

    The current study aimed to describe what proportion of variation in adult alcohol intake is attributable to genetic differences among individuals and what proportion to differences in environmental experiences individuals have been exposed to. Effects of age, gender, spousal resemblance, and cultural transmission of alcohol intake from parents to offspring were taken into account. In a twin-family design, the effects of genetic and cultural transmission and shared and nonshared environment on alcohol intake were estimated with genetic structural equation models. Data originated from adult twins, their siblings, parents (n = 12,587), and spouses (n = 429) registered with the population-based Netherlands Twin Register (63.5% female; ages 18-97 years). Alcohol intake (grams per day) was higher among men than women and increased with age. Broad-sense heritability estimates were similar across sex and age (53%). Spousal resemblance was observed (r = .39) but did not significantly affect the heritability estimates. No effects of cultural transmission were detected. In total, 23% of the variation in alcohol intake was explained by additive genetic effects, 30% by dominant (nonadditive) gene action, and 47% by environmental effects that were not shared among family members. Individual differences in adult alcohol intake are explained by genetic and individual-specific environmental effects. The same genes are expressed in males and females and in younger and older participants. A substantial part of the heritability of alcohol intake is attributable to nonadditive gene action. Effects of cultural transmission that have been reported in adolescence are not present in adulthood.

  16. Ecological factors influence population genetic structure of European grey wolves.

    Science.gov (United States)

    Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Branicki, Wojciech; Sidorovich, Vadim E; Jedrzejewska, Bogumila; Stachura, Krystyna; Funk, Stephan M

    2006-12-01

    Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

  17. Kin-Aggregations Explain Chaotic Genetic Patchiness, a Commonly Observed Genetic Pattern, in a Marine Fish.

    Directory of Open Access Journals (Sweden)

    Jason D Selwyn

    Full Text Available The phenomenon of chaotic genetic patchiness is a pattern commonly seen in marine organisms, particularly those with demersal adults and pelagic larvae. This pattern is usually associated with sweepstakes recruitment and variable reproductive success. Here we investigate the biological underpinnings of this pattern in a species of marine goby Coryphopterus personatus. We find that populations of this species show tell-tale signs of chaotic genetic patchiness including: small, but significant, differences in genetic structure over short distances; a non-equilibrium or "chaotic" pattern of differentiation among locations in space; and within locus, within population deviations from the expectations of Hardy-Weinberg equilibrium (HWE. We show that despite having a pelagic larval stage, and a wide distribution across Caribbean coral reefs, this species forms groups of highly related individuals at small spatial scales (<10 metres. These spatially clustered family groups cause the observed deviations from HWE and local population differentiation, a finding that is rarely demonstrated, but could be more common than previously thought.

  18. Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

    Science.gov (United States)

    Hand, Brian K; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

    2016-01-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  19. Microsatellite data analysis for population genetics

    Science.gov (United States)

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

  20. Genetic variation and population structure in Oryza ...

    Indian Academy of Sciences (India)

    Genetically isolated smaller populations and a narrow genetic base in O. malampuzhaensis point to its vulnerability to genetic drift and genetic depauperation. Thus O. malampuzhaensis appears to be under the threat of extinction and needs to be conserved by use of suitable methods. The present study also identified ...

  1. (Genetic structure of natural populations)

    Energy Technology Data Exchange (ETDEWEB)

    1988-01-01

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs.

  2. Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations.

    Science.gov (United States)

    Kim, Bernard Y; Lohmueller, Kirk E

    2015-03-05

    It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  3. A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space.

    Directory of Open Access Journals (Sweden)

    Luis Zea

    Full Text Available Bacteria behave differently in space, as indicated by reports of reduced lag phase, higher final cell counts, enhanced biofilm formation, increased virulence, and reduced susceptibility to antibiotics. These phenomena are theorized, at least in part, to result from reduced mass transport in the local extracellular environment, where movement of molecules consumed and excreted by the cell is limited to diffusion in the absence of gravity-dependent convection. However, to date neither empirical nor computational approaches have been able to provide sufficient evidence to confirm this explanation. Molecular genetic analysis findings, conducted as part of a recent spaceflight investigation, support the proposed model. This investigation indicated an overexpression of genes associated with starvation, the search for alternative energy sources, increased metabolism, enhanced acetate production, and other systematic responses to acidity-all of which can be associated with reduced extracellular mass transport.

  4. Conservation genetics of managed ungulate populations

    Science.gov (United States)

    Scribner, Kim T.

    1993-01-01

    Natural populations of many species are increasingly impacted by human activities. Perturbations are particularly pronunced for large ungulates due in part to sport and commercial harvest, to reductions and fragmentation of native habitat, and as the result of reintroductions. These perturbations affect population size, sex and age composition, and population breeding structure, and as a consequence affect the levels and partitioning of genetic variation. Three case histories highlighting long-term ecological genetic research on mule deer Odocoileus hemionus (Rafinesque, 1817), white-tailed deer O. virginianus (Zimmermann, 1780), and Alpine ibex Capra i. ibex Linnaeus, 1758 are presented. Joint examinations of population ecological and genetic data from several populations of each species reveal: (1) that populations are not in genetic equilibrium, but that allele frequencies and heterozygosity change dramatically over time and among cohorts produced in successive years, (2) populations are genetically structured over short and large geographic distances reflecting local breeding structure and patterns of gene flow, respectively; however, this structure is quite dynamic over time, due in part to population exploitation, and (3) restocking programs are often undertaken with small numbers of founding individuals resulting in dramatic declines in levels of genetic variability and increasing levels of genetic differentiation among populations due to genetic drift. Genetic characteristics have and will continue to provide valuable indirect sources of information relating enviromental and human perturbations to changes in population processes.

  5. High school students' understanding and problem solving in population genetics

    Science.gov (United States)

    Soderberg, Patti D.

    This study is an investigation of student understanding of population genetics and how students developed, used and revised conceptual models to solve problems. The students in this study participated in three rounds of problem solving. The first round involved the use of a population genetics model to predict the number of carriers in a population. The second round required them to revise their model of simple dominance population genetics to make inferences about populations containing three phenotype variations. The third round of problem solving required the students to revise their model of population genetics to explain anomalous data where the proportions of males and females with a trait varied significantly. As the students solved problems, they were involved in basic scientific processes as they observed population phenomena, constructed explanatory models to explain the data they observed, and attempted to persuade their peers as to the adequacy of their models. In this study, the students produced new knowledge about the genetics of a trait in a population through the revision and use of explanatory population genetics models using reasoning that was similar to what scientists do. The students learned, used and revised a model of Hardy-Weinberg equilibrium to generate and test hypotheses about the genetics of phenotypes given only population data. Students were also interviewed prior to and following instruction. This study suggests that a commonly held intuitive belief about the predominance of a dominant variation in populations is resistant to change, despite instruction and interferes with a student's ability to understand Hardy-Weinberg equilibrium and microevolution.

  6. Population Differences at MHC Do Not Explain Enhanced Resistance of Song Sparrows to Local Parasites.

    Science.gov (United States)

    Slade, Joel W G; Sarquis-Adamson, Yanina; Gloor, Gregory B; Lachance, Marc-André; MacDougall-Shackleton, Elizabeth A

    2017-03-01

    Infectious disease represents an emerging threat to natural populations, particularly when hosts are more susceptible to novel parasites (allopatric) than to parasites from the local area (sympatric). This pattern could arise through evolutionary processes (host populations become adapted to their local parasites and genetically differentiated from other populations at immune-related loci) and/or through ecological interactions (host individuals develop resistance to local parasites through previous exposure). The relative importance of these candidate mechanisms remains unclear. In jawed vertebrates, genes of the major histocompatibility complex (MHC) play a fundamental role in immunity and are compelling candidates for spatially varying selection. We recently showed that song sparrows (Melospiza melodia) are more susceptible to allopatric than to sympatric strains of malaria (Plasmodium). In the current study, to determine whether population differences at MHC explain this pattern, we characterized the peptide-binding regions of MHC (classes I and II) of birds that did or did not become infected in the previous experiment. We recovered up to 4 alleles per individual at class I, implying at least 2 loci, and up to 26 alleles per individual at class II, implying at least 13 loci. Individuals with more class I alleles were less likely to become infected by Plasmodium, consistent with parasite-mediated balancing selection. However, we found no evidence for population genetic differentiation at either class of MHC, based on 36 individuals sequenced. Resistance to sympatric parasites previously described for this system likely stems from individuals' prior immune experience, not from population differentiation and locally protective alleles at MHC. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Population genetics of sexual conflict in the genomic era.

    Science.gov (United States)

    Mank, Judith E

    2017-12-01

    Sexual conflict occurs when selection acts in opposing directions on males and females. Case studies in both vertebrates and invertebrates indicate that sexual conflict maintains genetic diversity through balancing selection, which might explain why many populations show more genetic variation than expected. Recent population genomic approaches based on different measures of balancing selection have suggested that sexual conflict can arise over survival, not just reproductive fitness as previously thought. A fuller understanding of sexual conflict will provide insight into its contribution to adaptive evolution and will reveal the constraints it might impose on populations.

  8. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    The results exhibit a strong genetic differentiation which is obviously due to genetic drift in the isolated populations. The genetic structure of M. quintuplinervia has probably been shaped by its breeding modes, biogeographic history and human impact (both grazing and collection for medicinal purposes). This research might ...

  9. The population genetics of cooperative gene regulation

    Directory of Open Access Journals (Sweden)

    Stewart Alexander J

    2012-09-01

    Full Text Available Abstract Background Changes in gene regulatory networks drive the evolution of phenotypic diversity both within and between species. Rewiring of transcriptional networks is achieved either by changes to transcription factor binding sites or by changes to the physical interactions among transcription factor proteins. It has been suggested that the evolution of cooperative binding among factors can facilitate the adaptive rewiring of a regulatory network. Results We use a population-genetic model to explore when cooperative binding of transcription factors is favored by evolution, and what effects cooperativity then has on the adaptive re-writing of regulatory networks. We consider a pair of transcription factors that regulate multiple targets and overlap in the sets of target genes they regulate. We show that, under stabilising selection, cooperative binding between the transcription factors is favoured provided the amount of overlap between their target genes exceeds a threshold. The value of this threshold depends on several population-genetic factors: strength of selection on binding sites, cost of pleiotropy associated with protein-protein interactions, rates of mutation and population size. Once it is established, we find that cooperative binding of transcription factors significantly accelerates the adaptive rewiring of transcriptional networks under positive selection. We compare our qualitative predictions to systematic data on Saccharomyces cerevisiae transcription factors, their binding sites, and their protein-protein interactions. Conclusions Our study reveals a rich set of evolutionary dynamics driven by a tradeoff between the beneficial effects of cooperative binding at targets shared by a pair of factors, and the detrimental effects of cooperative binding for non-shared targets. We find that cooperative regulation will evolve when transcription factors share a sufficient proportion of their target genes. These findings help to

  10. What Use Is Population Genetics?

    Science.gov (United States)

    Charlesworth, Brian

    2015-07-01

    The Genetic Society of America's Thomas Hunt Morgan Medal is awarded to an individual GSA member for lifetime achievement in the field of genetics. For over 40 years, 2015 recipient Brian Charlesworth has been a leader in both theoretical and empirical evolutionary genetics, making substantial contributions to our understanding of how evolution acts on genetic variation. Some of the areas in which Charlesworth's research has been most influential are the evolution of sex chromosomes, transposable elements, deleterious mutations, sexual reproduction, and life history. He also developed the influential theory of background selection, whereby the recurrent elimination of deleterious mutations reduces variation at linked sites, providing a general explanation for the correlation between recombination rate and genetic variation. Copyright © 2015 by the Genetics Society of America.

  11. Coexistence and population genetic structure of the whooper swan Cygnus cygnus and mute swan Cygnus olor in Lithuania and Latvia

    National Research Council Canada - National Science Library

    Butkauskas, Dalius; Švažas, Saulius; Tubelytė, Vaida; Morkūnas, Julius; Sruoga, Aniolas; Boiko, Dmitrijs; Paulauskas, Algimantas; Stanevičius, Vitas; Baublys, Vykintas

    2012-01-01

    .... Marked differences in the genetic population structure of both species may partially explain the dominance of the whooper swan, as genetic population divergence can be a major factor affecting inter...

  12. Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity

    Science.gov (United States)

    Yang, Melinda A.; Malaspinas, Anna-Sapfo; Durand, Eric Y.; Slatkin, Montgomery

    2012-01-01

    Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site frequency spectrum [dcfs]), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans. PMID:22513287

  13. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity.

    Science.gov (United States)

    Yang, Melinda A; Malaspinas, Anna-Sapfo; Durand, Eric Y; Slatkin, Montgomery

    2012-10-01

    Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site frequency spectrum [dcfs]), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans.

  14. Landscape genetics: combining landscape ecology and population genetics

    Science.gov (United States)

    Stephanie Manel; Michael K. Schwartz; Gordon Luikart; Pierre Taberlet

    2003-01-01

    Understanding the processes and patterns of gene flow and local adaptation requires a detailed knowledge of how landscape characteristics structure populations. This understanding is crucial, not only for improving ecological knowledge, but also for managing properly the genetic diversity of threatened and endangered populations. For nearly 80 years, population...

  15. [Maximum entropy principle and population genetic equilibrium].

    Science.gov (United States)

    Wang, Xiao-Long; Yuan, Zhi-Fa; Guo, Man-Cai; Song, Shi-De; Zhang, Quan-Qi; Bao, Zhen-Min

    2002-06-01

    A general mathematic model of population genetic equilibrium was constructed based on the maximum entropy principle. We proved that the maximum entropy probability distribution was equivalent to the Hardy-Weinberg equilibrium law. A population reached genetic equilibrium when the genotype entropy of the population reached the maximal possible value. In information theory, the entropy or the information content is used to measure the uncertainty of a system. In population genetics, we can use entropy to measure the uncertainty of the genotype of a population. The agreement of the maximum entropy principle and the hardy-Weinberg equilibrium law indicated that random crossing is an irreversible process, which increases the genotype entropy of the population, while inbreeding and selection decrease the genotype entropy of the population. In animal or plant breeding, we often use selection and/or inbreeding to decrease the entropy of a population, and use intercrossing to increase the entropy of the population. In this point of view, breeding is actually regulating the entropy of population. By applying the basic principle of informatics in population genetics, we revealed the biological significance of the genotype entropy and demonstrated that we can work over population genetic problems with the principles and methods of informatics and cybernetics.

  16. Heritability of blood pressure traits and the genetic contribution to blood pressure variance explained by four blood-pressure-related genes.

    NARCIS (Netherlands)

    Rijn, M.J. van; Schut, A.F.; Aulchenko, Y.S.; Deinum, J.; Sayed-Tabatabaei, F.A.; Yazdanpanah, M.; Isaacs, A.; Axenovich, T.I.; Zorkoltseva, I.V.; Zillikens, M.C.; Pols, H.A.; Witteman, J.C.; Oostra, B.A.; Duijn, C.M. van

    2007-01-01

    OBJECTIVE: To study the heritability of four blood pressure traits and the proportion of variance explained by four blood-pressure-related genes. METHODS: All participants are members of an extended pedigree from a Dutch genetically isolated population. Heritability and genetic correlations of

  17. Genetic composition of captive panda population.

    Science.gov (United States)

    Yang, Jiandong; Shen, Fujun; Hou, Rong; Da, Yang

    2016-10-03

    A major function of the captive panda population is to preserve the genetic diversity of wild panda populations in their natural habitats. Understanding the genetic composition of the captive panda population in terms of genetic contributions from the wild panda populations provides necessary knowledge for breeding plans to preserve the genetic diversity of the wild panda populations. The genetic contributions from different wild populations to the captive panda population were highly unbalanced, with Qionglai accounting for 52.2 % of the captive panda gene pool, followed by Minshan with 21.5 %, Qinling with 10.6 %, Liangshan with 8.2 %, and Xiaoxiangling with 3.6 %, whereas Daxiangling, which had similar population size as Xiaoxiangling, had no genetic representation in the captive population. The current breeding recommendations may increase the contribution of some small wild populations at the expense of decreasing the contributions of other small wild populations, i.e., increasing the Xiaoxiangling contribution while decreasing the contribution of Liangshan, or sharply increasing the Qinling contribution while decreasing the contributions of Xiaoxiangling and Liangshan, which were two of the three smallest wild populations and were already severely under-represented in the captive population. We developed three habitat-controlled breeding plans that could increase the genetic contributions from the smallest wild populations to 6.7-11.2 % for Xiaoxiangling, 11.5-12.3 % for Liangshan and 12.9-20.0 % for Qinling among the offspring of one breeding season while reducing the risk of hidden inbreeding due to related founders from the same habitat undetectable by pedigree data. The three smallest wild panda populations of Daxiangling, Xiaoxiangling and Liangshan either had no representation or were severely unrepresented in the current captive panda population. By incorporating the breeding goal of increasing the genetic contributions from the smallest wild

  18. Population genetics of African ungulates

    DEFF Research Database (Denmark)

    Lorenzen, Eline

    Molecular genetic techniques were used to gain insights into the evolutionary forces that have shaped the present day diversity of African savannah ungu-lates, which constitute the most species-rich mega faunal assemblage on earth. The studies included in this thesis represent individual species......-specific data sets, which are used to elucidate evolutionary processes of importance to the savannah ungulate community. Patterns of DNA variation were analyzed to assess the genetic signatures of Pleistocene refugia and investigate aspects of speciation, intraspecific structuring, hybridization, and historic...

  19. Does selection or genetic drift explain geographic differentiation of morphological characters in house sparrows Passer domesticus?

    Science.gov (United States)

    Holand, Anna M; Jensen, Henrik; Tufto, Jarle; Moe, Rune

    2011-10-01

    Understanding the relative influence of genetic drift and selection is fundamental in evolutionary biology. The theory of neutrality predicts that the genetic differentiation of a quantitative trait (QST) equals the genetic differentiation at neutral molecular markers (FST) if the quantitative trait has not been under selection. Thus, the relative magnitude of observed QST and expected QST under neutral expectations suggests the importance of selection and genetic drift for any observed phenotypic divergence. Because QST is based on additive genetic variance, estimating QST based on phenotypic measurements is problematic due to unknown environmental effects. To account for this, we used a model where the environmental component was allowed to vary when estimating QST. The model was used on data from 14 house sparrow (Passer domesticus) populations in Norway. In accordance with the significant phenotypic inter-population differences our analyses suggested that directional selection may have favoured different optimal phenotypes for some morphological traits across populations. In particular, different body mass and male ornamental phenotypes seemed to have been favoured. The conclusions are, however, dependent on assumptions regarding the proportion of the observed inter-population variation that is due to additive genetic differences, showing the importance of collecting such information in natural populations. By estimating QST, allowing the additive genetic proportion of phenotypic inter-population variation to vary, and by making use of recent statistical methods to compare observed QST with neutral expectations, we can use data that are relatively easy to collect to identify adaptive variation in natural populations.

  20. Population Genetics of Phytophthora infestans

    DEFF Research Database (Denmark)

    Montes, Melanie Sarah

    a high diversity of lineages, with different strains appearing from field to field. Different strains were also tested for their resistance to the fungicide metalaxyl, and it was shown that there is potential for linking genetic markers to resistance. In a pilot study it was then tested whether P...

  1. Molecular taxonomic, epidemiological and population genetic ...

    African Journals Online (AJOL)

    Admin

    African Journal of Biotechnology Vol. ... Review. Molecular taxonomic, epidemiological and population genetic approaches to understanding yam anthracnose disease. Mathew M. Abang1*, Stephan Winter2, Hodeba ... Key words: Anthracnose, Colletotrichum gloeosporioides, Dioscorea spp., molecular markers, molecular.

  2. Significant population genetic structuring of the holoplanktic ...

    African Journals Online (AJOL)

    Pelagia noctiluca is thought to have a global distribution, yet our understanding of genetic connectivity across the range of this problem animal is poor. Here, we investigate the genetic structure of populations off southern Africa using mitochondrial COI and nuclear ITS1 and ITS2 genes, and compare the results to recent ...

  3. The geometry of population genetics

    CERN Document Server

    Akin, Ethan

    1979-01-01

    The differential equations which model the action of selection and recombination are nonlinear equations which are impossible to It is even difficult to describe in general the solve explicitly. Recently, Shahshahani began using qualitative behavior of solutions. differential geometry to study these equations [28]. with this mono­ graph I hope to show that his ideas illuminate many aspects of pop­ ulation genetics. Among these are his proof and clarification of Fisher's Fundamental Theorem of Natural Selection and Kimura's Maximum Principle and also the effect of recombination on entropy. We also discover the relationship between two classic measures of 2 genetic distance: the x measure and the arc-cosine measure. There are two large applications. The first is a precise definition of the biological concept of degree of epistasis which applies to general (i.e. frequency dependent) forms of selection. The second is the unexpected appearance of cycling. We show that cycles can occur in the two-locus-two-allele...

  4. Population genetic analysis of cat populations from Mexico ...

    Indian Academy of Sciences (India)

    the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America,; the heterozygosity levels at these loci in the current Latin American cat populations,; the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and ...

  5. SMALL POPULATION GENETIC VARIABILITY AT LOCI UNDER STABILIZING SELECTION.

    Science.gov (United States)

    Foley, Patrick

    1992-06-01

    Genetic variability at a locus under stabilizing selection in a finite population is investigated using analytic methods and computer simulations. Three measures are examined: the number of alleles k, heterozygosity H, and additive genetic variance Vg. A nearly-neutral theory results. The composite parameter S = NVM /Vs (where N is the population size, VM the variance of new mutant allelic effects and Vs the weakness of stabilizing selection) figures prominently in the results. The equilibrium heterozygosity is similar to that of strictly neutral theory, H = 4Nμc / (1 + 4Nμc ), except that μc = μe=μ/1+cS where c is about 0.5. Simulations corroborate Vg=4μVs1+1/S except for very low N. Genetic variability attains similar equilibrium values at both a "lone" locus and at an "embedded" locus. This agrees with my earlier work concerning molecular clock rates. These results modify the neutralist interpretation of data concerning genetic variability and genetic distances between populations. Low H values are proportional not to N but to N. This may explain the narrow observed range of H among species. Heterozygosities need not be highly correlated to genetic variances. Genetic variances are not highly dependent on population size except in very small populations which are difficult to sample without bias because the smallest populations go extinct the fastest. Nearly neutral evolution will not be easily distinguished from strictly neutral theory under the Hudson-Kreitman-Aguade inter-/intraspecific variation ratio test, since a similar effective mutation rate holds for genetic distances and D = 2μc t, where μe=μ/1+S. As with strictly neutral theory, comparisons across loci should show D and H to be positively correlated because of the shared μc . But unlike neutral theory, for a given locus, comparisons across species should show D and H to be negatively correlated. There is no obvious threshold of population size below which genetic variability inevitably

  6. Embryonal Origin of MTSCC of Kidney May Explain its Morphological Heterogeneity: Diagnostic Impact of Genetic Analysis.

    Science.gov (United States)

    Banyai, Daniel; Vastag, Fanni; Yusenko, Maria; Bugert, Peter; Kovacs, Gyula

    2017-03-01

    Previous genetic and morphologic characterisation of mucinous tubular and spindle cell carcinoma (MTSCC) have yielded controversial results. The aim of this study was to explain the phenotypic heterogeneity of MTSCC diagnosed by genetic means. We analyzed 7 MTSCC by array CGH and microsatellite allelotyping and by histology for morphological variation. We worked-up two entire kidneys with MTSCC to find microscopic alterations. We confirmed the diagnosis of MTSCC by detecting copy number changes at chromosomes 1, 4, 6, 8, 13, 14, 15, 18 and 22. We detected 13 small, microscopic precursor lesions in the two kidneys and found similar histological structures in precursor lesions and MTSCC. MTSCC develops from embryonal rest-like lesions of impaired differentiation which may explain its morphological variations. Until diagnosis of a "malignant" MTSCC" is not confirmed by genetic means, it should not be called carcinoma. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  7. Philosophy of race meets population genetics.

    Science.gov (United States)

    Spencer, Quayshawn

    2015-08-01

    In this paper, I respond to four common semantic and metaphysical objections that philosophers of race have launched at scholars who interpret recent human genetic clustering results in population genetics as evidence for biological racial realism. I call these objections 'the discreteness objection', 'the visibility objection', 'the very important objection', and 'the objectively real objection.' After motivating each objection, I show that each one stems from implausible philosophical assumptions about the relevant meaning of 'race' or the nature of biological racial realism. In order to be constructive, I end by offering some advice for how we can productively critique attempts to defend biological racial realism based on recent human genetic clustering results. I also offer a clarification of the relevant human-population genetic research. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. The population genetics of evolutionary rescue.

    Directory of Open Access Journals (Sweden)

    H Allen Orr

    2014-08-01

    Full Text Available Evolutionary rescue occurs when a population that is threatened with extinction by an environmental change adapts to the change sufficiently rapidly to survive. Here we extend the mathematical theory of evolutionary rescue. In particular, we model evolutionary rescue to a sudden environmental change when adaptation involves evolution at a single locus. We consider adaptation using either new mutations or alleles from the standing genetic variation that begin rare. We obtain several results: i the total probability of evolutionary rescue from either new mutation or standing variation; ii the conditions under which rescue is more likely to involve a new mutation versus an allele from the standing genetic variation; iii a mathematical description of the U-shaped curve of total population size through time, conditional on rescue; and iv the time until the average population size begins to rebound as well as the minimal expected population size experienced by a rescued population. Our analysis requires taking into account a subtle population-genetic effect (familiar from the theory of genetic hitchhiking that involves "oversampling" of those lucky alleles that ultimately sweep to high frequency. Our results are relevant to conservation biology, experimental microbial evolution, and medicine (e.g., the dynamics of antibiotic resistance.

  9. Population genetics of fungal diseases of plants

    Directory of Open Access Journals (Sweden)

    Giraud T.

    2008-09-01

    Full Text Available Although parasitism is one of the most common lifestyles among eukaryotes, population genetics on parasites lag far behind those on free-living organisms. Yet, the advent of molecular markers offers great tools for studying important processes, such as dispersal, mating systems, adaptation to host and speciation. Here we highlight some studies that used molecular markers to address questions about the population genetics of fungal (including oomycetes plant pathogens. We conclude that population genetics approaches have provided tremendous insights into the biology of a few fungal parasites and warrant more wide use in phytopathology. However, theoretical advances are badly needed to best apply the existing methods. Fungi are of prime interest not only because they are major parasites of plants and animals, but they also constitute tractable and highly useful models for understanding evolutionary processes. We hope that the emerging field of fungal evolution will attract more evolutionary biologists in the near future.

  10. [Genetic structure of populations of the Colorado potato beetle Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)].

    Science.gov (United States)

    Sidorenko, A P; Berezovskaia, O P

    2002-11-01

    The genetic structure of a Colorado potato beetle population from Kiev oblast was examined by cluster analysis of individual RAPD patterns. The obtained clustering indicates that the population is structured. This may be explained by adaptation to pyrethroid insecticides used for controlling the population size of this pest. Micro-evolutionary factors affecting the genetic structure of local populations of Colorado potato beetle are discussed.

  11. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations

    Science.gov (United States)

    Pickup, M.; Field, D. L.; Rowell, D. M.; Young, A. G.

    2013-01-01

    Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations. PMID:23173202

  12. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor).

    Science.gov (United States)

    Burridge, Christopher P; Peucker, Amanda J; Valautham, Sureen K; Styan, Craig A; Dann, Peter

    2015-01-01

    Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. © The American Genetic Association 2015.

  13. Population genetic structure of Aldabra giant tortoises

    OpenAIRE

    Balmer, Oliver; Ciofi, Claudio; Galbraith, David A.; Swingland, Ian R.; Zug, George R.,; Caccone, Adalgisa

    2011-01-01

    Evolution of population structure on islands is the result of physical processes linked to volcanism, orogenic events, changes in sea level, as well as habitat variation. We assessed patterns of genetic structure in the giant tortoise of the Aldabra atoll, where previous ecological studies suggested population subdivisions as a result of landscape discontinuity due to unsuitable habitat and island separation. Analysis of mitochondrial DNA (mtDNA) control region sequences and allelic variation...

  14. Types of marriages, population structure and genetic disease.

    Science.gov (United States)

    Machado, T M B; Bomfim, T F; Souza, L V; Soares, N; Santos, F L; Acosta, A X; Abe-Sandes, K

    2013-07-01

    A high occurrence rate of consanguineous marriages may favour the onset and increased frequency of autosomal recessive diseases in a population. The population of Monte Santo, Bahia, Brazil, has a high frequency of rare genetic diseases such as mucopolysaccharidosis type VI, whose observed frequency in this population is 1:5000, while the incidence of this disease recorded in other regions of the world varies from 1:43,261 in Turkey to 1:1,505,160 in Switzerland. To verify the influence of consanguineous marriage on the increased frequency of observed genetic diseases in this population, the population structure and frequency of different types of marriage during different time periods were evaluated. A total of 9765 marriages were found in an analysis of parish marriage records from the city. Over three periods, 1860-1895, 1950-1961 and 1975-2010, the inbreeding rates were 37.1%, 13.2% and 4.2% respectively. Although there was a high rate of inbreeding, endogamic marriages were the dominant marriage type in all three periods. In the most recent period, there was an increase in the number of exogamous marriages and those among immigrants, but most of these occurred among individuals from cities that neighbour Monte Santo. The low rate of migration and high frequency of endogamic and consanguineous marriages show that growth of this population is predominantly internal and could explain the occurrence, and increase in frequency, of recessive genetic diseases in the city.

  15. Genetic Heterogeneity in Algerian Human Populations.

    Science.gov (United States)

    Bekada, Asmahan; Arauna, Lara R; Deba, Tahria; Calafell, Francesc; Benhamamouch, Soraya; Comas, David

    2015-01-01

    The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region.

  16. Genetic Heterogeneity in Algerian Human Populations.

    Directory of Open Access Journals (Sweden)

    Asmahan Bekada

    Full Text Available The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region.

  17. Genetic variation and population structure in Oryza ...

    Indian Academy of Sciences (India)

    Unknown

    [Thomas G., Sreejayan, Joseph L. and Kuriachan P. 2001 Genetic variation and population structure in Oryza malampuzhaensis. Krish. et .... (Promega). Southern hybridization was carried out as reported earlier (Thomas et al. 2000). Results. DNA fingerprinting. A total of 33 decamer primers randomly selected from C,.

  18. When population and evolutionary genetics met behaviour

    Directory of Open Access Journals (Sweden)

    Rodolfo Costa

    2013-01-01

    Full Text Available In this review, we analyse the impact of a population and evolutionary genetics approach on the study of insect behaviour. Our attention is focused on the model organism Drosophila melanogaster and several other insect species. In particular, we explore the relationship between rhythmic behaviours and the molecular evolution of clock and ion channel genes.

  19. Genetic sources of population epigenomic variation

    NARCIS (Netherlands)

    Taudt, Aaron; Colome-Tatche, Maria; Johannes, Frank

    The field of epigenomics has rapidly progressed from the study of individual reference epigenomes to surveying epigenomic variation in populations. Recent studies in a number of species, from yeast to humans, have begun to dissect the cis- and trans-regulatory genetic mechanisms that shape patterns

  20. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H.; Kidd, Jeffrey M.

    2013-01-01

    Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape...

  1. Simple life-history traits explain key effective population size ratios across diverse taxa.

    Science.gov (United States)

    Waples, Robin S; Luikart, Gordon; Faulkner, James R; Tallmon, David A

    2013-10-07

    Effective population size (Ne) controls both the rate of random genetic drift and the effectiveness of selection and migration, but it is difficult to estimate in nature. In particular, for species with overlapping generations, it is easier to estimate the effective number of breeders in one reproductive cycle (Nb) than Ne per generation. We empirically evaluated the relationship between life history and ratios of Ne, Nb and adult census size (N) using a recently developed model (agene) and published vital rates for 63 iteroparous animals and plants. Nb/Ne varied a surprising sixfold across species and, contrary to expectations, Nb was larger than Ne in over half the species. Up to two-thirds of the variance in Nb/Ne and up to half the variance in Ne/N was explained by just two life-history traits (age at maturity and adult lifespan) that have long interested both ecologists and evolutionary biologists. These results provide novel insights into, and demonstrate a close general linkage between, demographic and evolutionary processes across diverse taxa. For the first time, our results also make it possible to interpret rapidly accumulating estimates of Nb in the context of the rich body of evolutionary theory based on Ne per generation.

  2. Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor)

    Science.gov (United States)

    Peucker, Amanda J.; Valautham, Sureen K.; Styan, Craig A.; Dann, Peter

    2015-01-01

    Factors responsible for spatial structuring of population genetic variation are varied, and in many instances there may be no obvious explanations for genetic structuring observed, or those invoked may reflect spurious correlations. A study of little penguins (Eudyptula minor) in southeast Australia documented low spatial structuring of genetic variation with the exception of colonies at the western limit of sampling, and this distinction was attributed to an intervening oceanographic feature (Bonney Upwelling), differences in breeding phenology, or sea level change. Here, we conducted sampling across the entire Australian range, employing additional markers (12 microsatellites and mitochondrial DNA, 697 individuals, 17 colonies). The zone of elevated genetic structuring previously observed actually represents the eastern half of a genetic cline, within which structuring exists over much shorter spatial scales than elsewhere. Colonies separated by as little as 27 km in the zone are genetically distinguishable, while outside the zone, homogeneity cannot be rejected at scales of up to 1400 km. Given a lack of additional physical or environmental barriers to gene flow, the zone of elevated genetic structuring may reflect secondary contact of lineages (with or without selection against interbreeding), or recent colonization and expansion from this region. This study highlights the importance of sampling scale to reveal the cause of genetic structuring. PMID:25833231

  3. Ability of Matrix Models to Explain the Past and Predict the Future of Plant Populations

    NARCIS (Netherlands)

    Crone, E.E.; Ellis, M.M.; Morris, W.F.; Stanley, A.; Bell, T.; Bierzychudek, P.; Ehrlén, J.; Kaye, T.N.; Knight, T.M.; Lesica, P.; Oostermeijer, G.; Quintana-Ascencio, P.F.; Ticktin, T.; Valverde, T.; Williams, J.L.; Doak, D.F.; Ganesan, R.; McEachern, K.A.; Thorpe, A.; Menges, E.S.

    2013-01-01

    Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix

  4. HLA Population Genetics in Solid Organ Transplantation.

    Science.gov (United States)

    Kransdorf, Evan P; Pando, Marcelo J; Gragert, Loren; Kaplan, Bruce

    2017-09-01

    HLAs are fundamental to the adaptive immune response and play critical roles in the cellular and humoral response in solid organ transplantation. The genes encoding HLA proteins are the most polymorphic within the human genome, with thousands of different allelic variants known within the population. Application of the principles of population genetics to the HLA genes has resulted in the development of a numeric metric, the calculated panel-reactive antibody (CPRA) that predicts the likelihood of a positive crossmatch as a function of a transplant candidate's unacceptable HLA antigens. The CPRA is an indispensible measure of access to transplantation for sensitized candidates and is used as the official measure of sensitization for allocation of points in the US Kidney Allocation System and Eurotransplant. Here, we review HLA population genetics and detail the mathematical basis of the CPRA. An understanding of these principles by transplant clinicians will lay the foundation for continued innovation in the care of sensitized patients.

  5. Genetic classification of populations using supervised learning.

    LENUS (Irish Health Repository)

    Bridges, Michael

    2011-01-01

    There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

  6. Genetic classification of populations using supervised learning.

    Directory of Open Access Journals (Sweden)

    Michael Bridges

    Full Text Available There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories. This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines to the classification of three populations (two from Scotland and one from Bulgaria. The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.

  7. Genetic variation and population genetic structure of Rhizophora apiculata (Rhizophoraceae) in the Greater Sunda Islands, Indonesia using microsatellite markers.

    Science.gov (United States)

    Yahya, Andi Fadly; Hyun, Jung Oh; Lee, Jae Ho; Kim, Yong Yul; Lee, Kyung Mi; Hong, Kyung Nak; Kim, Seung-Chul

    2014-03-01

    Genetic variations within and among Rhizophora apiculata populations in the Greater Sunda Islands of Indonesia were studied using microsatellite markers. The study found 38 alleles on five loci in 15 populations. The observed (H(o)) and expected (H(e)) heterozygosity values are 0.338 and 0.378, respectively. Inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (F(ST) = 0.381) was similar to other mangrove species. The genetic diversity of R. apiculata populations along the coastline inside the archipelago (e.g., Buleleng, Donggala, Mamuju, and Takalar) was higher than those of population along the coastline outside the archipelago, especially northern Sumatra populations (i.e., Langkat, Tapanuli Tengah, Dumai, and Padang). The isolation by distances and sea currents directions as well as their connectivity might affect the gene flow and genetic exchange. The more isolated with fewer connections by sea currents, the smaller gene flow and genetic exchange observed between populations. The higher genetic exchange, on the contrary, occurred when population location was closer to the meeting point of the sea currents. The study also showed that the patterns of sea current movement seemed to have influence genetic clustering of populations which fell into three main groups (Sunda Shelf Mangroves) and one isolated population (New Guinea Mangroves).

  8. Genetic hitchhiking in a subdivided population of Mytilus edulis

    Directory of Open Access Journals (Sweden)

    David Patrice

    2008-05-01

    Full Text Available Abstract Background Few models of genetic hitchhiking in subdivided populations have been developed and the rarity of empirical examples is even more striking. We here provide evidences of genetic hitchhiking in a subdivided population of the marine mussel Mytilus edulis. In the Bay of Biscay (France, a patch of M. edulis populations happens to be separated from its North Sea conspecifics by a wide region occupied only by the sister species M. galloprovincialis. Although genetic differentiation between the two M. edulis regions is largely non-significant at ten marker loci (average FST~0.007, a strong genetic differentiation is observed at a single locus (FST = 0.25. We validated the outlier status of this locus, and analysed DNA sequence polymorphism in order to identify the nature of the selection responsible for the unusual differentiation. Results We first showed that introgression of M. galloprovincialis alleles was very weak in both populations and did not significantly affect their differentiation. Secondly, we observed the genetic signature of a selective sweep within both M. edulis populations in the form of a star-shaped clade of alleles. This clade was nearly fixed in the North Sea and was segregating at a moderate frequency in the Bay of Biscay, explaining their genetic differentiation. Incomplete fixation reveals that selection was not direct on the locus but that the studied sequence recombined with a positively selected allele at a linked locus while it was on its way to fixation. Finally, using a deterministic model we showed that the wave of advance of a favourable allele at a linked locus, when crossing a strong enough barrier to gene flow, generates a step in neutral allele frequencies comparable to the step observed between the two M. edulis populations at the outlier locus. In our case, the position of the barrier is now materialised by a large patch of heterospecific M. galloprovincialis populations. Conclusion High FST

  9. Quantitative genetics and evolution: Is our understanding of genetics sufficient to explain evolution?

    Science.gov (United States)

    Beilharz, R G; Luxford, B G; Wilkinson, J L

    1993-01-12

    We have provided a bridge between geneticists, who tend to concentrate on genes and their frequencies, and other biologists, who are much more aware of how severely the environment constrains and limits life. This bridge is the recognition that a . fitness is a product of important component traits, b . these and most other traits consume environmental resources and these resources are additively related and can sum to no more than the total resources an animal can obtain from the environment, c . allele frequencies can alter only to the degree that the phenotypes that carry the alleles reproduce themselves successfully, i. e. are fit, d . fitness must rise, because it is never free from natural selection upwards, to the point where it can rise no further, because all environmental resources available to an animal are being used most efficiently, e . in this state of adaptation, fitness is completely limited by the environment and all other traits important to the animal are constrained to a greater or lesser degree at intermediate, "optimal" values, and f . traits or molecules unimportant to animals, so that they are completely neutral with respect to fitness, are free to drift genetically and hence gene substitutions can occur at rates related to their mutation rates. This bridge between genetics and other parts of biology shows that the various theories apparently causing concern for the modern synthetic theory of evolution are entirely compatible with it. Bursts of rapid evolutionary change between long periods of evolutionary stasis are the necessary consequences of strong natural selection acting on fitness, in ecosystems that are stable until external forces cause them to change. Neutral (random) evolution describes the fate of genetic material that is unimportant for organisms, i. e. material that is truly neutral with respect to fitness. ZUSAMMENFASSUNG: Quantitative Genetik und Evolution. Genügt unser genetisches Verständnis um Evolution zu erkl

  10. Deep Learning for Population Genetic Inference.

    Directory of Open Access Journals (Sweden)

    Sara Sheehan

    2016-03-01

    Full Text Available Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data to the output (e.g., population genetic parameters of interest. We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history. Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

  11. Deep Learning for Population Genetic Inference

    Science.gov (United States)

    Sheehan, Sara; Song, Yun S.

    2016-01-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

  12. Extensive population genetic structure in the giraffe

    Directory of Open Access Journals (Sweden)

    Grether Gregory F

    2007-12-01

    Full Text Available Abstract Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

  13. Extensive population genetic structure in the giraffe

    Science.gov (United States)

    Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

    2007-01-01

    Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations. PMID:18154651

  14. Deep Learning for Population Genetic Inference.

    Science.gov (United States)

    Sheehan, Sara; Song, Yun S

    2016-03-01

    Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

  15. Bayesian analysis of genetic differentiation between populations.

    Science.gov (United States)

    Corander, Jukka; Waldmann, Patrik; Sillanpää, Mikko J

    2003-01-01

    We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.

  16. Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.

    Science.gov (United States)

    Cassel-Lundhagen, Anna; Ronnås, Cecilia; Battisti, Andrea; Wallén, Johan; Larsson, Stig

    2013-06-01

    It is challenging to unravel the history of organisms with highly scattered populations. Such species may have fragmented distributions because extant populations are remnants of a previously more continuous range, or because the species has narrow habitat requirements in combination with good dispersal capacity (naturally or vector borne). The northern pine processionary moth Thaumetopoea pinivora has a scattered distribution with fragmented populations in two separate regions, northern and south-western Europe. The aims of this study were to explore the glacial and postglacial history of T. pinivora, and add to the understanding of its current distribution and level of contemporary gene flow. We surveyed published records of its occurrence and analysed individuals from a representative subset of populations across the range. A 633 bp long fragment of the mtDNA COI gene was sequenced and nine polymorphic microsatellite loci were genotyped. Only nine nucleotide sites were polymorphic in the COI gene and 90% of the individuals from across its whole range shared the same haplotype. The microsatellite diversity gradually declined towards the north, and unique alleles were found in only three of the northern and three of southern sites. Genetic structuring did not indicate complete isolation among regions, but an increase of genetic isolation by geographic distance. Approximate Bayesian model choice suggested recent divergence during the postglacial period, but glacial refugia remain unidentified. The progressive reduction of suitable habitats is suggested to explain the genetic structure of the populations and we suggest that T. pinivora is a cold-tolerant relict species, with situation-dependent dispersal. © 2013 John Wiley & Sons Ltd.

  17. Population Genetics of Three Dimensional Range Expansions

    Science.gov (United States)

    Lavrentovich, Maxim; Nelson, David

    2014-03-01

    We develop a simple model of genetic diversity in growing spherical cell clusters, where the growth is confined to the cluster surface. This kind of growth occurs in cells growing in soft agar, and can also serve as a simple model of avascular tumors. Mutation-selection balance in these radial expansions is strongly influenced by scaling near a neutral, voter model critical point and by the inflating frontier. We develop a scaling theory to describe how the dynamics of mutation-selection balance is cut off by inflation. Genetic drift, i.e., local fluctuations in the genetic diversity, also plays an important role, and can lead to the extinction even of selectively advantageous strains. We calculate this extinction probability, taking into account the effect of rough population frontiers.

  18. A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species.

    Science.gov (United States)

    Souza, Helena Augusta Viana E; Collevatti, Rosane Garcia; Lima-Ribeiro, Matheus S; Lemos-Filho, José Pires de; Lovato, Maria Bernadete

    2017-01-01

    The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated. A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM). Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium. The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary

  19. Ability of matrix models to explain the past and predict the future of plant populations.

    Science.gov (United States)

    Crone, Elizabeth E; Ellis, Martha M; Morris, William F; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlén, Johan; Kaye, Thomas N; Knight, Tiffany M; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer L; Doak, Daniel F; Ganesan, Rengaian; McEachern, Kathyrn; Thorpe, Andrea S; Menges, Eric S

    2013-10-01

    Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models. © 2013 Society for Conservation Biology.

  20. Spatial and population genetic structure of microsatellites in white pine

    Science.gov (United States)

    Paula E. Marquardt; Bryan K. Epperson

    2004-01-01

    We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

  1. Linking genomics and population genetics with R.

    Science.gov (United States)

    Paradis, Emmanuel; Gosselin, Thierry; Goudet, Jérôme; Jombart, Thibaut; Schliep, Klaus

    2017-01-01

    Population genetics and genomics have developed and been treated as independent fields of study despite having common roots. The continuous progress of sequencing technologies is contributing to (re-)connect these two disciplines. We review the challenges faced by data analysts and software developers when handling very big genetic data sets collected on many individuals. We then expose how r, as a computing language and development environment, proposes some solutions to meet these challenges. We focus on some specific issues that are often encountered in practice: handling and analysing single-nucleotide polymorphism data, handling and reading variant call format files, analysing haplotypes and linkage disequilibrium and performing multivariate analyses. We illustrate these implementations with some analyses of three recently published data sets that contain between 60 000 and 1 000 000 loci. We conclude with some perspectives on future developments of r software for population genomics. © 2016 John Wiley & Sons Ltd.

  2. A new eigenfunction spatial analysis describing population genetic structure.

    Science.gov (United States)

    Diniz-Filho, José Alexandre Felizola; Diniz, João Vitor Barnez P L; Rangel, Thiago Fernando; Soares, Thannya Nascimento; Telles, Mariana Pires de Campos; Collevatti, Rosane Garcia; Bini, Luis Mauricio

    2013-12-01

    Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n). The relationship between the coefficient of determination (R(2)) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran's I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.

  3. Population genetic variation in sainfoin (Fabaceae) revealed by RAPD markers

    OpenAIRE

    Houshang NOSRATI; Mohammad Ali Hosseinpour FEIZI; Sona Seyed TARRAH; Ahmad Razban HAGHIGHI

    2012-01-01

    Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae) based on RA...

  4. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations

  5. Population genetics from 1966 to 2016.

    Science.gov (United States)

    Charlesworth, B; Charlesworth, D

    2017-01-01

    We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the first Population Genetics Group (PGG) meeting in January 1968. We review the major questions and controversies that have preoccupied population geneticists during this time (and were often hotly debated at PGG meetings). We show how theoretical and empirical work has combined to generate a highly productive interaction involving successive developments in the ability to characterise variability at the molecular level, to apply mathematical models to the interpretation of the data and to use the results to answer biologically important questions, even in nonmodel organisms. We also describe the changes from a field that was largely dominated by UK and North American biologists to a much more international one (with the PGG meetings having made important contributions to the increased number of population geneticists in several European countries). Although we concentrate on the earlier history of the field, because developments in recent years are more familiar to most contemporary researchers, we end with a brief outline of topics in which new understanding is still actively developing.

  6. Linking native and invader traits explains native spider population responses to plant invasion

    Science.gov (United States)

    Jennifer N. Smith; Douglas J. Emlen; Dean E. Pearson

    2016-01-01

    Theoretically, the functional traits of native species should determine how natives respond to invader-driven changes. To explore this idea, we simulated a large-scale plant invasion using dead spotted knapweed (Centaurea stoebe) stems to determine if native spiders' web-building behaviors could explain differences in spider population responses to...

  7. Explaining sex differences in chronic musculoskeletal pain in a general population

    NARCIS (Netherlands)

    Wijnhoven, Hanneke A H; de Vet, Henrica C W; Picavet, H. Susan J

    Many studies report a female predominance in the prevalence of chronic musculoskeletal pain (CMP) but the mechanisms explaining these sex differences are poorly understood. Data from a random postal questionnaire survey in the Dutch general population were used to examine whether sex differences in

  8. Explaining sex differences in chronic musculoskeletal pain in a general population.

    NARCIS (Netherlands)

    Wijnhoven, Hanneke A H; Vet, Henrica C W de; Picavet, H Susan J

    2006-01-01

    Many studies report a female predominance in the prevalence of chronic musculoskeletal pain (CMP) but the mechanisms explaining these sex differences are poorly understood. Data from a random postal questionnaire survey in the Dutch general population were used to examine whether sex differences in

  9. Explaining Inference on a Population of Independent Agents Using Bayesian Networks

    Science.gov (United States)

    Sutovsky, Peter

    2013-01-01

    The main goal of this research is to design, implement, and evaluate a novel explanation method, the hierarchical explanation method (HEM), for explaining Bayesian network (BN) inference when the network is modeling a population of conditionally independent agents, each of which is modeled as a subnetwork. For example, consider disease-outbreak…

  10. Population genetic study on common kilka (Clupeonella cultriventris ...

    African Journals Online (AJOL)

    A

    Accepted 16 October, 2012. This study represents population genetic analysis of the common kilka Clupeonella cultriventris ... of different genetic populations along the Caspian Sea coast (Guilan Province). Key words: Population ..... microsatellite linkage map of the European sea bass Dicentrarchus labrax L. Genetics ...

  11. Relationships among walleye population characteristics and genetic diversity in northern Wisconsin Lakes

    Science.gov (United States)

    Waterhouse, Matthew D.; Sloss, Brian L.; Isermann, Daniel A.

    2014-01-01

    The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age-0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density-dependent factors. An isolation-by-distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic

  12. Palaeoclimatic conditions in the Mediterranean explain genetic diversity of Posidonia oceanica seagrass meadows

    KAUST Repository

    Chefaoui, Rosa M.

    2017-05-26

    Past environmental conditions in the Mediterranean Sea have been proposed as main drivers of the current patterns of distribution of genetic structure of the seagrass Posidonia oceanica, the foundation species of one of the most important ecosystems in the Mediterranean Sea. Yet, the location of cold climate refugia (persistence regions) for this species during the Last Glacial Maximum (LGM) is not clear, precluding the understanding of its biogeographical history. We used Ecological Niche Modelling together with existing phylogeographic data to locate Pleistocene refugia in the Mediterranean Sea and to develop a hypothetical past biogeographical distribution able to explain the genetic diversity presently found in P. oceanica meadows. To do that, we used an ensemble approach of six predictive algorithms and two Ocean General Circulation Models. The minimum SST in winter and the maximum SST in summer allowed us to hindcast the species range during the LGM. We found separate glacial refugia in each Mediterranean basin and in the Central region. Altogether, the results suggest that the Central region of the Mediterranean Sea was the most relevant cold climate refugium, supporting the hypothesis that long-term persistence there allowed the region to develop and retain its presently high proportion of the global genetic diversity of P. oceanica.

  13. West Nile virus population genetics and evolution

    Science.gov (United States)

    Pesko, Kendra N.; Ebel, Gregory D.

    2015-01-01

    West Nile virus (WNV) (Flaviviridae: Flavivirus) is transmitted from mosquitoes to birds, but can cause fatal encephalitis in infected humans. Since its introduction into North America in New York in 1999, it has spread throughout the western hemisphere. Multiple outbreaks have also occurred in Europe over the last 20 years. This review highlights recent efforts to understand how host pressures impact viral population genetics, genotypic and phenotypic changes which have occurred in the WNV genome as it adapts to this novel environment, and molecular epidemiology of WNV worldwide. Future research directions are also discussed. PMID:22226703

  14. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species.

    Science.gov (United States)

    Hsiung, Huan-Yi; Huang, Bing-Hong; Chang, Jui-Tse; Huang, Yao-Moan; Huang, Chih-Wei; Liao, Pei-Chun

    2017-01-01

    Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

  15. Genetic structure of Hepatica nobilis var. japonica, focusing on within population flower color polymorphism.

    Science.gov (United States)

    Kameoka, Shinichiro; Sakio, Hitoshi; Abe, Harue; Ikeda, Hajime; Setoguchi, Hiroaki

    2017-03-01

    How phenotypic or genetic diversity is maintained in a natural habitat is a fundamental question in evolutionary biology. Flower color polymorphism in plants is a common polymorphism. Hepatica nobilis var. japonica on the Sea of Japan (SJ) side of the Japanese mainland exhibits within population flower color polymorphism (e.g., white, pink, and purple), while only white flowers are observed on the Pacific Ocean (PO) side. To determine the relationships between flower color polymorphism, within and among populations, and the genetic structure of H. nobilis var. japonica, we estimated the genetic variation using simple sequence repeat (SSR) markers. First, we examined whether cryptic lineages corresponding to distinct flower colors contribute to the flower color polymorphisms in H. nobilis var. japonica. In our field observations, no bias in color frequency was observed among populations on Sado Island, a region with high variation in flower color. Simple sequence repeat (SSR) analyses revealed that 18% of the genetic variance was explained by differences among populations, whereas no genetic variation was explained by flower color hue or intensity (0% for both components). These results indicate that the flower color polymorphism is likely not explained by cryptic lineages that have different flower colors. In contrast, populations in the SJ and PO regions were genetically distinguishable. As with the other plant species in these regions, refugial isolation and subsequent migration history may have caused the genetic structure as well as the spatially heterogeneous patterns of flower color polymorphisms in H. nobilis var. japonica.

  16. The Relevance of HLA Sequencing in Population Genetics Studies

    Directory of Open Access Journals (Sweden)

    Alicia Sanchez-Mazas

    2014-01-01

    Full Text Available Next generation sequencing (NGS is currently being adapted by different biotechnological platforms to the standard typing method for HLA polymorphism, the huge diversity of which makes this initiative particularly challenging. Boosting the molecular characterization of the HLA genes through efficient, rapid, and low-cost technologies is expected to amplify the success of tissue transplantation by enabling us to find donor-recipient matching for rare phenotypes. But the application of NGS technologies to the molecular mapping of the MHC region also anticipates essential changes in population genetic studies. Huge amounts of HLA sequence data will be available in the next years for different populations, with the potential to change our understanding of HLA variation in humans. In this review, we first explain how HLA sequencing allows a better assessment of the HLA diversity in human populations, taking also into account the methodological difficulties it introduces at the statistical level; secondly, we show how analyzing HLA sequence variation may improve our comprehension of population genetic relationships by facilitating the identification of demographic events that marked human evolution; finally, we discuss the interest of both HLA and genome-wide sequencing and genotyping in detecting functionally significant SNPs in the MHC region, the latter having also contributed to the makeup of the HLA molecular diversity observed today.

  17. The Etruscans: a population-genetic study

    DEFF Research Database (Denmark)

    Vernesi, Cristiano; Caramelli, David; Dupanloup, Isabelle

    2004-01-01

    The origins of the Etruscans, a non-Indo-European population of preclassical Italy, are unclear. There is broad agreement that their culture developed locally, but the Etruscans' evolutionary and migrational relationships are largely unknown. In this study, we determined mitochondrial DNA sequences...... a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically European...... or West Asian, but only a few haplotypes were found to have an exact match in a modern mitochondrial database, raising new questions about the Etruscans' fate after their assimilation into the Roman state....

  18. Iberia: population genetics, anthropology, and linguistics.

    Science.gov (United States)

    Arnaiz-Villena, A; Martínez-Laso, J; Alonso-García, J

    1999-10-01

    Basques, Portuguese, Spaniards, and Algerians have been studied for HLA and mitochondrial DNA markers, and the data analysis suggests that pre-Neolithic gene flow into Iberia came from ancient white North Africans (Hamites). The Basque language has also been used to translate the Iberian-Tartesian language and also Etruscan and Minoan Linear A. Physical anthropometry of Iberian Mesolithic and Neolithic skeletons does not support the demic replacement in Iberia of preexisting Mesolithic people by Neolithic people bearing new farming technologies from Europe and the Middle East. Also, the presence of cardial impressed pottery in western Mediterranean Europe and across the Maghreb (North Africa) coasts at the beginning of the Neolithic provides good evidence of pre-Neolithic circum-Mediterranean contacts by sea. In addition, pre-dynastic Egyptian El-Badari culture (4,500 years ago) is similar to southern Iberian Neolithic settlements with regard to pottery and animal domestication. Taking the genetic, linguistic, anthropological, and archeological evidence together with the documented Saharan area desiccation starting about 10,000 years ago, we believe that it is possible that a genetic and cultural pre-Neolithic flow coming from southern Mediterranean coasts existed toward northern Mediterranean areas, including at least Iberia and some Mediterranean islands. This model would substitute for the demic diffusion model put forward to explain Neolithic innovations in Western Europe.

  19. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Directory of Open Access Journals (Sweden)

    Rocío Pineda-Martos

    2014-01-01

    Full Text Available Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms.

  20. Capacities for population-genetic variation and ecological adaptations

    Directory of Open Access Journals (Sweden)

    Marinković Dragoslav

    2007-01-01

    Full Text Available In contemporary science of population genetics it is equally complex and important to visualize how adaptive limits of individual variation are determined, as well as to describe the amount and sort of this variation. Almost all century the scientists devoted their efforts to explain the principles and structure of biological variation (genetic, developmental, environmental, interactive, etc., basing its maintenance within existing limits mostly on equilibria proclaimed by Hardy-Weinberg rules. Among numerous model-organisms that have been used to prove these rules and demonstrate new variants within mentioned concepts, Drosophila melanogaster is a kind of queen that is used in thousands of experiments for almost exactly 100 years (CARPENTER 1905, with which numerous discoveries and principles were determined that later turned out to be applicable to all other organisms. It is both, in nature and in laboratory, that Drosophilids were used to demonstrate the basic principles of population-genetic variation that was later applied to other species of animals. In ecological-genetic variation their richness in different environments could be used as an exact indicator of the status of a determined habitat, and its population-genetic structure may definitely point out to a possibility that specific resources of the environment start to be in danger to deteriorate, or to disappear in the near future. This paper shows clear-cut differences among environmental habitats, when populations of Drosophilidae are quantitatively observed in different wild, semi-domestic and domestic environments, demonstrating a highly expressed mutual dependence of these two parameters. A crucial approach is how to estimate the causes that determine the limits of biological, i.e. of individual and population-genetic variation. The realized, i.e. adaptive variation, is much lesser than a total possible variation of a polygenic trait, and in this study, using a moderately

  1. Can genetic differences explain vocal dialect variation in sperm whales, Physeter macrocephalus?

    Science.gov (United States)

    Rendell, Luke; Mesnick, Sarah L; Dalebout, Merel L; Burtenshaw, Jessica; Whitehead, Hal

    2012-03-01

    Sperm whale social groups can be assigned to vocal clans based on their production of codas, short stereotyped patterns of clicks. It is currently unclear whether genetic variation could account for these behavioural differences. We studied mitochondrial DNA (mtDNA) variation among sympatric vocal clans in the Pacific Ocean, using sequences extracted from sloughed skin samples. We sampled 194 individuals from 30 social groups belonging to one of three vocal clans. As in previous studies of sperm whales, mtDNA control region diversity was low (π = 0.003), with just 14 haplotypes present in our sample. Both hierarchical AMOVAs and partial Mantel tests showed that vocal clan was a more important factor in matrilineal population genetic structure than geography, even though our sampling spanned thousands of kilometres. The variance component attributed to vocal dialects (7.7%) was an order of magnitude higher than those previously reported in birds, while the variance component attributed to geographic area was negligible. Despite this, the two most common haplotypes were present in significant quantities in each clan, meaning that variation in the control region cannot account for behavioural variation between clans, and instead parallels the situation in humans where parent-offspring transmission of language variation has resulted in correlations with neutral genes. Our results also raise questions for the management of sperm whale populations, which has traditionally been based on dividing populations into geographic 'stocks', suggesting that culturally-defined vocal clans may be more appropriate management units.

  2. Familial clustering and genetic risk for dementia in a genetically isolated Dutch population.

    NARCIS (Netherlands)

    K. Sleegers (Kristel); F. Forey; J. Theuns (Jessie); Y.S. Aulchenko (Yurii); S. Rademakers (Suzanne); M. Cruts (Marc); W.A. van Gool (Willem); P. Heutink (Peter); B.A. Oostra (Ben); J.C. van Swieten (John); C.M. van Duijn (Cornelia); C. van Broeckhoven (Christine)

    2004-01-01

    textabstractDespite advances in elucidating the genetic epidemiology of Alzheimer's disease and frontotemporal dementia, the aetiology for most patients with dementia remains unclear. We examined the genetic epidemiology of dementia in a recent genetically isolated Dutch population founded around

  3. Varying Intolerance of Gene Pathways to Mutational Classes Explain Genetic Convergence across Neuropsychiatric Disorders.

    Science.gov (United States)

    Shohat, Shahar; Ben-David, Eyal; Shifman, Sagiv

    2017-02-28

    Genetic susceptibility to intellectual disability (ID), autism spectrum disorder (ASD), and schizophrenia (SCZ) often arises from mutations in the same genes, suggesting that they share common mechanisms. We studied genes with de novo mutations in the three disorders and genes implicated in SCZ by genome-wide association study (GWAS). Using biological annotations and brain gene expression, we show that mutation class explains enrichment patterns more than specific disorder. Genes with loss-of-function mutations and genes with missense mutations were associated with different pathways across disorders. Conversely, gene expression patterns were specific for each disorder. ID genes were preferentially expressed in the cortex; ASD genes were expressed in the fetal cortex, cerebellum, and striatum; and genes associated with SCZ were expressed in the adolescent cortex. Our study suggests that convergence across neuropsychiatric disorders stems from common pathways that are consistently vulnerable to genetic variations but that spatiotemporal activity of genes contributes to specific phenotypes. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  4. Genetic diversity increases population productivity in a sessile marine invertebrate.

    Science.gov (United States)

    Aguirre, J David; Marshall, Dustin J

    2012-05-01

    Reductions in genetic diversity can have widespread ecological consequences: populations with higher genetic diversity are more stable, productive and resistant to disturbance or disease than populations with lower genetic diversity. These ecological effects of genetic diversity differ from the more familiar evolutionary consequences of depleting genetic diversity, because ecological effects manifest within a single generation. If common, genetic diversity effects have the potential to change the way we view and manage populations, but our understanding of these effects is far from complete, and the role of genetic diversity in sexually reproducing animals remains unclear. Here, we examined the effects of genetic diversity in a sexually reproducing marine invertebrate in the field. We manipulated the genetic diversity of experimental populations and then measured individual survival, growth, and fecundity, as well as the size of offspring produced by individuals in high and low genetic diversity populations. Overall, we found greater genetic diversity increased performance across all metrics, and that complementarity effects drove the increased productivity of our high-diversity populations. Our results show that differences in genetic diversity among populations can have pervasive effects on population productivity within remarkably short periods of time.

  5. Dynamics of genetic rescue in inbred Drosophila melanogaster populations

    NARCIS (Netherlands)

    Bijlsma, R.; Westerhof, M. D. D.; Roekx, L. P.; Pen, I.

    Genetic rescue has been proposed as a management strategy to improve the fitness of genetically eroded populations by alleviating inbreeding depression. We studied the dynamics of genetic rescue in inbred populations of Drosophila. Using balancer chromosomes, we show that the force of heterosis that

  6. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Si-Fa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  7. Conservation biology of the last Italian population of Cistus laurifolius (Cistaceae: demographic structure, reproductive success and population genetics

    Directory of Open Access Journals (Sweden)

    Giovanni Astuti

    2017-10-01

    Full Text Available Isolated populations are usually subject to low fitness and reduced genetic diversity, both of which may negatively affect their survival and adaptive potential. Hence, these issues cannot be neglected when planning conservation actions for isolated populations. The Italian population of Cistus laurifolius subsp. laurifolius is extremely isolated. Furthermore, it is affected by fragmentation, being constituted by a single larger subpopulation, surrounded by three much smaller subpopulations, a few hundred metres to a few kilometres apart. In order to fill gaps in demographic and genetic knowledge concerning the Italian population, its area of occupancy, size, age-stage structure and phenology were investigated and its reproductive fitness, pollination strategies and genetic variability were assessed. The population was inferred as fully xenogamous and showed good reproductive performance. Despite this, its genetic variability was low and it showed relatively high levels of inbreeding depression (Fis, seemingly not affected by sub-population size. These results suggest that the Italian population recently suffered fragmentation and reduction in size. The low genetic diversity observed could be explained by the high percentage of mature individuals found in the population, possibly established before fragmentation. For these reasons, the Italian population of C. laurifolius subsp. laurifolius should be monitored and concrete actions aimed at its conservation planned.

  8. Genetic variations between indigenous fat-tailed sheep populations

    African Journals Online (AJOL)

    ONOS

    2010-09-06

    Sep 6, 2010 ... In: Karlin S, Nevo E (Eds), Population Genetic and. Ecology.Acodemic Press, New York, pp. 723-7766. Nguyen TC, Morera L, Llanes D, Leger P (1992). Sheep blood polymorphism and genetic divergence between French Ramboullet and Spanish Merino: role of genetic, Drift Anim. Genet. 23: 325-332.

  9. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations.

    Directory of Open Access Journals (Sweden)

    Rachael Y Dudaniec

    Full Text Available With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus in two core regions (Washington State, United States versus the species' northern peripheral region (British Columbia, Canada where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a 'flat' landscape, but at the periphery, topography (slope and elevation had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.

  10. Genetic hitchhiking in spatially extended populations.

    Science.gov (United States)

    Barton, N H; Etheridge, A M; Kelleher, J; Véber, A

    2013-08-01

    When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(-2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and ℓ=σ2/s is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, η=ρσs/2. The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement σeff(2)/σ(2)=(8/3)(L/ℓ)(Λ/R); this can be substantial if the species' range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move

  11. Highlighting nonlinear patterns in population genetics datasets

    KAUST Repository

    Alanis Lobato, Gregorio

    2015-01-30

    Detecting structure in population genetics and case-control studies is important, as it exposes phenomena such as ecoclines, admixture and stratification. Principal Component Analysis (PCA) is a linear dimension-reduction technique commonly used for this purpose, but it struggles to reveal complex, nonlinear data patterns. In this paper we introduce non-centred Minimum Curvilinear Embedding (ncMCE), a nonlinear method to overcome this problem. Our analyses show that ncMCE can separate individuals into ethnic groups in cases in which PCA fails to reveal any clear structure. This increased discrimination power arises from ncMCE\\'s ability to better capture the phylogenetic signal in the samples, whereas PCA better reflects their geographic relation. We also demonstrate how ncMCE can discover interesting patterns, even when the data has been poorly pre-processed. The juxtaposition of PCA and ncMCE visualisations provides a new standard of analysis with utility for discovering and validating significant linear/nonlinear complementary patterns in genetic data.

  12. Population Genetics of Identifiler System in Malaysia.

    Science.gov (United States)

    Nakamura, Yasutaka; Samejima, Michinaga; Minaguchi, Kiyoshi; Nambiar, Phrabhakaran

    2016-01-01

    Short tandem repeat (STR) polymorphisms were investigated in 341 unrelated Malay individuals (218 males and 123 females) living in or around Kuala Lumpur by using a forensic analysts kit. The following STRs were targeted: D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA. The purpose of this study was to elucidate population genetics in Malaysia and calculate statistical parameters for forensic and anthropological research. Data on these STRs in the target population were obtained and subjected to statistical analysis. Accordance with the Hardy-Weinberg equilibrium was proven for all the loci targeted. The combined power of discrimination was greater than 0.9999999999, indicating that this multiplex system is an excellent tool for forensic casework. The allele frequency in the data were weighed against that in four other local populations (Chinese, Iranian, Belgian, and African). The average coefficient of correlation was strongest in the order of Africa (0.092522), Belgium (0.264822), Iran (0.404363), and China (0.706661). These results are consistent with what is known about the anthropological history of and prehistoric human migration in the Malay region. We believe that these data offer a valuable anthropological resource, being applicable to the statistical evaluation of DNA evidence in human identification, as well as the determination of ethnicity in healthy populations.

  13. Population genetic variation in sainfoin (Fabaceae revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    Houshang NOSRATI

    2012-05-01

    Full Text Available Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae based on RAPDs. Our results show that populations growing on he stressful environment i.e. saline soils indicated either the lowest 0.2466 or highest (0.3186 within-population genetic variation based on Nei’s diversity. That disagrees with Niche-Width Variation Theory, which expects highest genetic diversity within stressful populations. Partitioning the total genetic variation by analysis of molecular variance (AMOVA showed that 89.03% of total genetic diversity allocated to within populations while 10.97% of this variation dedicated to among populations, indicating predominantly outcrossing mode of pollination in sainfoin. The two population pairs growing under similar environmental stresses (cold climate and saline soil showed higher genetic similarity. This may suggest that RAPDs patterns reflex selection rather than random drift.

  14. Genetic variation among populations of Pythium irregulare in southern Australia

    National Research Council Canada - National Science Library

    Harvey, P. R; Butterworth, P. J; Hawke, B. G; Pankhurst, C. E

    2000-01-01

    Isolates of Pythium irregulare were sampled from seven cereal crops throughout South Australia to determine the extent of genetic diversity within this pathogen and the scale of genetic differentiation among populations...

  15. Genetic structure of Tribolium castaneum (Coleptera: Tenebrionidae) populations in mills

    Science.gov (United States)

    The red flour beetle, Tribolium castaneum, is primarily found associated with human structures such as wheat and rice mills, which are spatially isolated resource patches with apparently limited immigration that could produce genetically structured populations. We investigated genetic diversity and...

  16. Genetic variation in the population of three Polish cattle breeds ...

    African Journals Online (AJOL)

    Genetic variation in the population of three Polish cattle breeds included into the programme of genetic resources protection and Holstein-Friesian breed, estimation on the basis of polymorphism of 24 microsatellite DNA sequences.

  17. Population Genetic Structure and Gene Flow Among Nigerian Goats ...

    African Journals Online (AJOL)

    Population Genetic structure in 200 indigenous goats sampled across four states from the South-Western and South Southern region of Nigeria was assessed using 7 microsatellite DNA markers. Observed Analysis of molecular genetic variation (AMOVA) was higher within populations (3.47) than among populations (1.84) ...

  18. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations.

    Science.gov (United States)

    Angelone-Alasaad, Samer; Biebach, Iris; Pérez, Jesús M; Soriguer, Ramón C; Granados, José E

    2017-01-01

    Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies.

  19. Genetic Heterogeneity in Algerian Human Populations

    National Research Council Canada - National Science Library

    Bekada, Asmahan; Arauna, Lara R; Deba, Tahria; Calafell, Francesc; Benhamamouch, Soraya; Comas, David

    2015-01-01

    ...) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample...

  20. Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

    Science.gov (United States)

    Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  1. Common genetic variants explain the majority of the correlation between height and intelligence: the generation Scotland study.

    Science.gov (United States)

    Marioni, Riccardo E; Batty, G David; Hayward, Caroline; Kerr, Shona M; Campbell, Archie; Hocking, Lynne J; Porteous, David J; Visscher, Peter M; Deary, Ian J

    2014-03-01

    Greater height and higher intelligence test scores are predictors of better health outcomes. Here, we used molecular (single-nucleotide polymorphism) data to estimate the genetic correlation between height and general intelligence (g) in 6,815 unrelated subjects (median age 57, IQR 49-63) from the Generation Scotland: Scottish Family Health Study cohort. The phenotypic correlation between height and g was 0.16 (SE 0.01). The genetic correlation between height and g was 0.28 (SE 0.09) with a bivariate heritability estimate of 0.71. Understanding the molecular basis of the correlation between height and intelligence may help explain any shared role in determining health outcomes. This study identified a modest genetic correlation between height and intelligence with the majority of the phenotypic correlation being explained by shared genetic influences.

  2. Genetic Control of Mosquitoes: population suppression strategies

    Directory of Open Access Journals (Sweden)

    André Barretto Bruno Wilke

    2012-10-01

    Full Text Available Over the last two decades, morbidity and mortality from malaria and dengue fever among other pathogens are an increasing Public Health problem. The increase in the geographic distribution of vectors is accompanied by the emergence of viruses and diseases in new areas. There are insufficient specific therapeutic drugs available and there are no reliable vaccines for malaria or dengue, although some progress has been achieved, there is still a long way between its development and actual field use. Most mosquito control measures have failed to achieve their goals, mostly because of the mosquito's great reproductive capacity and genomic flexibility. Chemical control is increasingly restricted due to potential human toxicity, mortality in no target organisms, insecticide resistance, and other environmental impacts. Other strategies for mosquito control are desperately needed. The Sterile Insect Technique (SIT is a species-specific and environmentally benign method for insect population suppression, it is based on mass rearing, radiation mediated sterilization, and release of a large number of male insects. Releasing of Insects carrying a dominant lethal gene (RIDL offers a solution to many of the drawbacks of traditional SIT that have limited its application in mosquitoes while maintaining its environmentally friendly and species-specific utility. The self-limiting nature of sterile mosquitoes tends to make the issues related to field use of these somewhat less challenging than for self-spreading systems characteristic of population replacement strategies. They also are closer to field use, so might be appropriate to consider first. The prospect of genetic control methods against mosquito vectored human diseases is rapidly becoming a reality, many decisions will need to be made on a national, regional and international level regarding the biosafety, social, cultural and ethical aspects of the use and deployment of these vector control methods.

  3. A method for analyzing changing prison populations: explaining the growth of the elderly in prison.

    Science.gov (United States)

    Luallen, Jeremy; Kling, Ryan

    2014-12-01

    For the past several decades, the U.S. prison system has witnessed a steady and persistent increase in the ages of prison populations. Given the additional costs and burdens placed on prisons as they house older inmates, this aging trend has generated intense interest among policy makers and academics who seek to understand why prison populations are getting older. This article presents a method for evaluating drivers influencing the change in age distributions among prisoners. We define a methodological approach and demonstrate its application using prison data from four states reporting to the Bureau of Justice Statistics' National Corrections Reporting Program. We find that since 2000, the primary driver of overall growth in the elderly populations in prison (defined as inmates over 50) is the increasing admission age of offenders entering prison. Moreover, changes in offense mix and sentence length/time served over the last decade have had significantly less influence on the age composition of prison populations. We also find that the impact of explanatory factors varies across states and offense types. For example, prison admission and exit rates explain much of the change in elderly drug offenders in New York, but not elderly violent offenders, where admission age plays a much stronger explanatory role. Our analysis offers an effective demonstration that supports the use of this method as an important and informative first step toward understanding components of change that affect the problem of prison aging. © The Author(s) 2014.

  4. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... tant repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of ..... Peakall R. and Smouse P. E. 2012 GenAlEx 6.5: genetic analysis in. Excel. Population genetic software for teaching and research—an update. Bioinformatics 28, 2537–2539.

  5. AFLP analysis on genetic diversity and population structure of small ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism. (AFLP). Ninety-one ... Key words: Small yellow croaker, Larimichthys polyactis, genetic population structure, genetic diversity, AFLP. ... gene mapping, linkage and genetic diversity of species.

  6. Genetic study of scheduled caste populations of Tamil Nadu

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 87; Issue 2. Genetic study of scheduled caste populations of Tamil Nadu. M. Vijaya S. Kanthimathi A. Ramesh. Research Note Volume 87 Issue 2 ... Keywords. caste system; genetic affinity; scheduled castes; socio-economic groups; Tamil Nadu; principal component analysis.

  7. Population structure and genetic trends for indigenous African beef ...

    African Journals Online (AJOL)

    Population structure and genetic trends for indigenous African beef cattle breeds in South Africa. ... South African Journal of Animal Science ... This study has confirmed the benefits of having sufficient pedigree and performance data available for genetic evaluations and application in selection for genetic improvement.

  8. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    The endangered Aquilaria malaccensis, is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A.

  9. Genetic variability in the population of the endemic bee Anthophora ...

    African Journals Online (AJOL)

    The genetic diversity and spatial genetic population structure of the solitary bee Anthophora pauperata Walker 1871, a species endemic to St Katherine Protectorate, were studied by RAPD markers in seven wadis in the St Katherine Protectorate, South Sinai, Egypt. High levels of genetic diversity were found, mostly within ...

  10. Polygyny and strong genetic structuring within an isolated population of the wood ant Formica rufa

    Directory of Open Access Journals (Sweden)

    Wouter Dekoninck

    2014-12-01

    Full Text Available Social structuring of populations within some Formica species exhibits considerable variation going from monodomous and monogynous populations to polydomous, polygynous populations. The wood ant species Formica rufa appears to be mainly monodomous and monogynous throughout most of its distribution area in central and northern Europe. Only occasionally it was mentioned that F. rufa can have both polygynous and monogynous colonies in the same geographical region. We studied an isolated polydomous F. rufa population in a deciduous mixed forest in the north-west of Belgium. The level of polydomy within the colonies varied from monodomous to 11 nests per colony. Our genetic analysis of eight variable microsatellites suggest an oligo- to polygynous structure for at least the major part of the sampled nests. Relatedness amongst nest mate workers varies considerable within the population and colonies but confirms in general a polygynous structure. Additionally high genetic diversity (e.g. up to 8 out of 11 alleles per nest for the most variable locus and high within nest genetic variance (93% indicate that multiple queens contribute to the gene pool of workers of the same nest. Moreover significant genetic structuring among colonies indicates that gene flow between colonies is restricted and that exchange of workers between colonies is very limited. Finally we explain how possible factors as budding and the absence of Serviformica can explain the differences in genetic structure within this polygynous F. rufa population.

  11. Population Genetics and Natural Selection in Rheumatic Disease.

    Science.gov (United States)

    Ramos, Paula S

    2017-08-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Population genetic structure and phylogeography of the mud-flat ...

    African Journals Online (AJOL)

    Yomi

    2012-01-27

    Jan 27, 2012 ... Genetic structure and evolutionary demography of the mud-flat crabs (Helice tientsinensis and H. latimera) were investigated ... revealed significant genetic structure in the 10 populations of H. tientsinensis and H. latimera. For all populations, the ..... Yellow Sea depression (Chen, 1991). A large land bridge,.

  13. Identification of management units using population genetic data

    NARCIS (Netherlands)

    Palsboll, Per J.; Berube, Martine; Allendorf, Fred W.

    The identification of management units (MUs) is central to the management of natural populations and is crucial for monitoring the effects of human activity upon species abundance. Here, we propose that the identification of MUs from population genetic data should be based upon the amount of genetic

  14. AMOVA-based clustering of population genetic data

    NARCIS (Netherlands)

    Meirmans, P.G.

    2012-01-01

    Determining the genetic structure of populations is becoming an increasingly important aspect of genetic studies. One of the most frequently used methods is the calculation of F-statistics using an Analysis of Molecular Variance (AMOVA). However, this has the drawback that the population hierarchy

  15. Sam Karlin and multi-locus population genetics.

    Science.gov (United States)

    Feldman, Marcus W

    2009-06-01

    Between 1967 and 1982, Sam Karlin made fundamental contributions to many areas of deterministic population genetic theory. This remembrance focuses on his work in multi-locus population genetics, primarily on the interaction between genotypic selection and the rate of recombination.

  16. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  17. Mitochondrial DNA genetic variations among four horse populations in Egypt

    Directory of Open Access Journals (Sweden)

    Othman E. Othman

    2017-12-01

    It is concluded that sequence analysis of mtDNA control region is still the most informative tool for the identification of genetic biodiversity and phylogeny of different horse breeds and populations. The horse populations reared in Egypt possess low genetic diversity and all of them are belonged to Equus caballus breed.

  18. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

  19. Population genetics of bisexual and unisexual populations of the scaly-winged bark louse Echmepteryx hageni (Insecta: Psocoptera).

    Science.gov (United States)

    Shreve, Scott M; Johnson, Kevin P

    2014-10-01

    The scaly-winged bark louse, Echmepteryx hageni, exhibits a unique pattern of co-existence of apparently differnt reproductive modes. Unisexuality is widespread in eastern North America, while sexual populations are restricted to isolated rock out-croppings in southern Illinois and eastern Kentucky. Three of the four nuclear loci examined show greater genetic diversity in the unisexual form compared to the sexual form of E. hageni, in accordance with the pattern previously shown in mitochondrial genetic data. Neutrality tests of the nuclear loci indicate a consistent signal of demographic expansion in asexual populations, but not in sexual populations. There was evidence of inbreeding in the isolated sexual populations at three of the nuclear loci, and one locus had signs of gene specific balancing selection. However, there is no significant genetic differentiation between bisexual and unisexual populations, possibly due to the greater effective population size of nuclear loci relative to mitochondrial loci. The mitochondrial differentiation of E. hageni populations in the northwestern part of their range (Minnesota and Wisconsin) was also not reflected in the nuclear data. We present three hypotheses that may explain the disparity in observed nuclear and mitochondrial genetic diversity between the reproductive forms of E. hageni.

  20. Population Well-Being Measures Help Explain Geographic Disparities In Life Expectancy At The County Level

    Science.gov (United States)

    Arora, Anita; Spatz, Erica; Herrin, Jeph; Riley, Carley; Roy, Brita; Kell, Kenneth; Coberley, Carter; Rula, Elizabeth; Krumholz, Harlan M.

    2016-01-01

    Geographic disparities in life expectancy are substantial and not fully explained by differences in race and socioeconomic status. To develop policies that address these inequalities, it is essential to identify other factors that account for this variation. In this study we investigated whether population well-being—a comprehensive measure of physical, mental, and social health—helps explain geographic variation in life expectancy. At the county level, we found that for every 1-standarddeviation (4.2-point) increase in the well-being score, life expectancy was 1.9 years higher for females and 2.6 years higher for males. Life expectancy and well-being remained positively associated, even after race, poverty, and education were controlled for. In addition, well-being partially mediated the established associations of race, poverty, and education with life expectancy. These findings highlight well-being as an important metric of a population’s health and longevity and as a promising focus for intervention. PMID:27834249

  1. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... genetic structure of M. quintuplinervia has probably been shaped by its breeding modes, biogeographic history and human impact ... Key words: Meconopsis quintuplinervia Regel, genetic diversity, random amplified polymorphic DNA markers, ..... inbreeding depression and facilitate quality control of drug.

  2. Molecular taxonomic, epidemiological and population genetic ...

    African Journals Online (AJOL)

    Sexual recombination is a likely mechanism contributing to the high genetic diversity of C. gloeosporioides in yam-based cropping systems. Studies have been initiated to understand the mechanisms that generate genetic variation in C. gloeosporioides, and to gain some insight into the biochemistry of the interactions ...

  3. Genetic consequences of population decline in the Danish population of the little owl (Athene noctua)

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Pellegrino, Irene; Cucco, Maroc

    2012-01-01

    Background: Danish populations of the little owl (Athene noctua) have experienced dramaticdeclines in size over the past century. Before 1960 the little owl population was abundantin Denmark (estimated N>2000), but between 1960 and 1980 the population declinedrapidly, and since 1980 the little owl...... population has survived only in small and fragmentedareas. Question: Is the decline in population size associated with reduced genetic variation in theseDanish populations of the little owl? Are the populations genetically fragmented?Field site: Samples were collected from birds in Denmark (from 57457″N...... relatively little genetic variability, with more recent onesshowing even less. In addition, pairwise FST values showed evidence for genetic substructuringwith small but significant genetic differences between the extant population and the extinct owlpopulations on the Danish isle of Funen. The modest loss...

  4. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated......% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations.......The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  5. Detailed genetic structure of European bitterling populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Veronika Bartáková

    2015-11-01

    Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

  6. Landscape influences on genetic differentiation among bull trout populations in a stream-lake network

    Science.gov (United States)

    Meeuwig, M.H.; Guy, C.S.; Kalinowski, S.T.; Fredenberg, W.A.

    2010-01-01

    This study examined the influence of landscape heterogeneity on genetic differentiation between migratory bull trout (Salvelinus confluentus) populations in Glacier National Park, Montana. An information-theoretic approach was used to compare different conceptual models of dispersal associated with barriers, different models of isolation by distance, and the combined effects of barriers, waterway distance, patch size, and intra- and inter-drainage distribution of populations on genetic differentiation between bull trout populations. The effect of distance between populations on genetic differentiation was best explained by partitioning the effects of mainstem and tributary stream sections. Models that categorized barriers as having a one-way effect (i.e. allowed downstream dispersal) or a two-way effect were best supported. Additionally, patch size and the distribution of populations among drainages influenced genetic differentiation. Genetic differentiation between bull trout populations in Glacier National Park is linked to landscape features that restrict dispersal. However, this analysis illustrates that modelling variability within landscape features, such as dispersal corridors, will benefit landscape genetic analyses. Additionally, the framework used for evaluating the effects of barriers must consider not just barrier presence, but also potential asymmetries in barrier effects with respect to the organism under investigation.

  7. A Genetic Study of Wild Populations and Evolution A Genetic Study of Wild Populations and Evolution

    Directory of Open Access Journals (Sweden)

    Hovanitz William

    1944-06-01

    Full Text Available The determination of the scientific basis of heredity within the last two decades and the verification of the principal conclusions in many different plants and animals has made possible the application of analytical methods in the study of variations in wild populations. As with the physical and chemical sciences, genetics has been enabled to make use of mathematics to compound (often theoretically out of simple units, the genes, the complexity known as an organism, much in the same way as a chemist compounds molecules with atoms and the physicist compounds atoms with protons and electrons. The determination of the scientific basis of heredity within the last two decades and the verification of the principal conclusions in many different plants and animals has made possible the application of analytical methods in the study of variations in wild populations. As with the physical and chemical sciences, genetics has been enabled to make use of mathematics to compound (often theoretically out of simple units, the genes, the complexity known as an organism, much in the same way as a chemist compounds molecules with atoms and the physicist compounds atoms with protons and electrons.

  8. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer.

    Science.gov (United States)

    Timofeeva, Maria N; Kinnersley, Ben; Farrington, Susan M; Whiffin, Nicola; Palles, Claire; Svinti, Victoria; Lloyd, Amy; Gorman, Maggie; Ooi, Li-Yin; Hosking, Fay; Barclay, Ella; Zgaga, Lina; Dobbins, Sara; Martin, Lynn; Theodoratou, Evropi; Broderick, Peter; Tenesa, Albert; Smillie, Claire; Grimes, Graeme; Hayward, Caroline; Campbell, Archie; Porteous, David; Deary, Ian J; Harris, Sarah E; Northwood, Emma L; Barrett, Jennifer H; Smith, Gillian; Wolf, Roland; Forman, David; Morreau, Hans; Ruano, Dina; Tops, Carli; Wijnen, Juul; Schrumpf, Melanie; Boot, Arnoud; Vasen, Hans F A; Hes, Frederik J; van Wezel, Tom; Franke, Andre; Lieb, Wolgang; Schafmayer, Clemens; Hampe, Jochen; Buch, Stephan; Propping, Peter; Hemminki, Kari; Försti, Asta; Westers, Helga; Hofstra, Robert; Pinheiro, Manuela; Pinto, Carla; Teixeira, Manuel; Ruiz-Ponte, Clara; Fernández-Rozadilla, Ceres; Carracedo, Angel; Castells, Antoni; Castellví-Bel, Sergi; Campbell, Harry; Bishop, D Timothy; Tomlinson, Ian P M; Dunlop, Malcolm G; Houlston, Richard S

    2015-11-10

    Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10(-7)), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10(-7)); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10(-7) and OR = 1.09, P = 7.4 × 10(-8)); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 × 10(-9)), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P DNA mismatch repair genes (P = 6.1 × 10(-4)) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC.

  9. Locals, resettlers, and pilgrims: a genetic portrait of three pre-Columbian Andean populations.

    Science.gov (United States)

    Baca, Mateusz; Molak, Martyna; Sobczyk, Maciej; Węgleński, Piotr; Stankovic, Anna

    2014-07-01

    The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities. © 2014 Wiley Periodicals, Inc.

  10. Genetic variation and population structure in native Americans.

    Directory of Open Access Journals (Sweden)

    Sijia Wang

    2007-11-01

    Full Text Available We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1 a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2 a relative lack of differentiation between Mesoamerican and Andean populations, (3 a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4 a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

  11. The application of genetic indicators in wild populations: Potential and pitfalls for genetic monitoring [Chapter 15

    Science.gov (United States)

    Jennifer Pierson; Gordon Luikart; Michael Schwartz

    2015-01-01

    The genetic aspects of biodiversity and conservation have been long recognised as important to the viability of populations and evolutionary potential of species (Lande 1988). Yet incorporating genetic considerations into conservation, management, and decision making has lagged behind this recognition (Mace et al. 2003; Laikre et al. 2010). Gene-level (genetic...

  12. Genetic Component of Type 2 Diabetes in a Mexican Population.

    Science.gov (United States)

    Sánchez-Pozos, Katy; Menjívar, Marta

    2016-10-01

    Type 2 diabetes (T2D) is a complex disease caused by the interaction of genetic and environmental factors. In this regard, it has been demonstrated that Hispanics have a greater susceptibility to developing complex diseases like T2D, which has been attributed to their Amerindian component. Mexico has a wide population variety as a result of Amerindian (56-69%), European (26-41.8%) and African (1.8-6%) ancestral components. The stratification of the population has made difficult the study of T2D in the Mexican population. Despite advances, in Mexico the studies in this field are scarce; 9 of 88 loci associated with type 2 diabetes by genome-wide association studies (GWAS) in Caucasian populations have been replicated in the Mexican population. Currently, only 19 common variants and two variants of low frequency have been associated with T2D in Mexico. With respect to the private genetic variation in Mexican population, only one haplotype and two genetic variants have been described. This confirms the existence of new genetic variants not yet described, exclusive to the Mexican population, which suggests most likely, that there are more genetic variants to discover. Thus, in the present review we aim to bring together in one place all the studies about T2D in Mexico to understand the contribution of the genetic factors in the susceptibility to developing T2D in a Mexican population. Copyright © 2016 IMSS. Published by Elsevier Inc. All rights reserved.

  13. Physiological vagility: correlations with dispersal and population genetic structure of amphibians.

    Science.gov (United States)

    Hillman, Stanley S; Drewes, Robert C; Hedrick, Michael S; Hancock, Thomas V

    2014-01-01

    Physiological vagility represents the capacity to move sustainably and is central to fully explaining the processes involved in creating fine-scale genetic structure of amphibian populations, because movement (vagility) and the duration of movement determine the dispersal distance individuals can move to interbreed. The tendency for amphibians to maintain genetic differentiation over relatively short distances (isolation by distance) has been attributed to their limited dispersal capacity (low vagility) compared with other vertebrates. Earlier studies analyzing genetic isolation and population differentiation with distance treat all amphibians as equally vagile and attempt to explain genetic differentiation only in terms of physical environmental characteristics. We introduce a new quantitative metric for vagility that incorporates aerobic capacity, body size, body temperature, and the cost of transport and is independent of the physical characteristics of the environment. We test our metric for vagility with data for dispersal distance and body mass in amphibians and correlate vagility with data for genetic differentiation (F'(ST)). Both dispersal distance and vagility increase with body size. Differentiation (F'(ST)) of neutral microsatellite markers with distance was inversely and significantly (R2=0.61) related to ln vagility. Genetic differentiation with distance was not significantly related to body mass alone. Generalized observations are validated with several specific amphibian studies. These results suggest that interspecific differences in physiological capacity for movement (vagility) can contribute to genetic differentiation and metapopulation structure in amphibians.

  14. Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog (Rana temporaria?

    Directory of Open Access Journals (Sweden)

    Patrick P. Lenhardt

    2017-07-01

    Full Text Available Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria populations in Southern Palatinate (Germany. We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance. Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat

  15. Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog (Rana temporaria)?

    Science.gov (United States)

    Lenhardt, Patrick P; Brühl, Carsten A; Leeb, Christoph; Theissinger, Kathrin

    2017-01-01

    Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity) on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria) populations in Southern Palatinate (Germany). We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance) than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance). Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat, inhibiting genetic

  16. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

    2013-01-01

    method for quantifying population genetic differentiation from next-generation sequencing data. In addition, we present a strategy to investigate population structure via Principal Components Analysis. Through extensive simulations, we compare the new method herein proposed to approaches based...... individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage....... on genotype calling and demonstrate a marked improvement in estimation accuracy for a wide range of conditions. We apply the method to a large-scale genomic data set of domesticated and wild silkworms sequenced at low coverage. We find that we can infer the fine-scale genetic structure of the sampled...

  17. Genetic variation patterns of Medicago ruthenica populations from ...

    African Journals Online (AJOL)

    According to GST, gene flow at population level was 1.4427 for allozymes and 1.2040 for SSR markers, which indicated there was definite gene flow between populations. Low differentiations among ... in M. ruthenica populations. Key words: Medicago ruthenica, genetic diversity, allozyme, micro-satellite, North China.

  18. A biochemical genetic comparison of four populations of Breviceps ...

    African Journals Online (AJOL)

    Four populations of the bushveld rain frog, Breviceps adspersus, representing three northern populations (B. adspersus adspersus), and a southern population (B. adspersus pentheri), were analysed by electrophoresis to assess the extent of genetic variation and differentiation amongst them. Eighteen protein-coding loci ...

  19. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  20. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation

    Science.gov (United States)

    Tucker, Kimberly Pause; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.

    2012-01-01

    Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.

  1. Development of a communication aid for explaining hypertrophic cardiomyopathy genetic test results.

    Science.gov (United States)

    Smagarinsky, Yana; Burns, Charlotte; Spinks, Catherine; Semsarian, Christopher; Ingles, Jodie

    2017-01-01

    Large gene panels are now commonplace for hypertrophic cardiomyopathy (HCM), increasing the yield of uncertain genetic findings. Few resources exist which aim to facilitate communication of HCM genetic test results. We sought to develop, pilot, and refine a communication aid for probands receiving HCM genetic test results. Development was a multi-step process involving expertise of a multidisciplinary team, literature review, and empirical experience. The aid went through an iterative revision process throughout the piloting phase to incorporate feedback. HCM probands attending a specialized multidisciplinary HCM clinic, aged ≥ 18 years and genetic test results available for disclosure between May and August 2016, or recently received their gene results (January-April 2015) were eligible. A purposive sampling strategy was employed, recruiting those attending clinic during the study period or those who could attend without difficulty. We developed and pilot tested a genetic counsellor-led communication aid. Based on clinical expertise, the aid addresses (a) what genetic testing is, (b) implications for the patient, (c) reasoning for variant classification, and (d) implications for the family. Pilot data were sought to assess knowledge, feasibility, and acceptability using a self-report survey 2 weeks post-intervention. Twelve of 13 participants completed the follow-up questionnaire. Participants valued the individualised nature of the aid, recommended use of the aid, and indicated genetic knowledge, and family communication was better facilitated. Iterative modification of images helped to more simply depict important genetic concepts. We have developed a tool that is feasible, acceptable, and helpful to patients receiving genetic results. This is an important first step, and trial of the aid to assess effectiveness compared to usual care will follow.

  2. The genetic structure of a relict population of wood frogs

    Science.gov (United States)

    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.

  3. Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

    Science.gov (United States)

    Johnson, Ronald; Kennon, Tillman

    2009-01-01

    Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

  4. Analysis of genetic diversity and structure in Ethiopian populations of Phytolacca dodecandra using RAPD.

    Science.gov (United States)

    Semagn, K; Stedje, B; Bjornstad, A

    2001-01-01

    The genetic diversity and structure in 17 wild populations (249 individuals) of Phytolacca dodecandra (endod) sampled along altitudinal gradients of 1600-3000 meters above sea level (m.a.s.l.) in Ethiopia was studied using random amplified polymorphic DNA (RAPD). A total of 70 polymorphic loci (P) scored from 12 RAPD primers were used to calculate different diversity indices within and between populations, habitats, geographical regions, climatic zones and altitude groups. The number of polymorphic loci and overall Shannon information measure (H) in the populations varied from 30 to 55 and from 0.228 to 0.418, respectively. In general, differences in population variability were found significantly correlated to effective population size. Both P and H were significantly higher in an undisturbed than in a disturbed habitat, and in the lowland and central-highland than in the highland altitude group. However, for both parameters the differences were not statistically significant between regions and climatic zones. Genetic distance between populations varied from 0.301 to 0.628. Cluster analysis performed using the genetic distance matrix revealed a clear separation of the highland populations (2501-3000 m.a.s.l.) from those of the lowland/central-highlands (1600-2500 m.a.s.l.) irrespective of their geographical regions and climatic zones. Analysis of molecular variance (AMOVA) indicated that differences in habitat, geographical regions and climatic zones explained 4.6%, 2.5% and 4.6%, respectively. But none of these differences were significant. Altitude explained 17.2% of the total variance and was highly significant. The data, therefore, clearly indicated the association of genetic structure in endod with altitude. The proportion of RAPD variation found among populations (21.2-35.0%) was somewhat intermediate between values reported for selfing and outcrossing species. The fixation index (FST) values (0.350 to 0.384) indicated very high genetic differentiation among

  5. Genetic parameters in a Swine Population

    Directory of Open Access Journals (Sweden)

    Dana Popa

    2010-05-01

    Full Text Available The estimation of the variance-covariance components is a very important step in animal breeding because these components are necessary for: estimation of the genetic parameters, prediction of the breeding value and design of animal breeding programs. The estimation of genetic parameters is the first step in the development of a swine breeding program, using artificial insemination. Various procedures exist for estimation of heritability. There are three major procedures used for estimating heritability: analysis of variance (ANOVA, parents-offspring regression and restricted maximum likelihood (REML. By using ANOVA methodology or regression method it is possible to obtain aberrant values of genetic parameters (negative or over unit value of heritability coefficient, for example which can not be interpreting because is out of biological limits.

  6. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    Science.gov (United States)

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  7. Genetic population structure in an equatorial sparrow: roles for culture and geography.

    Science.gov (United States)

    Danner, J E; Fleischer, R C; Danner, R M; Moore, I T

    2017-06-01

    Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  8. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer

    Science.gov (United States)

    Timofeeva, Maria N.; Kinnersley, Ben; Farrington, Susan M.; Whiffin, Nicola; Palles, Claire; Svinti, Victoria; Lloyd, Amy; Gorman, Maggie; Ooi, Li-Yin; Hosking, Fay; Barclay, Ella; Zgaga, Lina; Dobbins, Sara; Martin, Lynn; Theodoratou, Evropi; Broderick, Peter; Tenesa, Albert; Smillie, Claire; Grimes, Graeme; Hayward, Caroline; Campbell, Archie; Porteous, David; Deary, Ian J.; Harris, Sarah E.; Northwood, Emma L.; Barrett, Jennifer H.; Smith, Gillian; Wolf, Roland; Forman, David; Morreau, Hans; Ruano, Dina; Tops, Carli; Wijnen, Juul; Schrumpf, Melanie; Boot, Arnoud; Vasen, Hans F A; Hes, Frederik J.; van Wezel, Tom; Franke, Andre; Lieb, Wolgang; Schafmayer, Clemens; Hampe, Jochen; Buch, Stephan; Propping, Peter; Hemminki, Kari; Försti, Asta; Westers, Helga; Hofstra, Robert; Pinheiro, Manuela; Pinto, Carla; Teixeira, Manuel; Ruiz-Ponte, Clara; Fernández-Rozadilla, Ceres; Carracedo, Angel; Castells, Antoni; Castellví-Bel, Sergi; Campbell, Harry; Bishop, D. Timothy; Tomlinson, Ian P M; Dunlop, Malcolm G.; Houlston, Richard S.

    2015-01-01

    Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10−7), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10−7); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10−7 and OR = 1.09, P = 7.4 × 10−8); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 × 10−9), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P < 2.90 × 10−6). We found an excess of rare, damaging variants in base-excision (P = 2.4 × 10−4) and DNA mismatch repair genes (P = 6.1 × 10−4) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC. PMID:26553438

  9. TreesimJ: a flexible, forward time population genetic simulator.

    Science.gov (United States)

    O'Fallon, Brendan

    2010-09-01

    Most population genetic simulators fall into one of two classes, backward time simulators that quickly generate trees but accommodate only relatively simple selective and demographic regimes, and forward simulators that allow for a broader range of evolutionary scenarios but which cannot produce genealogies. Thus, few tools are available that allow for producing genealogies under arbitrarily complex selective and demographic models. TreesimJ is a forward time population genetic simulator that allows for sampling of genealogies, genetic data and many population parameters from populations evolving under complex evolutionary scenarios. The application provides many fitness and demographic models and new models are easy to develop. Data collection is performed by a variety of independently configurable collectors which periodically sample the population and record statistics. Output options include writing traces, histograms and summary statistics from the data collectors in addition to sampled genetic sequences and genealogies. TreesimJ allows researchers to easily sample and analyze gene genealogies and related data from populations evolving under a wide variety of selective and demographic regimes. It is likely to be useful for population genetic researchers seeking to understand the links between evolutionary and demographic forces, genealogical structure and the resulting patterns of genetic variation. TreesimJ home : http://staff.washington.edu/brendano/treesimj. Source and developer resources: http://code.google.com/p/treesimj.

  10. Explaining the visible and the invisible : ancestry, appearance, race and genetics in Colombia.

    OpenAIRE

    Schwartz-Marin, Ernesto; Wade, Peter

    2015-01-01

    Using data from focus groups conducted in Colombia, we explore how educated lay audiences faced with scenarios about ancestry and genetics, draw on widespread and dominant notions of nation, race and belonging in Colombia to ascribe ancestry to collectivities and to themselves as individuals. People from a life sciences background tend to deploy idioms of race and genetics more readily than people from a humanities and race-critical background. When considering the individual level, people te...

  11. The estimation of recombination rates from population genetic data

    OpenAIRE

    2007-01-01

    Genetic recombination is an important process that generates new combinations of genes on which natural selection can operate. As such, an understanding of recombination in the human genome will provide insight into the evolutionary processes that have shaped our genetic history. The aim of this thesis is to use samples of population genetic data to explore the patterns of variation in the rate of recombination in the human genome. To do this I introduce a novel means of estimating recombinat...

  12. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

    Directory of Open Access Journals (Sweden)

    Jiali Zhao

    Full Text Available AIMS: We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1 determine the level of genetic diversity across the studied regions; (2 explore the likely origins of invasive populations in China; and (3 investigate whether there is the evidence of multiple introductions into China. METHODS: We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China. IMPORTANT FINDINGS: We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F IS or population differentiation (F ST. Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.

  13. Molecular species identification and population genetics of ...

    African Journals Online (AJOL)

    Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South ...

  14. Genetic disorders from an endogamous population

    African Journals Online (AJOL)

    Background: Marriage between close relatives has been practised globally since the early existence of human society. The role of consanguinity and inbreeding affecting human health is a topic of great interest in medical genetics. Objective: The objective of the study was to investigate the extent of consanguinity and its ...

  15. Genetic diversity and population structure among sorghum ...

    African Journals Online (AJOL)

    The Western Ethiopian region harbors a unique set of sorghum germplasm adapted to conditions not conventional to sorghums grown in other parts of the world. Accessions from the region possess unique resistance to multiple leaf and grain diseases. This study is aimed at exploring the extent of genetic variation and ...

  16. Speaker Input Variability Does Not Explain Why Larger Populations Have Simpler Languages.

    Science.gov (United States)

    Atkinson, Mark; Kirby, Simon; Smith, Kenny

    2015-01-01

    A learner's linguistic input is more variable if it comes from a greater number of speakers. Higher speaker input variability has been shown to facilitate the acquisition of phonemic boundaries, since data drawn from multiple speakers provides more information about the distribution of phonemes in a speech community. It has also been proposed that speaker input variability may have a systematic influence on individual-level learning of morphology, which can in turn influence the group-level characteristics of a language. Languages spoken by larger groups of people have less complex morphology than those spoken in smaller communities. While a mechanism by which the number of speakers could have such an effect is yet to be convincingly identified, differences in speaker input variability, which is thought to be larger in larger groups, may provide an explanation. By hindering the acquisition, and hence faithful cross-generational transfer, of complex morphology, higher speaker input variability may result in structural simplification. We assess this claim in two experiments which investigate the effect of such variability on language learning, considering its influence on a learner's ability to segment a continuous speech stream and acquire a morphologically complex miniature language. We ultimately find no evidence to support the proposal that speaker input variability influences language learning and so cannot support the hypothesis that it explains how population size determines the structural properties of language.

  17. Speaker Input Variability Does Not Explain Why Larger Populations Have Simpler Languages.

    Directory of Open Access Journals (Sweden)

    Mark Atkinson

    Full Text Available A learner's linguistic input is more variable if it comes from a greater number of speakers. Higher speaker input variability has been shown to facilitate the acquisition of phonemic boundaries, since data drawn from multiple speakers provides more information about the distribution of phonemes in a speech community. It has also been proposed that speaker input variability may have a systematic influence on individual-level learning of morphology, which can in turn influence the group-level characteristics of a language. Languages spoken by larger groups of people have less complex morphology than those spoken in smaller communities. While a mechanism by which the number of speakers could have such an effect is yet to be convincingly identified, differences in speaker input variability, which is thought to be larger in larger groups, may provide an explanation. By hindering the acquisition, and hence faithful cross-generational transfer, of complex morphology, higher speaker input variability may result in structural simplification. We assess this claim in two experiments which investigate the effect of such variability on language learning, considering its influence on a learner's ability to segment a continuous speech stream and acquire a morphologically complex miniature language. We ultimately find no evidence to support the proposal that speaker input variability influences language learning and so cannot support the hypothesis that it explains how population size determines the structural properties of language.

  18. Genetic variability of camel ( Camelus dromedarius ) populations in ...

    African Journals Online (AJOL)

    Camelus dromedarius) are poorly documented in Saudi Arabia. The present study was conducted to address some of these genetics using four Saudi Arabian camel populations namely; Magaheem (MG), Maghateer (MJ), Sofr (SO) and Shual (SH) ...

  19. Genetic variability of camel (Camelus dromedarius) populations in ...

    African Journals Online (AJOL)

    2010

    2012-06-26

    Camelus dromedarius) are poorly documented in Saudi Arabia. The present study was conducted to address some of these genetics using four Saudi Arabian camel populations namely; Magaheem (MG), Maghateer (MJ), Sofr.

  20. Population genetic diversity of marble goby (Oxyeleotris marmoratus ...

    Indian Academy of Sciences (India)

    Navya

    2017-03-31

    Innovation Center for Marine Bio-Industry Technology of Jiangsu Province,. Lianyungang, Jiangsu 222005, China. #These authors contributed equally to this work. Short title: Population genetic diversity analysis of marble goby.

  1. Theoretical population genetics of variable selection and migration

    Energy Technology Data Exchange (ETDEWEB)

    Felsenstein, J.

    1976-01-01

    Selection varying with time is reviewed with regard to infinite and finite populations. Geographic effects are reviewed with regard to migration versus selection; genetic drift and migration; and selection. Various models of geographic differentiation are described. (HLW)

  2. Genetic Variation Within and Among Populations of Delmarva Fox Squirrels

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The objective of this study was to provide important information about genetic variation in populations of the Delmarva Fox Squirrel in the context of a more general...

  3. [A genetically isolated population of Saccharomyces cerevisiae in Malaysia].

    Science.gov (United States)

    Naumov, G I; Serpova, E V; Naumova, E S

    2006-01-01

    A divergent population of Saccharomyces cerevisiae has been identified in Malaysia by molecular and genetic analysis. It has also demonstrated that the yeast S. bayanus may be found in South America. Problems of the origin of S. cerevisiae are discussed.

  4. Landscape, population structure and genetic diversity of Stomoxys calcitrans.

    Science.gov (United States)

    Dsouli Aymes, N; Mavoungou, J F; De Stordeur, E; Duvallet, G

    2009-03-01

    To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP) markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05). Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979) and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively). This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation.

  5. Genetic structure of fragmented November moth (Lepidoptera: Geometridae) populations in farmland

    DEFF Research Database (Denmark)

    Wynne, Ian Robert; Loxdale, Hugh D.; Brookes, Cliff P.

    2003-01-01

    allozymes, conservation genetics, Epirrita dilutata, Epirrita christyi, molecular markers, habitat fragmentation, population genetic structure......allozymes, conservation genetics, Epirrita dilutata, Epirrita christyi, molecular markers, habitat fragmentation, population genetic structure...

  6. Genetic differentiation of populations residing in areas of high ...

    Indian Academy of Sciences (India)

    ... Public Lectures · Lecture Workshops · Refresher Courses · Symposia. Home; Journals; Journal of Genetics; Volume 88; Issue 1. Genetic differentiation of populations residing in areas of high malaria endemicity in India. Swapnil Sinha Vandana Arya Sarita Agarwal Indian Genome Variation Consortium Saman Habib.

  7. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    Population structure was analyzed by means of genetic distances and probabilistic models; allelic frequencies were used in order to assess the genetic diversity indexes (Ht, Ho, PIC, % polymorphism and number of alleles) for each locus studied. All evaluated loci were polymorphic and the average was highly heterozygote ...

  8. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  9. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... Webb ex Christ and Helianthemum juliae Wildprett. Boletim do. Museo Municipal do Funchal. 2: 41-56. Barrett SCH, Kohn JR (1991). Genetic and evolutionary consequences of small population size in plants: implications for conservation. In: Falk DA, Holsinger KE (eds) Genetics and conservation of rare.

  10. Genetic diversity and population structure of blue-crested lizard ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 96; Issue 2. Genetic diversity and population structure of blue-crested lizard, Calotes ... These two lineages are separated by mountain ranges, which play an important role as natural barriers blocking gene flow. Our finding reveal at least two cryptic lineages represented in C.

  11. Genetic portrait of Lisboa immigrant population from Cabo Verde ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 94; Issue 3. Genetic portrait of Lisboa immigrant population from Cabo Verde with mitochondrial DNA analysis. Paulo Morais António Amorim Cláudia Vieira Da Silva Teresa Ribeiro Jorge Costa Santos Heloísa Afonso Costa. Research Note Volume 94 Issue 3 September 2015 ...

  12. Genetic variation within and among five natural populations of ...

    African Journals Online (AJOL)

    Knowledge of genetic diversity is important for successful conservation and domestication of species. In order to determine genetic diversity within and among Sclerocarya birrea (A. Rich.) Htochst. subsp. birrea populations in Sudan, random amplified polymorphic DNA (RAPD) markers were used. Leaf materials from 75 ...

  13. Genetic Identification and Population Structure of Juvenile Mullet ...

    African Journals Online (AJOL)

    Abstract—There is a growing demand for wild caught juvenile fish to supply the market for aquaculture. We investigated the local ... revealed a clear genetic population structure within the sampled fish community with a unique mainland cluster. ...... Genetic connectivity and historical demography of the blue barred parrotfish.

  14. Genetic diversity among natural populations of Ottelia acuminata ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... Genetic diversity among geographically separated populations of Nepenthes mirabilis. Biologia Brat. 61: 295-298. Farès K, Guasmi F, Touil L, Triki T, Ferchichi A (2009). Genetic diversity of pistochio tree using inter-simple sequence repeat markers. ISSR supported by morphological and chemical markers.

  15. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    The extent of genetic variation and the degree of genetic differentiation among seven ethnic populations from Karnataka, India (Bunt, Havyak, Iyengar, Lingayath, Smartha, Vaishya, Vokkaliga), was investigated using four single nucleotide polymorphisms (SNPs: IL-1A 4845, IL-1B 3954, IL-1B 511 and IL-1RA 2018) of the ...

  16. Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

    Directory of Open Access Journals (Sweden)

    Tamara Fernández-Calero

    2016-02-01

    Full Text Available Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.

  17. Genetic structure in four West African population groups

    Directory of Open Access Journals (Sweden)

    Chen Guanjie

    2005-06-01

    Full Text Available Abstract Background Africa contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa, we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes. Results There was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups. Conclusion There was little evidence for significant population substructure in the four major West African ethnic groups

  18. Broad-scale Population Genetics of the Host Sea Anemone, Heteractis magnifica

    KAUST Repository

    Emms, Madeleine

    2015-12-01

    Broad-scale population genetics can reveal population structure across an organism’s entire range, which can enable us to determine the most efficient population-wide management strategy depending on levels of connectivity. Genetic variation and differences in genetic diversity on small-scales have been reported in anemones, but nothing is known about their broad-scale population structure, including that of “host” anemone species, which are increasingly being targeted in the aquarium trade. In this study, microsatellite markers were used as a tool to determine the population structure of a sessile, host anemone species, Heteractis magnifica, across the Indo-Pacific region. In addition, two rDNA markers were used to identify Symbiodinium from the samples, and phylogenetic analyses were used to measure diversity and geographic distribution of Symbiodinium across the region. Significant population structure was identified in H. magnifica across the Indo-Pacific, with at least three genetic breaks, possibly the result of factors such as geographic distance, geographic isolation and environmental variation. Symbiodinium associations were also affected by environmental variation and supported the geographic isolation of some regions. These results suggests that management of H. magnifica must be implemented on a local scale, due to the lack of connectivity between clusters. This study also provides further evidence for the combined effects of geographic distance and environmental distance in explaining genetic variance.

  19. Genetic assessment of captive red panda (Ailurus fulgens) population.

    Science.gov (United States)

    Kumar, Arun; Rai, Upashna; Roka, Bhupen; Jha, Alankar K; Reddy, P Anuradha

    2016-01-01

    Red panda (Ailurus fulgens) is threatened across its range by detrimental human activities and rapid habitat changes necessitating captive breeding programs in various zoos globally to save this flagship species from extinction. One of the ultimate aims of ex situ conservation is reintroduction of endangered animals into their natural habitats while maintaining 90 % of the founder genetic diversity. Advances in molecular genetics and microsatellite genotyping techniques make it possible to accurately estimate genetic diversity of captive animals of unknown ancestry. Here we assess genetic diversity of the red panda population in Padmaja Naidu Himalayan Zoological Park, Darjeeling, which plays a pivotal role in ex situ conservation of red panda in India. We generated microsatellite genotypes of fifteen red pandas with a set of fourteen loci. This population is genetically diverse with 68 % observed heterozygosity (H O ) and mean inbreeding (F IS ) coefficient of 0.05. However population viability analysis reveals that this population has a very low survival probability (<2 %) and will rapidly loose its genetic diversity to 37 % mainly due to small population size and skewed male-biased sex ratio. Regular supplementation with a pair of adult individuals every five years will increase survival probability and genetic diversity to 99 and 61 % respectively and will also support future harvesting of individuals for reintroduction into the wild and exchange with other zoos.

  20. Population structure and genetic diversity of worldwide Nova Scotia Duck Tolling Retriever and Lancashire Heeler dog populations.

    Science.gov (United States)

    Mäki, K

    2010-08-01

    The aim of this study was to research the population structure and genetic diversity of the Nova Scotia Duck Tolling Retriever (NS) and the Lancashire Heeler (LH) dog breeds. Data consisted of nearly all the worldwide registration history for both breeds, including 28,668 NS and 4,782 LH individuals. A reference population, including the females born between 1999 and 2008, was defined for genetic analyses for each breed. Average depth of the pedigrees known for the reference population dogs was 12.9 complete generation equivalents in the NS and 6.0 in the LH. Only a small fraction of the born dogs were used later for breeding. Effective number of founders was 9.8 in the NS and 15.2 in the LH. More than 50% of the genetic diversity in the reference population was explained by two ancestors in the NS and five in the LH. Average inbreeding coefficients in the reference populations were 0.26 in the NS and 0.10 in the LH. Average kinships were 0.26 and 0.08 and realised effective population sizes 18 and 28, respectively. Failure to use available genetic resources for sustainable breeding has resulted in depletion of genetic variation in both breeds. To increase genetic variation, a larger proportion of the dogs should be used in reproduction and the contributions of reproducing animals should be equalized. In the LH, it is necessary to use the unregistered farm dogs in breeding. In the NS, crosses with another breed are needed.

  1. Culture, population structure, and low genetic diversity in Pleistocene hominins.

    Science.gov (United States)

    Premo, L S; Hublin, Jean-Jacques

    2009-01-06

    Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.

  2. Genetic population differentiation and connectivity among fragmented Moor frog (Rana arvalis) populations in The Netherlands

    NARCIS (Netherlands)

    Arens, P.F.P.; Sluis, van der T.; Westende, van 't W.P.C.; Vosman, B.; Vos, C.C.; Smulders, M.J.M.

    2007-01-01

    We studied the effects of landscape structure, habitat loss and fragmentation on genetic differentiation of Moor frog populations in two landscapes in The Netherlands (Drenthe and Noord-Brabant). Microsatellite data of eight loci showed small to moderate genetic differentiation among populations in

  3. Genetic signals of past demographic changes and the history of oak populations in California

    Science.gov (United States)

    Dodd, R. S.

    2009-04-01

    A retrospective view of species' demographic changes can inform on population stability through times of climatic change and the origins and spatial structure of genetic diversity in contemporary populations. The former provides the means to predict responses to future climatic change, while the latter allows us to infer the ability of populations to buffer the effects of reductions in population size and fragmentation. The approximately 1.8 my of the Pleistocene is believed to have had a significant impact on diversity through high rates of extinction during early glacial cycles and population expansions and contractions during the later cycles. In the Mediterranean basin, early emphasis on taxa with wide latitudinal ranges led to models of refugial sites and subsequent recolonization routes that could explain geographic patterns in genetic diversity, with a trend towards reduced genetic diversity in the north. More recently, the study of strictly Mediterranean taxa has revealed relictual sites that have persisted over very long periods of time, commonly relatively poor in diversity, but populations well differentiated from one site to another. In California, relatively little is known of the population dynamics of plant taxa during the Pleistocene glacial cycles, or to what extent differentiation today is a result of pre-Pleistocene events. For several animal taxa, differentiation between Coastal and Sierran taxa are believed to date to the Pliocene. Major demographic changes resulting in population isolation, bottlenecks, founder events and population expansions leave a genetic signal that can be detected through appropriate genetic markers and analyses. Such signals help to infer whether past climate fluctuations have had important effects on population demographics. Here, I will focus on key oak species of the California mediterranean climate zone. I will explore the likely effects of the last glacial maximum on oak populations using palaeoclimate and niche

  4. Medical Genetics and the First Studies of the Genetics of Populations in Mexico.

    Science.gov (United States)

    Barahona, Ana

    2016-09-01

    Following World War II (WWII), there was a new emphasis within genetics on studying the genetic composition of populations. This probably had a dual source in the growing strength of evolutionary biology and the new international interest in understanding the effects of radiation on human populations, following the atomic bombings in Japan. These global concerns were shared by Mexican physicians. Indeed, Mexico was one of the leading centers of this trend in human genetics. Three leading players in this story were Mario Salazar Mallén, Adolfo Karl, and Rubén Lisker. Their trajectories and the international networks in human genetics that were established after WWII, paved the way for the establishment of medical and population genetics in Mexico. Salazar Mallén's studies on the distribution and characterization of ABO blood groups in indigenous populations were the starting point while Karl's studies on the distribution of abnormal hemoglobin in Mexican indigenous populations showed the relationships observed in other laboratories at the time. It was Lisker's studies, however, that were instrumental in the development of population genetics in the context of national public policies for extending health care services to the Mexican population. In particular, he conducted studies on Mexican indigenous groups contributing to the knowledge of the biological diversity of human populations according to international trends that focused on the variability of human populations in terms of genetic frequencies. From the start, however, Lisker was as committed to the reconstruction of shared languages and practices as he was to building networks of collaboration in order to guarantee the necessary groundwork for establishing the study of the genetics of human populations in Mexico. This study also allows us to place Mexican science within a global context in which connected narratives describe the interplay between global trends and national contexts. Copyright © 2016 by

  5. Translating Population Difference: The Use and Re-Use of Genetic Ancestry in Brazilian Cancer Genetics.

    Science.gov (United States)

    Gibbon, Sahra

    2016-01-01

    In the past ten years, there has been an expansion of scientific interest in population genetics linked to both understanding histories of human migration and the way that population difference and diversity may account for and/or be implicated in health and disease. In this article, I examine how particular aspects of a globalizing research agenda related to population differences and genetic ancestry are taken up in locally variant ways in the nascent field of Brazilian cancer genetics. Drawing on a broad range of ethnographic data from clinical and nonclinical contexts in the south of Brazil, I examine the ambiguities that attention to genetic ancestry generates, so revealing the disjunctured and diverse ways a global research agenda increasingly orientated to questions of population difference and genetic ancestry is being used and reused.

  6. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

    Science.gov (United States)

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-09-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

  7. Mortality Rates in a Genetically Heterogeneous Population of Caenorhabditis elegans

    Science.gov (United States)

    Brooks, Anne; Lithgow, Gordon J.; Johnson, Thomas E.

    1994-02-01

    Age-specific mortality rates in isogenic populations of the nematode Caenorhabditis elegans increase exponentially throughout life. In genetically heterogeneous populations, age-specific mortality increases exponentially until about 17 days and then remains constant until the last death occurs at about 60 days. This period of constant age-specific mortality results from genetic heterogeneity. Subpopulations differ in mean life-span, but they all exhibit near exponential, albeit different, rates of increase in age-specific mortality. Thus, much of the observed heterogeneity in mortality rates later in life could result from genetic heterogeneity and not from an inherent effect of aging.

  8. The influence of climatic niche preferences on the population genetic structure of a mistletoe species complex.

    Science.gov (United States)

    Ramírez-Barahona, Santiago; González, Clementina; González-Rodríguez, Antonio; Ornelas, Juan Francisco

    2017-06-01

    The prevalent view on genetic structuring in parasitic plants is that host-race formation is caused by varying degrees of host specificity. However, the relative importance of ecological niche divergence and host specificity to population differentiation remains poorly understood. We evaluated the factors associated with population differentiation in mistletoes of the Psittacanthus schiedeanus complex (Loranthaceae) in Mexico. We used genetic data from chloroplast sequences and nuclear microsatellites to study population genetic structure and tested its association with host preferences and climatic niche variables. Pairwise genetic differentiation was associated with environmental and host preferences, independent of geography. However, environmental predictors appeared to be more important than host preferences to explain genetic structure, supporting the hypothesis that the occurrence of the parasite is largely determined by its own climatic niche and, to a lesser degree, by host specificity. Genetic structure is significant within this mistletoe species complex, but the processes associated with this structure appear to be more complex than previously thought. Although host specificity was not supported as the major determinant of population differentiation, we consider this to be part of a more comprehensive ecological model of mistletoe host-race formation that incorporates the effects of climatic niche evolution. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  9. Toward a Better Understanding of Population Genetics: Pop!World--A Virtual, Inquiry-Based Tool for Teaching Population Genetics

    Science.gov (United States)

    Poulin, Jessica; Ramamurthy, Bina; Dittmar, Katharina

    2013-01-01

    Population genetics is fundamental to understanding evolutionary theory, and is taught in most introductory biology/evolution courses. Many students are unaware that understanding this topic requires pertinent knowledge

  10. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations.

    Science.gov (United States)

    Marchi, Nina; Hegay, Tatyana; Mennecier, Philippe; Georges, Myriam; Laurent, Romain; Whitten, Mark; Endicott, Philipp; Aldashev, Almaz; Dorzhu, Choduraa; Nasyrova, Firuza; Chichlo, Boris; Ségurel, Laure; Heyer, Evelyne

    2017-04-01

    Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure. © 2017 Wiley Periodicals, Inc.

  11. Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

    NARCIS (Netherlands)

    McLaren, Paul J; Coulonges, Cedric; Bartha, István; Lenz, Tobias L; Deutsch, Aaron J; Bashirova, Arman; Buchbinder, Susan; Carrington, Mary N; Cossarizza, Andrea; Dalmau, Judith; De Luca, Andrea; Goedert, James J; Gurdasani, Deepti; Haas, David W; Herbeck, Joshua T; Johnson, Eric O; Kirk, Gregory D; Lambotte, Olivier; Luo, Ma; Mallal, Simon; van Manen, Daniëlle; Martinez-Picado, Javier; Meyer, Laurence; Miro, José M; Mullins, James I; Obel, Niels; Poli, Guido; Sandhu, Manjinder S; Schuitemaker, Hanneke; Shea, Patrick R; Theodorou, Ioannis; Walker, Bruce D; Weintrob, Amy C; Winkler, Cheryl A; Wolinsky, Steven M; Raychaudhuri, Soumya; Goldstein, David B; Telenti, Amalio; de Bakker, Paul I W; Zagury, Jean-François; Fellay, Jacques

    2015-01-01

    Previous genome-wide association studies (GWAS) of HIV-1-infected populations have been underpowered to detect common variants with moderate impact on disease outcome and have not assessed the phenotypic variance explained by genome-wide additive effects. By combining the majority of available

  12. Unexpectedly low rangewide population genetic structure of the imperiled eastern box turtle Terrapene c. carolina.

    Directory of Open Access Journals (Sweden)

    Steven J A Kimble

    Full Text Available Rangewide studies of genetic parameters can elucidate patterns and processes that operate only over large geographic scales. Herein, we present a rangewide population genetic assessment of the eastern box turtle Terrapene c. carolina, a species that is in steep decline across its range. To inform conservation planning for this species, we address the hypothesis that disruptions to demographic and movement parameters associated with the decline of the eastern box turtle has resulted in distinctive genetic signatures in the form of low genetic diversity, high population structuring, and decreased gene flow. We used microsatellite genotype data from (n = 799 individuals from across the species range to perform two Bayesian population assignment approaches, two methods for comparing historical and contemporary migration among populations, an evaluation of isolation by distance, and a method for detecting barriers to gene flow. Both Bayesian methods of population assignment indicated that there are two populations rangewide, both of which have maintained high levels of genetic diversity (HO = 0.756. Evidence of isolation by distance was detected in this species at a spatial scale of 300-500 km, and the Appalachian Mountains were identified as the primary barrier to gene flow across the species range. We also found evidence for historical but not contemporary migration between populations. Our prediction of many, highly structured populations across the range was not supported. This may point to cryptic contemporary gene flow, which might in turn be explained by the presence of rare transients in populations. However these data may be influenced by historical signatures of genetic connectivity because individuals of this species can be long-lived.

  13. Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis.

    Science.gov (United States)

    Cardoso, S R; Eloy, N B; Provan, J; Cardoso, M A; Ferreira, P C

    2000-11-01

    Heart-of-palm (Euterpe edulis Mart.) is a wild palm with a wide distribution throughout the Atlantic Rainforest. Populations of E. edulis represent important renewable natural resources but are currently under threat from predatory exploitation. Furthermore, because the species is indigenous to the Atlantic Rainforest, which is located in the most economically developed and populated region of Brazil, social and economic pressures have devastated heart-of-palm forests. In order to estimate the partitioning of genetic variation of endangered E. edulis populations, 429 AFLP markers were used to analyse 150 plants representing 11 populations of the species distribution range. Analysis of the genetic structure of populations carried out using analysis of molecular variance (AMOVA) revealed moderate genetic variation within populations (57. 4%). Genetic differentiation between populations (FST = 0.426) was positively correlated with geographical distance. These results could be explained by the historical fragmentation of the Atlantic coastal region, together with the life cycle and mating system. The data obtained in this work should have important implications for conservation and future breeding programmes of E. edulis.

  14. Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations.

    Science.gov (United States)

    Haber, Marc; Mezzavilla, Massimo; Xue, Yali; Comas, David; Gasparini, Paolo; Zalloua, Pierre; Tyler-Smith, Chris

    2016-06-01

    The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain under-represented in genetic studies and have a complex history including a major geographic displacement during World War I. Here, we analyse genome-wide variation in 173 Armenians and compare them with 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3000 and ~2000 bce, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1200 bce when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of Armenian ancestry may originate from an ancestral population that is best represented by Neolithic Europeans.

  15. Habitat continuity and geographic distance predict population genetic differentiation in giant kelp.

    Science.gov (United States)

    Alberto, Filipe; Raimondi, Peter T; Reed, Daniel C; Coelho, Nelson C; Leblois, Raphael; Whitmer, Allison; Serrão, Ester A

    2010-01-01

    Isolation by distance (IBD) models are widely used to predict levels of genetic connectivity as a function of Euclidean distance, and although recent studies have used GIS-landscape ecological approaches to improve the predictability of spatial genetic structure, few if any have addressed the effect of habitat continuity on gene flow. Landscape effects on genetic connectivity are even less understood in marine populations, where habitat mapping is particularly challenging. In this study, we model spatial genetic structure of a habitat-structuring species, the giant kelp Macrocystis pyrifera, using highly variable microsatellite markers. GIS mapping was used to characterize habitat continuity and distance between sampling sites along the mainland coast of the Santa Barbara Channel, and their roles as predictors of genetic differentiation were evaluated. Mean dispersal distance (sigma) and effective population size (Ne) were estimated by comparing our IBD slope with those from simulations incorporating habitat continuity and spore dispersal characteristics of the study area. We found an allelic richness of 7-50 alleles/locus, which to our knowledge is the highest reported for macroalgae. The best regression model relating genetic distance to habitat variables included both geographic distance and habitat continuity, which were respectively, positively and negatively related to genetic distance. Our results provide strong support for a dependence of gene flow on both distance and habitat continuity and elucidate the combination of Ne and a that explained genetic differentiation.

  16. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer

    NARCIS (Netherlands)

    Timofeeva, Maria N.; Ben Kinnersley, [Unknown; Farrington, Susan M.; Whiffin, Nicola; Palles, Claire; Svinti, Victoria; Lloyd, Amy; Gorman, Maggie; Ooi, Li-Yin; Hosking, Fay; Barclay, Ella; Zgaga, Lina; Dobbins, Sara; Martin, Lynn; Theodoratou, Evropi; Broderick, Peter; Tenesa, Albert; Smillie, Claire; Grimes, Graeme; Hayward, Caroline; Campbell, Archie; Porteous, David; Deary, Ian J.; Harris, Sarah E.; Northwood, Emma L.; Barrett, Jennifer H.; Smith, Gillian; Wolf, Roland; Forman, David; Morreau, Hans; Ruano, Dina; Tops, Carli; Wijnen, Juul; Schrumpf, Melanie; Boot, Arnoud; Vasen, Hans F. A.; Hes, Frederik J.; van Wezel, Tom; Franke, Andre; Lieb, Wolgang; Schafmayer, Clemens; Hampe, Jochen; Buch, Stephan; Propping, Peter; Hemminki, Kari; Foersti, Asta; Westers, Helga; Hofstra, Robert; Pinheiro, Manuela; Pinto, Carla; Teixeira, Manuel; Ruiz-Ponte, Clara; Fernandez-Rozadilla, Ceres; Carracedo, Angel; Castells, Antoni; Castellvi-Bel, Sergi; Campbell, Harry; Bishop, D. Timothy; Tomlinson, Ian P. M.; Dunlop, Malcolm G.; Houlston, Richard S.

    2015-01-01

    Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and

  17. Recurrent Coding Sequence Variation Explains only A Small Fraction of the Genetic Architecture of Colorectal Cancer

    NARCIS (Netherlands)

    M.N. Timofeeva (Maria N.); B. Kinnersley (Ben); S.M. Farrington (Susan M.); N. Whiffin (Nicola); C. Palles (Claire); V. Svinti (Victoria); A. Lloyd (Amy); M. Gorman (Maggie); L.-Y. Ooi (Li-Yin); F. Hosking (Fay); E. Barclay (Ella); L. Zgaga (Lina); S.E. Dobbins (Sara E.); L. Martin (Lynn); E. Theodoratou (Evropi); P. Broderick (Peter); A. Tenesa (Albert); C. Smillie (Claire); G. Grimes (Graeme); C. Hayward (Caroline); A. Campbell (Archie); D. Porteous (David); I.J. Deary (Ian J.); S.E. Harris (Sarah); J.B. Northwood (John Blackman); J.H. Barrett (Jennifer H.); G. Smith (Gillian); R. Wolf (Roland); D. Forman (David); H. Morreau (Hans); D. Ruano (Dina); C. Tops (Carli); J.T. Wijnen (Juul); M. Schrumpf (Melanie); A. Boot (Arnoud); H. Vasen (Hans); F.J. Hes (Frederik); T. van Wezel (Tom); A. Franke (Andre); W. Lieb (Wolgang); C. Schafmayer (Clemens); J. Hampe (Jochen); T. Buch (Thorsten); P. Propping (Peter); K. Hemminki (Kari); A. Försti (Asta); H. Westers (Helga); R.M.W. Hofstra (Robert); M. Pinheiro (Manuela); C. Pinto (Carla); P.J. Teixeira; C. Ruiz-Ponte (Clara); C. Fernández-Rozadilla (Ceres); A. Carracedo (Angel); A. Castells; S. Castellví-Bel; H. Campbell (Harry); D.T. Bishop (David Timothy); I. Tomlinson (Ian); M.G. Dunlop (Malcolm); R. Houlston (Richard)

    2015-01-01

    textabstractWhilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs

  18. Genetic variation in natural honeybee populations, Apis mellifera capensis

    Science.gov (United States)

    Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

    2004-09-01

    Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

  19. Humanity in a Dish: Population Genetics with iPSCs.

    Science.gov (United States)

    Warren, Curtis R; Cowan, Chad A

    2017-10-17

    Induced pluripotent stem cells (iPSCs) are powerful tools for investigating the relationship between genotype and phenotype. Recent publications have described iPSC cohort studies of common genetic variants and their effects on gene expression and cellular phenotypes. These in vitro quantitative trait locus (QTL) studies are the first experiments in a new paradigm with great potential: iPSC-based functional population genetic studies. iPSC collections from large cohorts are currently under development to facilitate the next wave of these studies, which have the potential to discover the effects of common genetic variants on cellular phenotypes and to uncover the molecular basis of common genetic diseases. Here, we describe the recent advances in this developing field, and provide a road map for future in vitro functional population genetic studies and trial-in-a-dish experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Explaining differences in perceived health-related quality of life: a study within the Spanish population.

    Science.gov (United States)

    Martín-Fernández, Jesús; Ariza-Cardiel, Gloria; Polentinos-Castro, Elena; Sanz-Cuesta, Teresa; Sarria-Santamera, Antonio; Del Cura-González, Isabel

    2017-09-25

    To assess the burden of several determinants on health-related quality of life (HRQOL) and to study its heterogeneity among the different Spanish regions. Cross-sectional study. Data were obtained from the Spanish National Health Survey (2012), and HRQOL was measured using the EQ-5D-5L questionnaire (utility and visual analogue scale -VAS- scores). Demographic variables, physical health condition, social variables, mental health status, and lifestyle were also analysed. Tobit regression models were employed to study the relationships between expressed HRQOL and personal characteristics. A total of 20,979 surveys were obtained. Of them, 62.4% expressed a utility score of 1, corresponding to perfect health (95%CI: 61.8%-63.2%), and 54.2% showed VAS scores ≥80 (95%CI: 53.5%-54.9%). HRQOL was mainly described as a function of age, chronic limitation in daily activities, and mental health status. Belonging to a higher-class strata and physical activity were related to better self-perceived HRQOL. Ageing worsened perceived HRQOL, but did not influence its determinants, and differences in HRQOL by regions were also not significant after model adjustment. HRQOL perception in the Spanish population varied slightly depending on the measure used (utilities index or VAS). Age, chronic limitations in daily life, and mental health status best explained the variability in perception, and no meaningful differences in HRQOL perception among regions were found after adjustment. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

  1. Explaining the disability paradox: a cross-sectional analysis of the Swiss general population

    Directory of Open Access Journals (Sweden)

    Fellinghauer Bernd

    2012-08-01

    Full Text Available Abstract Background Disability can be broken down into difficulties in different components of functioning such as impairments and limitations in activities and participation (A&P. Previous studies have produced the seemingly surprising result that persons with severe impairments tend to report high quality of life (QoL including perceived health regardless of their condition; the so-called “disability paradox”. We aim to study the role of contextual factors (i.e. the personal and environmental situation in explaining the disability paradox. Methods The Swiss Health Survey provides information on the perceived health of 18,760 participants from the general population. We construct a conditional independence graph applying random forests and stability selection in order to represent the structure of impairment, A&P limitation, contextual factors, and perceived health. Results We find that impairment and A&P limitations are not directly related but only via a cluster of contextual factors. Similarly, impairment and perceived health are not directly related. On the other hand, perceived health is directly connected with A&P limitations. We hypothesize that contextual factors have a moderating and/or mediating effect on the relationship of impairment, A&P limitations, and perceived health. Conclusion The disability paradox seems to dissolve when contextual factors are put into consideration. Contextual factors may be responsible for some persons with impairments developing A&P limitations and others not. In turn, persons with impairments may only then perceive bad health when they experience A&P limitation. Political interventions at the level of the environment may reduce the number of persons who perceive bad health.

  2. Genetic diversity in populations of asexual and sexual bag worm moths (Lepidoptera: Psychidae

    Directory of Open Access Journals (Sweden)

    Mappes Johanna

    2005-06-01

    Full Text Available Abstract Background Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two strictly sexual (Dahlica charlottae and Siederia rupicolella and one strictly asexual (D. fennicella. These species compete for the same resources and share the same parasitoids. Results Allelic richness was comparable between the sexual species but it was higher than in the asexual species. All species showed high heterozygote deficiency and a large variation was observed among FIS values across loci and populations. Large genetic differentiation was observed between populations confirming the poor dispersal ability of these species. The asexual species showed lower genotype diversity than the sexual species. Nevertheless, genotype diversity was high in all asexual populations. Conclusion The three different species show a similar population structure characterised by high genetic differentiation among populations and low dispersal. Most of the populations showed high heterozygote deficiency likely due to the presence of null alleles at most of the loci and/or to the Wahlund effect. Although the parthenogenetic D. fennicella shows reduced genetic diversity compared to the sexual species, it still shows surprisingly high genotype diversity. While we can not totally rule out the presence of cryptic sex, would explain this high genotype diversity, we never observed sex in the parthenogenetic D. fennicella, nor was there any other evidence of this. Alternatively, a non-clonal parthenogenetic reproduction, such as automictic thelytoky, could explain the high genotypic diversity observed in D. fennicella.

  3. Genetic population structure of muskellunge in the Great Lakes

    Science.gov (United States)

    Kapuscinski, Kevin L.; Sloss, Brian L.; Farrell, John M.

    2013-01-01

    We quantified genetic relationships among Muskellunge Esox masquinongy from 15 locations in the Great Lakes to determine the extent and distribution of measurable population structure and to identify appropriate spatial scales for fishery management and genetic conservation. We hypothesized that Muskellunge from each area represented genetically distinct populations, which would be evident from analyses of genotype data. A total of 691 Muskellunge were sampled (n = 10–127/site) and genetic data were collected at 13 microsatellite loci. Results from a suite of analyses (including pairwise genetic differentiation, Bayesian admixture prediction, analysis of molecular variance, and tests of isolation by distance) indicated the presence of nine distinct genetic groups, including two that were approximately 50 km apart. Geographic proximity and low habitat complexity seemed to facilitate genetic similarity among areas, whereas Muskellunge from areas of greater habitat heterogeneity exhibited high differentiation. Muskellunge from most areas contained private alleles, and mean within-area genetic variation was similar to that reported for other freshwater fishes. Management programs aimed at conserving the broader diversity and long-term sustainability of Muskellunge could benefit by considering the genetically distinct groups as independent fisheries, and individual spawning and nursery habitats could subsequently be protected to conserve the evolutionary potential of Muskellunge.

  4. Genetic diversity and population history of the endangered killifish Aphanius baeticus.

    Science.gov (United States)

    Gonzalez, Elena G; Pedraza-Lara, Carlos; Doadrio, Ignacio

    2014-01-01

    The secondary freshwater fish fauna of the western-Iberian Peninsula basin is primarily restricted to local coastal streams, and man-made salt evaporation ponds, etc., which are susceptible to periodical flood and drought events. Despite its uniqueness in ecological adaptation to high saltwater tolerance, very little is known about this fauna's population dynamics and evolutionary history. The killifish, Aphanius baeticus (Cyprinodontidae) is an endemic species restricted to river basins on Spain's southern Atlantic coastline, considered as "Endangered." In this study, the genetic structure, diversity and historical demography of A. baeticus were analyzed using mitochondrial (cytochrome b, N=131) and nuclear (4 out of 19 microsatellites tested, N=288) markers across its distribution range. The phylogenetic and networking reconstruction revealed subtle phylogeographic structuring. A scattered expansion at the beginning of the interglacial periods, coupled with posterior events of extinction and colonization caused by periodical cycles of flooding, could explain the absence of well-defined phylogenetic relationships among populations. Moreover, very low genetic diversity values and a weak population differentiation were detected. We proposed that dispersals allowed by periodic floods connecting river drainages may have promoted a wide genetic exchange among populations and could have contributed to the current genetic relatedness of these populations. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. The heterogeneous HLA genetic makeup of the Swiss population.

    Science.gov (United States)

    Buhler, Stéphane; Nunes, José Manuel; Nicoloso, Grazia; Tiercy, Jean-Marie; Sanchez-Mazas, Alicia

    2012-01-01

    This study aims at investigating the HLA molecular variation across Switzerland in order to determine possible regional differences, which would be highly relevant to several purposes: optimizing donor recruitment strategies in hematopoietic stem cell transplantation (HSCT), providing reliable reference data in HLA and disease association studies, and understanding the population genetic background(s) of this culturally heterogeneous country. HLA molecular data of more than 20,000 HSCT donors from 9-13 recruitment centers of the whole country were analyzed. Allele and haplotype frequencies were estimated by using new computer tools adapted to the heterogeneity and ambiguity of the data. Non-parametric and resampling statistical tests were performed to assess Hardy-Weinberg equilibrium, selective neutrality and linkage disequilibrium among different loci, both in each recruitment center and in the whole national registry. Genetic variation was explored through genetic distance and hierarchical analysis of variance taking into account both geographic and linguistic subdivisions in Switzerland. The results indicate a heterogeneous genetic makeup of the Swiss population: first, allele frequencies estimated on the whole national registry strongly deviate from Hardy-Weinberg equilibrium, by contrast with the results obtained for individual centers; second, a pronounced differentiation is observed for Ticino, Graubünden, and, to a lesser extent, Wallis, suggesting that the Alps represent(ed) a barrier to gene flow; finally, although cultural (linguistic) boundaries do not represent a main genetic differentiation factor in Switzerland, the genetic relatedness between population from south-eastern Switzerland and Italy agrees with historical and linguistic data. Overall, this study justifies the maintenance of a decentralized donor recruitment structure in Switzerland allowing increasing the genetic diversity of the national--and hence global--donor registry. It also

  6. Genetic resources of teak (Tectona grandis Linn. f.)—strong genetic structure among natural populations

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Changtragoon, Suchitra; Ponoy, Bundit

    2015-01-01

    Twenty-nine provenances of teak (Tectona grandis Linn. f.) representing the full natural distribution range of the species were genotyped with microsatellite DNA markers to analyse genetic diversity and population genetic structure. Provenances originating from the semi-moist east coast of India...... had the highest genetic diversity while provenances from Laos showed the lowest. In the eastern part of the natural distribution area, comprising Myanmar, Thailand and Laos, there was a strong clinal decrease in genetic diversity the further east the provenance was located. Overall, the pattern...... of the findings for conservation and use of genetic resources of the species are discussed....

  7. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  8. Genetic diversity and population structure of Caragana microphylla ...

    African Journals Online (AJOL)

    Caragana microphylla Lam. is a long-lived shrub species in the semi-arid, arid and desert regions. To determine the genetic diversity and population structure of C. microphylla Lam., 17 wild populations from the central and eastern part of Inner Mongolia were analyzed by inter-simple sequence repeat. 18 primers produced ...

  9. Ecological and population genetics of locally rare plants: A review

    Science.gov (United States)

    Simon A. Lei

    2001-01-01

    Plant species with limited dispersal ability, narrow geographical and physiological tolerance ranges, as well as with specific habitat and ecological requirements are likely to be rare. Small and isolated populations and species contain low levels of within-population genetic variation in many plant species. The gene pool of plants is a product of phenotype-environment...

  10. Genetic diversity and population structure of blue-crested lizard ...

    Indian Academy of Sciences (India)

    Weerachai Saijuntha

    2017-06-19

    Jun 19, 2017 ... Abstract. The blue-crested lizard, Calotes mystaceus Duméril & Bibron, 1837, is listed as a protected wild animal in Thailand. Its population is likely to be dramatically reduced due to massive hunting in several areas in this country. Basic information on its population genetics is therefore needed to facilitate ...

  11. Comparative analysis of inter population genetic diversity in Puntius ...

    African Journals Online (AJOL)

    The genetic variation in different population of the freshwater cyprinid Puntius filamentosus was studied using restriction fragment length polymorphism (RFLP) analysis. Samples were collected from five different locations of southern Western Ghats, India. The morphometric characters of population from Alancholai showed ...

  12. Inter-populations genetic and morphological diversity in three Silene ...

    African Journals Online (AJOL)

    The inter-populations morphological and genetic variations were studied in three species of Silene (Silene indeprensa, Silene gynodioica and Silene crispans) of the section Auriculatae, which grow and form several populations in different regions of Iran. Morphological analysis of variance (ANOVA) and analysis of ...

  13. Genetic diversity of Tamarindus indica populations: Any clues on the ...

    African Journals Online (AJOL)

    We have studied 10 populations using markers RAPDs with the seeds collected from Asia (India and Thailand), Africa (Burkina Faso, Senegal, Kenya and Tanzania), from three islands (Madagascar, Réunion and Guadeloupe). The results showed that T. indica has a high intra population genetic variability with a higher ...

  14. Effective population size and genetic conservation criteria for bull trout

    Science.gov (United States)

    Bruce E. Rieman; F. W. Allendorf

    2001-01-01

    Effective population size (Ne) is an important concept in the management of threatened species like bull trout Salvelinus confluentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively....

  15. Geographical distance and local environmental conditions drive the genetic population structure of a freshwater microalga (Bathycoccaceae; Chlorophyta) in Patagonian lakes.

    Science.gov (United States)

    Fernández, Leonardo D; Hernández, Cristián E; Schiaffino, M Romina; Izaguirre, Irina; Lara, Enrique

    2017-10-01

    The patterns and mechanisms underlying the genetic structure of microbial populations remain unresolved. Herein we investigated the role played by two non-mutually exclusive models (i.e. isolation by distance and isolation by environment) in shaping the genetic structure of lacustrine populations of a microalga (a freshwater Bathycoccaceae) in the Argentinean Patagonia. To our knowledge, this was the first study to investigate the genetic population structure in a South American microorganism. Population-level analyses based on ITS1-5.8S-ITS2 sequences revealed high levels of nucleotide and haplotype diversity within and among populations. Fixation index and a spatially explicit Bayesian analysis confirmed the occurrence of genetically distinct microalga populations in Patagonia. Isolation by distance and isolation by environment accounted for 38.5% and 17.7% of the genetic structure observed, respectively, whereas together these models accounted for 41% of the genetic differentiation. While our results highlighted isolation by distance and isolation by environment as important mechanisms in driving the genetic population structure of the microalga studied, none of these models (either alone or together) could explain the entire genetic differentiation observed. The unexplained variation in the genetic differentiation observed could be the result of founder events combined with rapid local adaptations, as proposed by the monopolisation hypothesis. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Within-population genetic structure in beech (Fagus sylvatica L.) stands characterized by different disturbance histories: does forest management simplify population substructure?

    Science.gov (United States)

    Piotti, Andrea; Leonardi, Stefano; Heuertz, Myriam; Buiteveld, Joukje; Geburek, Thomas; Gerber, Sophie; Kramer, Koen; Vettori, Cristina; Vendramin, Giovanni Giuseppe

    2013-01-01

    The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L.) plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs). Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θ ST ranged from 0.025 to 0.124). The proportion of within-population genetic variation due to genetic substructuring (F CluPlot = 0.067) was higher than the differentiation among the 10 plots (F PlotTot = 0.045). Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i) genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii) indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.

  17. Within-population genetic structure in beech (Fagus sylvatica L. stands characterized by different disturbance histories: does forest management simplify population substructure?

    Directory of Open Access Journals (Sweden)

    Andrea Piotti

    Full Text Available The fine-scale assessment of both spatially and non-spatially distributed genetic variation is crucial to preserve forest genetic resources through appropriate forest management. Cryptic within-population genetic structure may be more common than previously thought in forest tree populations, which has strong implications for the potential of forests to adapt to environmental change. The present study was aimed at comparing within-population genetic structure in European beech (Fagus sylvatica L. plots experiencing different disturbance levels. Five plot pairs made up by disturbed and undisturbed plots having the same biogeographic history were sampled throughout Europe. Overall, 1298 individuals were analyzed using four highly polymorphic nuclear microsatellite markers (SSRs. Bayesian clustering within plots identified 3 to 11 genetic clusters (within-plot θ ST ranged from 0.025 to 0.124. The proportion of within-population genetic variation due to genetic substructuring (F CluPlot = 0.067 was higher than the differentiation among the 10 plots (F PlotTot = 0.045. Focusing on the comparison between managed and unmanaged plots, disturbance mostly explains differences in the complexity of within-population genetic structure, determining a reduction of the number of genetic clusters present in a standardized area. Our results show that: i genetic substructuring needs to be investigated when studying the within-population genetic structure in forest tree populations, and ii indices describing subtle characteristics of the within-population genetic structure are good candidates for providing early signals of the consequences of forest management, and of disturbance events in general.

  18. [Study on Genetic Diversity of Twelve Natural Zanthoxylum dissitum Populations].

    Science.gov (United States)

    Li, Meng; Wang, Ping; Sun, Ji-kang; Zhou, Tao; Fe, Ming-liang

    2014-12-01

    The genetic diversity of twelve natural Zanthoxylum dissitum populations, which is a species of Chinese herbal medicines to four provinces of southwest China, has been investigated. By inter-simple sequence repeat markers (ISSR), the eight primers, which could amplify stable, clear and highly polymorphic bands, were screened from 100 candidate primers. 150 total ISSR discernible bands and 147 polymorphic were amplified by the eight checked primers. On one hand, the percentage of polymorphic bands was 98.0%, on the other hand, the population level the percent of polymorphic bands ranged from 26.0% to 62.0%. The Shannon's information index within species (Hsp) was 0.4175, while the values within population (Hpop) were ranged from 0.1328 to 0.3267. Analysis of molecular variance (ANOVA) revealed that the population genetic variation accounted for 47.98% but the intraspecific variation for 52.02%. The high level of genetic diversity exists not only in population but also in species. A high degree of genetic differentiation populations is approved to exist in Zanthoxylum dissitum. These results lay a theoretical foundation for genetic diversity analysis of Zanthoxylum dissitum.

  19. Unravelling parasitic nematode natural history using population genetics.

    Science.gov (United States)

    Gilabert, Aude; Wasmuth, James D

    2013-09-01

    The health and economic importance of parasitic nematodes cannot be overstated. Moreover, they offer a complex and diverse array of life strategies, raising a multitude of evolutionary questions. Researchers are applying population genetics to parasitic nematodes in order to disentangle some aspects of their life strategies, improve our knowledge about disease epidemiology, and design control strategies. However, population genetics studies of nematodes have been constrained due to the difficulty in sampling nematodes and developing molecular markers. In this context, new computational and sequencing technologies represent promising tools to investigate population genomics of parasitic, non-model, nematode species in an epidemiological context. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Global Population Genetic Analysis of Aspergillus fumigatus

    NARCIS (Netherlands)

    Ashu, E.E.; Hagen, F.; Chowdhary, A.; Meis, J.F.G.M.; Xu, J.

    2017-01-01

    Aspergillus fumigatus is a ubiquitous opportunistic fungal pathogen capable of causing invasive aspergillosis, a globally distributed disease with a mortality rate of up to 90% in high-risk populations. Effective control and prevention of this disease require a thorough understanding of its

  1. Population genetic structure analysis in endangered Hordeum ...

    African Journals Online (AJOL)

    Inbreeding index, gene flow values and cluster analysis revealed also significant differentiation between all populations. Gene flow decreased rapidly as the geographic distance increased. This may imply that seed exchange between farmers was limited to a regional scale. The lower correlation between the Euclidean ...

  2. GABAergic synapse properties may explain genetic variation in hippocampal network oscillations in mice

    Directory of Open Access Journals (Sweden)

    Tim S Heistek

    2010-06-01

    Full Text Available Cognitive ability and the properties of brain oscillation are highly heritable in humans. Genetic variation underlying oscillatory activity might give rise to differences in cognition and behavior. How genetic diversity translates into altered properties of oscillations and synchronization of neuronal activity is unknown. To address this issue, we investigated cellular and synaptic mechanisms of hippocampal fast network oscillations in eight genetically distinct inbred mouse strains. The frequency of carbachol-induced oscillations differed substantially between mouse strains. Since GABAergic inhibition sets oscillation frequency, we studied the properties of inhibitory synaptic inputs (IPSCs received by CA3 and CA1 pyramidal cells of three mouse strains that showed the highest, lowest and intermediate frequencies of oscillations. In CA3 pyramidal cells, the frequency of rhythmic IPSC input showed the same strain differences as the frequency of field oscillations. Furthermore, IPSC decay times in both CA1 and CA3 pyramidal cells were faster in mouse strains with higher oscillation frequencies than in mouse strains with lower oscillation frequency, suggesting that differences in GABAA-receptor subunit composition exist between these strains. Indeed, gene expression of GABAA-receptor β2 (Gabrb2 and β3 (Gabrb2 subunits was higher in mouse strains with faster decay kinetics compared with mouse strains with slower decay kinetics. Hippocampal pyramidal neurons in mouse strains with higher oscillation frequencies and faster decay kinetics fired action potential at higher frequencies. These data indicate that differences in genetic background may result in different GABAA-receptor subunit expression, which affects the rhythm of pyramidal neuron firing and fast network activity through GABA synapse kinetics.

  3. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong

    2013-01-01

    Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese......) to 17 (ETH185). The level of gene diversity was high indicated by a mean expected heterozygosity (He) across populations and loci of 0.73. Level of inbreeding (mean FIS=0.05) and genetic differentiation (mean FST=0.04) was moderate. The phylogenetic tree based on Reynolds genetic distance reflected...... of genetic diversity and distinct genetic structures. Based on these results, we recommend that for conservation homogenous populations (Nghe An, Thanh Hoa and Phu Yen) can be grouped to reduce costs and U Dau Riu, Lang Son and Ha Giang populations should be conserved separately to avoid loss of genetic...

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

    Directory of Open Access Journals (Sweden)

    Uriz Maria J

    2010-01-01

    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.

  5. Genetic mixture of multiple source populations accelerates invasive range expansion.

    Science.gov (United States)

    Wagner, Natalie K; Ochocki, Brad M; Crawford, Kerri M; Compagnoni, Aldo; Miller, Tom E X

    2017-01-01

    A wealth of population genetic studies have documented that many successful biological invasions stem from multiple introductions from genetically distinct source populations. Yet, mechanistic understanding of whether and how genetic mixture promotes invasiveness has lagged behind documentation that such mixture commonly occurs. We conducted a laboratory experiment to test the influence of genetic mixture on the velocity of invasive range expansion. The mechanistic basis for effects of genetic mixture could include evolutionary responses (mixed invasions may harbour greater genetic diversity and thus elevated evolutionary potential) and/or fitness advantages of between-population mating (heterosis). If driven by evolution, positive effects of source population mixture should increase through time, as selection sculpts genetic variation. If driven by heterosis, effects of mixture should peak following first reproductive contact and then dissipate. Using a laboratory model system (beetles spreading through artificial landscapes), we quantified the velocity of range expansion for invasions initiated with one, two, four or six genetic sources over six generations. Our experiment was designed to test predictions corresponding to the evolutionary and heterosis mechanisms, asking whether any effects of genetic mixture occurred in early or later generations of range expansion. We also quantified demography and dispersal for each experimental treatment, since any effects of mixture should be manifest in one or both of these traits. Over six generations, invasions with any amount of genetic mixture (two, four and six sources) spread farther than single-source invasions. Our data suggest that heterosis provided a 'catapult effect', leaving a lasting signature on range expansion even though the benefits of outcrossing were transient. Individual-level trait data indicated that genetic mixture had positive effects on local demography (reduced extinction risk and enhanced

  6. Population genetic structure in natural and reintroduced beaver (Castor fiber populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Kautenburger, R.

    2008-12-01

    Full Text Available Castor fiber Linnaeus, 1758 is the only indigenous species of the genus Castor in Europe and Asia. Due to extensive hunting until the beginning of the 20th century, the distribution of the formerly widespread Eurasian beaver was dramatically reduced. Only a few populations remained and these were in isolated locations, such as the region of the German Elbe River. The loss of genetic diversity in small or captive populations throughgenetic drift and inbreeding is a severe conservation problem. However, the reintroduction of beaver populations from several regions in Europe has shown high viability and populations today are growing fast. In the present study we analysed the population genetic structure of a natural and two reintroduced beaver populations in Germany and Austria. Furthermore, we studied the genetic differentiation between two beaver species, C. fiber and the American beaver (C. canadensis, using RAPD (Random Amplified Polymorphic DNA as a genetic marker. The reintroduced beaver populations of different origins and the autochthonous population of the Elbe River showed a similar low genetic heterogeneity. There was an overall high genetic similarity in the species C. fiber, and no evidence was found for a clear subspecific structure in the populations studied.

  7. Genetic analysis in the Collaborative Cross breeding population

    Energy Technology Data Exchange (ETDEWEB)

    Philip, Vivek [University of Tennessee, Knoxville (UTK); Sokoloff, Greta [ORNL; Ackert-Bicknell, Cheryl [Jackson Laboratory, The, Bar Harbor, ME; Striz, Martin [University of Kentucky, Lexington; Branstetter, Lisa R [ORNL; Beckmann, Melissa [ORNL; Spence, Jason S [ORNL; Jackson, Barbara L [ORNL; Galloway, Leslie D [ORNL; Barker, Gene [ORNL; Wymore, Ann M [Oak Ridge National Laboratory (ORNL); Hunsicker, Patricia R [ORNL; Durtschi, David W [University of Kentucky, Lexington; Shaw, Ginger S [University of Kentucky, Lexington; Shinpock, Sarah G [ORNL; Manly, Kenneth F [University of Kentucky, Lexington; Miller, Darla R [ORNL; Donahue, Kevin [University at Buffalo, NY; Culiat, Cymbeline T [ORNL; Churchill, Gary A [Jackson Laboratory, The, Bar Harbor, ME; Lariviere, William R [University of Pittsburgh; Palmer, Abraham [University of Chicago; O' Hara, Bruce [University of Kentucky; Voy, Brynn H [ORNL; Chesler, Elissa J [ORNL

    2011-01-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations. Supplementary material consists of Supplementary Table 1 Phenotypic means, variances, ranges and heritabilities for all traits and generations, Supplementary Table

  8. Smaller genetic risk in catabolic process explains lower energy expenditure, more athletic capability and higher prevalence of obesity in Africans.

    Directory of Open Access Journals (Sweden)

    Cheng Xue

    Full Text Available Lower energy expenditure (EE for physical activity was observed in Africans than in Europeans, which might contribute to the higher prevalence of obesity and more athletic capability in Africans. But it is still unclear why EE is lower among African populations. In this study we tried to explore the genetic mechanism underlying lower EE in Africans. We screened 231 common variants with possibly harmful impact on 182 genes in the catabolic process. The genetic risk, including the total number of mutations and the sum of harmful probabilities, was calculated and analyzed for the screened variants at a population level. Results of the genetic risk among human groups showed that most Africans (3 out of 4 groups had a significantly smaller genetic risk in the catabolic process than Europeans and Asians, which might result in higher efficiency of generating energy among Africans. In sport competitions, athletes need massive amounts of energy expenditure in a short period of time, so higher efficiency of energy generation might help make African-descendent athletes more powerful. On the other hand, higher efficiency of generating energy might also result in consuming smaller volumes of body mass. As a result, Africans might be more vulnerable to obesity compared to the other races when under the same or similar conditions. Therefore, the smaller genetic risk in the catabolic process might be at the core of understanding lower EE, more athletic capability and higher prevalence of obesity in Africans.

  9. Genetic concepts and uncertainties in restoring fish populations and species

    Science.gov (United States)

    Reisenbichler, R.R.; Utter, F.M.; Krueger, C.C.

    2003-01-01

    Genetic considerations can be crucially important to the success of reintroductions of lotic species. Current paradigms for conservation and population genetics provide guidance for reducing uncertainties in genetic issues and for increasing the likelihood of achieving restoration. Effective restoration is facilitated through specific goals and objectives developed from the definition that a restored or healthy population is (i) genetically adapted to the local environment, (ii) self-sustaining at abundances consistent with the carrying capacity of the river system, (iii) genetically compatible with neighboring populations so that substantial outbreeding depression does not result from straying and interbreeding between populations, and (iv) sufficiently diverse genetically to accommodate environmental variability over many decades. Genetic principles reveal the importance of describing and adhering to the ancestral lineages for the species to be restored and enabling genetic processes to maintain diversity and fitness in the populations under restoration. Newly established populations should be protected from unnecessary human sources of mortality, gene flow from maladapted (e.g., hatchery) or exotic populations, and inadvertent selection by fisheries or other human activities. Such protection facilitates initial, rapid adaptation of the population to its environment and should enhance the chances for persistence. Various uncertainties about specific restoration actions must be addressed on a case-by-case basis. Such uncertainties include whether to allow natural colonization or to introduce fish, which populations are suitable as sources for reintroduction, appropriate levels of gene flow from other populations, appropriate levels of artificial production, appropriate minimum numbers of individuals released or maintained in the population, and the best developmental stages for releasing fish into the restored stream. Rigorous evaluation or

  10. Population connectivity buffers genetic diversity loss in a seabird.

    Science.gov (United States)

    Ramírez, Oscar; Gómez-Díaz, Elena; Olalde, Iñigo; Illera, Juan Carlos; Rando, Juan Carlos; González-Solís, Jacob; Lalueza-Fox, Carles

    2013-05-20

    Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems' threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory's shearwater (Calonectris borealis). We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

  11. Genetic diversity in Chilean populations of rainbow trout, Oncorhynchus mykiss

    Directory of Open Access Journals (Sweden)

    Claudia B Cárcamo

    2015-03-01

    Full Text Available The rainbow trout Oncorhynchus mykiss, was first introduced in Chile between 1905 and 1920 and is currently widely distributed in Chile from Antofagasta (23°S to Patagonia (55°S. The broad range of the geographic and climatic distributions of this species in Chile offers a unique opportunity to study the effect of naturalization of an introduced species on its genetic variability. It is of particular importance to observe the genetic variability of populations in the northern range of this species distribution, in a transition zone where a Mediterranean-type climate changes to an arid climate. The present study analyzed allozymic variability and distribution within and between populations of O. mykiss from the river basins of Elqui and Limari rivers, and six culture strains, using starch-gel protein electrophoresis. Populations were found to be in Hardy-Weinberg equilibrium and the average values of He (0.045, polymorphism (13.9% and allele per locus (1.19 are similar to rainbow trout in its native distributional range. About 77.8% of the genetic variability was within population, similar to the variability reported for wild populations in the northern hemisphere. However, a marked genetic differentiation between wild populations was also found. This is likely to be the consequence of initial founder effects followed by subsequent introgression of resident populations caused by reseeding with trout of different origins in both basins.

  12. Population genetic analysis of Colombian Trypanosoma cruzi isolates revealed by enzyme electrophoretic profiles

    Directory of Open Access Journals (Sweden)

    Manuel Ruiz-Garcia

    2001-01-01

    Full Text Available Although Colombia presents an enormous biological diversity, few studies have been conducted on the population genetics of Trypanosoma cruzi. This study was carried out with 23 Colombian stocks of this protozoa analyzed for 13 isoenzymatic loci. The Hardy-Weinberg equilibrium, the genetic diversity and heterogeneity, the genetic relationships and the possible spatial structure of these 23 Colombian stocks of T. cruzi were estimated. The majority of results obtained are in agreement with a clonal population structure. Nevertheless, two aspects expected in a clonal structure were not discovered in the Colombian T. cruzi stocks. There was an absence of given zymodemes over-represented from a geographical point of view and the presumed temporal stabilizing selective phenomena was not observed either in the Colombian stocks sampled several times through the years of the study. Some hypotheses are discussed in order to explain the results found.

  13. Common variants explain a large fraction of the variability in the liability to psoriasis in a Han Chinese population

    OpenAIRE

    Yin, Xianyong; Wineinger, Nathan E; Cheng, Hui; Cui, Yong; Zhou, Fusheng; Zuo, Xianbo; Zheng, Xiaodong; Yang, Sen; Schork, Nicholas J; Zhang, Xuejun

    2014-01-01

    Background Psoriasis is a common inflammatory skin disease with a known genetic component. Our previously published psoriasis genome-wide association study identified dozens of novel susceptibility loci in Han Chinese. However, these markers explained only a small fraction of the estimated heritable component of psoriasis. To better understand the unknown yet likely polygenic architecture in psoriasis, we applied a linear mixed model to quantify the variation in the liability to psoriasis exp...

  14. Genetic Diversity among Ancient Nordic Populations

    Science.gov (United States)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R.; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  15. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13% than among extant Danes and Scandinavians (approximately 2.5% as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  16. Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore.

    Directory of Open Access Journals (Sweden)

    Małgorzata Pilot

    Full Text Available Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ(13C and δ(15N values for Eastern European wolves (Canis lupus as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure, to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.

  17. Population status and population genetics of northern leopard frogs in Arizona

    Science.gov (United States)

    Theimer, Tad C.; Drost, Charles A.; O'Donnell, Ryan P.; Mock, Karen E.

    2011-01-01

    Increasing isolation of populations by habitat fragmentation threatens the persistence of many species, both from stochastic loss of small isolated populations, and from inbreeding effects in populations that have become genetically isolated. In the southwestern United States, amphibian habitat is naturally patchy in occurrence because of the prevailing aridity of the region. Streams, rivers, and other wetlands are important both as habitat and as corridors that connect populations. However, populations of some species have become more fragmented and isolated by habitat degradation and loss. Northern leopard frogs (Rana pipiens) have experienced serious declines in the Southwest. We conducted an extensive survey across the known range of northern leopard frogs in Arizona to determine the current distribution and abundance of the species. From a range that once spanned much of the northern and central part of the State, northern leopard frogs have been reduced to three or four widely separated populations, near Lyman Lake in east-central Arizona, in the Stoneman Lake area south of Flagstaff, along Truxton Wash near Peach Springs, and a population of uncertain extent on Navajo Nation lands. The Lyman Lake and Truxton Wash populations are small and extremely isolated. The Stoneman Lake population, however, is an extensive metapopulation spread across several stream drainages, including numerous ponds, wetlands, and artificial tanks. This is the only population in Arizona that is increasing in extent and numbers, but there is concern about the apparent introduction of nonnative genetic stock from eastern North America into this area. We analyzed genetic diversity within and genetic divergence among populations of northern leopard frogs, across both extant and recently extirpated populations in Arizona. We also analyzed mitochondrial DNA to place these populations into a larger phylogenetic framework and to determine whether any populations contained genetic material

  18. Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh

    Directory of Open Access Journals (Sweden)

    Borkar Minal

    2007-04-01

    Full Text Available Abstract Background India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp. It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. Results We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119 as compared to the Asians (DA 0.1694 and Fst – 0.0718. The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20

  19. gPGA: GPU Accelerated Population Genetics Analyses.

    Directory of Open Access Journals (Sweden)

    Chunbao Zhou

    Full Text Available The isolation with migration (IM model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC simulations of gene genealogies. But computational burden of IM program has placed limits on its application.With strong computational power, Graphics Processing Unit (GPU has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA, which we call gPGA.Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.

  20. Quasispecies theory in the context of population genetics

    Directory of Open Access Journals (Sweden)

    Wilke Claus O

    2005-08-01

    Full Text Available Abstract Background A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory. Results I review the pertinent literature, and demonstrate for a number of cases that the quasispecies concept is equivalent to the concept of mutation-selection balance developed in population genetics, and that there is no disagreement between the population genetics of haploid, asexually-replicating organisms and quasispecies theory. Conclusion Since quasispecies theory and mutation-selection balance are two sides of the same medal, the discussion about which is more appropriate to describe virus evolution is moot. In future work on virus evolution, we would do good to focus on the important questions, such as whether we can develop accurate, quantitative models of virus evolution, and to leave aside discussions about the relative merits of perfectly equivalent concepts.

  1. Primer in Genetics and Genomics, Article 3-Explaining Human Diversity: The Role of DNA.

    Science.gov (United States)

    Read, Catherine Y

    2017-05-01

    Genetic variation lays the foundation for diversity and enables humans to adapt to changing environments. The order of the nucleotides adenine, guanine, cytosine, and thymine on the deoxyribonucleic acid (DNA) molecules of the nuclear chromosomes and mitochondrial DNA (mtDNA) plays an important role in normal cell division, tissue development, and reproduction but is susceptible to alteration from a large number of random, inherited, or environmental events. Variations can range from a change in a single nucleotide to duplication of entire chromosomes. Single nucleotide polymorphisms are the major source of human heterogeneity. Other variations that can alter phenotypes and adversely impact growth, development, and health include copy number variations, aneuploidies, and structural alterations such as deletions, translocations, inversions, duplications, insertions, or mutations in mtDNA. In addition, DNA rearrangements in somatic cells underlie the uncontrolled cell growth found in cancer. This article explores the mechanisms by which variations in DNA arise and the impact those changes can have on human health.

  2. Population history and its impact on medical genetics in Quebec.

    Science.gov (United States)

    Laberge, A-M; Michaud, J; Richter, A; Lemyre, E; Lambert, M; Brais, B; Mitchell, G A

    2005-10-01

    Knowledge of the genetic demography of Quebec is useful for gene mapping, diagnosis, treatment, community genetics and public health. The French-Canadian population of Quebec, currently about 6 million people, descends from about 8500 French settlers who arrived in Nouvelle-France between 1608 and 1759. The migrations of those settlers and their descendants led to a series of regional founder effects, reflected in the geographical distribution of genetic diseases in Quebec. This review describes elements of population history and clinical genetics pertinent to the treatment of French Canadians and other population groups from Quebec and summarizes the cardinal features of over 30 conditions reported in French Canadians. Some were discovered in French Canadians, such as autosomal recessive ataxia of the Charlevoix-Saguenay (MIM 270550), agenesis of corpus callosum and peripheral neuropathy (MIM 218000) and French-Canadian-type Leigh syndrome (MIM 220111). Other conditions are particularly frequent or have special genetic characteristics in French Canadians, including oculopharyngeal muscular dystrophy, hepatorenal tyrosinaemia, cystic fibrosis, Leber hereditary optic neuropathy and familial hypercholesterolaemia. Three genetic diseases of Quebec First Nations children are also discussed: Cree encephalitis (MIM 608505), Cree leukoencephalopathy (MIM 603896) and North American Indian childhood cirrhosis (MIM 604901).

  3. Emergent patterns of population genetic structure for a coral reef community.

    Science.gov (United States)

    Selkoe, Kimberly A; Gaggiotti, Oscar E; Bowen, Brian W; Toonen, Robert J

    2014-06-01

    What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R2=0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global FST (adjusted R2=0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species-specific abundance and migration patterns and/or seascape and historical factors. © 2014 John Wiley & Sons Ltd.

  4. The genetic consequences of selection in natural populations.

    Science.gov (United States)

    Thurman, Timothy J; Barrett, Rowan D H

    2016-04-01

    The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research. © 2016 John Wiley & Sons Ltd.

  5. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Science.gov (United States)

    Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

  6. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  7. [Study on the maximum entropy principle and population genetic equilibrium].

    Science.gov (United States)

    Zhang, Hong-Li; Zhang, Hong-Yan

    2006-03-01

    A general mathematic model of population genetic equilibrium about one locus was constructed based on the maximum entropy principle by WANG Xiao-Long et al. They proved that the maximum solve of the model was just the frequency distribution that a population reached Hardy-Weinberg genetic equilibrium. It can suggest that a population reached Hardy-Weinberg genetic equilibrium when the genotype entropy of the population reached the maximal possible value, and that the frequency distribution of the maximum entropy was equivalent to the distribution of Hardy-Weinberg equilibrium law about one locus. They further assumed that the frequency distribution of the maximum entropy was equivalent to all genetic equilibrium distributions. This is incorrect, however. The frequency distribution of the maximum entropy was only equivalent to the distribution of Hardy-Weinberg equilibrium with respect to one locus or several limited loci. The case with regard to limited loci was proved in this paper. Finally we also discussed an example where the maximum entropy principle was not the equivalent of other genetic equilibria.

  8. Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe

    DEFF Research Database (Denmark)

    Mucci, Nadia; Arrendal, Johanna; Ansorge, Hermann

    2010-01-01

    and landscape genetic analyses however indicate that local populations are genetically differentiated, perhaps as consequence of post-glacial demographic fluctuations and recent isolation. These results delineate a framework that should be used for implementing conservation programs in Europe, particularly......, should rely on sound knowledge of the historical or recent consequences of population genetic structuring. Here we present the results of a survey performed on 616 samples, collected from 19 European countries, genotyped at the mtDNA control-region and 11 autosomal microsatellites. The mtDNA variability...

  9. Unexpectedly high genetic diversity and divergence among populations of the apomictic Neotropical tree Miconia albicans.

    Science.gov (United States)

    Dias, A C C; Serra, A C; Sampaio, D S; Borba, E L; Bonetti, A M; Oliveira, P E

    2017-10-25

    Since tropical trees often have long generation times and relatively small reproductive populations, breeding systems and genetic variation are important for population viability and have consequences for conservation. Miconia albicans is an obligate, diplosporous, apomictic species widespread in the Brazilian Cerrado, the savanna areas in central Brazil and elsewhere in the Neotropics. The genetic variability would be, theoretically, low within these male-sterile and possibly clonal populations, although some variation would be expected due to recombination during restitutional meiosis. We used ISSR markers to assess genetic diversity of M. albicans and to compare with other tropical trees, including invasive species of Melastomataceae. A total of 120 individuals from six populations were analysed using ten ISSR primers, which produced 153 fully reproducible fragments. The populations of M. albicans presented mean Shannon's information index (I) of 0.244 and expected heterozygosity (H e ) of 0.168. Only two pairs of apparently clonal trees were identified, and genetic diversity was relatively high. A hierarchical amova for all ISSR datasets showed that 74% of the variance was found among populations, while only 26% of the variance was found within populations of this species. Multivariate and Bayesian analyses indicated marked separation between the studied populations. The genetic diversity generated by restitutional meiosis, polyploidy and possibly other genome changes may explain the morpho-physiological plasticity and the ability of these plants to differentiate and occupy such a wide territory and different environmental conditions. Producing enormous amounts of bird-dispersed fruits, M. albicans possess weedy potential that may rival other Melastomataceae alien invaders. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  10. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Directory of Open Access Journals (Sweden)

    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  11. Can behavioural differences in Platypus cylindrus (Coleoptera: Platypodinae) from Portugal and Tunisia be explained by genetic and morphological traits?

    Science.gov (United States)

    Bellahirech, A; Inácio, M L; Nóbrega, F; Henriques, J; Bonifácio, L; Sousa, E; Ben Jamâa, M L

    2016-02-01

    Platypus cylindrus is an important wood borer of cork oak trees (Quercus suber) in the Mediterranean region, namely Portugal, Morocco and Algeria where its presence has drastically increased in the past few decades. On the contrary, the insect is not a relevant pest in Tunisia. The aim of this work is to analyze morphological and genetic differences among Tunisian and Portuguese populations in order to understand their role in the diverse population dynamics (e.g., aggressiveness) of the insect. The information could be used as a novel tool to implement protective measures. Insects were collected from cork oak stands in Tunisia (Ain Beya, Babouch and Mzara) and Portugal (Chamusca and Crato). Morphological traits of female and male mycangial pits were determined, using scanning electron microscopy but no significant differences were found. Genetic differences were analyzed using nuclear (internal simple sequence repeat polymerase chain reaction) and mitochondrial (cytochrome oxidase I (COI)) molecular markers. The results showed a very low level of intraspecific polymorphism and genetic diversity. The alignment of COI sequences showed high percentage of identical sites (99%) indicating a very low variation in nucleotide composition. Other variables related with the ecology of the insect and its associated fungi must be studied for a better understanding of the differences in the insect population's dynamic in Mediterranean countries.

  12. Habitat type predicts genetic population differentiation in freshwater invertebrates.

    Science.gov (United States)

    Marten, Andreas; Brändle, Martin; Brandl, Roland

    2006-08-01

    A basic challenge in evolutionary biology is to establish links between ecology and evolution of species. One important link is the habitat template. It has been hypothesized, that the spatial and temporal settings of a habitat strongly influence the evolution of species dispersal propensity. Here, we evaluate the importance of the habitat type on genetic population differentiation of species using freshwater habitats as a model system. Freshwater habitats are either lentic (standing) or lotic (running). On average, lotic habitats are more stable and predictable over space and time than lentic habitats. Therefore, lentic habitats should favour the evolution of higher dispersal propensity which ensures population survival of lentic species. To test for such a relationship, we used extensive data on species' genetic population differentiation of lentic and lotic freshwater invertebrates retrieved from published allozyme studies. Overall, we analysed more than 150 species from all over the world. Controlling for several experimental, biological and geographical confounding effects, we always found that lentic invertebrates exhibit, on average, lower genetic population differentiation than lotic species. This pattern was consistent across insects, crustaceans and molluscs. Our results imply fundamental differences in genetic population differentiation among species adapted to either lentic or lotic habitats. We propose that such differences should occur in a number of other habitat types that differ in spatio-temporal stability. Furthermore, our results highlight the important role of lotic habitats as reservoirs for evolutionary processes and the potential for rapid speciation.

  13. Phenotypic divergence despite low genetic differentiation in house sparrow populations.

    Science.gov (United States)

    Ben Cohen, Shachar; Dor, Roi

    2018-01-10

    Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST) was lower in comparison to phenotypic variation (P ST), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.

  14. Enclaves of genetic diversity resisted Inca impacts on population history.

    Science.gov (United States)

    Barbieri, Chiara; Sandoval, José R; Valqui, Jairo; Shimelman, Aviva; Ziemendorff, Stefan; Schröder, Roland; Geppert, Maria; Roewer, Lutz; Gray, Russell; Stoneking, Mark; Fujita, Ricardo; Heggarty, Paul

    2017-12-12

    The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

  15. [Genetic polymorphisms of 19 STR loci in Shandong Han population].

    Science.gov (United States)

    Zhang, Mao-Xiui; Han, Shu-Yi; Gao, Hong-Mei; Sun, Shan-Hui; Xiao, Dong-Jie; Liu, Yang; Wang, Yun-Shan

    2013-12-01

    To investigate the genetic polymorphisms of 19 STR Loci in Shandong Han population in order to provide the genetic data for paternity testing. The genotypes of 205 unrelated individuals in Shandong Han population were typed by Goldeneye 20A kit to get the allele frequencies and population genetic parameters of 19 STR loci. Four kits, Identifiler kit, SinoFiler kit, PowerPlex 16 kit, and Goldeneye 20A kit, were compared with each other and used in the analysis of a special paternity test case. The population genetic parameters of 19 STR loci in Shandong Han Population were obtained. The cumulative discrimination power (CDP) and cumulative probability of exclusion (CPE) ranked from high to low were Goldeneye 20A kit, SinoFiler kit, PowerPlex 16 kit and Identifiler kit, respectively. As duo case, the result of the real case showed that Identifiler kit had no excluding loci, and none of the SinoFiler kit, PowerPlex 16 kit or Goldeneye 20A kit could exclude fatherhood. Compared with Identifiler kit, SinoFiler kit, and PowerPlex 16 kit, Goldeneye 20A kit shows the higher efficiency than the others, but is not completely satisfied for duo cases.

  16. The ecology of population dispersal: Modeling alternative basin-plateau foraging strategies to explain the Numic expansion.

    Science.gov (United States)

    Magargal, Kate E; Parker, Ashley K; Vernon, Kenneth Blake; Rath, Will; Codding, Brian F

    2017-07-08

    The expansion of Numic speaking populations into the Great Basin required individuals to adapt to a relatively unproductive landscape. Researchers have proposed numerous social and subsistence strategies to explain how and why these settlers were able to replace any established populations, including private property and intensive plant processing. Here we evaluate these hypotheses and propose a new strategy involving the use of landscape fire to increase resource encounter rates. Implementing a novel, spatially explicit, multi-scalar prey choice model, we examine how individual decisions approximating each alternative strategy (private property, anthropogenic fire, and intensive plant processing) would aggregate at the patch and band level to confer an overall benefit to this colonizing population. Analysis relies on experimental data reporting resource profitability and abundance, ecological data on the historic distribution of vegetation patches, and ethnohistoric data on the distribution of Numic bands. Model results show that while resource privatization and landscape fires produce a substantial advantage, intensified plant processing garners the greatest benefit. The relative benefits of alternative strategies vary significantly across ecological patches resulting in variation across ethnographic band ranges. Combined, a Numic strategy including all three alternatives would substantially increase subsistence yields. The application of a strategy set that includes landscape fire, privatization and intensified processing of seeds and nuts, explains why the Numa were able to outcompete local populations. This approach provides a framework to help explain how individual decisions can result in such population replacement events throughout human history. © 2017 Wiley Periodicals, Inc.

  17. Population genetic correlates of declining transmission in a human pathogen.

    Science.gov (United States)

    Nkhoma, Standwell C; Nair, Shalini; Al-Saai, Salma; Ashley, Elizabeth; McGready, Rose; Phyo, Aung P; Nosten, François; Anderson, Tim J C

    2013-01-01

    Pathogen control programs provide a valuable, but rarely exploited, opportunity to directly examine the relationship between population decline and population genetics. We investigated the impact of an ~12-fold decline in transmission on the population genetics of Plasmodium falciparum infections (n = 1731) sampled from four clinics on the Thai-Burma border over 10 years and genotyped using 96 genome-wide SNPs. The most striking associated genetic change was a reduction in the frequency of infections containing multiple parasite genotypes from 63% in 2001 to 14% in 2010 (P = 3 × 10(-15)). Two measures of the clonal composition of populations (genotypic richness and the β-parameter of the Pareto distribution) declined over time as more people were infected by parasites with identical multilocus genotypes, consistent with increased selfing and a reduction in the rate at which multilocus genotypes are broken apart by recombination. We predicted that the reduction in transmission, multiple clone carriage and outbreeding would be mirrored by an increased influence of genetic drift. However, geographical differentiation and expected heterozygosity remained stable across the sampling period. Furthermore, N(e) estimates derived from allele frequencies fluctuation between years remained high (582 to ∞) and showed no downward trend. These results demonstrate how genetic data can compliment epidemiological assessments of infectious disease control programs. The temporal changes in a single declining population parallel to those seen in comparisons of parasite genetics in regions of differing endemicity, strongly supporting the notion that reduced opportunity for outbreeding is the key driver of these patterns. © 2012 Blackwell Publishing Ltd.

  18. Explaining density-dependent regulation in earthworm populations using life-history analysis

    NARCIS (Netherlands)

    Kammenga, J.E.; Spurgeon, D.J.; Svendsen, C.; Weeks, J.M.

    2003-01-01

    At present there is little knowledge about how density regulates population growth rate and to what extent this is determined by life-history patterns. We compared density dependent population consequences in the Nicholsonian sense based oil experimental observations and life-history modeling for

  19. An alternative covariance estimator to investigate genetic heterogeneity in populations.

    Science.gov (United States)

    Heslot, Nicolas; Jannink, Jean-Luc

    2015-11-26

    For genomic prediction and genome-wide association studies (GWAS) using mixed models, covariance between individuals is estimated using molecular markers. Based on the properties of mixed models, using available molecular data for prediction is optimal if this covariance is known. Under this assumption, adding individuals to the analysis should never be detrimental. However, some empirical studies showed that increasing training population size decreased prediction accuracy. Recently, results from theoretical models indicated that even if marker density is high and the genetic architecture of traits is controlled by many loci with small additive effects, the covariance between individuals, which depends on relationships at causal loci, is not always well estimated by the whole-genome kinship. We propose an alternative covariance estimator named K-kernel, to account for potential genetic heterogeneity between populations that is characterized by a lack of genetic correlation, and to limit the information flow between a priori unknown populations in a trait-specific manner. This is similar to a multi-trait model and parameters are estimated by REML and, in extreme cases, it can allow for an independent genetic architecture between populations. As such, K-kernel is useful to study the problem of the design of training populations. K-kernel was compared to other covariance estimators or kernels to examine its fit to the data, cross-validated accuracy and suitability for GWAS on several datasets. It provides a significantly better fit to the data than the genomic best linear unbiased prediction model and, in some cases it performs better than other kernels such as the Gaussian kernel, as shown by an empirical null distribution. In GWAS simulations, alternative kernels control type I errors as well as or better than the classical whole-genome kinship and increase statistical power. No or small gains were observed in cross-validated prediction accuracy. This alternative

  20. Climate and ecosystem linkages explain widespread declines in North American Atlantic salmon populations.

    Science.gov (United States)

    Mills, Katherine E; Pershing, Andrew J; Sheehan, Timothy F; Mountain, David

    2013-10-01

    North American Atlantic salmon (Salmo salar) populations experienced substantial declines in the early 1990s, and many populations have persisted at low abundances in recent years. Abundance and productivity declined in a coherent manner across major regions of North America, and this coherence points toward a potential shift in marine survivorship, rather than local, river-specific factors. The major declines in Atlantic salmon populations occurred against a backdrop of physical and biological shifts in Northwest Atlantic ecosystems. Analyses of changes in climate, physical, and lower trophic level biological factors provide substantial evidence that climate conditions directly and indirectly influence the abundance and productivity of North American Atlantic salmon populations. A major decline in salmon abundance after 1990 was preceded by a series of changes across multiple levels of the ecosystem, and a subsequent population change in 1997, primarily related to salmon productivity, followed an unusually low NAO event. Pairwise correlations further demonstrate that climate and physical conditions are associated with changes in plankton communities and prey availability, which are ultimately linked to Atlantic salmon populations. Results suggest that poor trophic conditions, likely due to climate-driven environmental factors, and warmer ocean temperatures throughout their marine habitat area are constraining the productivity and recovery of North American Atlantic salmon populations. © 2013 John Wiley & Sons Ltd.

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

    Science.gov (United States)

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

    2013-01-01

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

  2. Rooms for genetic improvement in Indonesian Bali cattle population

    Science.gov (United States)

    Widyas, N.; Nugroho, T.; Prastowo, S.

    2017-04-01

    Bali cattle is a species of Bos javanicus d’Alton, a local cattle in Indonesia. They are loaded with potential as meat producer and well adapted to tropical climate and limited feed resources. Studies have been made to characterize the species. This paper presents a rough estimate of the opportunity to improve the Bali cattle population genetically. Our aim is to endorse that the Bali cattle could be both superior and efficient as tropical meat producer cattle. Results shows that Bali cattle population size is decreasing for the last years with a possibility to be accompanied by genetic quality decline. However, there is hope in improving Bali cattle genetically by a proper breeding strategy. This could also be an answer to the challenge of climate change which leads to global warming; where species adaptable to such environment is more beneficial in the future.

  3. Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays.

    Science.gov (United States)

    Gross, Arnd; Tönjes, Anke; Kovacs, Peter; Veeramah, Krishna R; Ahnert, Peter; Roshyara, Nab R; Gieger, Christian; Rueckert, Ina-Maria; Loeffler, Markus; Stoneking, Mark; Wichmann, Heinz-Erich; Novembre, John; Stumvoll, Michael; Scholz, Markus

    2011-07-28

    The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples. The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses. Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable. Regarding LD

  4. Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays

    Directory of Open Access Journals (Sweden)

    Gieger Christian

    2011-07-01

    Full Text Available Abstract Background The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644 and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples. Results The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses. Conclusions Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the

  5. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline

    2017-02-15

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  6. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands.

    Science.gov (United States)

    Pailles, Yveline; Ho, Shwen; Pires, Inês S; Tester, Mark; Negrão, Sónia; Schmöckel, Sandra M

    2017-01-01

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense , are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  7. Genetic diversity in two populations of Limicolaria aurora (Jay, 1839 ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-06-22

    Jun 22, 2016 ... 1993; Madec et al., 1998). Genetic drift and natural selection are the two primary evolutionary mechanisms that cause population differen- tiation (Hufford and Mazer, 2003). Natural selection by ecological factors will result in development of ecological adaptation or ecotypes. It remains to be determined.

  8. Genetic study of scheduled caste populations of Tamil Nadu

    Indian Academy of Sciences (India)

    The present study aims to describe the genetic structure of the scheduled caste populations in Tamil Nadu state, ... phisms) in DNA samples from five Tamil Nadu caste groups using phylogenetic and principal component analysis ... 1997), a mitochondrial DNA insert in the human nuclear genome (Zischler et al. 1995), and ...

  9. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... This study compared the genetic diversity within and among six naturally growing coastal and inland populations of Peganum harmala by using random amplified polymorphic DNA (RAPD) technique. Seven primers generated a total of 63 RAPD bands (loci) of which 60 (95.24%) were polymorphic across.

  10. Population genetic structure based on SSR markers in alfalfa ...

    Indian Academy of Sciences (India)

    1988). Cultivated alfalfa is autotetraploid (2n = 4x = 32) (McCoy and Bingham 1988), cross-pollinated (allogamous) and seed propagated. Severe inbreeding depression and tetrasomic inheritance make it dif- ficult to carry out many types of population-genetic stud- ies in this species. Therefore, breeding approaches to de-.

  11. Population genetic structure and demographic history of small ...

    African Journals Online (AJOL)

    Small yellow croaker, Larimichthys polyactis (Bleeker, 1877), a commercially important benthopelagic fish, is widely distributed in the Bohai, Yellow and East China Seas. To evaluate the population genetic structure and demographic history of L. polyactis, we sequenced the complete mitochondrial deoxyribonucleic acid ...

  12. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    Full Length Research Paper ... The study was conducted to assess the genetic diversity of L. sativum population from Ethiopia using inter simple sequence repeat (ISSR) marker. Molecular data generated from ISSR ... the ISSR data was used to construct unweighted pair group method with arithmetic mean (UPGMA) and.

  13. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 individuals were collected from 12 coral reefs in Xisha, Zhongsha and Nansha archipelagos and 22 haplotypes were obtained.

  14. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Directory of Open Access Journals (Sweden)

    Sara Melito

    Full Text Available BACKGROUND: Helichrysum italicum (Asteraceae is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. METHODS: H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. KEY RESULTS: The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. CONCLUSIONS: The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

  15. Population Genetic Status of the Western Indian Ocean

    African Journals Online (AJOL)

    Whatever the system, whether coral reefs, sea grasses or mangroves, the general consensus appears to be that .... populations from the Red Sea, Mauritius and South. Africa showed no genetic separation from Pacific ..... seas: Global phylogeography of the sea urchin. Diadema. Evolution. 55: 955-975. Lessios, H.A., Kane ...

  16. Population Genetic Structure and Connectivity of the Abundant Sea ...

    African Journals Online (AJOL)

    Uncontrolled growth of sea urchin populations may have a negative effect on coral reefs, making them barren. To avoid this, different methods of sea urchin reduction have been developed but, without knowledge of their genetic structure and connectivity, these methods may be ineffective. The aim of this study was to ...

  17. Population genetic study on common kilka ( Clupeonella cultriventris ...

    African Journals Online (AJOL)

    All sampled regions contained private alleles. The average observed and expected heterozygosity were 0.153 and 0.888, respectively. All loci significantly deviated from Hardy-Weinberg equilibrium (HWE). Based on AMOVA, RST values was found to be 0.113 (Nm=1.96, P<0.01). The genetic distance between populations ...

  18. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    Genetic diversity analysis in the Hypericum perforatum populations in the Kashmir valley by using inter-simple sequence repeats (ISSR) markers. Shazia Farooq, MA Siddiqui, PC Ray, MQ Sheikh, Sheikh Shahnawaz, M Ashraf Bhat, MR Mir, MZ Abdin, Imtiyaz Ahmad, Jamsheed Javid, Prasant Yadav, M Masroor, Mariyam ...

  19. Population genetics related to adaptation in elite oat germplasm

    Science.gov (United States)

    Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 2...

  20. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    Late blight, caused by Phytophthora infestans is the most important disease of potato (Solanum tuberosum). This study reveals the genetic diversity of P. infestans population in north China. A total of 134 strains of P. infestans were isolated from different agricultural fields in Hebei, Liaoning, Jinlin and Heilongjiang Provinces ...

  1. AFLP analysis on genetic diversity and population structure of small ...

    African Journals Online (AJOL)

    The population genetic structure and diversity of small yellow croaker Larimichthys polyactis in the Bohai Bay, Yellow Sea and East China Sea were analyzed using amplified fragment length polymorphism (AFLP). Ninety-one individuals were collected from six locations representing three stocks of small yellow croaker.

  2. Development of mapping populations for genetic analysis in yams ...

    African Journals Online (AJOL)

    Progress is being made at the International Institute of Tropical Agriculture (IITA, Ibadan, Nigeria) to develop molecular tools for marker-assisted selection that would complement and expedite conventional breeding approaches for genetic improvement of yams (Dioscorea spp.). F1 full-sib mapping populations were ...

  3. Analyzing Population Genetics Data: A Comparison of the Software

    Science.gov (United States)

    Choosing a software program for analyzing population genetic data can be a challenge without prior knowledge of the methods used by each program. There are numerous web sites listing programs by type of data analyzed, type of analyses performed, or other criteria. Even with programs categorized in ...

  4. Population genetics of Setaria viridis, a new model system

    Science.gov (United States)

    An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new mod...

  5. Analysis of genetic diversity and population structure among exotic ...

    African Journals Online (AJOL)

    The present study was performed to study genetic relationships and population differentiation of 90 introduced sugarcane accessions in Ethiopia by means of 22 SSR molecular markers. The 22 SSR markers amplified a total of 260 alleles, of which 230 were polymorphic with a mean of 10.45 alleles per SSR locus.

  6. Genetic diversity of Kenyan Prosopis populations based on random ...

    African Journals Online (AJOL)

    MUTURI

    In combination, these traits may enhance the invasiveness of plant hybrids. The introduction of Prosopis ... Description of sample populations, plant sampling and reference species. Six naturally established Prosopis ...... boosted genetic diversity in the invasive range of black cherry. (Prunus serotina; Rosaceae). Ann. Bot.

  7. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    AJL

    compositions and changes in population genetic structure of P. infestans, especially the .... Allele frequencies for SSR markers in 134 P. infestans strains from the four provinces collected in 2008 and 2009. SSR locus Allele Hebei Liaoning Jilin Heilongjiang 2008 2009 Overall Gene diversity. G11. 156. 0.02. 0.00. 0.13. 0.03.

  8. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    ) was applied to analyze the genetic variation of the 2 populations of Mystus vittatus (Bloch) of Madhya Pradesh, India. 10 random 10-mer primers were primarily scored in 3 individuals from each of the 2 locations. Five primers, which gave ...

  9. Genetic diversity of endangered populations of Butia capitata ...

    African Journals Online (AJOL)

    The flora and fauna of the Cerrado biome in central Brazil both show great diversity and high levels of endemism. Butia capitata is a palm native to this biome that has significant economic, social, and environmental value. We sought to identify and quantify the genetic diversity of four fragmented populations of B. capitata ...

  10. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  11. Genetic variation and population structure of willowy flounder ...

    African Journals Online (AJOL)

    The first hypervariable region (HVR-1) of the mitochondrial DNA control region was utilized for determination of genetic variation and population structure in willowy flounder (Tanakius kitaharai) collected from Aomori, Ibaraki and Niigata. A total of 35 haplotypes were detected among 66 individuals with a total of 30 variable ...

  12. Population genetic structure and cladistic analysis of Trypanosoma brucei isolates

    NARCIS (Netherlands)

    Agbo, E.C.; Clausen, P.H.; Buscher, P.; Majiwa, P.A.O.; Pas, te M.F.W.; Claassen, E.

    2003-01-01

    Using a novel multilocus DNA marker analysis method, we studied the population genetic structure of Trypansoma brucei stocks and derived clones isolated from animal and rhodesiense sleeping sickness patients during a national sleeping sickness control program in Mukono district, Uganda. We then

  13. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    was conducted to assess the genetic diversity of L. sativum population from Ethiopia using inter simple sequence repeat (ISSR) marker. Molecular ... human abdominal ache and diarrhea. Moreover, L. sativum is also used to treat ..... Composition and Physical Properties of Cress (Lepidium sativum L.) and Field Pennycress ...

  14. Inter-populations genetic and morphological diversity in three Silene ...

    African Journals Online (AJOL)

    enoho

    2012-03-30

    Mar 30, 2012 ... The inter-populations morphological and genetic variations were studied in three species of Silene. (Silene indeprensa, Silene gynodioica and ... Morphological analysis of variance (ANOVA) and analysis of molecular (AMOVA) analyses ..... In general, considering our previous cytological work (Sheidaei et ...

  15. Short communication Population structure and genetic trends for ...

    African Journals Online (AJOL)

    user

    2016-05-23

    May 23, 2016 ... Population structure and genetic trends for indigenous African beef cattle breeds in South Africa ... and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger,. Nguni and Tuli) in ..... circumference and semen characteristics of Line 1 Hereford bulls. J. Anim. Sci.

  16. Genetic diversity of Annona senegalensis Pers. populations as ...

    African Journals Online (AJOL)

    Annona senegalensis Pers. is one of the wild fruit tree for domestication in southern Africa. An assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasm collection, conservation and fruit domestication programmes. During 2004 to 2006 nine populations were collected from different ...

  17. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... Res. 5: 643-652. Capili JB (1990). Isozyme and mitochondrial DNA restriction endonuclease analysis of three strains of O. nilitocus. Dissertation,. University of Wales. D'Amato ME, Corach D (1996). Genetic diversity of populations of the freshwater shrimp Macrobrachium bordello (Caridae: Palaemonidae).

  18. Insights into metabolic disease from studying genetics in isolated populations

    DEFF Research Database (Denmark)

    Zeggini, Ele; Gloyn, A L; Hansen, Torben

    2016-01-01

    variation on disease risk. Current efforts are now focused on extending this to genetic variants in the rare and low-frequency spectrum by capitalising on next-generation sequencing technologies. This review discusses the important contributions that studies in isolated populations are making to this effort...

  19. ECOLOGO-GENETIC MONITORING OF CULTIVATED AND WILD PLANT POPULATION

    Directory of Open Access Journals (Sweden)

    A. E. SHPAKOV

    2010-01-01

    Full Text Available Quantitative estimation of genotypic structure dynamic of three plant species: Nicotiana tabacum L., Anacamptus pyramidalis (L. Rich., Teucrium chamaedrys L. in different ecological conditions has been conducted. The effectiveness of systemic analyses of the trait complex with the aim of ecologo-genetic monitoring of the plant population has been established.

  20. Genetic diversity of Jatropha curcas L. populations in Kenya using ...

    African Journals Online (AJOL)

    Jatropha curcas L is an economically potential tree species gaining interest globally because of its feasible contribution towards production of commercial biofuel. Little is known however, of its genetic variation patterns within Kenyan accessions for maximum exploitation. Eight populations covering most of its distribution ...

  1. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Review: Genetic diversity and population structure of cotton ( Gossypium hirsutum L. race latifolium H. ) using microsatellite markers. ... African Journal of Biotechnology ... Four groups were identified applying different methods (the probabilistic method, Principal Coordinates Analysis and Neighbor Joining tree). American ...

  2. Genomic Insights into Campylobacter jejuni Virulence and Population Genetics

    Directory of Open Access Journals (Sweden)

    Zuowei Wu

    2016-11-01

    Full Text Available Campylobacter jejuni has long been recognized as a main food-borne pathogen in many parts of the world. Natural reservoirs include a wide variety of domestic and wild birds and mammals, whose intestines offer a suitable biological niche for the survival and dissemination of the organism. Understanding the genetic basis of the biology and pathogenicity of C. jejuni is vital to prevent and control Campylobacter-associated infections. The recent progress in sequencing techniques has allowed for a rapid increase in our knowledge of the molecular biology and the genetic structures of Campylobacter. Single-molecule realtime (SMRT sequencing, which goes beyond four-base sequencing, revealed the role of DNA methylation in modulating the biology and virulence of C. jejuni at the level of epigenetics. In this review, we will provide an up-to-date review on recent advances in understanding C. jejuni genomics, including structural features of genomes, genetic traits of virulence, population genetics, and epigenetics.

  3. Acceptance of genetic testing in a general population

    DEFF Research Database (Denmark)

    Aro, A R; Hakonen, A; Hietala, M

    1997-01-01

    The aim of the study was to analyze effects of age, education and gender on acceptance of genetic testing. Subjects, n = 1967 aged 15-69, were a stratified random sample of the Finnish population. One thousand, one hundred and sixty nine subjects, 530 men and 639 women, returned the questionnaire....... The majority of the respondents approved of the availability of genetic testing. Young, aged 15-24, were more favourable towards testing and more willing to undergo suggested tests, but they were also more worried than others about the misuse of test results. Men aged 45-69 with only basic education were more...... in favour of mandatory genetic testing than other respondents. Respondents with university education were more critical towards genetic testing and expressed their worry about eugenics more often than other education groups. In conclusion, there are age, education and gender related differences...

  4. Different metabolic and genetic responses in citrus may explain relative susceptibility to Tetranychus urticae.

    Science.gov (United States)

    Agut, Blas; Gamir, Jordi; Jacas, Josep A; Hurtado, Mónica; Flors, Victor

    2014-11-01

    Life history parameters of the phytophagous spider mite Tetranychus urticae in citrus depend on the rootstock where the cultivar is grafted. To unveil the mechanisms responsible for this effect, the authors have carried out comparative experiments of T. urticae performance on two citrus rootstocks, the highly T. urticae-sensitive Cleopatra mandarin and the more tolerant sour orange. Sour orange showed reduced leaf damage symptoms, supported lower mite populations and reduced oviposition rates compared with Cleopatra mandarin. Hormonal, metabolomic and gene expression analyses of the main defence pathways suggest a relevant role of the oxylipin and the flavonoid pathways in the response against T. urticae. Sour orange showed an increased activity of the JA pathway, which was hardly active in the most susceptible rootstock. Moreover, treatments with the LOX inhibitor Phenidone abolished the enhanced tolerance of sour orange. Therefore, oxylipin-dependent defence seems to be rootstock dependent. The metabolomic analysis showed the importance of the flavonoid pathway, which is implicated in the interaction between plants and their environment. The findings suggest that sour-orange enhanced tolerance to spider mites can be sustained by a combination of pre-existing and induced responses depending on high levels of flavonoids and a fast and effective activation of the oxylipin pathway. © 2013 Society of Chemical Industry. © 2013 Society of Chemical Industry.

  5. A survey of Lolium rigidum populations in citrus orchards: Factors explaining infestation levels

    OpenAIRE

    Atanackovic, Valentina; Juárez Escario, Alejandro; Recasens i Guinjuan, Jordi; Torra Farré, Joel

    2015-01-01

    The presence of herbicide-resistant Lolium rigidum in Mediterranean (Spanish) citrus orchards was reported in 2005 and it poses a serious threat to crop management. The main objective of this research was to investigate which components could be responsible for the persistence of annual ryegrass populations in Mediterranean mandarin and orange orchards. This is the first study regarding L. rigidum populations in Mediterranean citrus orchards. Surveys were con- ducted in 55 comme...

  6. Population genetic history of Aristeus antennatus (Crustacea: Decapoda) in the Western and Central Mediterranean Sea.

    Science.gov (United States)

    Marra, Annamaria; Mona, Stefano; Sà, Rui M; D'Onghia, Gianfranco; Maiorano, Porzia

    2015-01-01

    Aristeus antennatus is an ecologically and economically important deep-water species in the Mediterranean Sea. In this study we investigated the genetic variability of A. antennatus sampled from 10 sampling stations in the Western and Central Mediterranean. By comparing our new samples with available data from the Western area, we aim to identify potential genetic stocks of A. antennatus and to reconstruct its historical demography in the Mediterranean. We analyzed two regions of mitochondrial DNA in 319 individuals, namely COI and 16S. We found two main results: i) the genetic diversity values consistent with previous data within the Mediterranean and the absence of barriers to gene flow within the Mediterranean Sea; ii) a constant long-term effective population size in almost all demes but a strong signature of population expansion in the pooled sample about 50,000 years B.P./ago. We propose two explanation for our results. The first is based on the ecology of A. antennatus. We suggest the existence of a complex meta-population structured into two layers: a deeper-dwelling stock, not affected by fishing, which preserves the pattern of historical demography; and genetically homogeneous demes inhabiting the fishing grounds. The larval dispersal, adult migration and continuous movements of individuals from "virgin" deeper grounds not affected by fishing to upper fishing areas support an effective 'rescue effect' contributing to the recovery of the exploited stocks and explain their genetic homogeneity throughout the Mediterranean Sea. The second is based on the reproduction model of this shrimp: the high variance in offspring production calls for a careful interpretation of the data observed under classical population genetics and Kingman's coalescent. In both cases, management policies for A. antennatus will therefore require careful evaluation of the meta-population dynamics of all stocks in the Mediterranean. In the future, it will be particularly relevant to

  7. Population genetic history of Aristeus antennatus (Crustacea: Decapoda in the Western and Central Mediterranean Sea.

    Directory of Open Access Journals (Sweden)

    Annamaria Marra

    Full Text Available Aristeus antennatus is an ecologically and economically important deep-water species in the Mediterranean Sea. In this study we investigated the genetic variability of A. antennatus sampled from 10 sampling stations in the Western and Central Mediterranean. By comparing our new samples with available data from the Western area, we aim to identify potential genetic stocks of A. antennatus and to reconstruct its historical demography in the Mediterranean. We analyzed two regions of mitochondrial DNA in 319 individuals, namely COI and 16S. We found two main results: i the genetic diversity values consistent with previous data within the Mediterranean and the absence of barriers to gene flow within the Mediterranean Sea; ii a constant long-term effective population size in almost all demes but a strong signature of population expansion in the pooled sample about 50,000 years B.P./ago. We propose two explanation for our results. The first is based on the ecology of A. antennatus. We suggest the existence of a complex meta-population structured into two layers: a deeper-dwelling stock, not affected by fishing, which preserves the pattern of historical demography; and genetically homogeneous demes inhabiting the fishing grounds. The larval dispersal, adult migration and continuous movements of individuals from "virgin" deeper grounds not affected by fishing to upper fishing areas support an effective 'rescue effect' contributing to the recovery of the exploited stocks and explain their genetic homogeneity throughout the Mediterranean Sea. The second is based on the reproduction model of this shrimp: the high variance in offspring production calls for a careful interpretation of the data observed under classical population genetics and Kingman's coalescent. In both cases, management policies for A. antennatus will therefore require careful evaluation of the meta-population dynamics of all stocks in the Mediterranean. In the future, it will be

  8. Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches.

    Science.gov (United States)

    Aguilar, Ramiro; Quesada, Mauricio; Ashworth, Lorena; Herrerias-Diego, Yvonne; Lobo, Jorge

    2008-12-01

    Conservation of genetic diversity, one of the three main forms of biodiversity, is a fundamental concern in conservation biology as it provides the raw material for evolutionary change and thus the potential to adapt to changing environments. By means of meta-analyses, we tested the generality of the hypotheses that habitat fragmentation affects genetic diversity of plant populations and that certain life history and ecological traits of plants can determine differential susceptibility to genetic erosion in fragmented habitats. Additionally, we assessed whether certain methodological approaches used by authors influence the ability to detect fragmentation effects on plant genetic diversity. We found overall large and negative effects of fragmentation on genetic diversity and outcrossing rates but no effects on inbreeding coefficients. Significant increases in inbreeding coefficient in fragmented habitats were only observed in studies analyzing progenies. The mating system and the rarity status of plants explained the highest proportion of variation in the effect sizes among species. The age of the fragment was also decisive in explaining variability among effect sizes: the larger the number of generations elapsed in fragmentation conditions, the larger the negative magnitude of effect sizes on heterozygosity. Our results also suggest that fragmentation is shifting mating patterns towards increased selfing. We conclude that current conservation efforts in fragmented habitats should be focused on common or recently rare species and mainly outcrossing species and outline important issues that need to be addressed in future research on this area.

  9. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations.

    Science.gov (United States)

    Martin, Alicia R; Gignoux, Christopher R; Walters, Raymond K; Wojcik, Genevieve L; Neale, Benjamin M; Gravel, Simon; Daly, Mark J; Bustamante, Carlos D; Kenny, Eimear E

    2017-04-06

    The vast majority of genome-wide association studies (GWASs) are performed in Europeans, and their transferability to other populations is dependent on many factors (e.g., linkage disequilibrium, allele frequencies, genetic architecture). As medical genomics studies become increasingly large and diverse, gaining insights into population history and consequently the transferability of disease risk measurement is critical. Here, we disentangle recent population history in the widely used 1000 Genomes Project reference panel, with an emphasis on populations underrepresented in medical studies. To examine the transferability of single-ancestry GWASs, we used published summary statistics to calculate polygenic risk scores for eight well-studied phenotypes. We identify directional inconsistencies in all scores; for example, height is predicted to decrease with genetic distance from Europeans, despite robust anthropological evidence that West Africans are as tall as Europeans on average. To gain deeper quantitative insights into GWAS transferability, we developed a complex trait coalescent-based simulation framework considering effects of polygenicity, causal allele frequency divergence, and heritability. As expected, correlations between true and inferred risk are typically highest in the population from which summary statistics were derived. We demonstrate that scores inferred from European GWASs are biased by genetic drift in other populations even when choosing the same causal variants and that biases in any direction are possible and unpredictable. This work cautions that summarizing findings from large-scale GWASs may have limited portability to other populations using standard approaches and highlights the need for generalized risk prediction methods and the inclusion of more diverse individuals in medical genomics. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  10. Analysis of the genetic effects for several traits in oil palm (Elaeis guineensis Jacq.) populations. I. Population means.

    Science.gov (United States)

    Baudouin, L; Cao, T V; Gallais, A

    1995-03-01

    An oil palm experiment was set up in the Ivory Coast to compare the effects of crossing and selfing within two origins, Deli and La Mé, on the mean and the variability of Deli x Mé between-origin hybrids. The originality of the experiment lay in the crossing plan, which provided access to genetic parameters related to additivity, dominance and different components of epistasis. This first part covers the analysis of the components of the mean. The parents used were obtained from four palms, two from each origin. Those of La Mé origin were half-sibs. The common parent came from a wild stand in the Ivory Coast. Those of Deli origin were from two different populations bred in Southeast Asia for several generations from a narrow genetic base. These four parents gave rise to nine Deli x La Mé hybrid populations with double-cousintype links. The additive component is more important within the Deli origin than within the La Mé origin. This may be explained by the large genetic divergence between the two Deli parent palms. On the other hand, the additive(*) additive epistasis is more substantial within the La Mé origin, probably because of inbreeding. The discussion concentrates on how this information should be used when choosing parents to be crossed and tested and to produce improved populations. The crossing plan proposed can be of general use and is suitable for other species in a reciprocal recurrent selection programme.

  11. Using classical population genetics tools with heterochroneous data: time matters!

    Directory of Open Access Journals (Sweden)

    Frantz Depaulis

    Full Text Available BACKGROUND: New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA. However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. METHODOLOGY/PRINCIPAL FINDINGS: We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck. Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus, for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA. CONCLUSIONS/SIGNIFICANCE: Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of

  12. Genetic Diversity and Population Structure of Ethiopian Sheep Populations Revealed by High-Density SNP Markers.

    Science.gov (United States)

    Edea, Zewdu; Dessie, Tadelle; Dadi, Hailu; Do, Kyoung-Tag; Kim, Kwan-Suk

    2017-01-01

    Sheep in Ethiopia are adapted to a wide range of environments, including extreme habitats. Elucidating their genetic diversity is critical for improving breeding strategies and mapping quantitative trait loci associated with productivity. To this end, the present study investigated the genetic diversity and population structure of five Ethiopian sheep populations exhibiting distinct phenotypes and sampled from distinct production environments, including arid lowlands and highlands. To investigate the genetic relationships in greater detail and infer population structure of Ethiopian sheep breeds at the continental and global levels, we analyzed genotypic data of selected sheep breeds from the Ovine SNP50K HapMap dataset. All Ethiopian sheep samples were genotyped with Ovine Infinium HD SNP BeadChip (600K). Mean genetic diversity ranged from 0.29 in Arsi-Bale to 0.32 in Menz sheep, while estimates of genetic differentiation among populations ranged from 0.02 to 0.07, indicating low to moderate differentiation. An analysis of molecular variance revealed that 94.62 and 5.38% of the genetic variation was attributable to differences within and among populations, respectively. Our population structure analysis revealed clustering of five Ethiopian sheep populations according to tail phenotype and geographic origin-i.e., short fat-tailed (very cool high-altitude), long fat-tailed (mid to high-altitude), and fat-rumped (arid low-altitude), with clear evidence of admixture between long fat-tailed populations. North African sheep breeds showed higher levels of within-breed diversity, but were less differentiated than breeds from Eastern and Southern Africa. When African breeds were grouped according to geographic origin (North, South, and East), statistically significant differences were detected among groups (regions). A comparison of population structure between Ethiopian and global sheep breeds showed that fat-tailed breeds from Eastern and Southern Africa clustered

  13. Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

    KAUST Repository

    Mineta, Katsuhiko

    2015-05-01

    The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

  14. The Effect of Multiple Paternity on Genetic Diversity of Small Populations during and after Colonisation

    KAUST Repository

    Rafajlović, Marina

    2013-10-28

    Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration) has been reached. During colonisation, multiple mating by 2-10 males increased the heterozygosity by 10-300% in comparison with single paternity, while in the steady state the increase was 10-50% compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity. 2013 Rafajlovi? et al.

  15. Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea.

    Science.gov (United States)

    Casabianca, Silvia; Penna, Antonella; Pecchioli, Elena; Jordi, Antoni; Basterretxea, Gotzon; Vernesi, Cristiano

    2012-01-07

    The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity (C(i)) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea.

  16. Genetic rescue of an insular population of large mammals.

    Science.gov (United States)

    Hogg, John T; Forbes, Stephen H; Steele, Brian M; Luikart, Gordon

    2006-06-22

    Natural populations worldwide are increasingly fragmented by habitat loss. Isolation at small population size is thought to reduce individual and population fitness via inbreeding depression. However, little is known about the time-scale over which adverse genetic effects may develop in natural populations or the number and types of traits likely to be affected. The benefits of restoring gene flow to isolates are therefore also largely unknown. In contrast, the potential costs of migration (e.g. disease spread) are readily apparent. Management for ecological connectivity has therefore been controversial and sometimes avoided. Using pedigree and life-history data collected during 25 years of study, we evaluated genetic decline and rescue in a population of bighorn sheep founded by 12 individuals in 1922 and isolated at an average size of 42 animals for 10-12 generations. Immigration was restored experimentally, beginning in 1985. We detected marked improvements in reproduction, survival and five fitness-related traits among descendants of the 15 recent migrants. Trait values were increased by 23-257% in maximally outbred individuals. This is the first demonstration, to our knowledge, of increased male and female fitness attributable to outbreeding realized in a fully competitive natural setting. Our findings suggest that genetic principles deserve broader recognition as practical management tools with near-term consequences for large-mammal conservation.

  17. Coccidian infection may explain the differences in the life history of octopus host populations.

    Science.gov (United States)

    Storero, Lorena P; Narvarte, Maite A

    2013-11-01

    The prevalence of coccidian parasites in three Octopus tehuelchus populations from San Matías Gulf (Patagonia, Argentina) is compared. The prevalence was similar between sexes, but varied between seasons (being highest during cold months) and sites. Islote Lobos had the highest prevalence (42.7-100%) followed by San Antonio Bay (0-66%) and El Fuerte (0-24.5%). Octopuses under 27 mm of dorsal mantle length showed a low prevalence (less than 50%), which increased with size. We hypothesize that the high prevalence of parasites, which affect the three populations differentially, could account for the observed variability in life-span and growth, size-frequency distributions, reproduction and densities of O. tehuelchus populations. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. Working with the Hmong Population in a Genetics Setting: Genetic Counselor Perspectives.

    Science.gov (United States)

    Agather, Aime; Rietzler, Jennifer; Reiser, Catherine A; Petty, Elizabeth M

    2017-12-01

    The Hmong language lacks words for many familiar Western medical genetic concepts which may impact genetic counseling sessions with individuals of Hmong ancestry who have limited English proficiency. To study this interaction, a qualitative, semi-structured interview was designed to address genetic counselors' experiences of genetic counseling sessions working with individuals with Hmong ancestry. Genetic counselors in the three states with the largest population of Hmong individuals (California, Minnesota and Wisconsin) were invited via email to participate in a telephone interview. Eleven counselors' interviews were transcribed and analyzed for emergent themes. Each of the counselors had served Hmong patients in a variety of clinics and possessed counseling experience ranging from approximately one to greater than 20 years. Interviews highlighted strengths and challenges in genetic counseling sessions with Hmong patients with limited English proficiency in each of five categories: 1) relevant training during graduate school, 2) session preparation, 3) content of the counseling session, 4) perception of Hmong culture, and 5) reflections on working with Hmong interpreters. Cultural awareness and education in training programs were highlighted by all genetic counselors as valued components to patient care. All interviewees had worked with professional Hmong medical interpreters, but had different expectations for the interpreter with whom they worked. To help improve genetic services for Hmong individuals in the United States, we offer suggestions to improve some of the challenges mentioned, and recommend further studies to investigate the genetic counselor and interpreter relationship.

  19. Population Genetic Structure of the People of Qatar

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A.; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W.; Fuller, Jennifer; Hackett, Neil R.; Crystal, Ronald G.; Clark, Andrew G.

    2010-01-01

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. PMID:20579625

  20. Population genetic structure in the paddyfield warbler (Acrocephalus agricola Jerd.

    Directory of Open Access Journals (Sweden)

    Pavel ZEHTINDJIEV, Mihaela ILIEVA, Bengt HANSSON, Olga OPARINA,Mihail OPARIN, Staffan BENSCH

    2011-02-01

    Full Text Available Population genetic structure was studied in paddyfield warblers Acrocephalus agricola breeding in NE Bulgaria, SE Russia and S Kazakhstan. We were particularly interested in the degree of genetic differentiation and gene flow of the Bulgarian population due to its geographical isolation, recent origin and unique migratory strategy. Analyses of mitochondrial DNA (mtDNA showed that there was no divergence between Bulgarian and Russian populations (FST = 0.007, whereas those in Kazakhstan differed significantly from the European breeding populations (Russia: FST = 0.058; Bulgaria: FST = 0.114. The degree of differentiation between populations at nuclear markers (five microsatellite loci; FST ≈ 0 was weaker than for mtDNA. We suggest that this relatively weak differentiation over the range of this species reflects a recent postglacial expansion, and results from mismatch distribution analyses and Fu’s FS tests are in agreement. Preservation of small and geographically isolated populations which may contain individuals with unique adaptive traits, such as the studied Bulgarian population of paddyfield warbler, is valuable for the long-term conservation of expanding migratory bird species [Current Zoology 57 (1: 63–71, 2011].

  1. The probability of genetic parallelism and convergence in natural populations.

    Science.gov (United States)

    Conte, Gina L; Arnegard, Matthew E; Peichel, Catherine L; Schluter, Dolph

    2012-12-22

    Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1-0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.

  2. A stochastic step model of replicative senescence explains ROS production rate in ageing cell populations.

    Directory of Open Access Journals (Sweden)

    Conor Lawless

    Full Text Available Increases in cellular Reactive Oxygen Species (ROS concentration with age have been observed repeatedly in mammalian tissues. Concomitant increases in the proportion of replicatively senescent cells in ageing mammalian tissues have also been observed. Populations of mitotic human fibroblasts cultured in vitro, undergoing transition from proliferation competence to replicative senescence are useful models of ageing human tissues. Similar exponential increases in ROS with age have been observed in this model system. Tracking individual cells in dividing populations is difficult, and so the vast majority of observations have been cross-sectional, at the population level, rather than longitudinal observations of individual cells.One possible explanation for these observations is an exponential increase in ROS in individual fibroblasts with time (e.g. resulting from a vicious cycle between cellular ROS and damage. However, we demonstrate an alternative, simple hypothesis, equally consistent with these observations which does not depend on any gradual increase in ROS concentration: the Stochastic Step Model of Replicative Senescence (SSMRS. We also demonstrate that, consistent with the SSMRS, neither proliferation-competent human fibroblasts of any age, nor populations of hTERT overexpressing human fibroblasts passaged beyond the Hayflick limit, display high ROS concentrations. We conclude that longitudinal studies of single cells and their lineages are now required for testing hypotheses about roles and mechanisms of ROS increase during replicative senescence.

  3. Do differences in inducible resistance explain the population dynamics of birch and pine defoliators?

    Science.gov (United States)

    Seppo Neuvonen; Pekka Niemela

    1991-01-01

    Damage inflicted by insects may trigger responses in their host plants resulting either in immediate effects on herbivores either rapidly or in effects upon subsequent herbivore generations. Differentiation between rapid and delayed inducible resistance is essential since the two responses affect the population dynamics of herbivores in fundamentally different ways (...

  4. Using life-history traits to explain bird population responses to changing weather variability

    NARCIS (Netherlands)

    Cormont, A.; Vos, C.C.; Turnhout, van C.A.M.; Foppen, R.P.B.; Braak, ter C.J.F.

    2011-01-01

    Bird population dynamics are expected to change in response to increased weather variability, an expression of climate change. The extent to which species are sensitive to effects of weather on survival and reproduction depends on their life-history traits. We investigated how breeding bird species

  5. Geography, the Integrating Discipline: Explaining China's Population-Driven Geopolitics to Students

    Science.gov (United States)

    Bouchat, Clarence J.

    2008-01-01

    This article demonstrates geography's role as an integrative discipline and its utility in connecting students to the world around them. A case study links China's demography and its geopolitics to the lives of U.S. students. The relationship of China's population pressures to its resulting economic growth, need for economic resources, and…

  6. [Genetic ecological monitoring in human populations: heterozygosity, mtDNA haplotype variation, and genetic load].

    Science.gov (United States)

    Balanovskiĭ, O P; Koshel', S M; Zaporozhchenko, V V; Pshenichnov, A S; Frolova, S A; Kuznetsova, M A; Baranova, E E; Teuchezh, I E; Kuznetsova, A A; Romashkina, M V; Utevskaia, O M; Churnosov, M I; Villems, R; Balanovskaia, E V

    2011-11-01

    Yu. P. Altukhov suggested that heterozygosity is an indicator of the state of the gene pool. The idea and a linked concept of genetic ecological monitoring were applied to a new dataset on mtDNA variation in East European ethnic groups. Haplotype diversity (an analog of the average heterozygosity) was shown to gradually decrease northwards. Since a similar trend is known for population density, interlinked changes were assumed for a set of parameters, which were ordered to form a causative chain: latitude increases, land productivity decreases, population density decreases, effective population size decreases, isolation of subpopulations increases, genetic drift increases, and mtDNA haplotype diversity decreases. An increase in genetic drift increases the random inbreeding rate and, consequently, the genetic load. This was confirmed by a significant correlation observed between the incidence of autosomal recessive hereditary diseases and mtDNA haplotype diversity. Based on the findings, mtDNA was assumed to provide an informative genetic system for genetic ecological monitoring; e.g., analyzing the ecology-driven changes in the gene pool.

  7. Genetic Structure of Loach Population in Yatsu Paddy Field

    Science.gov (United States)

    Koizumi, Noriyuki; Takemura, Takeshi; Mori, Atsushi; Okushima, Shuji

    Using repeated sequences of microsatellite DNA, we investigated genetic variation and spatial structure of the loach Misgurnus anguillicaudatus population in drainage canals including a main stream in the Shitada River basin composed of Yatsu paddy fields, Chiba Prefecture. Loach population samples of nine to 48 individuals were collected from 54 sampling sites in eight canals and the main stream, and genotype data in eight microsatellite loci were obtained for each sample in the genetic analysis. The average number of alleles per locus was 3.9 to 9.0, and the average observed and expected heterozygosities were 0.444-0.647 and 0.463-0.628, respectively, across samples. All samples seemed to be random mating, which conformed to the Hardy-Weinberg equilibrium. Values of the fixation index FST, were estimated to range between 0-0.161 among all samples, and a part of these values were significant. The pattern of genetic differentiation between samples with principal component analysis indicated that samples in three distinct canals appeared to differentiate, suggesting that the genetic spatial structure of the loach population in Yatsu paddy fields must be complex.

  8. Changes in Habitat Structure May Explain Decrease in Reintroduced Mohor Gazelle Population in the Guembeul Fauna Reserve, Senegal

    OpenAIRE

    Eulalia Moreno; Abibou Sane; Jesús Benzal; Belén Ibáñez; Joaquín Sanz-Zuasti; Gerardo Espeso

    2012-01-01

    Simple Summary The reintroduction of plants and animals to the wild is an important technique to save endangered species from extinction. To perform post release monitoring is crucial to evaluate reintroduction outcomes. A Mohor gazelle reintroduction programme took place in Senegal in 1984. We attempt to explain why the size of the reintroduced gazelle population has diminished in recent years. We suggest that changes in habitat structure occurred over time and have very likely reduced the a...

  9. Change in genetic size of small-closed populations: lessons from a domestic mammal population

    Directory of Open Access Journals (Sweden)

    Farhad Ghafouri-Kesbi

    2010-01-01

    Full Text Available The aim of this study was to monitor changes in genetic size of a small-closed population of Iranian Zandi sheep, by using pedigree information from animals born between 1991 and 2005. The genetic size was assessed by using measures based on the probability of identity-by-descend of genes (coancestry, f, and effective population size, Ne, as well as measures based on probability of gene origin (effective number of founders, f e, effective number of founder genomes, f g, and effective number of non-founder genomes, f ne. Average coancestry, or the degree of genetic similarity of individuals, increased from 0.81% to 1.44% during the period 1993 to 2005, at the same time that Ne decreased from 263 to 93. The observed trend for f e was irregular throughout the experiment in a way that f e was 68, 87, 77, 92, and 80 in 1993, 1996, 1999, 2002, and 2005, respectively. Simultaneously, f g, the most informative effective number, decreased from 61 to 35. The index of genetic diversity (GD which was obtained from estimates of f g,decreased about 2% throughout the period studied. In addition, a noticeable reduction was observed in the estimates of f ne from 595 in 1993 to 61 in 2005. The higher than 1 ratio of f e to f g indicated the presence of bottlenecks and genetic drift in the development of this population of Zandi sheep. From 1993 to 1999, f ne was much higher than f e, thereby indicating that with respect to loss of genetic diversity, the unequal contribution of founders was more important than the random genetic drift in non-founder generations. Subsequently, random genetic drift in non-founder generations was the major reason for f e> f ne. The minimization of average coancestry in new reproductive individuals was recommended as a means of preserving the population against a further loss in genetic diversity.

  10. [Population genetics of hereditary diseases in the child population of the Republic of Bashkortostan, Chuvashia, and Udmurtia].

    Science.gov (United States)

    Bessonova, L A; El'chinova, G I; Zinchenko, R A

    2012-05-01

    The results of integrated study of the genetic structure and prevalence of monogenic hereditary diseases (MHDs) in the child population of three republics of Russia are summarized. Eight raions (districts) of the Republic of Bashkortostan and six districts of each Republic of Chuvashia and Republic of Udmurtia has been surveyed. The total population surveyed was 782184 people, with children accounting for 24.67% of them (192992 children). The loads of autosomal dominant (AD), autosomal recessive (AR), and X-linked MHDs have been calculated separately for urban and rural populations; differences between individual populations in the MHD load have been found. The differentiation of subpopulations with respect to MHD prevalence is explained by differences in the degree of subdivision. The MHD spectrum in the child population of the three republics comprises 222 disease entities, including 121 AD, 83 AR, and 18 X-linked diseases. Group of highly prevalent MHDs in regional child populations have been determined. The mean fitness of MHD patients in Bashkortostan has been calculated; it is 0.87, 0.04 and 0.16 for AD, AR, and X-linked diseases, respectively. Analysis has demonstrated that the prevalence rates of MHDs in the child populations of the republics of Chuvashia, Udmurtia, and Bashkortostan are 1, 1.2, and 1.4%, respectively.

  11. Genetic population structure of Anopheles gambiae in Equatorial Guinea

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    Caccone Adalgisa

    2007-10-01

    Full Text Available Abstract Background Patterns of genetic structure among mosquito vector populations in islands have received particular attention as these are considered potentially suitable sites for experimental trials on transgenic-based malaria control strategies. In this study, levels of genetic differentiation have been estimated between populations of Anopheles gambiae s.s. from the islands of Bioko and Annobón, and from continental Equatorial Guinea (EG and Gabon. Methods Genotyping of 11 microsatellite loci located in chromosome 3 was performed in three island samples (two in Bioko and one in Annobón and three mainland samples (two in EG and one in Gabon. Four samples belonged to the M molecular form and two to the S-form. Microsatellite data was used to estimate genetic diversity parameters, perform demographic equilibrium tests and analyse population differentiation. Results High levels of genetic differentiation were found between the more geographically remote island of Annobón and the continent, contrasting with the shallow differentiation between Bioko island, closest to mainland, and continental localities. In Bioko, differentiation between M and S forms was higher than that observed between island and mainland samples of the same molecular form. Conclusion The observed patterns of population structure seem to be governed by the presence of both physical (the ocean and biological (the M-S form discontinuity barriers to gene flow. The significant degree of genetic isolation between M and S forms detected by microsatellite loci located outside the "genomic islands" of speciation identified in A. gambiae s.s. further supports the hypothesis of on-going incipient speciation within this species. The implications of these findings regarding vector control strategies are discussed.

  12. Genetic, ecological and morphological divergence between populations of the endangered Mexican Sheartail hummingbird (Doricha eliza).

    Science.gov (United States)

    Licona-Vera, Yuyini; Ornelas, Juan Francisco

    2014-01-01

    The Mexican Sheartail (Doricha eliza), an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.

  13. Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci

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    Solano Philippe

    2011-07-01

    Full Text Available Abstract Background Glossina palpalis palpalis (Diptera: Glossinidae is widespread in west Africa, and is the main vector of sleeping sickness in Cameroon as well as in the Bas Congo Province of the Democratic Republic of Congo. However, little is known on the structure of its populations. We investigated G. p. palpalis population genetic structure in five sleeping sickness foci (four in Cameroon, one in Democratic Republic of Congo using eight microsatellite DNA markers. Results A strong isolation by distance explains most of the population structure observed in our sampling sites of Cameroon and DRC. The populations here are composed of panmictic subpopulations occupying fairly wide zones with a very strong isolation by distance. Effective population sizes are probably between 20 and 300 individuals and if we assume densities between 120 and 2000 individuals per km2, dispersal distance between reproducing adults and their parents extends between 60 and 300 meters. Conclusions This first investigation of population genetic structure of G. p. palpalis in Central Africa has evidenced random mating subpopulations over fairly large areas and is thus at variance with that found in West African populations of G. p. palpalis. This study brings new information on the isolation by distance at a macrogeographic scale which in turn brings useful information on how to organise regional tsetse control. Future investigations should be directed at temporal sampling to have more accurate measures of demographic parameters in order to help vector control decision.

  14. Genetic, ecological and morphological divergence between populations of the endangered Mexican Sheartail hummingbird (Doricha eliza.

    Directory of Open Access Journals (Sweden)

    Yuyini Licona-Vera

    Full Text Available The Mexican Sheartail (Doricha eliza, an endangered hummingbird, is endemic to Mexico where two populations have a disjunct distribution. One population is distributed along the northern tip of the Yucatan Peninsula whereas the other is mostly restricted to central Veracruz. Despite their disjunct distribution, previous work has failed to detect morphological or behavioral differences between these populations. Here we use variation in morphology, mtDNA and nuDNA sequences to determine the degree of morphological and molecular divergence between populations, their divergence time, and historical demography. We use species distribution modeling and niche divergence tests to infer the relative roles of vicariance and dispersal in driving divergence in the genus. Our Bayesian and maximum likelihood phylogenetic analyses revealed that Doricha eliza populations form a monophyletic clade and support their sister relationship with D. enicura. We found marked genetic differentiation, with reciprocal monophyly of haplotypes and highly restricted gene flow, supporting a history of isolation over the last 120,000 years. Genetic divergence between populations is consistent with the lack of overlap in environmental space and slight morphological differences between males. Our findings indicate that the divergence of the Veracruz and Yucatan populations is best explained by a combination of a short period of isolation exacerbated by subsequent divergence in climate conditions, and that rather than vicariance, the two isolated ranges of D. eliza are the product of recent colonization and divergence in isolation.

  15. Retinitis pigmentosa genetics: A study in Indian population

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    Vinchurkar Manisha

    1996-01-01

    Full Text Available A total of 151 retinitis pigmentosa (RP patients from 83 families were screened and the frequencies of different genetic categories studied. One hundred and ten patients out of 151 had a positive inheritance pattern, and autosomal recessive (AR emerged as the predominant (53 out of 151, genetic pattern followed by isolated or sporadic (41 out of 151 cases. Further study of autosomal recessive cases revealed consanguinity as the main characteristic (49 out of 53 in the Indian population studied. Early onset and severe progression of disease was seen in the consanguineous group.

  16. Inter-chromosomal variation in the pattern of human population genetic structure

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    Baye Tesfaye M

    2011-05-01

    Full Text Available Abstract Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC, cluster, discriminant, fixation index (FST and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (OCA2, hect domain and RLD 2 (HERC2, ectodysplasin A receptor (EDAR and solute carrier family 45, member 2 (SLC45A2. These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (IFNG and death-associated protein kinase 1 (DAPK1, which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the

  17. Two invasive populations of the dry rot fungus Serpula lacrymans show divergent population genetic structures.

    Science.gov (United States)

    Engh, Ingeborg Bjorvand; Carlsen, Tor; Saetre, Glenn-Peter; Högberg, Nils; Doi, Shuichi; Kauserud, Håvard

    2010-02-01

    The dry rot fungus Serpula lacrymans is a devastating basidiomycete occurring in wooden constructions in temperate regions worldwide. In this study, we compare the genetic structures of two invasive populations from Europe and Japan. Microsatellite data from 14 loci and DNA sequences from four loci demonstrated that the two populations were highly differentiated. Significant isolation by distance effect was observed in Europe and Japan. Higher genetic variation was observed within the Japanese population than within the European population, corresponding with the observed higher richness of vegetative compatibility types in Japan, indicating that there has been a higher level of gene flow from the Asian source populations to Japan than to Europe. The European population is genetically more homogenous with only six detected vegetative compatibility types. Various tests indicate that both the European and the Japanese populations have gone through population bottlenecks prior to population expansion. No identical multi-locus genotypes were observed within Japan and very few within Europe, indicating limited clonal dispersal. Deviations from Hardy Weinberg expectations were observed both in Europe and Japan and heterozygote excess were observed at several loci, especially in Europe. Possible explanations for this pattern are discussed.

  18. Genetic population substructure in bison at Yellowstone National Park.

    Science.gov (United States)

    Halbert, Natalie D; Gogan, Peter J P; Hedrick, Philip W; Wahl, Jacquelyn M; Derr, James N

    2012-01-01

    The Yellowstone National Park bison herd is 1 of only 2 populations known to have continually persisted on their current landscape since pre-Columbian times. Over the last century, the census size of this herd has fluctuated from around 100 individuals to over 3000 animals. Previous studies involving radiotelemetry, tooth wear, and parturition timing provide evidence of at least 2 distinct groups of bison within Yellowstone National Park. To better understand the biology of Yellowstone bison, we investigated the potential for limited gene flow across this population using multilocus Bayesian clustering analysis. Two genetically distinct and clearly defined subpopulations were identified based on both genotypic diversity and allelic distributions. Genetic cluster assignments were highly correlated with sampling locations for a subgroup of live capture individuals. Furthermore, a comparison of the cluster assignments to the 2 principle winter cull sites revealed critical differences in migration patterns across years. The 2 Yellowstone subpopulations display levels of differentiation that are only slightly less than that between populations which have been geographically and reproductively isolated for over 40 years. The identification of cryptic population subdivision and genetic differentiation of this magnitude highlights the importance of this biological phenomenon in the management of wildlife species.

  19. Demography and genetic structure of a recovering grizzly bear population

    Science.gov (United States)

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

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

    Science.gov (United States)

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

    2004-11-01

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

  1. Identification of genetic and epigenetic marks involved in population structure.

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    Jingyu Liu

    2010-10-01

    Full Text Available Population structure is well known as a prevalent and important factor in genetic studies, but its relevance in epigenetics is unclear. Very little is known about the affected epigenetic markers and their connections with genetics. In this study we assessed the impact of population diversity on genome wide single nucleotide polymorphisms (SNPs and DNA methylation levels in 196 participants from five ethnic groups, using principle and independent component analyses. Three population stratification factors (PSFs were identified in the genomic SNP dataset, accounting for a relatively large portion of total variance (6%. In contrast, only one PSF was identified in genomic methylation dataset accounting for 0.2% of total variance. This methylation PSF, however, was significantly correlated with the largest SNP PSF (r = 0.72, p<1E-23. We then investigated the top contributing markers in these two linked PSFs. The SNP PSF predominantly consists of 8 SNPs from three genes, SLC45A2, HERC2 and CTNNA2, known to encode skin/hair/eye color. The methylation PSF includes 48 methylated sites in 44 genes coding for basic molecular functions, including transcription regulation, DNA binding, cytokine, and transferase activity. Among them, 8 sites are either hypo- or hyper-methylated correlating to minor alleles of SNPs in the SNP PSF. We found that the genes in SNP and methylation PSFs share common biological processes including sexual/multicellular organism reproduction, cell-cell signaling and cytoskeleton organization. We further investigated the transcription regulatory network operating at these genes and identified that most of genes closely interact with ID2, which encodes for a helix-loop-helix inhibitor of DNA binding. Overall, our results show a significant correlation between genetic and epigenetic population stratification, and suggest that the interrelationship between genetic and epigenetic population structure is mediated via complex multiple

  2. The contribution of genetic diversity to subdivide populations living in the silk road of China.

    Science.gov (United States)

    Zhang, Zhe; Wei, Shuguang; Gui, Hongsheng; Yuan, Zuyi; Li, Shengbin

    2014-01-01

    There are several indigenous ethnic populations along the silk road in the Northwest of China that display clear differences in culture and social customs, perhaps as a result of geographic isolation and different linguistic traditions. However, extensive trade and other interactions probably facilitated the admixture of different gene pools between these populations over the last two millennia. To further explore the evolutionary relationships of the 13 ethnic populations residing in Northwest China and to reveal the features of population admixture, the 9 most-commonly employed CODIS loci (D3S1358, TH01, D5S818, D13S317, D7S820, CSF1PO, vWA, TPOX, FGA) were selected for genotyping and further analysis. Phylogenetic tree and principal component analysis revealed clear pattern of population differentiation between 4 populations living in Sinkiang Uighur Autonomous Region and other 9 populations dwelled in the upper regions of Silk Road. R matrix regression showed high-level gene flow and population admixture dose exist among these ethic populations in the Northwest region of China. Furthermore, the Mantel test suggests that larger percent of genetic variance (21.58% versus 2.3%) can be explained by geographic isolation than linguistic barriers, which matched with the contribution of geographic factors to other world populations.

  3. A population genetic study of Pasqueflower: In situ and Ex situ Conservation Genetics of a Vulnerable UK Plant Species

    OpenAIRE

    Worswick, Gemma

    2016-01-01

    The population genetic structure of the vulnerable UK plant species Anemone pulsatilla L. reflects geographic patterns of historical range fragmentation and the influence of population decline and restoration intervention. Positive spatial auto-correlation of natural in situ populations of A. pulsatilla lends support to a scenario for genetic drift (i.e. random drift of allelic frequencies) driving the emergence of population genetic structure as a consequence of fragmentation. Multivariate a...

  4. Distribution and population genetics of walleye and sauger

    Science.gov (United States)

    Haponski, Amanda E.; Sloss, Brian L.

    2014-01-01

    Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the “blue pike”.

  5. Genetic Parameter Estimation in Seedstock Swine Population for Growth Performances

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    Jae Gwan Choi

    2013-04-01

    Full Text Available The objective of this study was to estimate genetic parameters that are to be used for across-herd genetic evaluations of seed stock pigs at GGP level. Performance data with pedigree information collected from swine breeder farms in Korea were provided by Korea Animal Improvement Association (AIAK. Performance data were composed of final body weights at test days and ultrasound measures of back fat thickness (BF, rib eye area (EMA and retail cut percentage (RCP. Breeds of swine tested were Landrace, Yorkshire and Duroc. Days to 90 kg body weight (DAYS90 were estimated with linear function of age and ADG calculated from body weights at test days. Ultrasound measures were taken with A-mode ultrasound scanners by trained technicians. Number of performance records after censoring outliers and keeping records pigs only born from year 2000 were of 78,068 Duroc pigs, 101,821 Landrace pigs and 281,421 Yorkshire pigs. Models included contemporary groups defined by the same herd and the same seasons of births of the same year, which was regarded as fixed along with the effect of sex for all traits and body weight at test day as a linear covariate for ultrasound measures. REML estimation was processed with REMLF90 program. Heritability estimates were 0.40, 0.32, 0.21 0.39 for DAYS90, ADG, BF, EMA, RCP, respectively for Duroc population. Respective heritability estimates for Landrace population were 0.43, 0.41, 0.22, and 0.43 and for Yorkshire population were 0.36, 0.38, 0.22, and 0.42. Genetic correlation coefficients of DAYS90 with BF, EMA, or RCP were estimated to be 0.00 to 0.09, −0.15 to −0.25, 0.22 to 0.28, respectively for three breeds populations. Genetic correlation coefficients estimated between BF and EMA was −0.33 to −0.39. Genetic correlation coefficient estimated between BF and RCP was high and negative (−0.78 to −0.85 but the environmental correlation coefficients between these two traits was medium and negative (near −0

  6. Restoration of genetic connectivity among Northern Rockies wolf populations.

    Science.gov (United States)

    Hebblewhite, Mark; Musiani, Marco; Mills, L Scott

    2010-10-01

    Probably no conservation genetics issue is currently more controversial than the question of whether grey wolves (Canis lupus) in the Northern Rockies have recovered to genetically effective levels. Following the dispersal-based recolonization of Northwestern Montana from Canada, and reintroductions to Yellowstone and Central Idaho, wolves have vastly exceeded population recovery goals of 300 wolves distributed in at least 10 breeding pairs in each of Wyoming, Idaho and Montana. With >1700 wolves currently, efforts to delist wolves from endangered status have become mired in legal battles over the distinct population segment (DPS) clause of the Endangered Species Act (ESA), and whether subpopulations within the DPS were genetically isolated. An earlier study by vonHoldt et al. (2008) suggested Yellowstone National Park wolves were indeed isolated and was used against delisting in 2008. Since then, wolves were temporarily delisted, and a first controversial hunting season occurred in fall of 2009. Yet, concerns over the genetic recovery of wolves in the Northern Rockies remain, and upcoming District court rulings in the summer of 2010 will probably include consideration of gene flow between subpopulations. In this issue of Molecular Ecology, vonHoldt et al. (2010) conduct the largest analysis of gene flow and population structure of the Northern Rockies wolves to date. Using an impressive sampling design and novel analytic methods, vonHoldt et al. (2010) show substantial levels of gene flow between three identified subpopulations of wolves within the Northern Rockies, clarifying previous analyses and convincingly showing genetic recovery. © 2010 Blackwell Publishing Ltd.

  7. The Individual and Population Genetics of Antibody Immunity.

    Science.gov (United States)

    Watson, Corey T; Glanville, Jacob; Marasco, Wayne A

    2017-07-01

    Antibodies (Abs) produced by immunoglobulin (IG) genes are the most diverse proteins expressed in humans. While part of this diversity is generated by recombination during B-cell development and mutations during affinity maturation, the germ-line IG loci are also diverse across human populations and ethnicities. Recently, proof-of-concept studies have demonstrated genotype-phenotype correlations between specific IG germ-line variants and the quality of Ab responses during vaccination and disease. However, the functional consequences of IG genetic variation in Ab function and immunological outcomes remain underexplored. In this opinion article, we outline interconnections between IG genomic diversity and Ab-expressed repertoires and structure. We further propose a strategy for integrating IG genotyping with functional Ab profiling data as a means to better predict and optimize humoral responses in genetically diverse human populations, with immediate implications for personalized medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Genetic analysis of drought adaptive traits in maize synthetic populations

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    Bekavac Goran

    2006-01-01

    Full Text Available Maize breeders consider tolerance to drought as an important criterion in commercial breeding programs. Two traits, stay green and anthesis-silking interval seem to be closely associated with drought tolerance. The main objective of this study was to obtain estimates of means, variability, heritability and estimates of genetic correlations for several traits in two maize synthetic populations. S1 progenies were evaluated in an incomplete block design in four environments. Large genetic variability existed for all traits in both populations but highest variability was found for anthesis-silking interval. Strong, highly significant correlations between drought adaptive traits and grain moisture may cause some undesirable correlative response throughout cycles of selection.

  9. Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset.

    Science.gov (United States)

    Sengupta, Dhriti; Choudhury, Ananyo; Basu, Analabha; Ramsay, Michèle

    2016-12-31

    Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto-Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Population genetic segmentation of MHC-correlated perfume preferences.

    Science.gov (United States)

    Hämmerli, A; Schweisgut, C; Kaegi, M

    2012-04-01

    It has become difficult to find a matching perfume. An overwhelming number of 300 new perfumes launch each year, and marketing campaigns target pre-defined groups based on gender, age or income rather than on individual preferences. Recent evidence for a genetic basis of perfume preferences, however, could be the starting point for a novel population genetic approach to better match perfumes with people's preferences. With a total of 116 participants genotyped for alleles of three loci of the major histocompatibility complex (MHC), the aim of this study was to test whether common MHC alleles could be used as genetic markers to segment a given population into preference types. Significant deviations from random expectations for a set of 10 common perfume ingredients indicate how such segmentation could be achieved. In addition, preference patterns of participants confronted with images that contained a sexual communication context significantly differed in their ratings for some of the scents compared with participants confronted with images of perfume bottles. This strongly supports the assumption that genetically correlated perfume preferences evolved in the context of sexual communication. The results are discussed in the light of perfume customization. © 2011 The Authors. ICS © 2011 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

  11. Spontaneous genetic clustering in populations of competing organisms.

    Science.gov (United States)

    Rogers, Tim; McKane, Alan J; Rossberg, Axel G

    2012-12-01

    We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the model exhibits a pattern-forming instability which is highly amplified by the effects of demographic noise, leading to the spontaneous formation of genotypic clusters. This mechanism supports the thesis that stochasticity has a central role in the formation and coherence of species.

  12. Adapting populations in space: clonal interference and genetic diversity

    Science.gov (United States)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  13. An individual-based approach to explain plasmid invasion in bacterial populations

    DEFF Research Database (Denmark)

    Seoane, Jose Miguel; Yankelevich, Tatiana; Dechesne, Arnaud

    2011-01-01

    of the growth cycle and that nongrowing cells, even when exposed to high nutrient concentrations, do not display conjugal activity. These results do not support previous hypotheses relating conjugation decay in the deeper cell layers of bacterial biofilms to nutrient depletion and low physiological activity. We......We present an individual-based experimental framework to identify and estimate the main parameters governing bacterial conjugation at the individual cell scale. From this analysis, we have established that transient periods of unregulated plasmid transfer within newly formed transconjugant cells......, together with contact mechanics arising from cellular growth and division, are the two main processes determining the emergent inability of the pWW0 TOL plasmid to fully invade spatially structured Pseudomonas putida populations. We have also shown that pWW0 conjugation occurs mainly at advanced stages...

  14. Genetic Variability of Apolipoprotein E in Different Populations from Venezuela

    Directory of Open Access Journals (Sweden)

    M. T. Fernández-Mestre

    2005-01-01

    Full Text Available The genetic variation at the Apolipoprotein E locus (APOE is an important determinant of plasma lipids and has been implicated in various human pathological conditions. The objective of the present study was to estimate the distribution of APOE alleles in five Venezuelan communities: two Amerindian tribes (Bari and Yucpa, one Negroid population from Curiepe, one Caucasoid population from Colonia Tovar and the mestizo urban population living in Caracas. The APOE*3 allele was the most common allele in all populations studied. However, a significant increase in the APOE*2 allele frequency in the Mestizo (18.96% and Negroid (16.25% populations was found. Similar to results reported in other Native American populations we have found that the APOE*2 allele is completely absent in the Bari and Yucpa Amerindians. Frequencies found in the Colonia Tovar population are in agreement with those reported in the population of Germany, indicating a high degree of relatedness. The results support the notion that the distribution of the APOE alleles shows ethnic variability.

  15. Reconstructing the population genetic history of the Caribbean.

    Science.gov (United States)

    Moreno-Estrada, Andrés; Gravel, Simon; Zakharia, Fouad; McCauley, Jacob L; Byrnes, Jake K; Gignoux, Christopher R; Ortiz-Tello, Patricia A; Martínez, Ricardo J; Hedges, Dale J; Morris, Richard W; Eng, Celeste; Sandoval, Karla; Acevedo-Acevedo, Suehelay; Norman, Paul J; Layrisse, Zulay; Parham, Peter; Martínez-Cruzado, Juan Carlos; Burchard, Esteban González; Cuccaro, Michael L; Martin, Eden R; Bustamante, Carlos D

    2013-11-01

    The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse--which today is reflected by shorter, older ancestry tracts--consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse--reflected by longer, younger tracts--is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source

  16. Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura.

    Science.gov (United States)

    Wallace, Andre G; Detweiler, Don; Schaeffer, Stephen W

    2013-07-08

    Paracentric inversions in populations can have a profound effect on the pattern and organization of nucleotide variability along a chromosome. Regions near inversion breakpoints are expected to have greater levels of differentiation because of reduced genetic exchange between different gene arrangements whereas central regions in the inverted segments are predicted to have lower levels of nucleotide differentiation due to greater levels of genetic flux among different karyotypes. We used the inversion polymorphism on the third chromosome of Drosophila pseudoobscura to test these predictions with an analysis of nucleotide diversity of 18 genetic markers near and away from inversion breakpoints. We tested hypotheses about how the presence of different chromosomal arrangements affects the pattern and organization of nucleotide variation. Overall, markers in the distal segment of the chromosome had greater levels of nucleotide heterozygosity than markers within the proximal segment of the chromosome. In addition, our results rejected the hypothesis that the breakpoints of derived inversions will have lower levels of nucleotide variability than breakpoints of ancestral inversions, even when strains with gene conversion events were removed. High levels of linkage disequilibrium were observed within all 11 breakpoint regions as well as between the ends of most proximal and distal breakpoints. The central region of the chromosome had the greatest levels of linkage disequilibrium compared with the proximal and distal regions because this is the region that experiences the highest level of recombination suppression. These data do not fully support the idea that genetic exchange is the sole force that influences genetic variation on inverted chromosomes.

  17. Invasion success in Cogongrass (Imperata cylindrica): A population genetic approach exploring genetic diversity and historical introductions

    Science.gov (United States)

    Rima D. Lucardi; Lisa E. Wallace; Gary N. Ervin

    2014-01-01

    Propagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied...

  18. Boosting forward-time population genetic simulators through genotype compression.

    Science.gov (United States)

    Ruths, Troy; Nakhleh, Luay

    2013-06-14

    Forward-time population genetic simulations play a central role in deriving and testing evolutionary hypotheses. Such simulations may be data-intensive, depending on the settings to the various parameters controlling them. In particular, for certain settings, the data footprint may quickly exceed the memory of a single compute node. We develop a novel and general method for addressing the memory issue inherent in forward-time simulations by compressing and decompressing, in real-time, active and ancestral genotypes, while carefully accounting for the time overhead. We propose a general graph data structure for compressing the genotype space explored during a simulation run, along with efficient algorithms for constructing and updating compressed genotypes which support both mutation and recombination. We tested the performance of our method in very large-scale simulations. Results show that our method not only scales well, but that it also overcomes memory issues that would cripple existing tools. As evolutionary analyses are being increasingly performed on genomes, pathways, and networks, particularly in the era of systems biology, scaling population genetic simulators to handle large-scale simulations is crucial. We believe our method offers a significant step in that direction. Further, the techniques we provide are generic and can be integrated with existing population genetic simulators to boost their performance in terms of memory usage.

  19. Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (Capros aper).

    Science.gov (United States)

    Farrell, Edward D; Carlsson, Jeanette E L; Carlsson, Jens

    2016-12-01

    The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (Capros aper) across the species' range. Microsatellite loci were developed de novo and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies-a crucial element for assessment, sustainable management and conservation of valuable biological resources.

  20. Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea

    KAUST Repository

    Nanninga, Gerrit B.

    2014-01-20

    The relatively recent fields of terrestrial landscape and marine seascape genetics seek to identify the influence of biophysical habitat features on the spatial genetic structure of populations or individuals. Over the last few years, there has been accumulating evidence for the effect of environmental heterogeneity on patterns of gene flow and connectivity in marine systems. Here, we investigate the population genetic patterns of an anemonefish, Amphiprion bicinctus, along the Saudi Arabian coast of the Red Sea. We collected nearly one thousand samples from 19 locations, spanning approximately 1500 km, and genotyped them at 38 microsatellite loci. Patterns of gene flow appeared to follow a stepping-stone model along the northern and central Red Sea, which was disrupted by a distinct genetic break at a latitude of approximately 19°N. The Red Sea is characterized by pronounced environmental gradients along its axis, roughly separating the northern and central from the southern basin. Using mean chlorophyll-a concentrations as a proxy for this gradient, we ran tests of isolation by distance (IBD, R2 = 0.52) and isolation by environment (IBE, R2 = 0.64), as well as combined models using partial Mantel tests and multiple matrix regression with randomization (MMRR). We found that genetic structure across our sampling sites may be best explained by a combined model of IBD and IBE (Mantel: R2 = 0.71, MMRR: R2 = 0.86). Our results highlight the potential key role of environmental patchiness in shaping patterns of gene flow in species with pelagic larval dispersal. We support growing calls for the integration of biophysical habitat characteristics into future studies of population genetic structure. © 2014 John Wiley & Sons Ltd.

  1. GENETIC CONSEQUENCES OF OUTCROSSING IN THE CLEISTOGAMOUS ANNUAL, IMPATIENS CAPENSIS. I. POPULATION-GENETIC STRUCTURE.

    Science.gov (United States)

    Knight, Susan E; Waller, Donald M

    1987-09-01

    We examined the genetic structure of 11 populations of Impatiens capensis, a cleistogamous annual herb, using starch gel electrophoresis. We sampled both cleistogamous (CL) and chasmogamous (CH) progeny (if present) from maternal parents in each population to infer maternal genotypes and to estimate the extent and pattern of inbreeding within and among populations. Only eight of 31 loci were polymorphic, with one to six (mean = 3.1) loci varying within each population. Mean heterozygosity per individual is quite low (mean = 3.9%) and comparable to highly self-fertilized species. Gene flow is low, and genetic distances do not parallel geographical distances, suggesting a population structure similar to Wright's Island model with drift among the populations. Fixation indexes within populations (f̂ or FIS ) span the largest range yet reported for a plant species (0.26 to 0.94, mean = 0.57). Further inbreeding results from population substructuring (θ^ or FST=0.46), resulting in a total average inbreeding coefficient (F̂ or FIT ) of 0.77. Despite these high overall levels of inbreeding, chasmogamy significantly reduces fixation, which may account for the observed greater fitness of CH progeny. © 1987 The Society for the Study of Evolution.

  2. Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

    Science.gov (United States)

    Costantini, Federica; Abbiati, Marco

    2016-03-01

    Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

  3. Documenting and explaining the HIV decline in east Zimbabwe: the Manicaland General Population Cohort

    Science.gov (United States)

    Gregson, Simon; Mugurungi, Owen; Eaton, Jeffrey; Takaruza, Albert; Rhead, Rebecca; Maswera, Rufurwokuda; Mutsvangwa, Junior; Mayini, Justin; Skovdal, Morten; Schaefer, Robin; Hallett, Timothy; Sherr, Lorraine; Munyati, Shungu; Mason, Peter; Campbell, Catherine; Garnett, Geoffrey P; Nyamukapa, Constance Anesu

    2017-01-01

    Purpose The Manicaland cohort was established to provide robust scientific data on HIV prevalence and incidence, patterns of sexual risk behaviour and the demographic impact of HIV in a sub-Saharan African population subject to a generalised HIV epidemic. The aims were later broadened to include provision of data on the coverage and effectiveness of national HIV control programmes including antiretroviral therapy (ART). Participants General population open cohort located in 12 sites in Manicaland, east Zimbabwe, representing 4 major socioeconomic strata (small towns, agricultural estates, roadside settlements and subsistence farming areas). 9,109 of 11,453 (79.5%) eligible adults (men 17-54 years; women 15–44 years) were recruited in a phased household census between July 1998 and January 2000. Five rounds of follow-up of the prospective household census and the open cohort were conducted at 2-year or 3-year intervals between July 2001 and November 2013. Follow-up rates among surviving residents ranged between 77.0% (over 3 years) and 96.4% (2 years). Findings to date HIV prevalence was 25.1% at baseline and had a substantial demographic impact with 10-fold higher mortality in HIV-infected adults than in uninfected adults and a reduction in the growth rate in the worst affected areas (towns) from 2.9% to 1.0%pa. HIV infection rates have been highest in young adults with earlier commencement of sexual activity and in those with older sexual partners and larger numbers of lifetime partners. HIV prevalence has since fallen to 15.8% and HIV incidence has also declined from 2.1% (1998-2003) to 0.63% (2009-2013) largely due to reduced sexual risk behaviour. HIV-associated mortality fell substantially after 2009 with increased availability of ART. Future plans We plan to extend the cohort to measure the effects on the epidemic of current and future HIV prevention and treatment programmes. Proposals for access to these data and for collaboration are welcome. PMID

  4. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units.

    Science.gov (United States)

    Olsen, Morten T; Andersen, Liselotte W; Dietz, Rune; Teilmann, Jonas; Härkönen, Tero; Siegismund, Hans R

    2014-02-01

    Identification of populations and management units is an essential step in the study of natural systems. Still, there is limited consensus regarding how to define populations and management units, and whether genetic methods allow for inference at the relevant spatial and temporal scale. Here, we present a novel approach, integrating genetic, life history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic structure in harbour seals. Second, we used harbour seal demographic and life history data to conduct population viability analyses (PVAs) in the vortex simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (Molecular Ecology, 19, 2010, 3038) 'population viability criterion' for demographic independence. The genetic analyses revealed fine-scale population structuring in southern Scandinavian harbour seals and pointed to the existence of several genetic units. The PVAs indicated that the census population size of each of these genetic units was sufficiently large for long-term population viability, and hence that the units could be classified as demographically independent management units. Our study suggests that population genetic inference can offer the same degree of temporal and spatial resolution as 'nongenetic' methods and that the combined use of genetic data and PVAs constitutes a promising approach for delineating populations and management units. © 2013 John Wiley & Sons Ltd.

  5. Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae).

    Science.gov (United States)

    Thornhill, D J; Howells, E J; Wham, D C; Steury, T D; Santos, S R

    2017-05-01

    Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broadscale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population-level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations. Here, we present a synthesis of population-level characteristics for Symbiodinium, with an emphasis on how phylogenetic affinities, dynamics within and among host individuals, and a propensity towards clonality shape patterns on and across reefs. Major inferences include the following: (i) Symbiodinium populations within individual hosts are comprised mainly of cells belonging to a single or few genetic clones. (ii) Symbiont populations exhibit a mixed mode of reproduction, wherein at least one sexual recombination event occurs in the genealogy between most genotypes, but clonal propagation predominates overall. (iii) Mutualistic Symbiodinium do not perpetually persist outside their hosts, instead undergoing turnover and replacement via the continuous shedding of viable clonal cells from host individuals. (iv) Symbiont populations living in the same host, but on different reefs, are often genetically subdivided, suggesting low connectivity, adaptation to local conditions, or prolific asexual reproduction and low effective population sizes leading to disproportionate success within and among hosts. Overall, this synthesis forms a basis for future investigations of coral symbiosis ecology and evolution as well as delimitation of species boundaries in Symbiodinium and other eukaryotic microorganisms. © 2017 John Wiley & Sons Ltd.

  6. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    DEFF Research Database (Denmark)

    Olsen, Morten Tange; Andersen, Liselotte Wesley; Dietz, Rune

    2014-01-01

    present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic...... structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010......) "population viability criterion" for demographic independence. The genetic analyses revealed fine-scale population structuring in southern Scandinavian harbour seals and pointed to the existence of six genetic units. The PVAs indicated that the census population size of each of these genetic units...

  7. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

    Directory of Open Access Journals (Sweden)

    S Elizabeth Alter

    Full Text Available Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  8. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    Science.gov (United States)

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

    2011-01-01

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

  9. Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations.

    Science.gov (United States)

    Hodoğlugil, Uğur; Mahley, Robert W

    2012-03-01

    Turkey has experienced major population movements. Population structure and genetic relatedness of samples from three regions of Turkey, using over 500,000 SNP genotypes, were compared together with Human Genome Diversity Panel (HGDP) data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analysed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K=3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42-49), 40% European (95% CI, 36-44) and 15% Central Asian (95% CI, 13-16), whereas at K=4 the genetic ancestry of the Turks was 38% European (95% CI, 35-42), 35% Middle Eastern (95% CI, 33-38), 18% South Asian (95% CI, 16-19) and 9% Central Asian (95% CI, 7-11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul and Kayseri) were superimposed, without clear subpopulation structure, suggesting sample homogeneity. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns. © 2012 The Authors Annals of Human Genetics © 2012 Blackwell Publishing Ltd/University College London.

  10. Connecting Palau's marine protected areas: a population genetic approach to conservation

    Science.gov (United States)

    Cros, Annick; Toonen, Robert J.; Donahue, Megan J.; Karl, Stephen A.

    2017-09-01

    Bleaching events are becoming more frequent and are projected to become annual in Micronesia by 2040. To prepare for this threat, the Government of Palau is reviewing its marine protected area network to increase the resilience of the reefs by integrating connectivity into the network design. To support their effort, we used high-throughput sequencing of microsatellites to create genotypes of colonies of the coral Acropora hyacinthus to characterize population genetic structure and dispersal patterns that led to the recovery of Palau's reefs from a 1998 bleaching event. We found no evidence of a founder effect or refugium where colonies may have survived to recolonize the reef. Instead, we found significant pairwise F' st values, indicating population structure and low connectivity among most of the 25 sites around Palau. We used kinship to measure genetic differences at the individual level among sites and found that differences were best explained by the degree of exposure to the ocean [ F 1,20 = 3.015, Pr(> F) = 0.01], but with little of the total variation explained. A permutation test of the pairwise kinship coefficients revealed that there was self-seeding within sites. Overall, the data point to the population of A. hyacinthus in Palau recovering from a handful of surviving colonies with population growth primarily from self-seeding and little exchange among sites. This finding has significant implications for the management strategies for the reefs of Palau, and we recommend increasing the number and distribution of management areas around Palau to capture the genetic architecture and increase the chances of protecting potential refuges in the future.

  11. Contrasting genetic structure of rear edge and continuous range populations of a parasitic butterfly infected by Wolbachia

    Directory of Open Access Journals (Sweden)

    Patricelli Dario

    2013-01-01

    Full Text Available Abstract Background Climatic oscillations are among the long-term factors shaping the molecular features of animals and plants and it is generally supposed that the rear edges (i.e., the low-latitude limits of distribution of any given specialised species situated closer to glacial refugia are vital long-term stores of genetic diversity. In the present study, we compared the genetic structure of several populations of an endangered and obligate myrmecophilous butterfly (Maculinea arion from two distinct and geographically distant parts of its European distribution (i.e., Italy and Poland, which fully represent the ecological and morphological variation occurring across the continent. Results We sequenced the COI mitochondrial DNA gene (the ‘barcoding gene’ and the EF-1α nuclear gene and found substantial genetic differentiation among M. arion Italian populations in both markers. Eleven mtDNA haplotypes were present in Italy. In contrast, almost no mtDNA polymorphisms was found in the Polish M. arion populations, where genetic differentiation at the nuclear gene was low to moderate. Interestingly, the within-population diversity levels in the EF-1α gene observed in Italy and in Poland were comparable. The genetic data did not support any subspecies divisions or any ecological specialisations. All of the populations studied were infected with a single strain of Wolbachia and our screening suggested 100% prevalence of the bacterium. Conclusions Differences in the genetic structure of M. arion observed in Italy and in Poland may be explained by the rear edge theory. Although we were not able to pinpoint any specific evolutionarily significant units, we suggest that the Italian peninsula should be considered as a region of special conservation concern and one that is important for maintaining the genetic diversity of M. arion in Europe. The observed pattern of mtDNA differentiation among the populations could not be explained by an

  12. Genetic variation and population structure in the endangered Hermann's tortoise: the roles of geography and human-mediated processes.

    Science.gov (United States)

    Perez, Melanie; Livoreil, Barbara; Mantovani, Sara; Boisselier, Marie-Catherine; Crestanello, Barbara; Abdelkrim, Jawad; Bonillo, Céline; Goutner, Vassilis; Lambourdière, Josie; Pierpaoli, Massimo; Sterijovski, Bogoljub; Tomovic, Ljiljana; Vilaça, Sibelle T; Mazzotti, Stefano; Bertorelle, Giorgio

    2014-01-01

    The Hermann's tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing 1 mitochondrial locus and 9 nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure and to identify the genetic priorities for the conservation of this species. We found that 1) all geographic areas are highly differentiated, mainly as a function of their distance but with a clear genetic discontinuity (F st values larger than 0.4) between the Eastern and the Western subspecies; 2) the contact zone between subspecies is located farthest to the west than previously believed, and it probably coincides with the delta of the largest Italian river; 3) extinction events due to climatic conditions in the Upper Palaeolithic and subsequent human-mediated translocations in the Neolithic possibly explain the unexpected similarity among Spain, Sicily, and Corsica. For conservation purposes, the large majority of genetic pools appears native although hybridization among subspecies, related to extensive 20th century trade of tortoises across Europe, is observed in Spain and some Italian samples. Most populations do not seem at immediate risk of low genetic variation, except the French population, which has very low nuclear genetic diversity (heterozygosity = 0.25) and where 50 out of 51 sampled animals shared the same mitochondrial sequence. In general, restocking and reintroduction plans should carefully consider the genetic background of the individuals.

  13. Population genetic structure of a microalgal species under expansion.

    Directory of Open Access Journals (Sweden)

    Karen Lebret

    Full Text Available Biological invasions often cause major perturbations in the environment and are well studied among macroorganisms. Less is known about invasion by free-living microbes. Gonyostomum semen (Raphidophyceae is a freshwater phytoplankton species that has increased in abundance in Northern Europe since the 1980's and has expanded its habitat range. In this study, we aimed to determine the genetic population structure of G. semen in Northern Europe and to what extent it reflects the species' recent expansion. We sampled lakes from 12 locations (11 lakes in Norway, Sweden and Finland. Multiple strains from each location were genotyped using Amplified Fragment Length Polymorphism (AFLP. We found low differentiation between locations, and low gene diversity within each location. Moreover, there was an absence of genetic isolation with distance (Mantel test, p = 0.50. According to a Bayesian clustering method all the isolates belonged to the same genetic population. Together our data suggest the presence of one metapopulation and an overall low diversity, which is coherent with a recent expansion of G. semen.

  14. Genetic differentiation in red-bellied piranha populations (Pygocentrus nattereri, Kner, 1858) from the Solimões-Amazonas River.

    Science.gov (United States)

    Dos Santos, Carlos Henrique Dos A; de Sá Leitão, Carolina S; Paula-Silva, Maria de N; Almeida-Val, Vera Maria F

    2016-06-01

    Red-bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões-Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red-bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red-bellied piranha populations collected at different locations of Solimões-Amazonas River system. We collected 234 red-bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões-Amazonas River system, with significant genetic differentiation between them. The red-bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing.

  15. Determining causes of genetic isolation in a large carnivore (Ursus americanus population to direct contemporary conservation measures.

    Directory of Open Access Journals (Sweden)

    Agnès Pelletier

    Full Text Available The processes leading to genetic isolation influence a population's local extinction risk, and should thus be identified before conservation actions are implemented. Natural or human-induced circumstances can result in historical or contemporary barriers to gene flow and/or demographic bottlenecks. Distinguishing between these hypotheses can be achieved by comparing genetic diversity and differentiation in isolated vs. continuous neighboring populations. In Ontario, American black bears (Ursus americanus are continuously distributed, genetically diverse, and exhibit an isolation-by-distance structuring pattern, except on the Bruce Peninsula (BP. To identify the processes that led to the genetic isolation of BP black bears, we modelled various levels of historical and contemporary migration and population size reductions using forward simulations. We compared simulation results with empirical genetic indices from Ontario black bear populations under different levels of geographic isolation, and conducted additional simulations to determine if translocations could help achieve genetic restoration. From a genetic standpoint, conservation concerns for BP black bears are warranted because our results show that: i a recent demographic bottleneck associated with recently reduced migration best explains the low genetic diversity on the BP; and ii under sustained isolation, BP black bears could lose between 70% and 80% of their rare alleles within 100 years. Although restoring migration corridors would be the most effective method to enhance long-term genetic diversity and prevent inbreeding, it is unrealistic to expect connectivity to be re-established. Current levels of genetic diversity could be maintained by successfully translocating 10 bears onto the peninsula every 5 years. Such regular translocations may be more practical than landscape restoration, because areas connecting the peninsula to nearby mainland black bear populations have been

  16. Modified Multi-Population Genetic Algorithm for Yeast Fed-batch Cultivation Parameter Identification

    Directory of Open Access Journals (Sweden)

    Angelova M.

    2009-12-01

    Full Text Available In this work, a modified multi-population genetic algorithm is developed for the purpose of parameter identification of fermentation process model. Modified multi-population genetic algorithm is similar to the multi-population one and its development is instigated by modified genetic algorithm, similar to simple one. A comparison of four types of genetic algorithms, namely simple, modified, multipopulation and modified multi-population is presented for parameter identification of a fed-batch cultivation of Saccharomyces cerevisiae

  17. Population Genetic Structure of the Tropical Two-Wing Flyingfish (Exocoetus volitans.

    Directory of Open Access Journals (Sweden)

    Eric A Lewallen

    Full Text Available Delineating populations of pantropical marine fish is a difficult process, due to widespread geographic ranges and complex life history traits in most species. Exocoetus volitans, a species of two-winged flyingfish, is a good model for understanding large-scale patterns of epipelagic fish population structure because it has a circumtropical geographic range and completes its entire life cycle in the epipelagic zone. Buoyant pelagic eggs should dictate high local dispersal capacity in this species, although a brief larval phase, small body size, and short lifespan may limit the dispersal of individuals over large spatial scales. Based on these biological features, we hypothesized that E. volitans would exhibit statistically and biologically significant population structure defined by recognized oceanographic barriers. We tested this hypothesis by analyzing cytochrome b mtDNA sequence data (1106 bps from specimens collected in the Pacific, Atlantic and Indian oceans (n = 266. AMOVA, Bayesian, and coalescent analytical approaches were used to assess and interpret population-level genetic variability. A parsimony-based haplotype network did not reveal population subdivision among ocean basins, but AMOVA revealed limited, statistically significant population structure between the Pacific and Atlantic Oceans (ΦST = 0.035, p<0.001. A spatially-unbiased Bayesian approach identified two circumtropical population clusters north and south of the Equator (ΦST = 0.026, p<0.001, a previously unknown dispersal barrier for an epipelagic fish. Bayesian demographic modeling suggested the effective population size of this species increased by at least an order of magnitude ~150,000 years ago, to more than 1 billion individuals currently. Thus, high levels of genetic similarity observed in E. volitans can be explained by high rates of gene flow, a dramatic and recent population expansion, as well as extensive and consistent dispersal throughout the geographic

  18. Analysis of population genetic structure from Bucaramanga (Colombia) based on gene polymorphisms associated with the regulation of blood pressure.

    Science.gov (United States)

    León, Francisco Javier; Rondón, Fernando; Vargas, Clara Inés; Oróstegui, Myriam; Bautista, Leonelo; Serrano, Norma Cecilia; Páez, María C; Castillo, Adriana

    2012-04-01

    In spite of nearly 40% of variability in blood pressure being explained by genetic factors, the identification of genes associated with essential high blood pressure is difficult to determine in populations where individuals have different genetic backgrounds. In these circumstances it is necessary to determinate whether the population is sub-structured because this can bias studies associated with this disease. TO DETERMINE THE GENETIC STRUCTURE OF THE POPULATION IN BUCARAMANGA FROM GENETIC POLYMORPHISMS ASSOCIATED WITH THE REGULATION OF BLOOD PRESSURE: 448G>T, 679C>T y 1711C>T from the gene kinase 4 of the dopaminergic receptor linked to the protein G and Glu298Asp, -786T>C and the VNTR of the intron 4 of the gene of endothelial nitric oxide. A sample of 552 unrelated individuals was studied through analysis of restriction fragment length polymorphism. The allelic, haplotypic and genotypic frequencies were calculated, the Hardy-Weinberg equilibrium was determined and a molecular analysis of variance was performed to determine the genetic structure. Thirty-eight (38) Haplotypes were identified with GCCTG4b being the most frequent (21.2%). The most diverse polymorphism was 448G>T with a frequency of 49.9% for heterozygous. The six polymorphisms were found in genetic equilibrium and a genetic structure of populations was not evidenced (FST= 0.0038). The population studied does not present a genetic sub-structure and the polymorphisms analyzed were found in genetic equilibrium. This indicates that the population mixes randomly and there are no sub-groups capable of affecting the results of the association studies.

  19. Medically unexplained and explained physical symptoms in the general population: association with prevalent and incident mental disorders.

    Directory of Open Access Journals (Sweden)

    Jonna van Eck van der Sluijs

    Full Text Available Clinical studies have shown that Medically Unexplained Symptoms (MUS are related to common mental disorders. It is unknown how often common mental disorders occur in subjects who have explained physical symptoms (PHY, MUS or both, in the general population, what the incidence rates are, and whether there is a difference between PHY and MUS in this respect.To study the prevalence and incidence rates of mood, anxiety and substance use disorders in groups with PHY, MUS and combined MUS and PHY compared to a no-symptoms reference group in the general population.Data were derived from the Netherlands Mental Health Survey and Incidence Study-2 (NEMESIS-2, a nationally representative face-to-face survey of the general population aged 18-64 years. We selected subjects with explained physical symptoms only (n=1952, with MUS only (n=177, with both MUS and PHY (n=209, and a reference group with no physical symptoms (n=4168. The assessment of common mental disorders was through the Composite International Diagnostic Interview 3.0. Multivariate logistic regression analyses were used to examine the association between group membership and the prevalence and first-incidence rates of comorbid mental disorders, adjusted for socio-demographic characteristics.MUS were associated with the highest prevalence rates of mood and anxiety disorders, and combined MUS and PHY with the highest prevalence rates of substance disorder. Combined MUS and PHY were associated with a higher incidence rate of mood disorder only (OR 2.9 (95%CI:1.27,6.74.In the general population, PHY, MUS and the combination of both are related to mood and anxiety disorder, but odds are highest for combined MUS and PHY in relation to substance use disorder. Combined MUS and PHY are related to a greater incidence of mood disorder. These findings warrant further research into possibilities to improve recognition and early intervention in subjects with combined MUS and PHY.

  20. Molecular markers for genetic diversity, gene flow and genetic population structure of freshwater mussel species.

    Science.gov (United States)

    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.

  1. Genetic structure and molecular variability of potato virus M populations.

    Science.gov (United States)

    Tabasinejad, Fatemeh; Jafarpour, Behrooz; Zakiaghl, Mohammad; Siampour, Majid; Rouhani, Hamid; Mehrvar, Mohsen

    2014-08-01

    To investigate the genetic diversity of potato virus M (PVM; genus Carlavirus, family Betaflexiviridae), the complete nucleotide sequence of the coat protein gene of 30 PVM isolates from a major potato-growing region in Iran were determined. Phylogenetic analysis of these Iranian PVM isolates together with those available in the GenBank database suggested two divergent evolutionary lineages that did not reflect the origin of the isolates, and these were designated as PVM-o and PVM-d. Examination of the genetic variability of the coat protein of Iranian isolates and their counterparts whose sequences are available in the Genbank database revealed 16 genotype groups in the PVM population. Analysis of the synonymous-tononsynonymous ratio showed strong purifying selection in the CP gene in the genotype groups of divergent clades.

  2. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

  3. Population composition, public policy, and the genetics of smoking.

    Science.gov (United States)

    Boardman, Jason D; Blalock, Casey L; Pampel, Fred C; Hatemi, Peter K; Heath, Andrew C; Eaves, Lindon J

    2011-11-01

    In this article, we explore the effect of public policy on the extent to which genes influence smoking desistance. Using a sample of adult twins (n(mz) = 363, n(dz) = 233) from a large population registry, we estimate Cox proportional hazards models that describe similarity in the timing of smoking desistance among adult twin pairs. We show that identical twin pairs are significantly more likely to quit smoking within a similar time frame compared with fraternal twin pairs. Importantly, we then show that genetic factors for smoking desistance increase in importance following restrictive legislation on smoking behaviors that occurred in the early and mid-1970s. These findings support the social push perspective and make important contributions to the social demography and genetic epidemiology of smoking as well as to the gene-environment interaction literatures.

  4. Population Composition, Public Policy, and the Genetics of Smoking*

    Science.gov (United States)

    Boardman, Jason D.; Blalock, Casey L.; Pampel, Fred C.; Hatemi, Peter K.; Heath, Andrew C.; Eaves, Lindon J.

    2012-01-01

    In this paper we explore the effect public policy on the extent to which genes may influence smoking desistance. Using a sample of adult twins (nmz=363, ndz=233) from a large population registry, we estimate Cox proportional hazards models that describe similarity in the timing of smoking desistance among adult twin pairs and we show that identical twin pairs are significantly more likely to quit smoking within a similar time frame compared to fraternal twin pairs. Importantly, we then show that genetic factors for smoking desistance increase in importance following restrictive legislation on smoking behaviors that occurred in the early and mid 1970s. These findings support the social push perspective and make important contributions to the social demography and genetic epidemiology of smoking as well as to the gene-environment interaction literatures. PMID:21845502

  5. Population genetics of foxtail millet and its wild ancestor

    Directory of Open Access Journals (Sweden)

    Wang Yongfang

    2010-10-01

    Full Text Available Abstract Background Foxtail millet (Setaria italica (L. P. Beauv., one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L. P. Beauv.. Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. Results In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059, θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027 when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively. The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. Conclusions The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population

  6. Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris.

    Science.gov (United States)

    Abadía-Cardoso, Alicia; Freimer, Nelson B; Deiner, Kristy; Garza, John Carlos

    2017-09-01

    The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species. Published by Oxford University Press on behalf of The American Genetic Association 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  7. Genetic architecture of skin and eye color in an African-European admixed population.

    Science.gov (United States)

    Beleza, Sandra; Johnson, Nicholas A; Candille, Sophie I; Absher, Devin M; Coram, Marc A; Lopes, Jailson; Campos, Joana; Araújo, Isabel Inês; Anderson, Tovi M; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Correia E Silva, António; Shriver, Mark D; Rocha, Jorge; Barsh, Gregory S; Tang, Hua

    2013-03-01

    Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3 × 10(-62), SLC24A5 P = 9.6 × 10(-9)) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4 × 10(-27), TYR P = 1.1 × 10(-9), APBA2[OCA2] P = 1.5 × 10(-8), SLC45A2 P = 6 × 10(-9)) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

  8. Genetic architecture of skin and eye color in an African-European admixed population.

    Directory of Open Access Journals (Sweden)

    Sandra Beleza

    2013-03-01

    Full Text Available Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3 × 10(-62, SLC24A5 P = 9.6 × 10(-9 that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4 × 10(-27, TYR P = 1.1 × 10(-9, APBA2[OCA2] P = 1.5 × 10(-8, SLC45A2 P = 6 × 10(-9 for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44% is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

  9. Genetic structure of Chilean populations of Seriola lalandi for the diversification of the national aquaculture in the north of Chile

    Directory of Open Access Journals (Sweden)

    Gonzalo Fernández

    2015-05-01

    Full Text Available Seriola lalandi has been recognized as a potential aquaculture species in Chile, however, little is known about the genetic structure of local populations. This is important, as the current production system is based on an initial wild catching and ill management of these stocks can cause reduced genetic variability. To assess the genetic structure of local S. lalandi we evaluated 27 published microsatellite markers developed from genomic libraries of other species of the genera. However only 12 markers could be used to properly assess the populations, most of these markers showed deviations from Hardy-Weinberg equilibrium with moderate inbreeding (F = 0.12. This species tends to show schooling behavior, so in all likelihood mating between relatives within small groups of fish is not unexpected. The population structure was assessed using Structure software, showing the presence of admixture with varying levels of individual ancestry. This was seen in both populations, without significant genetic differentiation. This may be explained by the migratory behavior, with mating between different populations likely to happen in small groups. Management of aquaculture resources is essential to secure a sustainable production system; this study is the first to provide estimates of genetic diversity of Chilean populations of S. lalandi.

  10. Distinct genetic structure in populations of Chrysoperla externa (Hagen (Neuroptera, Chrysopidae shown by genetic markers ISSR and COI gene

    Directory of Open Access Journals (Sweden)

    Nara C. C. P. Barbosa

    2014-06-01

    Full Text Available Distinct genetic structure in populations of Chrysoperla externa (Hagen (Neuroptera, Chrysopidae shown by genetic markers ISSR and COI gene. Green lacewings are generalist predators, and the species Chrysoperla externa presents a great potential for use in biological control of agricultural pests due to its high predation and reproduction capacities, as well as its easy mass rearing in the laboratory. The adaptive success of a species is related to genetic variability, so that population genetic studies are extremely important in order to maximize success of the biological control. Thus, the present study used nuclear (Inter Simple Sequence Repeat - ISSR and mitochondrial (Cytochrome Oxidase I - COI molecular markers to estimate the genetic variability of 12 populations in the São Paulo State, Brazil, as well as the genetic relationships between populations. High levels of genetic diversity were observed for both markers, and the highest values of genetic diversity appear associated with municipalities that have the greatest areas of native vegetation. There was high haplotype sharing, and there was no correlation between the markers and the geographic distribution of the populations. The AMOVA indicated absence of genetic structure for the COI gene, suggesting that the sampled areas formed a single population unit. However, the great genetic differentiation among populations showed by ISSR demonstrates that these have been under differentiation after their expansion or may also reflect distinct dispersal behavior between males and females.

  11. Population Genetic Structure of red mullet (Mullus barbatus L. in Turkish Sea Based on Mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Fevzi Bardakci

    2014-06-01

    Full Text Available Aim: Mullus barbatus (red mullet is a commercial fish species naturally distributed from Eastern Atlantic: British Isles to Dakar, Senegal, Canary Islands, Mediterranean and Black Sea. There is no study in our knowledge aimed to determine population genetic structuring and genetic stocks of M. barbatus species in territorial waters of Turkey. Only a few studies have been carried out on their genetics in Turkey which are limited to determination of phylogenetic relationships between species in familia of Mullidae. In this study population genetic structure and genetic diversity of red mullet (Mullus barbatus L. in Turkish Seas was determined using sequence data of mitochondrial DNA control region. Material and Methods: Red mullet sample were collected from the Mediterranean Sea (Mersin, Antalya, the Aegean Sea (Ayvalık, Marmara Sea (Bandırma, the Black Sea (Zonguldak, Trabzon, Fatsa and Hopa. mtDNA control region of 410 bp in length were amplified and subsequently sequenced. The sequences were aligned in Bioedit ver 7.1.3.0 (Hall, 1999. Genetic distance between populations (γst (Nei, 1982, haplotype diversities (h, nucleotide diversities(π were detected by DNAsp ver. 5.10 (Rozas et al., 2003. Based on pairwise distance matrix data a UPGMA dendogram was constructed by MEGA 5.05 (Kumar et al., 2004. To explain genetic structuring of samples we performed analysis of molecular variance (AMOVA using Arlequin ver. 3.5 (Excoffier et al., 2010. Results: In total 190 individuals were studied and alignment of partial control region of mtDNA revealed 98 mtDNA haplotypes with 75 polymorphic sites. The average of nucleotide diversities and haplotype diversities were calculated 0,015 and 0,963 respectively. Haplotype and nucleotide (π diversities among the populations ranged from 0,907 (Zonguldak to 0,972 (Trabzon and from 0.0155 (Trabzon to 0,0114 (Bandırma, respectively. Distance tree based on gammast pairwise comparisons revealed two main clades, the

  12. The genetic structure of populations of an invading pest fruit fly, Bactrocera tryoni, at the species climatic range limit.

    Science.gov (United States)

    Gilchrist, A S; Meats, A W

    2010-08-01

    Previous population genetic studies of the Queensland fruit fly, Bactrocera tryoni Froggatt (Diptera: Tephritidae), in its central range have shown barely detectable genetic differentiation across distances of almost 3000 km (F(st)=0.003). In this study, we investigated the genetic structuring of southern border populations of B. tryoni, in the region extending from the central population to the recently colonized southern range limit. The expectation was that marginal populations would be small, fragmented population sinks, with local adaptation limited by gene flow or drift. Unexpectedly, we found that the population at the southern extreme of the range was a source population, rather than a sink, for the surrounding region. This was shown by assignment testing of recent outbreaks in an adjoining quarantine area and by indirect migration estimates. Furthermore, populations in the region had formed a latitudinal cline in microsatellite allele frequencies, spanning the region between the central population and the southern range limit. The cline has formed within 250 generations of the initial invasion and appears stable between years. We show that there is restricted gene flow in the region and that effective population sizes are of the order of 10(2)-10(3). Although the cline may result from natural selection, neutral evolutionary processes may also explain our findings.

  13. Genetics of Plasminogen Activator Inhibitor-1 (PAI-1 in a Ghanaian Population.

    Directory of Open Access Journals (Sweden)

    Marquitta J White

    Full Text Available Plasminogen activator inhibitor 1 (PAI-1, a major modulator of the fibrinolytic system, is an important factor in cardiovascular disease (CVD susceptibility and severity. PAI-1 is highly heritable, but the few genes associated with it explain only a small portion of its variation. Studies of PAI-1 typically employ linear regression to estimate the effects of genetic variants on PAI-1 levels, but PAI-1 is not normally distributed, even after transformation. Therefore, alternative statistical methods may provide greater power to identify important genetic variants. Additionally, most genetic studies of PAI-1 have been performed on populations of European descent, limiting the generalizability of their results. We analyzed >30,000 variants for association with PAI-1 in a Ghanaian population, using median regression, a non-parametric alternative to linear regression. Three variants associated with median PAI-1, the most significant of which was in the gene arylsulfatase B (ARSB (p = 1.09 x 10(-7. We also analyzed the upper quartile of PAI-1, the most clinically relevant part of the distribution, and found 19 SNPs significantly associated in this quartile. Of note an association was found in period circadian clock 3 (PER3. Our results reveal novel associations with median and elevated PAI-1 in an understudied population. The lack of overlap between the two analyses indicates that the genetic effects on PAI-1 are not uniform across its distribution. They also provide evidence of the generalizability of the circadian pathway's effect on PAI-1, as a recent meta-analysis performed in Caucasian populations identified another circadian clock gene (ARNTL.

  14. Elucidating the multiple genetic lineages and population genetic structure of the brooding coral Seriatopora (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago

    Science.gov (United States)

    Nakajima, Yuichi; Nishikawa, Akira; Iguchi, Akira; Nagata, Tomofumi; Uyeno, Daisuke; Sakai, Kazuhiko; Mitarai, Satoshi

    2017-06-01

    The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F ST = 0.064-0.116 (all P = 0.001), pairwise G''ST = 0.107-0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.

  15. Genetics in an isolated population like Finland: a different basis for genomic medicine?

    Science.gov (United States)

    Kääriäinen, Helena; Muilu, Juha; Perola, Markus; Kristiansson, Kati

    2017-10-01

    A unique genetic background in an isolated population like that of Finland offers special opportunities for genetic research as well as for applying the genetic developments to the health care. On the other hand, the different genetic background may require local attempts to develop diagnostics and treatment as the selection of diseases and mutations differs from that in the other populations. In this review, we describe the experiences of research and health care in this genetic isolate starting from the identification of specific monogenic diseases enriched in the Finnish population all the way to implementing the knowledge of the unique genetic background to genomic medicine at population level.

  16. [Geography of genetic processes in the population: genetic migration in Northern Eurasia (Central Asia region)].

    Science.gov (United States)

    Evsiukov, A N; Zhukova, O V; Rychkov, Iu B

    1999-01-01

    Based on the data of the census of 1970, a map of the rates of gene migrations in the rural population of Central Asia and Kazakhstan was drawn. The corrected average value for 35 populations of oblasts (administrative regions) and autonomous republics was m = 0.0606 +/- 0.0102. The estimate obtained from the mapped data was 0.0799 +/- 0.0014, which is 1.2-fold higher than similar values for Europe. The relationship between the rate of gene migration m, the genetically effective population size Ne, and the density of elementary populations in the studied area Pp was analyzed by means of correlation and regression analyses. The following relationship was obtained: m = A/Ne + BPp, where A > 0 and B migration flow is mainly directed to the less densely populated rural areas. Given that the region was chosen somewhat artificially, studying gene migrations in Central Asia and Kazakhstan as separate historical, geographic, and genetic subregions of northern Eurasia might be a better approach.

  17. Population Genetics and Demography Unite Ecology and Evolution.

    Science.gov (United States)

    Lowe, Winsor H; Kovach, Ryan P; Allendorf, Fred W

    2017-02-01

    The interplay of ecology and evolution has been a rich area of research for decades. A surge of interest in this area was catalyzed by the observation that evolution by natural selection can operate at the same contemporary timescales as ecological dynamics. Specifically, recent eco-evolutionary research focuses on how rapid adaptation influences ecology, and vice versa. Evolution by non-adaptive forces also occurs quickly, with ecological consequences, but understanding the full scope of ecology-evolution (eco-evo) interactions requires explicitly addressing population-level processes - genetic and demographic. We show the strong ecological effects of non-adaptive evolutionary forces and, more broadly, the value of population-level research for gaining a mechanistic understanding of eco-evo interactions. The breadth of eco-evolutionary research should expand to incorporate the breadth of evolution itself. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Population genetics and demography unite ecology and evolution

    Science.gov (United States)

    Lowe, Winsor H.; Kovach, Ryan; Allendorf, Fred W.

    2017-01-01

    The interplay of ecology and evolution has been a rich area of research for decades. A surge of interest in this area was catalyzed by the observation that evolution by natural selection can operate at the same contemporary timescales as ecological dynamics. Specifically, recent eco-evolutionary research focuses on how rapid adaptation influences ecology, and vice versa. Evolution by non-adaptive forces also occurs quickly, with ecological consequences, but understanding the full scope of ecology–evolution (eco–evo) interactions requires explicitly addressing population-level processes – genetic and demographic. We show the strong ecological effects of non-adaptive evolutionary forces and, more broadly, the value of population-level research for gaining a mechanistic understanding of eco–evo interactions. The breadth of eco-evolutionary research should expand to incorporate the breadth of evolution itself.

  19. Transferrin variation and genetic structure of reindeer populations in Scandinavia

    Directory of Open Access Journals (Sweden)

    Knut H. Røed

    1987-06-01

    Full Text Available Polyacrylamide gel electrophoresis was used to analyse transferrin variation in herds of semi-domestic reindeer from Scandinavia. The results are compared with previously reported values for other populations of both semi-domestic and wild reindeer using the same techniques as in the present study. In all populations the number of alleles was high, ranging from seven to eleven, and the heterozygosity was correspondingly high, with a mean of 0.749. This high genetic variation in all populations suggests that inbreeding is not widespread among Scandinavian reindeer. The pattern of allele frequency distribution indicates a high degree of genetic heterogeneity in the transferrin locus, both between the different semi-domestic herds and between the different wild populations. The mean value of genetic distance was 0.069 between semi-domestic herds and 0.091 between wild populations. Between semi-domestic and wild populations the genetic distance was particularly high, with a mean of 0.188. This high value was mainly due to a different pattern in the distribution of the two most common transferrin alleles: Tfu was most common among semi-domestic herds, while TfEI was most common among wild populations. These differences in transferrin allele distribution are discussed in relation to possible different origins of semi-domestic and wild reindeer in Scandinavia, or alternatively, to different selection forces acting on transferrin genotypes in semi-domestic and wild populations.Transferrin-variasjon og genetisk struktur hos rein i Skandinavia.Abstact in Norwegian / Sammendrag: Transferrin-variasjon i tamreinflokker ble analysert ved hjelp av polyacrylamid gel elektroforese. Resultatene er sammenlignet med verdier som tidligere er beskrevet for både tamrein og villrein hvor det ble benyttet samme metode som i denne undersøkelsen. I alle populasjonene ble det registrert et høyt antall alleler (7-11 og heterozygositeten var tilsvarende høy med en

  20. Genetic admixture and population substructure in Guanacaste Costa Rica.

    Directory of Open Access Journals (Sweden)

    Zhaoming Wang

    2010-10-01

    Full Text Available The population of Costa Rica (CR represents an admixture of major continental populations. An investigation of the CR population structure would provide an important foundation for mapping genetic variants underlying common diseases and traits. We conducted an analysis of 1,301 women from the Guanacaste region of CR using 27,904 single nucleotide polymorphisms (SNPs genotyped on a custom Illumina InfiniumII iSelect chip. The program STRUCTURE was used to compare the CR Guanacaste sample with four continental reference samples, including HapMap Europeans (CEU, East Asians (JPT+CHB, West African Yoruba (YRI, as well as Native Americans (NA from the Illumina iControl database. Our results show that the CR Guanacaste sample comprises a three-way admixture estimated to be 43% European, 38% Native American and 15% West African. An estimated 4% residual Asian ancestry may be within the error range. Results from principal components analysis reveal a correlation between genetic and geographic distance. The magnitude of linkage disequilibrium (LD measured by the number of tagging SNPs required to cover the same region in the genome in the CR Guanacaste sample appeared to be weaker than that observed in CEU, JPT+CHB and NA reference samples but stronger than that of the HapMap YRI sample. Based on the clustering pattern observed in both STRUCTURE and principal components analysis, two subpopulations were identified that differ by approximately 20% in LD block size averaged over all LD blocks identified by Haploview. We also show in a simulated association study conducted within the two subpopulations, that the failure to account for population stratification (PS could lead to a noticeable inflation in the false positive rate. However, we further demonstrate that existing PS adjustment approaches can reduce the inflation to an acceptable level for gene discovery.

  1. Paternal genetic history of the Basque population of Spain.

    Science.gov (United States)

    Young, Kristin L; Sun, Guangyun; Deka, Ranjan; Crawford, Michael H

    2011-08-01

    This study examines the genetic variation in Basque Y chromosome lineages using data on 12 Y-short tandem repeat (STR) loci in a sample of 158 males from four Basque provinces of Spain (Alava, Vizcaya, Guipuzcoa, and Navarre). As reported in previous studies, the Basques are characterized by high frequencies of haplogroup R1b (83%). AMOVA analysis demonstrates genetic homogeneity, with a small but significant amount of genetic structure between provinces (Y-short tandem repeat loci STRs: 1.71%, p = 0.0369). Gene and haplotype diversity levels in the Basque population are on the low end of the European distribution (gene diversity: 0.4268; haplotype diversity: 0.9421). Post-Neolithic contribution to the paternal Basque gene pool was estimated by measuring the proportion of those haplogroups with a Time to Most Recent Common Ancestor (TMRCA) previously dated either prior (R1b, I2a2) or subsequent to (E1b1b, G2a, J2a) the Neolithic. Based on these estimates, the Basque provinces show varying degrees of post-Neolithic contribution in the paternal lineages (10.9% in the combined sample).

  2. Population genetics of the invasive cryptogenic anemone, Anemonia alicemartinae, along the southeastern Pacific coast

    Science.gov (United States)

    Canales-Aguirre, C. B.; Quiñones, A.; Hernández, C. E.; Neill, P. E.; Brante, A.

    2015-08-01

    One of the most important issues in biological invasions is understanding the factors and mechanisms determining the invasion success of non-native species. Theoretical and empirical works have shown that genetic diversity is a determinant of invasion success; thus, studying spatial patterns of genetic diversity, and exploring how biological and physical factors shape this population trait, are fundamental for understanding this phenomenon. Coastal marine ecosystems are one of the most susceptible habitats to invasion given the complex network of maritime transport. In this work we study the cryptogenic anemone, Anemonia alicemartinae, which has rapidly increased its geographical range southward during the last 50 years (approx. 2000 km) along the southeastern Pacific coast. Based on COI mtDNA sequences we evaluated three main hypotheses: a) the genetic diversity of A. alicemartinae decreases according to the direction of invasion (from north to south); b) there is biogeographic-phylogeographic concordance at the 30°S biogeographic break; and c) the demographic history is coherent with a recent geographic expansion. A total of 161 individual samples of A. alicemartinae were collected along the southeastern Pacific coast range of distribution, covering more than 2000 km, including samples along the 30°S biogeographical break. Results showed low genetic diversity (Hd = 0.253; π = 0.08) and a lack of geographic population genetic structure (FST = - 0.009, p-value = 0.656). The highest genetic diversity was observed in Peru (Chero and Mesas) and at localities close to the main Chilean seaports. We did not observe concordance between biogeographic and phylogeographic patterns or isolation by distance. Demographic indices (D = - 2.604, p < 0.001; Fu's = - 26.619, p < 0.001), as well as a star-like configuration of the haplotype network support recent population expansion of this species. Our results, together with historical field observations, support the idea that

  3. A genetic algorithm based global search strategy for population pharmacokinetic/pharmacodynamic model selection.

    Science.gov (United States)

    Sale, Mark; Sherer, Eric A

    2015-01-01

    The current algorithm for selecting a population pharmacokinetic/pharmacodynamic model is based on the well-established forward addition/backward elimination method. A central strength of this approach is the opportunity for a modeller to continuously examine the data and postulate new hypotheses to explain observed biases. This algorithm has served the modelling community well, but the model selection process has essentially remained unchanged for the last 30 years. During this time, more robust approaches to model selection have been made feasible by new technology and dramatic increases in computation speed. We review these methods, with emphasis on genetic algorithm approaches and discuss the role these methods may play in population pharmacokinetic/pharmacodynamic model selection. © 2013 The British Pharmacological Society.

  4. Historical and anthropogenic factors affecting the population genetic structure of Ontario's inland lake populations of Walleye (Sander vitreus).

    Science.gov (United States)

    Walter, Ryan P; Cena, Christopher J; Morgan, George E; Heath, Daniel D

    2012-01-01

    Populations existing in formerly glaciated areas often display composite historical and contemporary patterns of genetic structure. For Canadian freshwater fishes, population genetic structure is largely reflective of dispersal from glacial refugia and isolation within drainage basins across a range of scales. Enhancement of sport fisheries via hatchery stocking programs and other means has the potential to alter signatures of natural evolutionary processes. Using 11 microsatellite loci genotyped from 2182 individuals, we analyzed the genetic structure of 46 inland lake walleye (Sander vitreus) populations spanning five major drainage basins within the province of Ontario, Canada. Population genetic analyses coupled with genotype assignment allowed us to: 1) characterize broad- and fine-scale genetic structure among Ontario walleye populations; and 2) determine if the observed population divergence is primarily due to natural or historical processes, or recent anthropogenic events. The partitioning of genetic variation revealed higher genetic divergence among lakes than among drainage basins or proposed ancestries-indicative of relatively high isolation among lakes, study-wide. Walleye genotypes were clustered into three major groups, likely reflective of Missourian, Mississippian, and Atlantic glacial refugial ancestry. Despite detectable genetic signatures indicative of anthropogenic influences, province-wide spatial genetic structure remains consistent with the hypothesis of dispersal from distinct glacial refugia and subsequent isolation of lakes within primary drainage basins. Our results provide a novel example of minimal impacts from fishery enhancement to the broad-scale genetic structure of inland fish populations.

  5. Population genetics of the Chilean frog Batrachyla Leptopus (Leptodactylidae

    Directory of Open Access Journals (Sweden)

    J.R. Formas

    2000-03-01

    Full Text Available Electrophoretic variation of proteins encoded by 14 loci was analyzed in eight (five continental and three insular populations of the Chilean leptodactylid frog Batrachyla leptopus. The overall proportion of polymorphic loci was estimated to be 18.7% and the average number of alleles per locus, 1.2, while observed and expected heterozygosities were 1.7 and 5.1%, respectively. The estimated coefficient of genetic identity was 0.940; the corresponding figure for genetic distance was 0.063. F-statistics analysis showed a total inbreeding coefficient (Fit of 0.855 and high levels of genetic subdivision (Fst = 0.596 as well as of inbreeding within populations (Fis = 0.640. However, there was only a moderate level of genetic differentiation (Fst = 0.181 between the insular group of populations and the continental group.A variação eletroforética de proteínas codificadas por 14 loci foi analisada em oito populações (5 continentais e 3 insulares da rã leptodactilídea chilena Batrachyla leptopus. A proporção geral de loci polimórficos foi estimada como sendo de 18,7% e o número médio de alelos por loco, 1,2, enquanto que as heterozigosidades observada e esperada foram 1,7 e 5,1%, respectivamente. O coeficiente esperado de identidade genética foi 0,940; o número correspondente para a distância genética foi 0,063. A análise estatística F mostrou um coeficiente de endogamia total (Fit de 0,855 e altos níveis de subdivisão genética (Fst = 0,596, assim como de endogamia dentro das populações (Fis = 0,640. Contudo, houve apenas um nível moderado de diferenciação genética (Fst = 0,181 entre o grupo insular de populações e o grupo continental.

  6. Genetic signature of anthropogenic population collapse in orang-utans.

    Directory of Open Access Journals (Sweden)

    Benoît Goossens

    2006-02-01

    Full Text Available Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.

  7. Genetic Signature of Anthropogenic Population Collapse in Orang-utans.

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.

  8. Dissecting malaria biology and epidemiology using population genetics and genomics.

    Science.gov (United States)

    Auburn, Sarah; Barry, Alyssa E

    2017-02-01

    Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches. Copyright © 2016. Published by Elsevier Ltd.

  9. Genetic parameter estimates and identification of superior white maize populations

    Directory of Open Access Journals (Sweden)

    Sara Regina Silvestrin Rovaris

    2017-04-01

    Full Text Available In Brazil, there is a shortage of white maize cultivars and genetic studies for special maize breeding programs. This study aimed to identify populations and promising hybrid white maize for main agronomic traits and grits processing and to estimate the genetic parameters of parents and heterosis. In the 2012/13 growing season, fifteen hybrids were obtained by complete diallel crosses, and six parental and commercial check varieties were evaluated for: female flowering (FF, ear height (EH, grain yield (GY, ear length (EL, volumetric mass (VM and grits processing (GP in two locations in São Paulo State, Campinas and Mococa, using a randomized block design. Analyses of variance were carried out, and diallel crosses were performed using the Gardner and Eberhart model. The populations P3 and P6 stood out because of the estimated effects of the parents and of heterosis; the studied characters are promising for obtaining new lines and forming composites. For GP, the treatments showed no differences, implying the need to introduce new sources of germplasm.

  10. Expanding the population genetic perspective of cnidarian-Symbiodinium symbioses.

    Science.gov (United States)

    Santos, Scott R

    2014-09-01

    The modern synthesis was a seminal period in the biological sciences, establishing many of the core principles of evolutionary biology that we know today. Significant catalysts were the contributions of R.A. Fisher, J.B.S. Haldane and Sewall Wright (and others) developing the theoretical underpinning of population genetics, thus demonstrating adaptive evolution resulted from the interplay of forces such as natural selection and mutation within groups of individuals occupying the same space and time (i.e. a population). Given its importance, it is surprising that detailed population genetic data remain lacking for numerous organisms vital to many ecosystems. For example, the coral reef ecosystem is well recognized for its high biodiversity and productivity, numerous ecological services and significant economic and societal values (Moberg & Folke 1999;Cinner 2014). Many coral reef invertebrates form symbiotic relationships with single-celled dinoflagellates within the genus Symbiodinium Freudenthal (Taylor 1974), with hosts providing these (typically) intracellular symbionts with by-products of metabolism and in turn receiving photosynthetically fixed carbon capable of meeting hosts' respiratory demands (Falkowski et al. 1984; Muscatine et al. 1984). Unfortunately, the health and integrity of the coral reef ecosystem has been significantly and negatively impacted by onslaughts like anthropogenic eutrophication and disease in addition to global climate change, with increased incidences of 'bleaching' events (characterized as the loss of photosynthetic pigments from the algal cell or massive reduction of Symbiodinium density from hosts' tissue) and host mortality leading to staggering declines in geographic coverage (Bruno & Selig 2007) that have raised questions on the viability of this ecosystem as we know it (Bellwood et al. 2004; Parmesan 2006). One avenue towards anticipating the future of the coral reef ecosystem is by developing a broader and deeper

  11. Integration of population genetic structure and plant response to climate change: sustaining genetic resources through evaluation of projected threats

    Science.gov (United States)

    Bryce A. Richardson; Marcus V. Warwell; Mee-Sook Kim; Ned B. Klopfenstein; Geral I. McDonald

    2010-01-01

    To assess threats or predict responses to disturbances, or both, it is essential to recognize and characterize the population structures of forest species in relation to changing environments. Appropriate management of these genetic resources in the future will require (1) understanding the existing genetic diversity/variation and population structure of forest trees...

  12. Genetic determinants of circulating sphingolipid concentrations in European populations.

    Directory of Open Access Journals (Sweden)

    Andrew A Hicks

    2009-10-01

    Full Text Available Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI, cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS between 318,237 single-nucleotide polymorphisms (SNPs and levels of circulating sphingomyelin (SM, dihydrosphingomyelin (Dih-SM, ceramide (Cer, and glucosylceramide (GluCer single lipid species (33 traits; and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32 in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08x10(-66. The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3 associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4 or less. Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be

  13. Stuck in fragments: Population genetics of the Endangered collared brown lemur Eulemur collaris in the Malagasy littoral forest.

    Science.gov (United States)

    Bertoncini, Stefania; D'Ercole, Jacopo; Brisighelli, Francesca; Ramanamanjato, Jean-Baptiste; Capelli, Cristian; Tofanelli, Sergio; Donati, Giuseppe

    2017-07-01

    The Endangered collared brown lemur (Eulemur collaris) is the largest primate living in the littoral forest of southeastern Madagascar, a top priority habitat for biodiversity conservation on the island. Because this lemur is a key seed-disperser, an evaluation of the structure and connectivity of the populations surviving in the forest fragments is urgently needed to guide conservation plans. Genetic variability at autosomal microsatellites and mitochondrial DNA was investigated in a total of 49 collared brown lemurs sampled by non-invasive methods in three littoral forest fragments and in the nearby lowland humid forest. The overall genetic diversity of E. collaris in the southeastern coastal region of Madagascar was lower than in other populations, as well as in other lemur species. The population appears highly structured, with less variable and more inbred groups inhabiting the littoral forest fragments compared to the inland area. Major barriers to gene flow were identified isolating littoral forest fragments from each other and from the inland lowland humid forest. Medium to long-term drift and scarce gene flow is the scenario that best explains the current genetic distribution. Habitat discontinuities such as rivers and grassland between forest fragments played a major role in structuring the population. A common history of size contraction is pointed out by several genetic estimators, indicating a possible ecological crisis triggered around 1,300 years ago. The adoption of strategies aimed at facilitating gene flow and population growth appears crucial to delay further loss of genetic diversity. © 2017 Wiley Periodicals, Inc.

  14. An Underlying Common Factor, Influenced by Genetics and Unique Environment, Explains the Covariation Between Major Depressive Disorder, Generalized Anxiety Disorder, and Burnout: A Swedish Twin Study.

    Science.gov (United States)

    Mather, Lisa; Blom, Victoria; Bergström, Gunnar; Svedberg, Pia

    2016-12-01

    Depression and anxiety are highly comorbid due to shared genetic risk factors, but less is known about whether burnout shares these risk factors. We aimed to examine whether the covariation between major depressive disorder (MDD), generalized anxiety disorder (GAD), and burnout is explained by common genetic and/or environmental factors. This cross-sectional study included 25,378 Swedish twins responding to a survey in 2005-2006. Structural equation models were used to analyze whether the trait variances and covariances were due to additive genetics, non-additive genetics, shared environment, and unique environment. Univariate analyses tested sex limitation models and multivariate analysis tested Cholesky, independent pathway, and common pathway models. The phenotypic correlations were 0.71 (0.69-0.74) between MDD and GAD, 0.58 (0.56-0.60) between MDD and burnout, and 0.53 (0.50-0.56) between GAD and burnout. Heritabilities were 45% for MDD, 49% for GAD, and 38% for burnout; no statistically significant sex differences were found. A common pathway model was chosen as the final model. The common factor was influenced by genetics (58%) and unique environment (42%), and explained 77% of the variation in MDD, 69% in GAD, and 44% in burnout. GAD and burnout had additive genetic factors unique to the phenotypes (11% each), while MDD did not. Unique environment explained 23% of the variability in MDD, 20% in GAD, and 45% in burnout. In conclusion, the covariation was explained by an underlying common factor, largely influenced by genetics. Burnout was to a large degree influenced by unique environmental factors not shared with MDD and GAD.

  15. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    Science.gov (United States)

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

  16. Low genetic differentiation in a sedentary bird: house sparrow population genetics in a contiguous landscape.

    Science.gov (United States)

    Kekkonen, J; Seppä, P; Hanski, I K; Jensen, H; Väisänen, R A; Brommer, J E

    2011-01-01

    The house sparrow Passer domesticus has been declining in abundance in many localities, including Finland. We studied the genetic diversity and differentiation of the house sparrow populations across Finland in the 1980s, at the onset of the species' decline in abundance. We genotyped 472 adult males (the less dispersive sex) from 13 locations in Finland (covering a range of 400 × 800 km) and one in Sweden (Stockholm) for 13 polymorphic microsatellite markers. Our analysis of Finnish ringing records showed that natal dispersal distances are limited (90% genetically very homogeneous and the limited dispersal was sufficiently large to maintain their connectivity. However, all Finnish populations differed significantly from the Stockholm population, even though direct geographical distance to it was often smaller than among Finnish populations. Hence, the open sea between Finland and Sweden appears to form a dispersal barrier for this species, whereas dispersal is much less constrained across the Finnish mainland (which lacks geographical barriers). Our findings provide a benchmark for conservation biologists and emphasize the influence of landscape structure on gene flow.

  17. [Genetic demography of populations of three megalopolises in relation to the problem of creating genetic databases].

    Science.gov (United States)

    Kurbatova, O L; Pobedonostseva, E Iu; Veremeĭchik, V M; Prudnikova, A S; Atramentova, L A; Tsybovskiĭ, I S; Udina, I G

    2013-04-01

    Based on data collected from urban residents by questionnaire, the basic parameters of the genetic-demographic structure of populations of the three megalopolises, i.e., Moscow, Kharkov, and Minsk, have been calculated, including the migration coefficients and their dynamics in generations, the radius of the cities migration attraction, the parameters of marriage structure (the proportion ofinterethnic marriages, the level of intraethnic assortative mating, the marital distances), and the gene flow between the ethnic groups. It is shown that the representatives of the most numerous ethnic groups in each megalopolis have considerable amount of admixture. For Russians of Moscow, Ukrainians of Kharkov, and Belarusians of Minsk, the proportion of individuals whose ancestors were all born in the given city for at least three generations and belonged to the same nationality turned out to be very low (4.75% in Moscow, 1.83% in Kharkov, and 3.13% in Minsk). This finding questions the formation of a reference population in the megalopolis as a sampling of aboriginals of certain ethnic origins. In the paper, we justify principles of creating genetic databases for the population of the megalopolis taking into account the complexity and dynamism of its population structure.

  18. Novel Synthetic Medea Selfish Genetic Elements Drive Population Replacement in Drosophila; a Theoretical Exploration of Medea-Dependent Population Suppression

    OpenAIRE

    Akbari, Omar S.; Chen, Chun-Hong; Marshall, John M.; Huang, Haixia; Antoshechkin, Igor; Hay, Bruce A.

    2014-01-01

    Insects act as vectors for diseases of plants, animals, and humans. Replacement of wild insect populations with genetically modified individuals unable to transmit disease provides a potentially self-perpetuating method of disease prevention. Population replacement requires a gene drive mechanism in order to spread linked genes mediating disease refractoriness through wild populations. We previously reported the creation of synthetic Medea selfish genetic elements able to drive population rep...

  19. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.

    Science.gov (United States)

    Wilson, Benjamin A; Garud, Nandita R; Feder, Alison F; Assaf, Zoe J; Pennings, Pleuni S

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance. © 2015 John Wiley & Sons Ltd.

  20. Mental health care use in medically unexplained and explained physical symptoms: findings from a general population study

    Science.gov (United States)

    van Eck van der Sluijs, Jonna F; ten Have, Margreet; Rijnders, Cees A; van Marwijk, Harm WJ; de Graaf, Ron; van der Feltz-Cornelis, Christina M

    2016-01-01

    Objective The aim of this study was to explore mental health care utilization patterns in primary and specialized mental health care of people with unexplained or explained physical symptoms. Methods Data were derived from the first wave of the Netherlands Mental Health Survey and Incidence Study-2, a nationally representative face-to-face cohort study among the general population aged 18–64 years. We selected subjects with medically unexplained symptoms (MUS) only (MUSonly; n=177), explained physical symptoms only (PHYonly, n=1,952), combined MUS and explained physical symptoms (MUS + PHY, n=209), and controls without physical symptoms (NONE, n=4,168). We studied entry into mental health care and the number of treatment contacts for mental problems, in both primary care and specialized mental health care. Analyses were adjusted for sociodemographic characteristics and presence of any 12-month mental disorder assessed with the Composite International Diagnostic Interview 3.0. Results At the primary care level, all three groups of subjects with physical symptoms showed entry into care for mental health problems significantly more often than controls. The adjusted odds ratios were 2.29 (1.33, 3.95) for MUSonly, 1.55 (1.13, 2.12) for PHYonly, and 2.25 (1.41, 3.57) for MUS + PHY. At the specialized mental health care level, this was the case only for MUSonly subjects (adjusted odds ratio 1.65 [1.04, 2.61]). In both the primary and specialized mental health care, there were no significant differences between the four groups in the number of treatment contacts once they entered into treatment. Conclusion All sorts of physical symptoms, unexplained as well as explained, were associated with significant higher entry into primary care for mental problems. In specialized mental health care, this was true only for MUSonly. No differences were found in the number of treatment contacts. This warrants further research aimed at the content of the treatment contacts. PMID

  1. Genetic diversity and population structure of Anastrepha striata (Diptera: Tephritidae) in three natural regions of southwestern Colombia using mitochondrial sequences.

    Science.gov (United States)

    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.

  2. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman.

    Science.gov (United States)

    Coia, V; Cipollini, G; Anagnostou, P; Maixner, F; Battaggia, C; Brisighelli, F; Gómez-Carballa, A; Destro Bisol, G; Salas, A; Zink, A

    2016-01-14

    The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.

  3. Big mountains but small barriers: Population genetic structure of the Chinese wood frog (Rana chensinensis in the Tsinling and Daba Mountain region of northern China

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    Li Cheng

    2009-04-01

    Full Text Available Abstract Background Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Results Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. Conclusion The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high

  4. Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

    Science.gov (United States)

    Zhan, Aibin; Li, Cheng; Fu, Jinzhong

    2009-04-09

    Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the

  5. Estimating the contribution of genetic variants to difference in incidence of disease between population groups.

    Science.gov (United States)

    Moonesinghe, Ramal; Ioannidis, John P A; Flanders, W Dana; Yang, Quanhe; Truman, Benedict I; Khoury, Muin J

    2012-08-01

    Genome-wide association studies have identified multiple genetic susceptibility variants to several complex human diseases. However, risk-genotype frequency at loci showing robust associations might differ substantially among different populations. In this paper, we present methods to assess the contribution of genetic variants to the difference in the incidence of disease between different population groups for different scenarios. We derive expressions for the contribution of a single genetic variant, multiple genetic variants, and the contribution of the joint effect of a genetic variant and an environmental factor to the difference in the incidence of disease. The contribution of genetic variants to the difference in incidence increases with increasing difference in risk-genotype frequency, but declines with increasing difference in incidence between the two populations. The contribution of genetic variants also increases with increasing relative risk and the contribution of joint effect of genetic and environmental factors increases with increasing relative risk of the gene-environmental interaction. The contribution of genetic variants to the difference in incidence between two populations can be expressed as a function of the population attributable risks of the genetic variants in the two populations. The contribution of a group of genetic variants to the disparity in incidence of disease could change considerably by adding one more genetic variant to the group. Any estimate of genetic contribution to the disparity in incidence of disease between two populations at this stage seems to be an elusive goal.

  6. Peach genetic resources: diversity, population structure and linkage disequilibrium

    Science.gov (United States)

    2013-01-01

    was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. Conclusions Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach. PMID:24041442

  7. Living on the edge: the role of geography and environment in structuring genetic variation in the southernmost populations of a tropical oak.

    Science.gov (United States)

    Ortego, J; Bonal, R; Muñoz, A; Espelta, J M

    2015-05-01

    Understanding the factors determining genetic diversity and structure in peripheral populations is a long-standing goal of evolutionary biogeography, yet little empirical information is available for tropical species. In this study, we combine information from nuclear microsatellite markers and niche modelling to analyse the factors structuring genetic variation across the southernmost populations of the tropical oak Quercus segoviensis. First, we tested the hypothesis that genetic variability decreases with population isolation and increases with local habitat suitability and stability since the Last Glacial Maximum (LGM). Second, we employed a recently developed multiple matrix regression with randomisation (MMRR) approach to study the factors associated with genetic divergence among the studied populations and test the relative contribution of environmental and geographic isolation to contemporary patterns of genetic differentiation. We found that genetic diversity was negatively correlated with average genetic differentiation with other populations, indicating that isolation and limited gene flow have contributed to erode genetic variability in some populations. Considering the relatively small size of the study area (<120 km), analyses of genetic structure indicate a remarkable inter-population genetic differentiation. Environmental dissimilarity and differences in current and past climate niche suitability and their additive effects were not associated with genetic differentiation after controlling for geographic distance, indicating that local climate does not contribute to explain spatial patterns of genetic structure. Overall, our data indicate that geographic isolation, but not current or past climate, is the main factor determining contemporary patterns of genetic diversity and structure within the southernmost peripheral populations of this tropical oak. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  8. Genetic structure of honeybee populations from southern Brazil and Uruguay

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    Diniz Nilza Maria

    2003-01-01

    Full Text Available Apis mellifera scutellata was introduced to Brazil in 1956 and Africanized honeybee populations have now spread from Argentina to the southwestern United States. Temperate climatic restrictions seem to be a natural limit to Africanized honeybee expansion around parallels 35° to 40° SL. We used allozyme loci (Mdh-1 and Hk-1 and mtDNA haplotypes to characterize honeybee populations in southern Brazil and Uruguay and define a possible transition area between Africanized and European bees. Samples of 194 bee colonies were collected from ten localities between 30°-35° SL and 52°-59° WL. The mtDNA restriction patterns of these colonies were obtained through digestion of the mitochondrial genome by Eco RI, or by digestion by Bgl II and Xba I of the cytochrome B locus and the COI-COII intergenic region, respectively. The distribution limit of African bee colonies, i.e., those populations with only the African mtDNA haplotype and with a high proportion of African genes as shown by allozyme analysis, is located in northern Uruguay, with a hybridization zone located farther south in Uruguay. A gradual cline from north to south was observed, confirmed by mtDNA, racial admixture, and genetic distance analyses. No evidence of either gametic disequilibrium between nuclear markers or cytonuclear disequilibrium among the nuclear and mtDNA genotypes was detected, suggesting that the hybridization process has been completed.

  9. Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations.

    Science.gov (United States)

    Sanchez-Mazas, A; Vidan-Jeras, B; Nunes, J M; Fischer, G; Little, A-M; Bekmane, U; Buhler, S; Buus, S; Claas, F H J; Dormoy, A; Dubois, V; Eglite, E; Eliaou, J F; Gonzalez-Galarza, F; Grubic, Z; Ivanova, M; Lie, B; Ligeiro, D; Lokki, M L; da Silva, B Martins; Martorell, J; Mendonça, D; Middleton, D; Voniatis, D Papioannou; Papasteriades, C; Poli, F; Riccio, M E; Vlachou, M Spyropoulou; Sulcebe, G; Tonks, S; Nevessignsky, M Toungouz; Vangenot, C; van Walraven, A-M; Tiercy, J-M

    2012-12-01

    HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics' analyses) recommends avoiding outdated racial classifications and population names (e.g. 'Caucasian') and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. 'pan-European'). A standard 'HLA-NET POPULATION DATA QUESTIONNAIRE' has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in 'HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS'. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable

  10. Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers

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    Ágnes Ősz

    2015-12-01

    4 University of West Hungary, Mosonmagyaróvár Vár 2., 9200 Mosonmagyaróvár, Hungary Based on the analyses of the mitochondrial DNA of several European brown trout populations, five evolutionary lineages of brown trout were indentified (Atlantic, Danubian, Mediterranean, Adriatic, Marble. The species is bred primarily for stock enhancement of natural waters, however the most hatchery-maintained broodstocks originate from the Atlantic lineage. Due to the hydrogeography of Hungary our stocks should theoretically belong to the Danubian lineage; however, this has not been investigated earlier by genetic studies. For our genetic analysis, 702 fin clips were collected from two brown trout broodstocks (Lillafüred and Szilvásvárad as well as populations of natural streams (Bán, Jósva, Kemence, Apátkút, Bittva and Kölöntés in Hungary. Sequencing of the control region in mitochondrial DNA, three PCR-RFLP (mitochondrial DNA control region, lactate dehydrogenase and somatolactin genes and five microsatellite markers were used to distinguish between Danubian and Atlantic lineages of brown trout. The proportion of the mitochondrial haplotype of the Danubian lineage was low, with the exception of the Apátkúti, Kölöntés streams and Szilvásvárad broodstock. Analyses of nuclear PCR-RFLP and microsatellites markers showed various distributions of alleles characteristic of the Atlantic or Danubian lineages, although the Atlantic genotype has dominated in all population. In case of the analyses of microsatellites the polymorphism varied greatly at all locations. In addition we found several alleles that were not described earlier in other populations. Those alleles probably would be typical of Hungarian brown trout populations. Overall the populations were effectively in Hardy-Weinberg equilibrium for both PCR-RFLP and microsatellite markers. The remarkably high proportion of allochthonous Atlantic alleles in the analyzed sites is a clear indicator of the import

  11. Population genetics of the deep-sea bluntnose sixgill shark, Hexanchus griseus, revealing spatial genetic heterogeneity.

    Science.gov (United States)

    Vella, Noel; Vella, Adriana

    2017-06-08

    Hexanchus griseus is a globally distributed deep-water shark species. It inhabits tropical and temperate waters throughout the world, including the Mediterranean Sea where it is by-caught by small-scale fisheries in the region. In this study, we analysed the genetic variation of H. griseus specimens collected from different areas within and outside the Mediterranean region, to assess its genetic connectivity. The mitochondrial DNA (mtDNA) sequence analysed in this study ranged from cytochrome b to 16S rRNA genes including the control region, the 12S rRNA gene and the interspersed tRNA genes in the region, covering a total of 3731 to 3914 nucleotides. Results have shown that this species exhibits geographically distinct maternal lineages, indicating population structure along geographical ranges. These findings reveal population subdivisions not only between the Pacific Ocean and the Atlantic Ocean, but also within the oceans and on a smaller scale within the Mediterranean Sea. This highlights the need to consider each population subdivision separately when designing management plans for the conservation of this species. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Fatty Acid Diversity is Not Associated with Neutral Genetic Diversity in Native Populations of the Biodiesel Plant Jatropha curcas L.

    Science.gov (United States)

    Martínez-Díaz, Yesenia; González-Rodríguez, Antonio; Rico-Ponce, Héctor Rómulo; Rocha-Ramírez, Víctor; Ovando-Medina, Isidro; Espinosa-García, Francisco J

    2017-01-01

    Jatropha curcas L. (Euphorbiaceae) is a shrub native to Mexico and Central America, which produces seeds with a high oil content that can be converted to biodiesel. The genetic diversity of this plant has been widely studied, but it is not known whether the diversity of the seed oil chemical composition correlates with neutral genetic diversity. The total seed oil content, the diversity of profiles of fatty acids and phorbol esters were quantified, also, the genetic diversity obtained from simple sequence repeats was analyzed in native populations of J. curcas in Mexico. Using the fatty acids profiles, a discriminant analysis recognized three groups of individuals according to geographical origin. Bayesian assignment analysis revealed two genetic groups, while the genetic structure of the populations could not be explained by isolation-by-distance. Genetic and fatty acid profile data were not correlated based on Mantel test. Also, phorbol ester content and genetic diversity were not associated. Multiple linear regression analysis showed that total oil content was associated with altitude and seasonality of temperature. The content of unsaturated fatty acids was associated with altitude. Therefore, the cultivation planning of J. curcas should take into account chemical variation related to environmental factors. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  13. Spatial genetic structure in natural populations of Phragmites australis in a mosaic of saline habitats in the Yellow River Delta, China.

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    Lexuan Gao

    Full Text Available Determination of spatial genetic structure (SGS in natural populations is important for both theoretical aspects of evolutionary genetics and their application in species conservation and ecological restoration. In this study, we examined genetic diversity within and among the natural populations of a cosmopolitan grass Phragmites australis (common reed in the Yellow River Delta (YRD, China, where a mosaic of habitat patches varying in soil salinity was detected. We demonstrated that, despite their close geographic proximity, the common reed populations in the YRD significantly diverged at six microsatellite loci, exhibiting a strong association of genetic variation with habitat heterogeneity. Genetic distances among populations were best explained as a function of environmental difference, rather than geographical distance. Although the level of genetic divergence among populations was relatively low (F'(ST =0.073, weak but significant genetic differentiation, as well as the concordance between ecological and genetic landscapes, suggests spatial structuring of genotypes in relation to patchy habitats. These findings not only provided insights into the population dynamics of common reed in changing environments, but also demonstrated the feasibility of using habitat patches in a mosaic landscape as test systems to identify appropriate genetic sources for ecological restoration.

  14. Understanding population structure and historical demography in a conservation context: population genetics of the endangered Kirengeshoma palmata (Hydrangeaceae).

    Science.gov (United States)

    Yuan, Na; Sun, Yi; Comes, Hans-Peter; Fu, Cheng-Xin; Qiu, Ying-Xiong

    2014-03-01

    Both historical and contemporary microevolutionary processes greatly influence the genetic patterns of East Asian plant endemics, but the spatial and temporal contexts of these processes remain poorly understood. Here, we investigate the relative influences of historical and contemporary gene flow and drift on the population genetic structure of Kirengeshoma palmata, a perennial herb from East China and South Japan. We used data from nine polymorphic microsatellite loci to assess the levels of genetic diversity, effective population size, and contemporary and historical gene flow for six of the seven known populations. We found high levels of inbreeding and allelic diversity within populations. Both contemporary and historical migration rates among populations were low, and a test of alternate models of population history strongly favored a model of long-term drift-migration equilibrium. We inferred declines in population size ca. 10,000-100,000 yr ago, but failed to detect recent declines. Bayesian clustering divided K. palmata populations into three genetic clusters, two of which were consistent with a glacial refugium hypothesis for two mountain ranges in East China. These results suggest that anthropogenic fragmentation has had little effect on the genetic characteristics of Chinese K. palmata. Rather, past decline in population size due to Late Pleistocene climate change as well as restricted pollen and seed dispersal may have contributed to low levels of both historical and contemporary gene flow, resulting in high genetic differentiation between adjacent mountain ranges due to genetic drift and inbreeding.

  15. The genetics of a putative social trait in natural populations of yeast

    Science.gov (United States)

    Bozdag, G O; Greig, D

    2014-01-01

    The sharing of secreted invertase by yeast cells is a well-established laboratory model for cooperation, but the only evidence that such cooperation occurs in nature is that the SUC loci, which encode invertase, vary in number and functionality. Genotypes that do not produce invertase can act as ‘cheats’ in laboratory experiments, growing on the glucose that is released when invertase producers, or ‘cooperators’, digest sucrose. However, genetic variation for invertase production might instead be explained by adaptation of different populations to different local availabilities of sucrose, the substrate for invertase. Here we find that 110 wild yeast strains isolated from natural habitats, and all contained a single SUC locus and produced invertase; none were ‘cheats’. The only genetic variants we found were three strains isolated instead from sucrose-rich nectar, which produced higher levels of invertase from three additional SUC loci at their subtelomeres. We argue that the pattern of SUC gene variation is better explained by local adaptation than by social conflict. PMID:25169714

  16. Quantifying population genetic differentiation from next-generation sequencing data

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Garrett Vieira, Filipe Jorge; Korneliussen, Thorfinn Sand

    2013-01-01

    Over the last few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of these sequencing technologies is often challenged by errors and biases associated with the bioinformatical methods used for analyzing the data...... individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage........ In particular, the use of naïve methods to identify polymorphic sites and infer genotypes can inflate downstream analyses. Recently, explicit modeling of genotype probability distributions has been proposed as a method for taking genotype call uncertainty into account. Based on this idea, we propose a novel...

  17. Genetic structure of autochthonous populations of Meso-America: Mexico.

    Science.gov (United States)

    Lisker, R; Ramírez, E; Babinsky, V

    1996-06-01

    We analyze the possible effect of gene flow on the genetic structure of present-day Mexicans. For this purpose we reviewed previous admixture estimates for various Indian and Mestizo groups. Several facts seem clear: (1) There are no pure Indian groups in Mexico, because all Indian groups show variable degrees of admixture, mostly with whites (range, 0.088 in the Huichol to 0.373 in the Huasteco); (2) the main ancestral contribution to the noncoastal lower middle class Mestizo populations is Indian (above 50%) so that from a genetic standpoint Indians and lower middle class Mestizos are not much different; and (3) black ancestry is quite high on the coasts, ranging from 0.127 to 0.405 on the east coast, and is present in other Mestizos, ranging in large urban centers from 0.027 in Oaxaca to 0.107 in Puebla and in smaller cities from 0.08 in Tlaxcala to 0.181 in Cuanalán.

  18. Optimization of genomic selection training populations with a genetic algorithm.

    Science.gov (United States)

    Akdemir, Deniz; Sanchez, Julio I; Jannink, Jean-Luc

    2015-05-06

    In this article, we imagine a breeding scenario with a population of individuals that have been genotyped but not phenotyped. We derived a computationally efficient statistic that uses this genetic information to measure the reliability of genomic estimated breeding values (GEBV) for a given set of individuals (test set) based on a training set of individuals. We used this reliability measure with a genetic algorithm scheme to find an optimized training set from a larger set of candidate individuals. This subset was phenotyped to create the training set that was used in a genomic selection model to estimate GEBV in the test set. Our results show that, compared to a random sample of the same size, the use of a set of individuals selected by our method improved accuracies. We implemented the proposed training selection methodology on four sets of data on Arabidopsis, wheat, rice and maize. This dynamic model building process that takes genotypes of the individuals in the test sample into account while selecting the training individuals improves the performance of genomic selection models.

  19. Population genetics of the Schistosoma snail host Bulinus truncatus in Egypt.

    Science.gov (United States)

    Zein-Eddine, Rima; Djuikwo-Teukeng, Félicité F; Dar, Yasser; Dreyfuss, Gilles; Van den Broeck, Frederik

    2017-08-01

    The tropical freshwater snail Bulinus truncatus serves as an important intermediate host of several human and cattle Schistosoma species in many African regions. Despite some ecological and malacological studies, there is no information on the genetic diversity of B. truncatus in Egypt. Here, we sampled 70-100 snails in ten localities in Upper Egypt and the Nile Delta. Per locality, we sequenced 10 snails at a partial fragment of the cytochrome c oxidase subunit 1 gene (cox1) and we genotyped 25-30 snails at six microsatellite markers. A total of nine mitochondrial haplotypes were detected, of which five were unique to the Nile Delta and three were unique to Upper Egypt, indicating that snail populations may have evolved independently in both regions. Bayesian clustering and hierarchical F-statistics using microsatellite markers further revealed strong population genetic structure at the level of locality. Observed heterozygosity was much lower compared to what is expected under random mating, which could be explained by high selfing rates, population size reductions and to a lesser extent by the Wahlund effect. Despite these observations, we found signatures of gene flow and cross-fertilization, even between snails from the Nile Delta and Upper Egypt, indicating that B. truncatus can travel across large distances in Egypt. These observations could have serious consequences for disease epidemiology, as it means that infected snails from one region could rapidly and unexpectedly spark a new epidemic in another distant region. This could be one of the factors explaining the rebound of human Schistosoma infections in the Nile Delta, despite decades of sustained schistosomiasis control. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Genetic diversity in different populations of sloths assessed by DNA fingerprinting

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    MORAES N.

    2002-01-01

    Full Text Available In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

  1. Juvenile resilience and adult longevity explain residual populations of the Andean wax palm Ceroxylon quindiuense after deforestation.

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    María José Sanín

    Full Text Available Wax palms are an important element of the cloud forests in the tropical Andes. Despite heavy deforestation, the density of adults seems to be similar in deforested pastures as in forests. We aimed to infer the mechanisms responsible for this apparent resilience in pastures and we tested two hypotheses to explain it: 1 adult palms survived in pastures because they were spared from logging, and 2 adults occurred in pastures through the resilience of large juvenile rosettes, which survived through subterranean meristems and later developed into adults. For this purpose, we characterized the demographic structure of C. quindiuense in a total of 122 plots of 400 m(2 in forests and pastures at two sites with contrasted land use histories in Colombia and Peru. Additionally, we implemented growth models that allowed us to estimate the age of individuals at four sites. These data were combined with information collected from local land managers in order to complete our knowledge on the land use history at each site. At two sites, the presence of old individuals up to 169 years and a wide age range evidenced that, at least, a portion of current adults in pastures were spared from logging at the time of deforestation. However, at the two other sites, the absence of older adults in pastures and the narrow age range of the populations indicated that individuals came exclusively from rosette resilience. These interpretations were consistent with the land use history of sites. In consequence, the combination of the two hypotheses (spared individuals and rosette resilience explained patterns of C. quindiuense in pastures on a regional scale. Regeneration through subterranean meristems in palms is an important, yet overlooked mechanism of resilience, which occurs in a number of palm species and deserves being integrated in the conceptual framework of disturbance ecology.

  2. Comment on Gohli et al. : "Does promiscuity explain differences in levels of genetic diversity across passerine birds?"

    NARCIS (Netherlands)

    Spurgin, Lewis G.

    2013-01-01

    Gohli et al. (2013) report a positive relationship between genetic diversity and promiscuity across passerine birds, and suggest that female promiscuity acts as a form of balancing selection, maintaining differences in genetic variation across species. This is an interesting hypothesis, but the

  3. A variant in the ABO gene explains the variation in soluble E-selectin levels-results from dense genotyping in two independent populations.

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    Mahir Karakas

    Full Text Available BACKGROUND: Elevated soluble (s E-selectin levels have been associated with various cardiovascular diseases. Recently, genetic variants in the ABO blood group have been related to E-selectin levels in a small cohort of patients with type 1 diabetes. We evaluated whether this association is reproducible in two large samples of Caucasians. METHODOLOGY/ PRINCIPAL FINDINGS: Data of the present study was drawn from the population-based MONICA/KORA Augsburg study (n = 1,482 and the patients-based LURIC study (n = 1,546. A high-density genotyping array (50K IBC Chip containing single-nucleotide polymorphisms (SNPs from E-selectin candidate genes selected on known biology of E-selectin metabolism, mouse genetic studies, and human genetic association studies, was used for genotyping. Linear regression analyses with adjustment for age and sex (and survey in KORA were applied to assess associations between gene variants and sE-selectin concentrations. A number of 12 SNPs (in KORA and 13 SNPs (in LURIC, all from the ABO blood group gene, were significantly associated with the log-transformed concentration of E-selectin. The strongest association was observed for rs651007 with a change of log-transformed sE-selectin per one copy of the minor allele of -0.37 ng/ml (p = 1.87×10(-103 in KORA and -0.35 ng/ml (p = 5.11×10(-84 in LURIC. Inclusion of rs651007 increased the explained sE-selectin variance by 0.256 in KORA and 0.213 in LURIC. All SNPs had minor allele frequencies above 20% showing a substantial gene variation. CONCLUSIONS/ SIGNIFICANCE: Our findings in two independent samples indicate that the genetic variants at the ABO locus affect sE-selectin levels. Since distinct genome-wide association studies linked the ABO gene with myocardial infarction (MI in the presence of coronary atherosclerosis and with coronary artery disease, these findings may not only enhance our understanding of adhesion molecule biology, but may also provide a focus for several

  4. Genetic diversity and population differentiation of Sclerotinia sclerotiorum collected from canola in China and in USA

    Science.gov (United States)

    Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity wa...

  5. Comment on Gohli et al. (2013): "Does promiscuity explain differences in levels of genetic diversity across passerine birds?".

    Science.gov (United States)

    Spurgin, Lewis G

    2013-10-01

    Gohli et al. (2013) report a positive relationship between genetic diversity and promiscuity across passerine birds, and suggest that female promiscuity acts as a form of balancing selection, maintaining differences in genetic variation across species. This is an interesting hypothesis, but the enormous variation in genetic diversity present within species is not taken into account in their analyses. This, combined with a small sample size at several levels, makes the relationship between genetic diversity and promiscuity very difficult to interpret. Demonstrating that species-level differences in genetic diversity (if they occur at all) are affected by promiscuity would require a far more comprehensive study than is presently possible. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  6. Population Structure and Genetic Relationships of Melia Taxa in China Assayed with Sequence-Related Amplified Polymorphism (SRAP Markers

    Directory of Open Access Journals (Sweden)

    Boyong Liao

    2016-04-01

    Full Text Available The uncertainty about whether, in China, the genus Melia (Meliaceae consists of one species (M. azedarach Linnaeus or two species (M. azedarach and M. toosendan Siebold & Zuccarini remains to be clarified. Although the two putative species are morphologically distinguishable, genetic evidence supporting their taxonomic separation is lacking. Here, we investigated the genetic diversity and population structure of 31 Melia populations across the natural distribution range of the genus in China. We used sequence-related amplified polymorphism (SRAP markers and obtained 257 clearly defined bands amplified by 20 primers from 461 individuals. The polymorphic loci (P varied from 35.17% to 76.55%, with an overall mean of 58.24%. Nei’s gene diversity (H ranged from 0.13 to 0.31, with an overall mean of 0.20. Shannon’s information index (I ranged from 0.18 to 0.45, with an average of 0.30. The genetic diversity of the total population (Ht and within populations (Hs was 0.37 ± 0.01 and 0.20 ± 0.01, respectively. Population differentiation was substantial (Gst = 0.45, and gene flow was low. Of the total variation, 31.41% was explained by differences among putative species, 19.17% among populations within putative species, and 49.42% within populations. Our results support the division of genus Melia into two species, which is consistent with the classification based on the morphological differentiation.

  7. [Develop a statistics analysis software in population genetics using VBA language].

    Science.gov (United States)

    Cai, Ying; Zhou, Ni; Xu, Ye-li; Xiang, Da-peng; Su, Jiang-hui; Zhang, Lin-tian

    2006-12-01

    To develop a statistics analysis software that can be used in STR population genetics for the purpose of promoting and fastening the basic research of STR population genetics. Selecting the Microsoft VBA for Excel, which is simple and easy to use, as the program language and using its macro function to develop a statistics analysis software used in STR population genetics. The software "Easy STR Genetics" based on VBA language, by which the population genetic analysis of STR data can be made, were developed. The developed software "Easy STR Genetics" based on VBA language, can be spread in the domain of STR population genetics research domestically and internationally, due to its feature of full function, good compatibility for different formats of input data, distinct and easy to understand outputs for statistics and calculation results.

  8. Genetic variation in time and space : Microsatellite analysis of extinct and extant populations of Atlantic salmon

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Michael Møller; Loeschcke, V.

    1999-01-01

    Information on genetic composition of past and present populations may be obtained by analyzing DNA from archival samples. A study is presented on the genetic population structure of extant and extinct local populations of Atlantic salmon from 1913 to 1989 using dried scales as a source of DNA...

  9. Genetic structure of American chestnut populations based on neutral DNA markers

    Science.gov (United States)

    Thomas L. Kubisiak; James H. Roberds

    2006-01-01

    Microsatellite and RAPD markers suggest that American chestnut exists as a highly variable species. Even at the margins of its natural range, with a large proportion of its genetic variability occurring within populations (~95%). A statistically significant proportion also exists among population. Although genetic differentiation among populations has taken place, no...

  10. Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies

    NARCIS (Netherlands)

    Pham, H.T.M.; Berthouly-Salazar, C.; Crooijmans, R.P.M.A.

    2013-01-01

    The aims of this study were to assess the genetic diversity of 17 populations of Vietnamese local chickens (VNN) and one Red Jungle Fowl population, together with six chicken populations of Chinese origin (CNO), and to provide priorities supporting the conservation of genetic resources using 20

  11. Genetic diversity and population structure of sickleweed (Falcaria vulgaris; Apiaceae) in the upper Midwest USA

    Science.gov (United States)

    Sarbottam Piya; Madhav P. Nepal; Jack L. Butler; Gary E. Larson; Achal Neupane

    2014-01-01

    Sickleweed (Falcaria vulgaris), an introduced species native to Europe and Asia, grows as an aggressive weed in some areas of the upper Midwest in the United States. We are reporting genetic diversity and population structure of sickleweed populations using microsatellite markers and nuclear and chloroplast DNA sequences. Populations showed high genetic differentiation...

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

    Science.gov (United States)

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

    2012-01-01

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

  13. Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history.

    Directory of Open Access Journals (Sweden)

    Jeffrey L Peters

    Full Text Available Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect to test for deviations from selective neutrality in the gadwall (Anas strepera, a Holarctic duck. Nucleotide diversity among these loci varied by nearly two orders of magnitude (from 0.0004 to 0.029, and this heterogeneity could not be explained by differences in substitution rates alone. Using two different coalescent methods to infer models of population history and then simulating neutral genetic diversity under these models, we found that the observed among-locus heterogeneity in nucleotide diversity was significantly higher than expected for these simple models. Defining more complex models of population history demonstrated that a pre-divergence bottleneck was also unlikely to explain this heterogeneity. However, both selection and interspecific hybridization could account for the heterogeneity observed among loci. Regardless of the cause of the deviation, our results illustrate that violating key assumptions of coalescent models can mislead inferences of population history.

  14. Contrasting effects of summer and winter warming on body mass explain population dynamics in a food-limited Arctic herbivore.

    Science.gov (United States)

    Albon, Steve D; Irvine, R Justin; Halvorsen, Odd; Langvatn, Rolf; Loe, Leif E; Ropstad, Erik; Veiberg, Vebjørn; van der Wal, René; Bjørkvoll, Eirin M; Duff, Elizabeth I; Hansen, Brage B; Lee, Aline M; Tveraa, Torkild; Stien, Audun

    2017-04-01

    The cumulative effects of climate warming on herbivore vital rates and population dynamics are hard to predict, given that the expected effects differ between seasons. In the Arctic, warmer summers enhance plant growth which should lead to heavier and more fertile individuals in the autumn. Conversely, warm spells in winter with rainfall (rain-on-snow) can cause 'icing', restricting access to forage, resulting in starvation, lower survival and fecundity. As body condition is a 'barometer' of energy demands relative to energy intake, we explored the causes and consequences of variation in body mass of wild female Svalbard reindeer (Rangifer tarandus platyrhynchus) from 1994 to 2015, a period of marked climate warming. Late winter (April) body mass explained 88% of the between-year variation in population growth rate, because it strongly influenced reproductive loss, and hence subsequent fecundity (92%), as well as survival (94%) and recruitment (93%). Autumn (October) bod