WorldWideScience

Sample records for classification population genetics

  1. 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.

  2. Molecular Population Genetics

    Science.gov (United States)

    Casillas, Sònia; 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 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. PMID:28270526

  3. Population Genetics with Fluctuating Population Sizes

    CERN Document Server

    Chotibut, Thiparat

    2016-01-01

    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 fluctuations-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  4. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

    Science.gov (United States)

    Maglo, Koffi N.; Mersha, Tesfaye B.; Martin, Lisa J.

    2016-01-01

    The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to “frictional” effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the “cluster” and “cline” constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response. PMID:26925096

  5. Population Genomics and the Statistical Values of Race:An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

    Directory of Open Access Journals (Sweden)

    Koffi N. Maglo

    2016-02-01

    Full Text Available The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to frictional effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the cluster and cline constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin’s argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors and evolutionary forces affecting disease causation and treatment response.

  6. Genetic Feature Selection for Texture Classification

    Institute of Scientific and Technical Information of China (English)

    PAN Li; ZHENG Hong; ZHANG Zuxun; ZHANG Jianqing

    2004-01-01

    This paper presents a novel approach to feature subset selection using genetic algorithms. This approach has the ability to accommodate multiple criteria such as the accuracy and cost of classification into the process of feature selection and finds the effective feature subset for texture classification. On the basis of the effective feature subset selected, a method is described to extract the objects which are higher than their surroundings, such as trees or forest, in the color aerial images. The methodology presented in this paper is illustrated by its application to the problem of trees extraction from aerial images.

  7. A Descriptive Genetic Classification for Glaciovolcanoes

    Science.gov (United States)

    Edwards, B. R.; Russell, K.; Porritt, L. A.

    2014-12-01

    We review the recently published descriptive genetic classification for glaciovolcanoes (Russell et al., Quat Sci Rv, 2014). The new classification uses 'tuya' as a root word for all glaciovolcanic edifices, and with modifiers that make the classification descriptive (e.g., andesitic, lava-dominated, flat topped tuya). Although tuyas can range in composition from basaltic to rhyolitic, many of the characteristics diagnostic of glaciovolcanic environments are largely independent of lava composition (e.g., edifice morphology, columnar jointing patterns, glass distributions, pyroclast shapes). Tuya subtypes are first classified on the basis of variations in edifice-scale morphologies (e.g., conical tuya) then, on the proportions of the essential lithofacies (e.g., tephra-dominated conical tuya), and lastly on magma composition (e.g., basaltic, tephra-dominated, conical tuya). The lithofacies associations within tuyas broadly record the interplay between magmatic and glaciohydraulic conditions extent during the active phases of the eruption, including the dominant style of eruption (e.g., explosive vs. effusive). We present nine distinct, endmember models for glaciovolcanic edifices that simultaneously record changes in eruption conditions (explosive, transitional, effusive) for different general glaciohydraulic conditions (closed/sealed, leaky/partly sealed, open/well-drained). To date we have identified potential examples for 7 of the 9 models. Use of a simplified, descriptive classification scheme for glaciovolcanoes will facilitate communications amongst volcanologists and planetary scientists and the use of tuyas for recovering critical paleo-environmental information, particularly the local glaciohydraulics extent during eruptions.

  8. Wolf population genetics in Europe

    DEFF Research Database (Denmark)

    Hindrikson, Maris; Remm, Jaanus; Pilot, Malgorzata

    2017-01-01

    The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human–carnivore conflict, which has led to long-term persecution of wolves......, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population...... (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included...

  9. Population genetics without intraspecific data

    DEFF Research Database (Denmark)

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

    2007-01-01

    A central goal of computational biology is the prediction of phenotype from DNA and protein sequence data. Recent models of sequence change use in silico prediction systems to incorporate the effects of phenotype on evolutionary rates. These models have been designed for analyzing sequence data...... 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...... reflects the tendency for protein tertiary structure to influence nonsynonymous substitution rates. We argue that statistical fit to data should not be the sole criterion for assessing models of sequence change. A good interspecific model should also yield a clear and biologically plausible population...

  10. Microsatellite data analysis for population genetics.

    Science.gov (United States)

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    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 variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  11. 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...

  12. 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.

  13. (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.

  14. Microbial diversity - insights from population genetics

    NARCIS (Netherlands)

    Mes, T.H.M.

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, Ne, is one of the parameters that determines population genetic

  15. 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.

  16. Genetic programming and serial processing for time series classification.

    Science.gov (United States)

    Alfaro-Cid, Eva; Sharman, Ken; Esparcia-Alcázar, Anna I

    2014-01-01

    This work describes an approach devised by the authors for time series classification. In our approach genetic programming is used in combination with a serial processing of data, where the last output is the result of the classification. The use of genetic programming for classification, although still a field where more research in needed, is not new. However, the application of genetic programming to classification tasks is normally done by considering the input data as a feature vector. That is, to the best of our knowledge, there are not examples in the genetic programming literature of approaches where the time series data are processed serially and the last output is considered as the classification result. The serial processing approach presented here fills a gap in the existing literature. This approach was tested in three different problems. Two of them are real world problems whose data were gathered for online or conference competitions. As there are published results of these two problems this gives us the chance to compare the performance of our approach against top performing methods. The serial processing of data in combination with genetic programming obtained competitive results in both competitions, showing its potential for solving time series classification problems. The main advantage of our serial processing approach is that it can easily handle very large datasets.

  17. Genetic variation among white croaker populations

    Science.gov (United States)

    Han, Zhiqiang; Gao, Tianxiang; Zhuang, Zhimeng; Tang, Qisheng

    2008-02-01

    To investigate the genetic structures and differentiation of different wild populations of white croaker ( Pennahia argentata), horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 loci, of which eleven were polymorphic. The percentage of polymorphic loci of white croaker populations varied from 6.67% to 53.33%; the mean observed and expected heterozygosity ranged from 0.0033 to 0.0133 and 0.0032 to 0.0191, respectively. The expected heterozygosity revealed a low genetic variability for white croaker in comparison with other marine fishes. The genetic distances between populations ranged from 0.00005 to 0.00026. A weak differentiation was observed within each clade and between clades; and no significant differences in gene frequencies among populations were observed in white croaker. Among the five populations, three Chinese populations showed more genetic diversity than that in Japanese populations.

  18. Discovering Fuzzy Censored Classification Rules (Fccrs: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Renu Bala

    2012-08-01

    Full Text Available Classification Rules (CRs are often discovered in the form of ‘If-Then’ Production Rules (PRs. PRs, beinghigh level symbolic rules, are comprehensible and easy to implement. However, they are not capable ofdealing with cognitive uncertainties like vagueness and ambiguity imperative to real word decision makingsituations. Fuzzy Classification Rules (FCRs based on fuzzy logic provide a framework for a flexiblehuman like reasoning involving linguistic variables. Moreover, a classification system consisting of simple‘If-Then’ rules is not competent in handling exceptional circumstances. In this paper, we propose aGenetic Algorithm approach to discover Fuzzy Censored Classification Rules (FCCRs. A FCCR is aFuzzy Classification Rule (FCRs augmented with censors. Here, censors are exceptional conditions inwhich the behaviour of a rule gets modified. The proposed algorithm works in two phases. In the firstphase, the Genetic Algorithm discovers Fuzzy Classification Rules. Subsequently, these FuzzyClassification Rules are mutated to produce FCCRs in the second phase. The appropriate encodingscheme, fitness function and genetic operators are designed for the discovery of FCCRs. The proposedapproach for discovering FCCRs is then illustrated on a synthetic dataset.

  19. Protein fold classification with genetic algorithms and feature selection.

    Science.gov (United States)

    Chen, Peng; Liu, Chunmei; Burge, Legand; Mahmood, Mohammad; Southerland, William; Gloster, Clay

    2009-10-01

    Protein fold classification is a key step to predicting protein tertiary structures. This paper proposes a novel approach based on genetic algorithms and feature selection to classifying protein folds. Our dataset is divided into a training dataset and a test dataset. Each individual for the genetic algorithms represents a selection function of the feature vectors of the training dataset. A support vector machine is applied to each individual to evaluate the fitness value (fold classification rate) of each individual. The aim of the genetic algorithms is to search for the best individual that produces the highest fold classification rate. The best individual is then applied to the feature vectors of the test dataset and a support vector machine is built to classify protein folds based on selected features. Our experimental results on Ding and Dubchak's benchmark dataset of 27-class folds show that our approach achieves an accuracy of 71.28%, which outperforms current state-of-the-art protein fold predictors.

  20. 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.

  1. Mass spectrometry cancer data classification using wavelets and genetic algorithm.

    Science.gov (United States)

    Nguyen, Thanh; Nahavandi, Saeid; Creighton, Douglas; Khosravi, Abbas

    2015-12-21

    This paper introduces a hybrid feature extraction method applied to mass spectrometry (MS) data for cancer classification. Haar wavelets are employed to transform MS data into orthogonal wavelet coefficients. The most prominent discriminant wavelets are then selected by genetic algorithm (GA) to form feature sets. The combination of wavelets and GA yields highly distinct feature sets that serve as inputs to classification algorithms. Experimental results show the robustness and significant dominance of the wavelet-GA against competitive methods. The proposed method therefore can be applied to cancer classification models that are useful as real clinical decision support systems for medical practitioners.

  2. Genetic drift of HIV populations in culture.

    Directory of Open Access Journals (Sweden)

    Yegor Voronin

    2009-03-01

    Full Text Available Populations of Human Immunodeficiency Virus type 1 (HIV-1 undergo a surprisingly large amount of genetic drift in infected patients despite very large population sizes, which are predicted to be mostly deterministic. Several models have been proposed to explain this phenomenon, but all of them implicitly assume that the process of virus replication itself does not contribute to genetic drift. We developed an assay to measure the amount of genetic drift for HIV populations replicating in cell culture. The assay relies on creation of HIV populations of known size and measurements of variation in frequency of a neutral allele. Using this assay, we show that HIV undergoes approximately ten times more genetic drift than would be expected from its population size, which we defined as the number of infected cells in the culture. We showed that a large portion of the increase in genetic drift is due to non-synchronous infection of target cells. When infections are synchronized, genetic drift for the virus is only 3-fold higher than expected from its population size. Thus, the stochastic nature of biological processes involved in viral replication contributes to increased genetic drift in HIV populations. We propose that appreciation of these effects will allow better understanding of the evolutionary forces acting on HIV in infected patients.

  3. Genetics of autoimmune diseases: insights from population genetics.

    Science.gov (United States)

    Ramos, Paula S; Shedlock, Andrew M; Langefeld, Carl D

    2015-11-01

    Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Autoimmune diseases (ADs) are a family of complex heterogeneous disorders with similar underlying mechanisms characterized by immune responses against self. Collectively, ADs are common, exhibit gender and ethnic disparities, and increasing incidence. As natural selection is an important influence on human genetic variation, and immune function genes are enriched for signals of positive selection, it is thought that the prevalence of AD risk alleles seen in different population is partially the result of differing selective pressures (for example, due to pathogens). With the advent of high-throughput technologies, new analytical methodologies and large-scale projects, evidence for the role of natural selection in contributing to the heritable component of ADs keeps growing. This review summarizes the genetic regions associated with susceptibility to different ADs and concomitant evidence for selection, including known agents of selection exerting selective pressure in these regions. Examples of specific adaptive variants with phenotypic effects are included as an evidence of natural selection increasing AD susceptibility. Many of the complexities of gene effects in different ADs can be explained by population genetics phenomena. Integrating AD susceptibility studies with population genetics to investigate how natural selection has contributed to genetic variation that influences disease risk will help to identify functional variants and elucidate biological mechanisms. As such, the study of population genetics in human population holds untapped potential for elucidating the genetic causes of human disease and more rapidly focusing to personalized medicine.

  4. Ocean currents help explain population genetic structure

    Science.gov (United States)

    White, Crow; Selkoe, Kimberly A.; Watson, James; Siegel, David A.; Zacherl, Danielle C.; Toonen, Robert J.

    2010-01-01

    Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management. PMID:20133354

  5. Microbial diversity--insights from population genetics.

    Science.gov (United States)

    Mes, Ted H M

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

  6. 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...

  7. 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...... species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central....../eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost...

  8. The genetic structure of the Swedish population.

    Directory of Open Access Journals (Sweden)

    Keith Humphreys

    Full Text Available Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise F(st indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to

  9. Population Dynamics of Genetic Regulatory Networks

    Science.gov (United States)

    Braun, Erez

    2005-03-01

    Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

  10. 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...

  11. 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.

  12. 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.

  13. The Genetic Deafness in Chinese Population

    Institute of Scientific and Technical Information of China (English)

    LIU Xuezhong; Ouyang Xiaomei; Denise Yan

    2006-01-01

    Deafness is an etiologically heterogeneous trait with many known genetic, environmental causes or a combination thereof. The identification of more than 120 independent genes for deafness has provided profound new insights into the pathophysiology of hearing. However, recent findings indicate that a large proportion of both syndromic and nonsyndromic forms of deafness in Chinese population are caused by a small number of mutations.This review is focused on syndromic and nonsyndromic deafness as well as on the latest information linking inherited mitochondrial pathologies to a variety of etiologies of sensorineural deafness in Chinese population. Better understanding of the genetic causes of deafness in Chinese population is important for accurate genetics counseling and early diagnosis for timely intervention and treatment options.

  14. Genetic Structure of the Spanish Population

    Directory of Open Access Journals (Sweden)

    Gutiérrez Marta

    2010-05-01

    Full Text Available Abstract Background Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias. Results In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV analyses, and have compared these estimates of the Spanish population with existing data from similar efforts. Conclusions In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community.

  15. Genetic classification and molecular mechanisms of primary dystonia

    Institute of Scientific and Technical Information of China (English)

    Xueping Chen; Huifang Shang; Zuming Luo

    2008-01-01

    BACKGROUND: Primary dystonia is a heterogeneous disease, with a complex genetic basis. In previous studies, primary dystonia was classified according to age of onset, involved regions, and other clinical characteristics. With the development of molecular genetics, new virulence genes and sites have been discovered. Therefore, there is a gradual understanding of the various forms of dystonia, based on new viewpoints. There are 15 subtypes of dystonia, based on the molecular level, i.e., DYT1 to DYT15. OBJECTIVE: To analyze the genetic development of dystonia in detail, and to further investigate molecular mechanisms of dystonia. RETRIEVAL STRATEGY: A computer-based online search was conducted in PubMed for English language publications containing the keywords "dystonia and genetic" from January 1980 to March 2007. There were 105 articles in total. Inclusion criteria: ① the contents of the articles should closely address genetic classification and molecular mechanisms of primary dystonia; ② the articles published in recent years or in high-impact journals took preference. Exclusion criteria: duplicated articles. LITERATURE EVALUATION: The selected articles were on genetic classification and molecular genetics mechanism of primary dystonia. Of those, 27 were basic or clinical studies. DATA SYNTHESIS: ① Dystonia is a heterogeneous disease, with a complex genetic basis. According to the classification of the Human Genome Organization, there are 15 dystonia subtypes, based on genetics, i.e., DYT1-DYT15,including primary dystonia, dystonia plus syndrome, degeneration plus dystonia, and paroxysmal dyskinesia plus dystonia. ② To date, the chromosomes of 13 subtypes have been localized; however, DYT2 and DYT4 remain unclear. Six subtypes have been located within virulence genes. Specifically, torsinA gene expression results in the DYT1 genotype; autosomal dominant GTP cyclohydrolase I gene expression and recessive tyrosine hydroxylase expression result in the DYT5

  16. 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

  17. 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.

  18. Alignment-free phylogenetics and population genetics.

    Science.gov (United States)

    Haubold, Bernhard

    2014-05-01

    Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.

  19. A population genetics model of linkage disequilibrium in admixed populations

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Understanding linkage disequilibrium (LD) created in admixed population and the rate of decay in the disequilibrium over evolution is an important subject in population genetics theory and in disease gene mapping in human populations. The present study represents the theoretical investigation of effects of gene frequencies, levels of LD and admixture proportions of donor populations on the evolutionary dynamics of the LD of the admixed population. We examined the conditions under which the admixed population reached linkage equilibrium or the peak level of the LD. The study reveals the inappropriateness in approximating the dynamics of the LD generated by population admixture by the commonly used formula in literature. An appropriate equation for the dynamics is proposed. The distinct feature of the newly suggested formula is that the value of the nonlinear component of the LD remains constant in the first generation of the population evolution. Comparison between the predicted disequilibrium dynamics shows that the error will be caused by using the old formula, and thus resulting in a misguidance in using the evolutionary information of the admixed population in gene mapping.

  20. 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.

  1. 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.

  2. 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.

  3. A new crossover operator in genetic programming for object classification.

    Science.gov (United States)

    Zhang, Mengjie; Gao, Xiaoying; Lou, Weijun

    2007-10-01

    The crossover operator has been considered "the centre of the storm" in genetic programming (GP). However, many existing GP approaches to object recognition suggest that the standard GP crossover is not sufficiently powerful in producing good child programs due to the totally random choice of the crossover points. To deal with this problem, this paper introduces an approach with a new crossover operator in GP for object recognition, particularly object classification. In this approach, a local hill-climbing search is used in constructing good building blocks, a weight called looseness is introduced to identify the good building blocks in individual programs, and the looseness values are used as heuristics in choosing appropriate crossover points to preserve good building blocks. This approach is examined and compared with the standard crossover operator and the headless chicken crossover (HCC) method on a sequence of object classification problems. The results suggest that this approach outperforms the HCC, the standard crossover, and the standard crossover operator with hill climbing on all of these problems in terms of the classification accuracy. Although this approach spends a bit longer time than the standard crossover operator, it significantly improves the system efficiency over the HCC method.

  4. Medical Image Classification Using Genetic Optimized Elman Network

    Directory of Open Access Journals (Sweden)

    T. Baranidharan

    2012-01-01

    Full Text Available Problem statement: Advancements in the internet and digital images have resulted in a huge database of images. Most of the current search engines found in the web depends only on images that can be retrieved using metadata, which generates a lot of unwanted results in the results got. Content-Based Image Retrieval (CBIR system is the utilization of computer vision techniques in the predicament of image retrieval. In other words, it is used for searching and retrieving of the right digital image among a huge database using query image. CBIR finds extensive applications in the field of medicine as it helps medical professionals in diagnosis and plan treatment. Approach: Various methods have been proposed for CBIR using the images low level features like histogram, color, texture and shape. Similarly various classification algorithms like Naive Bayes classifier, Support Vector Machine, Decision tree induction algorithms and Neural Network based classifiers have been studied extensively. In this study it is proposed to extract global features using Hilbert Transform (HT, select features based on the correlation of the extracted vectors with respect to the class label and propose a enhanced Elman Neural Network Genetic Algorithm Optimized Elman (GAOE Neural Network. Results and Conclusion: The proposed method for feature extraction and the classification algorithm was tested on a dataset consisting of 180 medical images. The classification accuracy of 92.22% was obtained in the proposed method.

  5. 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

  6. Reliability of genetic bottleneck tests for detecting recent population declines

    NARCIS (Netherlands)

    Peery, M. Zachariah; Kirby, Rebecca; Reid, Brendan N.; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    2012-01-01

    The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popula

  7. A novel hybrid classification model of genetic algorithms, modified k-Nearest Neighbor and developed backpropagation neural network.

    Science.gov (United States)

    Salari, Nader; Shohaimi, Shamarina; Najafi, Farid; Nallappan, Meenakshii; Karishnarajah, Isthrinayagy

    2014-01-01

    Among numerous artificial intelligence approaches, k-Nearest Neighbor algorithms, genetic algorithms, and artificial neural networks are considered as the most common and effective methods in classification problems in numerous studies. In the present study, the results of the implementation of a novel hybrid feature selection-classification model using the above mentioned methods are presented. The purpose is benefitting from the synergies obtained from combining these technologies for the development of classification models. Such a combination creates an opportunity to invest in the strength of each algorithm, and is an approach to make up for their deficiencies. To develop proposed model, with the aim of obtaining the best array of features, first, feature ranking techniques such as the Fisher's discriminant ratio and class separability criteria were used to prioritize features. Second, the obtained results that included arrays of the top-ranked features were used as the initial population of a genetic algorithm to produce optimum arrays of features. Third, using a modified k-Nearest Neighbor method as well as an improved method of backpropagation neural networks, the classification process was advanced based on optimum arrays of the features selected by genetic algorithms. The performance of the proposed model was compared with thirteen well-known classification models based on seven datasets. Furthermore, the statistical analysis was performed using the Friedman test followed by post-hoc tests. The experimental findings indicated that the novel proposed hybrid model resulted in significantly better classification performance compared with all 13 classification methods. Finally, the performance results of the proposed model was benchmarked against the best ones reported as the state-of-the-art classifiers in terms of classification accuracy for the same data sets. The substantial findings of the comprehensive comparative study revealed that performance of the

  8. Towards a genetic classification of uranium deposits; Vers une classification genetique des gisements d'uranium

    Energy Technology Data Exchange (ETDEWEB)

    Cuney, M. [G2R, Nancy Universite, CNRS, CREGU, 54 - Vandoeuvre les Nancy (France)

    2009-07-01

    As the IAEA's uranium deposit classification is based on the deposit nature and morphology, some deposits which have been formed by very different genetic processes and located in very different geological environments, are grouped according to this classification. In order to build up a reliable genetic classification based on the mechanism at the origin of the formation of the deposit, the author presents the five main categories according to which uranium deposits can be classified: magmatic, hydrothermal, evapotranspiration, syn-sedimentary, and infiltration of meteoric water

  9. Genetic diversity in introduced populations with an Allee effect.

    Science.gov (United States)

    Wittmann, Meike J; Gabriel, Wilfried; Metzler, Dirk

    2014-09-01

    A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations.

  10. A population genetics view of animal domestication.

    Science.gov (United States)

    Larson, Greger; Burger, Joachim

    2013-04-01

    The fundamental shift associated with the domestication of plants and animals allowed for a dramatic increase in human population sizes and the emergence of modern society. Despite its importance and the decades of research devoted to studying it, questions regarding the origins and processes of domestication remain. Here, we review recent theoretical advances and present a perspective that underscores the crucial role that population admixture has played in influencing the genomes of domestic animals over the past 10000 years. We then discuss novel approaches to generating and analysing genetic data, emphasising the importance of an explicit hypothesis-testing approach for the inference of the origins and subsequent evolution and demography of domestic animals. By applying next-generation sequencing technology alongside appropriate biostatistical methodologies, a substantially deeper understanding of domestication is on the horizon.

  11. Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations.

    Science.gov (United States)

    Torkzaban, Bahareh; Kayvanjoo, Amir Hossein; Ardalan, Arman; Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi

    2015-01-01

    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two '4-targeted' and '16-targeted' experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations.

  12. What is new in genetics and osteogenesis imperfecta classification?

    Directory of Open Access Journals (Sweden)

    Eugênia R. Valadares

    2014-12-01

    Full Text Available OBJECTIVE: Literature review of new genes related to osteogenesis imperfecta (OI and update of its classification. SOURCES: Literature review in the PubMed and OMIM databases, followed by selection of relevant references. SUMMARY OF THE FINDINGS: In 1979, Sillence et al. developed a classification of OI subtypes based on clinical features and disease severity: OI type I, mild, common, with blue sclera; OI type II, perinatal lethal form; OI type III, severe and progressively deforming, with normal sclera; and OI type IV, moderate severity with normal sclera. Approximately 90% of individuals with OI are heterozygous for mutations in the COL1A1 and COL1A2 genes, with dominant pattern of inheritance or sporadic mutations. After 2006, mutations were identified in the CRTAP, FKBP10, LEPRE1, PLOD2, PPIB, SERPINF1, SERPINH1, SP7, WNT1, BMP1, and TMEM38B genes, associated with recessive OI and mutation in the IFITM5 gene associated with dominant OI. Mutations in PLS3 were recently identified in families with osteoporosis and fractures, with X-linked inheritance pattern. In addition to the genetic complexity of the molecular basis of OI, extensive phenotypic variability resulting from individual loci has also been documented. CONCLUSIONS: Considering the discovery of new genes and limited genotype-phenotype correlation, the use of next-generation sequencing tools has become useful in molecular studies of OI cases. The recommendation of the Nosology Group of the International Society of Skeletal Dysplasias is to maintain the classification of Sillence as the prototypical form, universally accepted to classify the degree of severity in OI, while maintaining it free from direct molecular reference.

  13. Classification of Big Data with Application to Imaging Genetics

    CERN Document Server

    Ulfarsson, Magnus O; Sigurdsson, Jakob; Sveinsson, Johannes R

    2016-01-01

    Big data applications, such as medical imaging and genetics, typically generate datasets that consist of few observations n on many more variables p, a scenario that we denote as p>>n. Traditional data processing methods are often insufficient for extracting information out of big data. This calls for the development of new algorithms that can deal with the size, complexity, and the special structure of such datasets. In this paper, we consider the problem of classifying p>>n data and propose a classification method based on linear discriminant analysis (LDA). Traditional LDA depends on the covariance estimate of the data, but when p>>n the sample covariance estimate is singular. The proposed method estimates the covariance by using a sparse version of noisy principal component analysis (nPCA). The use of sparsity in this setting aims at automatically selecting variables that are relevant for classification. In experiments, the new method is compared to state-of-the art methods for big data problems using bot...

  14. 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

  15. Genetic Diversity of RAPD Mark for Natural Davidia involucrata Populations

    Institute of Scientific and Technical Information of China (English)

    Congwen Song; Manzhu Bao

    2006-01-01

    The genetic diversity and genetic variation within and among populations of five natural Davidia involucrata populations were studied from 13 primers based on random amplified polymorphic DNA (RAPD) analysis.The results show that natural D.involucrata population has a rich genetic diversity,and the differences among populations are significant.Twenty-six percent of genetic variation exists among D.involucrata populations,which is similar to that of the endangered tree species Liriodendron chinense and Cathaya argyrophylla in China,but different from more widely distributed tree species.The analysis of the impacts of sampling method on genetic diversity parameters shows that the number of sampled individuals has little effect on the effective number of alleles and genetic diversity,but has a marked effect on the genetic differentiation among populations and gene flows.This study divides the provenances of D.involucrata into two parts,namely,a southeast and a northwest provenance.

  16. Population size and time since island isolation determine genetic diversity loss in insular frog populations.

    Science.gov (United States)

    Wang, Supen; Zhu, Wei; Gao, Xu; Li, Xianping; Yan, Shaofei; Liu, Xuan; Yang, Ji; Gao, Zengxiang; Li, Yiming

    2014-02-01

    Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used nine microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square-root-transformed) and population size (log-transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations.

  17. Genetic drift and the population history of the Irish travellers.

    Science.gov (United States)

    Relethford, John H; Crawford, Michael H

    2013-02-01

    The Irish Travellers are an itinerant group in Ireland that has been socially isolated. Two hypotheses have been proposed concerning the genetic origin of the Travellers: (1) they are genetically related to Roma populations in Europe that share a nomadic lifestyle or (2) they are of Irish origin, and genetic differences from the rest of Ireland reflect genetic drift. These hypotheses were tested using data on 33 alleles from 12 red blood cell polymorphism loci. Comparison with other European, Roma, and Indian populations shows that the Travellers are genetically distinct from the Roma and Indian populations and most genetically similar to Ireland, in agreement with earlier genetic analyses of the Travellers. However, the Travellers are still genetically distinct from other Irish populations, which could reflect some external gene flow and/or the action of genetic drift in a small group that was descended from a small number of founders. In order to test the drift hypothesis, we analyzed genetic distances comparing the Travellers to four geographic regions in Ireland. These distances were then compared with adjusted distances that account for differential genetic drift using a method developed by Relethford (Hum Biol 68 (1996) 29-44). The unadjusted distances show the genetic distinctiveness of the Travellers. After adjustment for the expected effects of genetic drift, the Travellers are equidistant from the other Irish samples, showing their Irish origins and population history. The observed genetic differences are thus a reflection of genetic drift, and there is no evidence of any external gene flow.

  18. 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.

  19. Transmission function models of finite population genetic algorithms

    NARCIS (Netherlands)

    Kemenade, C.H.M. van; Kok, J.N.; La Poutré, J.A.; Thierens, D.

    1998-01-01

    Infinite population models show a deterministic behaviour. Genetic algorithms with finite populations behave non-deterministicly. For small population sizes, the results obtained with these models differ strongly from the results predicted by the infinite population model. When the population size i

  20. Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations.

    Science.gov (United States)

    Gomaa, Nasr H; Montesinos-Navarro, Alicia; Alonso-Blanco, Carlos; Picó, F Xavier

    2011-09-01

    Currently, there exists a limited knowledge on the extent of temporal variation in population genetic parameters of natural populations. Here, we study the extent of temporal variation in population genetics by genotyping 151 genome-wide SNP markers polymorphic in 466 individuals collected from nine populations of the annual plant Arabidopsis thaliana during 4 years. Populations are located along an altitudinal climatic gradient from Mediterranean to subalpine environments in NE Spain, which has been shown to influence key demographic attributes and life cycle adaptations. Genetically, A. thaliana populations were more variable across space than over time. Common multilocus genotypes were detected several years in the same population, whereas low-frequency multilocus genotypes appeared only 1 year. High-elevation populations were genetically poorer and more variable over time than low-elevation populations, which might be caused by a higher overall demographic instability at higher altitudes. Estimated effective population sizes were low but also showed a significant decreasing trend with increasing altitude, suggesting a deeper impact of genetic drift at high-elevation populations. In comparison with single-year samplings, repeated genotyping over time captured substantially higher amount of genetic variation contained in A. thaliana populations. Furthermore, repeated genotyping of populations provided novel information on the genetic properties of A. thaliana populations and allowed hypothesizing on their underlying mechanisms. Therefore, including temporal genotyping programmes into traditional population genetic studies can significantly increase our understanding of the dynamics of natural populations.

  1. Genetic Differentiation of Different Geographical Populations of Bemisia tabaci (Gennadius) Complex

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; LIU Guo-xia; FAN Zhong-xue; TAO Yun-li; ZHANG You-jun

    2007-01-01

    Bemisia tabaci (Gennadius) is a species complex, which includes different geographical populations with genetic differentiation. The recent progress on the genetic differentiation of various geographical populations of B. tabaci complex was introduced. The genetic differentiation was further analyzed on the basis of the sequences of mtDNA COI and rDNA ITSl recorded in the world's GenBank. Five groups are defined on the basis of mtDNA COI and rDNA ITS1, including the Asia group, America group, Africa group, Australia group, and Biotype B/Mediterranean/Middle East/ Northern Africa/Biotype Ms group. There are several ungrouped geographical classifications, such as the Uganda population, Ivory Coast population, and Taiwan population. Geographical isolation may be the most important factor that contributed to the genetic differentiation of various geographical populations of B. tabaci. Many populations with biological advantages invaded new regions and caused severe economic losses within human activity. It is necessary to strengthen the research of B. tabaci biotype to prevent the spread of invaded populations and the invasion of potentially dangerous populations.

  2. Study on genetic coadaptability of wild quail populations in China

    Institute of Scientific and Technical Information of China (English)

    CHANG; Guobin; CHANG; Hong; LIU; Xiangping; YANG; Zhangping; CHEN; Guohong; ZHAO; Wenming; JI; Dejun; XUE; Yan; HUANG; Feng; HASSAN; Hussein

    2006-01-01

    Genetic coadaptability of wild Japanese quail, wild Common quail and Domestic quail populations in China was studied using 7 microsatellite DNA markers and Monte Carlo method to test genetic disequilibrium. The molecular effects of genetic coadaptability were analyzed through a new statistical model of neutral site. The results showed that genetic coadaptability dominated the genetic disequilibrium of the three quail populations, and totally 16.67%, 9.66% and 10.05% of non-allelic combinations were in the genetic disequilibrium in wild Japanese quail, wild Common quail and Domestic quail populations, respectively. Genetic coadaptability existed at almost all the tested sites. In the molecular point of view, genetic coadaptability plays an important role of keeping lots of polymorphisms in natural populations. Therefore, it is another key factor to the genetic disequilibrium in the population except for linkage. The results enrich the conceptions and connotations of genetic disequilibrium, and help us know more about genetic coadaptability and its effects, and lay a foundation of evaluation and protection of wild quail genetic resources in China.

  3. Integrating genetic algorithm method with neural network for land use classification using SZ-3 CMODIS data

    Institute of Scientific and Technical Information of China (English)

    WANG Changyao; LUO Chengfeng; LIU Zhengjun

    2005-01-01

    This paper presents a methodology on land use mapping using CMODIS (Chinese Moderate Resolution Imaging Spectroradiometer ) data on-board SZ-3 (Shenzhou 3) spacecraft. The integrated method is composed of genetic algorithm (GA) for feature extraction and neural network classifier for land use classification. In the data preprocessing, a moment matching method was adopted to reuse classification was obtained. To generate a land use map, the three layers back propagation neural network classifier is used for training the samples and classification. Compared with the Maximum Likelihood classification algorithm, the results show that the accuracy of land use classification is obviously improved by using our proposed method, the selected band number in the classification process is reduced,and the computational performance for training and classification is improved. The result also shows that the CMODIS data can be effectively used for land use/land cover classification and change monitoring at regional and global scale.

  4. Extreme genetic diversity in asexual grass thrips populations.

    Science.gov (United States)

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.

  5. Identification of management units using population genetic data

    NARCIS (Netherlands)

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

    2007-01-01

    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

  6. 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

  7. Multiscale modeling for classification of SAR imagery using hybrid EM algorithm and genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    Xianbin Wen; Hua Zhang; Jianguang Zhang; Xu Jiao; Lei Wang

    2009-01-01

    A novel method that hybridizes genetic algorithm (GA) and expectation maximization (EM) algorithm for the classification of syn-thetic aperture radar (SAR) imagery is proposed by the finite Gaussian mixtures model (GMM) and multiscale autoregressive (MAR)model. This algorithm is capable of improving the global optimality and consistency of the classification performance. The experiments on the SAR images show that the proposed algorithm outperforms the standard EM method significantly in classification accuracy.

  8. Classification of Noisy Data: An Approach Based on Genetic Algorithms and Voronoi Tessellation

    DEFF Research Database (Denmark)

    Khan, Abdul Rauf; Schiøler, Henrik; Knudsen, Torben

    2016-01-01

    on the portioning of information space; and (2) use of the genetic algorithm to solve combinatorial problems for classification. In particular, we will implement our methodology to solve complex classification problems and compare the performance of our classifier with other well-known methods (SVM, KNN, and ANN...

  9. Genetic diversity of natural Hepatacodium miconioides populations in Zhejiang Province

    Institute of Scientific and Technical Information of China (English)

    LI Junmin; JIN Zexin

    2006-01-01

    Hepatacodium miconioides is the Class Ⅱ protected plant species in China.This paper studies the genetic diversity and differentiation of its nine natural populations in Zhejiang Province by using random amplified polymorphic DNA (RAPD) technique.Twelve random primers were selected in the amplification,and 164 repetitive loci were produced.The percentage of polymorphic loci in each H.miconioides population ranged from 14.60% to 27.44%,with an average of 20.73%.Among the test populations,Kuochangshan had the highest percentage of polymorphic loci,Simingshan took the second place,and Guanyinping had the lowest percentage.As estimated by Shannon index,the genetic diversity within H.miconioides populations accounted for 27.28% of the total genetic diversity,while that among H.miconioides populations accounted for 72.72%.The genetic differentiation among H.miconioides populations as estimated by Nei index was 0.715,7.This figure was generally consistent with that estimated by Shannon index,i.e.,the genetic differentiation among populations was relatively high,but that within populations was relatively low.The gene flow among H.miconioides populations was relatively low (0.198,7),and the genetic similarity ranged from 0.655,7 to 0.811,9,with an average of 0.730,6.The highest genetic distance among populations was 0.422,9,while the lowest was 0.208,3.All the results showed that there was a distinct genetic differentiation among H.miconioides populations.The genetic distance matrix of nine test populations was calculated using this method,and the clustering analysis was made using the unweighted pair group method with arithmetic mean (UPGMA).The cluster analysis suggested that the ninepopulations of H.miconioides in Zhejiang Province could be divided into two groups,the eastern Zhejiang group and the western Zhejiang group.

  10. GENETICS OF INDO-EUROPEAN POPULATIONS: THE PAST, THE FUTURE

    OpenAIRE

    Balanovsky, Oleg; Utevska, Olga; Balanovska, Elena

    2013-01-01

    We describe our experience of comparing genetic and linguistic data in relation to the Indo-European problem. Our recent comparison of the genetic variation with lexicostatistical data on North Caucasian populations identified the parallel evolution of genes and languages; one can say that history of the populations was reflected in the linguistic and the genetic mirrors. For other linguistic families one can also expect this similarity, though it could be blurred by elite dominance and other...

  11. Hybrid model based on Genetic Algorithms and SVM applied to variable selection within fruit juice classification.

    Science.gov (United States)

    Fernandez-Lozano, C; Canto, C; Gestal, M; Andrade-Garda, J M; Rabuñal, J R; Dorado, J; Pazos, A

    2013-01-01

    Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM). Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA), the most representative variables for a specific classification problem can be selected.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Genetic structure of a unique admixed population: implications for medical research.

    Science.gov (United States)

    Patterson, Nick; Petersen, Desiree C; van der Ross, Richard E; Sudoyo, Herawati; Glashoff, Richard H; Marzuki, Sangkot; Reich, David; Hayes, Vanessa M

    2010-02-01

    STATEMENT: In naming population groups, we think a chief aim is to use terms that the group members use themselves, or find familiar and comfortable. The terms used in this manuscript to describe populations are as historically correct as possible and are chosen so as not to offend any population group. Two of the authors (DCP and REvdR) belong to the Coloured population, with one of the authors (REvdR) having contributed extensively to current literature on the history of the Coloured people of South Africa and served as Vice-President of the South African Institute of Race Relations. According to the 2001 South African census (http://www.statssa.gov.za/census01/HTML/CInBrief/CIB2001.pdf), "Statistics South Africa continues to classify people by population group, in order to monitor progress in moving away from the apartheid-based discrimination of the past. However, membership of a population group is now based on self-perception and self-classification, not on a legal definition. Five options were provided on the questionnaire, Black African, Coloured, Indian or Asian, White and Other. Responses in the category 'Other' were very few and were therefore imputed". We have elected to use the term Bushmen rather than San to refer to the hunter-gatherer people of Southern Africa. Although they have no collective name for themselves, this decision was based on the term Bushmen (or Bossiesman) being the more familiar to the communities themselves, while the term San is the more accepted academic classification. Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising approximately 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected

  14. Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

    Science.gov (United States)

    Lauber, Chris; Gorbalenya, Alexander E

    2012-04-01

    Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

  15. 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

  16. Population genetic structure of Aedes albopictus in Penang, Malaysia.

    Science.gov (United States)

    Zawani, M K N; Abu, H A; Sazaly, A B; Zary, S Y; Darlina, M N

    2014-10-07

    The mosquito Aedes albopictus is indigenous to Southeast Asian and is a vector for arbovirus diseases. Studies examining the population genetics structure of A. albopictus have been conducted worldwide; however, there are no documented reports on the population genetic structure of A. albopictus in Malaysia, particularly in Penang. We examined the population genetics of A. albopictus based on a 445-base pair segment of the mitochondrial DNA cytochrome oxidase 1 gene among 77 individuals from 9 localities representing 4 regions (Seberang Perai Utara, Seberang Perai Tengah, Northeast, and Southwest) of Penang. A total of 37 haplotypes were detected, including 28 unique haplotypes. The other 9 haplotypes were shared among various populations. These shared haplotypes reflect the weak population genetic structure of A. albopictus. The phylogenetic tree showed a low bootstrap value with no genetic structure, which was supported by minimum spanning network analysis. Analysis of mismatch distribution showed poor fit of equilibrium distribution. The genetic distance showed low genetic variation, while pairwise FST values showed no significant difference between all regions in Penang except for some localities. High haplotype diversity and low nucleotide diversity was observed for cytochrome oxidase 1 mtDNA. We conclude that there is no population genetic structure of A. albopictus mosquitoes in the Penang area.

  17. Analysis of Distributed and Adaptive Genetic Algorithm for Mining Interesting Classification Rules

    Institute of Scientific and Technical Information of China (English)

    YI Yunfei; LIN Fang; QIN Jun

    2008-01-01

    Distributed genetic algorithm can be combined with the adaptive genetic algorithm for mining the interesting and comprehensible classification rules. The paper gives the method to encode for the rules, the fitness function, the selecting, crossover, mutation and migration operator for the DAGA at the same time are designed.

  18. Genetic analysis in the Collaborative Cross breeding population.

    Science.gov (United States)

    Philip, Vivek M; Sokoloff, Greta; Ackert-Bicknell, Cheryl L; Striz, Martin; Branstetter, Lisa; Beckmann, Melissa A; Spence, Jason S; Jackson, Barbara L; Galloway, Leslie D; Barker, Paul; Wymore, Ann M; Hunsicker, Patricia R; Durtschi, David C; Shaw, Ginger S; Shinpock, Sarah; Manly, Kenneth F; Miller, Darla R; Donohue, Kevin D; Culiat, Cymbeline T; Churchill, Gary A; Lariviere, William R; Palmer, Abraham A; O'Hara, Bruce F; Voy, Brynn H; Chesler, Elissa J

    2011-08-01

    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.

  19. Ssr analysis for genetic structure and diversity determination of maize local populations from former Yugoslavia territories.

    Science.gov (United States)

    Ignjatović-Micić, D; Drinić, S Mladenović; Nikolić, A; Lazić-Jancić, V

    2008-11-01

    A collection of 2178 local populations from ex-Yugoslavia territories is maintained in Maize Research Institute (MRI) gene bank. These populations were characterized mainly by morphological markers. In this work 21 local populations belonging to seven different agro-ecological groups have been subjected to SSR analysis using a DNA-pooling strategy. The objective of this work was to develop genetic fingerprints for characterization, identification and classification of the populations, as well as for estimation of their genetic diversity. Also, a DNA-pooling strategy was employed with the aim to certify if it could be applied for population analysis with SSR markers. Statistical analysis of 25 informative SSR primers revealing 224 alleles (bands) showed that the average within-population mean number of alleles was 2.55, the average values for total and within-population diversity were 0.784 and 0.502, respectively and G(ST) value was 0.360. Genetic distance values calculated using Modified Rogers' Distance were in the range from 0.35 to 0.60. The silver staining method of DNA used for bulked samples showed some weakness that could be overcome with a more sensitive staining method. Nevertheless, the results in this work indicate that the SSR analysis of bulks could be used for characterizing a large number of populations in gene banks.

  20. 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.

  1. 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...

  2. Genetic variation and population history of three Carassius auratus populations in Huaihe River, China.

    Science.gov (United States)

    Chen, Wei; Zhao, Yuanjun; Yang, Chengzhong

    2016-11-01

    In order to investigate the relationships of drainage history of Huaihe River with the genetic history of Carassius auratus along the river, we examined the genetic variations and population histories of three wild C. auratus populations in Huaihe River based on the D-loop gene. The results showed that their nucleotide and haplotype diversities were ranged from 0.00268 to 0.00651 and from 0.863 to 0.902, respectively, and their genetic distance was quite small. The analysis of molecular variance demonstrated that a frequent inter-population connection and large historic gene flows occurred among the three populations. Demographic analysis indicated that expansions had been happened in three populations. After investigating the historic process of the Huaihe River, we presumed that both nature and artificial factors may play important roles in shaping the genetic structure of the three populations. The present study also provided genetic information of C. auratus for further conservation of its germplasm resources.

  3. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  4. 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.

  5. Text Classification using Association Rule with a Hybrid Concept of Naive Bayes Classifier and Genetic Algorithm

    CERN Document Server

    Kamruzzaman, S M; Hasan, Ahmed Ryadh

    2010-01-01

    Text classification is the automated assignment of natural language texts to predefined categories based on their content. Text classification is the primary requirement of text retrieval systems, which retrieve texts in response to a user query, and text understanding systems, which transform text in some way such as producing summaries, answering questions or extracting data. Now a day the demand of text classification is increasing tremendously. Keeping this demand into consideration, new and updated techniques are being developed for the purpose of automated text classification. This paper presents a new algorithm for text classification. Instead of using words, word relation i.e. association rules is used to derive feature set from pre-classified text documents. The concept of Naive Bayes Classifier is then used on derived features and finally a concept of Genetic Algorithm has been added for final classification. A system based on the proposed algorithm has been implemented and tested. The experimental ...

  6. Classification of Noisy Data: An Approach Based on Genetic Algorithms and Voronoi Tessellation

    DEFF Research Database (Denmark)

    Khan, Abdul Rauf; Schiøler, Henrik; Knudsen, Torben;

    2016-01-01

    Classification is one of the major constituents of the data-mining toolkit. The well-known methods for classification are built on either the principle of logic or statistical/mathematical reasoning for classification. In this article we propose: (1) a different strategy, which is based......). The results of this study suggest that our proposed methodology is specialized to deal with the classification problem of highly imbalanced classes with significant overlap....... on the portioning of information space; and (2) use of the genetic algorithm to solve combinatorial problems for classification. In particular, we will implement our methodology to solve complex classification problems and compare the performance of our classifier with other well-known methods (SVM, KNN, and ANN...

  7. 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.

  8. Genetic Variation of Host Populations of Liriomyza sativae Blanchard

    Institute of Scientific and Technical Information of China (English)

    WANG Li-ping; DU Yu-zhou; HE Ya-ting; ZHENG Fu-shan; LU Zi-qiang

    2008-01-01

    In this study, partial sequences of the mitochondrial cytochrome oxidase subunit Ⅰ (mtDNA-COI) gene and the ribosomal internal transcribed spacer 1 (rDNA-ITS1) gene, isolated from five artificial populations of Liriomyza sativae (Diptera:Agromyzidae), were sequenced and compared, to analyze their genetic variation. Analysis of the mtDNA-CO1 gene showed that a low genetic variation was detected among the five populations and only five variable sites were found in the nucleotide sequences. Most of the observed variations that occurred within the populations were because of nucleotide transitions, whereas, the interpopulation variation was because of the differences in haplotype frequencies occurring among the host populations. Analysis of the rDNA-ITS1 gene revealed a small diversity in the five host populations. The trend of genetic differentiation in the host populations was consistent with the preference of L. sativae to the plant hosts.

  9. GESP: A computer program for modeling genetic effective population size, inbreeding, and divergence in substructured populations.

    Science.gov (United States)

    Olsson, Fredrik; Laikre, Linda; Hössjer, Ola; Ryman, Nils

    2017-03-24

    The genetically effective population size (Ne) is of key importance for quantifying rates of inbreeding and genetic drift, and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analyzing the expected Ne in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here. GESP (Genetic Effective population size, inbreeding, and divergence in Substructured Populations) is R-based and designed to model short and long term patterns of genetic differentiation and effective population size of subdivided populations. The algorithms performed by GESP allow exact computation of global and local inbreeding and eigenvalue effective population size, predictions of genetic divergence among populations (GST) as well as departures from random mating (FIS, FIT) while varying i) subpopulation census and effective size, separately or including trend of the global population size, ii) rate and direction of migration between all pairs of subpopulations, iii) degree of relatedness and divergence among subpopulations, iv) ploidy (haploid or diploid), and v) degree of selfing. Here, we describe GESP and exemplify its use in conservation genetics modeling. This article is protected by copyright. All rights reserved.

  10. Genetic diversity in wild populations of Paulownia fortune.

    Science.gov (United States)

    Li, H Y; Ru, G X; Zhang, J; Lu, Y Y

    2014-11-01

    The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138-1.2726), Nei's genetic diversity (0.1566-0.1887), and Shannon's information index (0.2692-0.3117) indicated a plentiful genetic diversity and different among Paulownia fortunei populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.

  11. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

    NARCIS (Netherlands)

    Dobon, B.; Hassan, H.Y.; Laayouni, H.; Luisi, P.; Ricano-Ponce, I.; Zhernakova, A.; Wijmenga, C.; Tahir, H.; Comas, D.; Netea, M.G.; Bertranpetit, J.

    2015-01-01

    East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic gro

  12. 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…

  13. 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...

  14. Thirty years of tick population genetics: a comprehensive review.

    Science.gov (United States)

    Araya-Anchetta, Ana; Busch, Joseph D; Scoles, Glen A; Wagner, David M

    2015-01-01

    Population genetic studies provide insights into the basic biology of arthropod disease vectors by estimating dispersal patterns and their potential to spread pathogens. In wingless vectors, such as ticks, gene flow will be defined in large part by the mobility of their hosts. However, tick behaviors and life cycle strategies can limit their dispersal even on highly mobile hosts and lead to an increase in genetic structure. In this review we synthesize the published literature from three decades of tick population genetic studies. Based on studies from 22 tick species (including representatives from Amblyomma, Bothriocroton, Dermacentor, Ixodes, Ornithodoros, and Rhipicephalus), observed levels of population genetic structure in ticks varied from no structure to very high levels. In about half of the species (including representatives from Amblyomma, Bothriocroton, Dermacentor, and Ornithodoros), tick genetic structure appeared to be determined primarily by the movement capacity of hosts, with low gene flow observed in ticks that use smaller bodied less mobile hosts and high gene flow in ticks using highly mobile hosts. In a number of other species (primarily from Ixodes, Ornithodoros, and Rhipicephalus), behavioral limitations to gene flow appeared to result in greater genetic structure than expected based upon host movement capability alone. We also discuss the strengths and limitations of genetic markers and their applicability to ticks and suggest possible analyses when planning population genetic studies for ticks.

  15. 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 (HO) and mean inbreeding (FIS) 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.

  16. Modernization, Population Dispersion, and Papago Genetic Integrity

    Science.gov (United States)

    Smith, David G.

    1972-01-01

    That residents of Papago villages were less closely related in the 19th century than during recent decades is considered in historical and genetic perspectives. A preliminary version of this paper was read at the annual meeting of the American Anthropological Association, New York City, 1971. (FF)

  17. Genetic diversity and population structure of cucumber (Cucumis sativus L..

    Directory of Open Access Journals (Sweden)

    Jing Lv

    Full Text Available Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

  18. Application of a Genetic Algorithm to Nearest Neighbour Classification

    NARCIS (Netherlands)

    Simkin, S.; Verwaart, D.; Vrolijk, H.C.J.

    2005-01-01

    This paper describes the application of a genetic algorithm to nearest-neighbour based imputation of sample data into a census data dataset. The genetic algorithm optimises the selection and weights of variables used for measuring distance. The results show that the measure of fit can be improved by

  19. Population Genetic Structure of Aedes fluviatilis (Diptera: Culicidae)

    Science.gov (United States)

    Multini, Laura Cristina; Suesdek, Lincoln; Marrelli, Mauro Toledo

    2016-01-01

    Although Aedes fluviatilis is an anthropophilic mosquito found abundantly in urban environments, its biology, epidemiological potential and genetic characteristics are poorly understood. Climate change and urbanization processes that result in environmental modifications benefit certain anthropophilic mosquito species such as Ae. fluviatilis, greatly increasing their abundance in urban areas. To gain a better understanding of whether urbanization processes modulate the genetic structure of this species in the city of São Paulo, we used eight microsatellite loci to genetically characterize Ae. fluviatilis populations collected in nine urban parks in the city of São Paulo. Our results show that there is high gene flow among the populations of this species, heterozygosity deficiency and low genetic structure and that the species may have undergone a recent population expansion. There are two main hypotheses to explain these findings: (i) Ae. fluviatilis populations have undergone a population expansion as a result of urbanization; and (ii) as urbanization of the city of São Paulo occurred recently and was quite intense, the structuring of these populations cannot be observed yet, apart from in the populations of Ibirapuera and Piqueri parks, where the first signs of structuring have appeared. We believe that the expansion found in Ae. fluviatilis populations is probably correlated with the unplanned urbanization of the city of São Paulo, which transformed green areas into urbanized areas, as well as the increasing population density in the city. PMID:27598889

  20. 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

  1. Population genetics of Wolbachia-infected, parthenogenetic and uninfected, sexual populations of Tetrastichus coeruleus (Hymenoptera: Eulophidae).

    Science.gov (United States)

    Reumer, Barbara M; van Alphen, Jacques J M; Kraaijeveld, Ken

    2013-09-01

    Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. These manipulations are expected to have consequences on the population genetics of the host, such as heterozygosity levels, genetic diversity and gene flow. The parasitoid wasp Tetrastichus coeruleus has populations that are infected with parthenogenesis-inducing Wolbachia and populations that are not infected. We studied the population genetics of T. coeruleus between and within Wolbachia-infected and uninfected populations, using nuclear microsatellites and mitochondrial DNA. We expected reduced genetic diversity in both DNA types in infected populations. However, migration and gene flow could introduce new DNA variants into populations. We therefore paid special attention to individuals with unexpected (genetic) characteristics. Based on nuclear and mitochondrial DNA, two genetic clusters were evident: a thelytokous cluster containing all Wolbachia-infected, parthenogenetic populations and an arrhenotokous cluster containing all uninfected, sexual populations. Nuclear and mitochondrial DNA did not exhibit concordant patterns of variation, although there was reduced genetic diversity in infected populations for both DNA types. Within the thelytokous cluster, there was nuclear DNA variation, but no mitochondrial DNA variation. This nuclear DNA variation may be explained by occasional sex between infected females and males, by horizontal transmission of Wolbachia, and/or by novel mutations. Several females from thelytokous populations were uninfected and/or heterozygous for microsatellite loci. These unexpected characteristics may be explained by migration, by inefficient transmission of Wolbachia, by horizontal transmission of Wolbachia, and/or by novel mutations. However, migration has not prevented the build-up of considerable genetic differentiation between thelytokous and arrhenotokous populations.

  2. Molecular Population Genetics of Rice Domestication

    Institute of Scientific and Technical Information of China (English)

    Tian Tang; Suhua Shi

    2007-01-01

    Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations? Another notable outcome of artificial selection is the reduction in the fitness of domesticated species when they live in the wild without human assistance. The complete sequences of the two subspecies of rice cultivars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non-synonymous (N) than synonymous (S) substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication-associated Hill-Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza ruflpogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A-genome wild species. Genes from the highly polymorphic regions also provide strong support for the independent domestication of the two subspecies. The genomic variation in rice has revealing

  3. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape.

    Science.gov (United States)

    Dobon, Begoña; Hassan, Hisham Y; Laayouni, Hafid; Luisi, Pierre; Ricaño-Ponce, Isis; Zhernakova, Alexandra; Wijmenga, Cisca; Tahir, Hanan; Comas, David; Netea, Mihai G; Bertranpetit, Jaume

    2015-01-01

    East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

  4. 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.

  5. Land cover classification using random forest with genetic algorithm-based parameter optimization

    Science.gov (United States)

    Ming, Dongping; Zhou, Tianning; Wang, Min; Tan, Tian

    2016-07-01

    Land cover classification based on remote sensing imagery is an important means to monitor, evaluate, and manage land resources. However, it requires robust classification methods that allow accurate mapping of complex land cover categories. Random forest (RF) is a powerful machine-learning classifier that can be used in land remote sensing. However, two important parameters of RF classification, namely, the number of trees and the number of variables tried at each split, affect classification accuracy. Thus, optimal parameter selection is an inevitable problem in RF-based image classification. This study uses the genetic algorithm (GA) to optimize the two parameters of RF to produce optimal land cover classification accuracy. HJ-1B CCD2 image data are used to classify six different land cover categories in Changping, Beijing, China. Experimental results show that GA-RF can avoid arbitrariness in the selection of parameters. The experiments also compare land cover classification results by using GA-RF method, traditional RF method (with default parameters), and support vector machine method. When the GA-RF method is used, classification accuracies, respectively, improved by 1.02% and 6.64%. The comparison results show that GA-RF is a feasible solution for land cover classification without compromising accuracy or incurring excessive time.

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

    Science.gov (United States)

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

    2014-01-01

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

  7. Genetic analysis of population differentiation and adaptation in Leuciscus waleckii.

    Science.gov (United States)

    Chang, Yumei; Tang, Ran; Sun, Xiaowen; Liang, Liqun; Chen, Jinping; Huang, Jinfeng; Dou, Xinjie; Tao, Ran

    2013-12-01

    Demographic events and natural selection both influence animal phenotypic and genetic variation; exploring the effects of demography and selection on population divergence is of great significance in evolutionary biology. To uncover the causes behind the patterns of genetic differentiation and adaptation among six populations of Leuciscus waleckii from Dali Basin (two populations, alkaline vs. freshwater) and Amur Basin (four populations, freshwater rivers vs. alkaline lake), a set of 21 unlinked polymorphic microsatellite markers and two mitochondrial DNA sequences (Cytb and D-loop) were applied to examine whether populations from different environments or habitats have distinct genetic differentiation and whether alkalinity is the major factor that caused population divergence. Bayesian analysis and principal component analysis as well as haplotype network analysis showed that these populations are primarily divided into two groups, which are congruent with geographic separation but not inconsistent with the habitat environment (alkalinity). Using three different approaches, outlier detection indicated that one locus, HLJYL017, may be under directional selection and involved in local adaptation processes. Overall, this study suggested that demographic events and selection of local environmental conditions including of alkalinity are jointly responsible for population divergence. These findings constitute an important step towards the understanding of the genetic basis of differentiation and adaptation, as well as towards the conservation of L. waleckii.

  8. 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.

  9. 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.

  10. Population genetic structure of Venezuelan chiropterophilous columnar cacti (Cactaceae).

    Science.gov (United States)

    Nassar, Jafet M; Hamrick, J L; Fleming, Theodore H

    2003-11-01

    We conducted allozyme surveys of three Venezuelan self-incompatible chiropterophilous columnar cacti: two diploid species, Stenocereus griseus and Cereus repandus, and one tetraploid, Pilosocereus lanuginosus. The three cacti are pollinated by bats, and both bats and birds disperse seeds. Population sampling comprised two spatial scales: all Venezuelan arid zones (macrogeographic) and two arid regions in northwestern Venezuela (regional). Ten to 15 populations and 17-23 loci were analyzed per species. Estimates of genetic diversity were compared with those of other allozyme surveys in the Cactaceae to examine how bat-mediated gene dispersal affects the population genetic attributes of the three cacti. Genetic diversity was high for both diploid (P(s) = 94.1-100, P(p) = 56.7-72.3, H(s) = 0.182-0.242, H(p) = 0.161-0.205) and tetraploid (P(s) = 93.1, P(p) = 76.1, H(s) = 0.274, H(p) = 0.253) species. Within-population heterozygote deficit was detected in the three cacti at macrogeographic (F(IS) = 0.145-0.182) and regional (F(IS) = 0.057-0.174) levels. Low genetic differentiation was detected at both macrogeographic (G(ST) = 0.043-0.126) and regional (G(ST) = 0.009-0.061) levels for the three species, suggesting substantial gene flow among populations. Gene exchange among populations seems to be regulated by distance among populations. Our results support the hypothesis that bat-mediated gene dispersal confers high levels of genetic exchange among populations of the three columnar cacti, a process that enhances levels of genetic diversity within their populations.

  11. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

    Melchior, Linea Cecilie; Lynnerup, Niels; Siegismund, Hans Redlef

    2010-01-01

    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....

  12. Weighted K-Nearest Neighbor Classification Algorithm Based on Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Xuesong Yan

    2013-10-01

    Full Text Available K-Nearest Neighbor (KNN is one of the most popular algorithms for data classification. Many researchers have found that the KNN algorithm accomplishes very good performance in their experiments on different datasets. The traditional KNN text classification algorithm has limitations: calculation complexity, the performance is solely dependent on the training set, and so on. To overcome these limitations, an improved version of KNN is proposed in this paper, we use genetic algorithm combined with weighted KNN to improve its classification performance. and the experiment results shown that our proposed algorithm outperforms the KNN with greater accuracy.

  13. A RBF classification method of remote sensing image based on genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The remote sensing image classification has stimulated considerable interest as an effective method for better retrieving information from the rapidly increasing large volume, complex and distributed satellite remote imaging data of large scale and cross-time, due to the increase of remote image quantities and image resolutions. In the paper, the genetic algorithms were employed to solve the weighting of the radial basis faction networks in order to improve the precision of remote sensing image classification. The remote sensing image classification was also introduced for the GIS spatial analysis and the spatial online analytical processing (OLAP) ,and the resulted effectiveness was demonstrated in the analysis of land utilization variation of Daqing city.

  14. Stellar Population Analysis of Galaxies based on Genetic Algorithms

    Institute of Scientific and Technical Information of China (English)

    Abdel-Fattah Attia; H.A.Ismail; I.M.Selim; A.M.Osman; I.A.Isaa; M.A.Marie; A.A.Shaker

    2005-01-01

    We present a new method for determining the age and relative contribution of different stellar populations in galaxies based on the genetic algorithm.We apply this method to the barred spiral galaxy NGC 3384, using CCD images in U, B, V, R and I bands. This analysis indicates that the galaxy NGC 3384 is mainly inhabited by old stellar population (age > 109 yr). Some problems were encountered when numerical simulations are used for determining the contribution of different stellar populations in the integrated color of a galaxy. The results show that the proposed genetic algorithm can search efficiently through the very large space of the possible ages.

  15. Population genetics in minority children with type 2 diabetes mellitus.

    Science.gov (United States)

    Wallerstein, Robert

    2002-04-01

    Non-insulin dependent (type 2) diabetes mellitus (DM) is a rapidly emerging health threat in minority populations in the United States, with the African-American, Hispanic, and Native American populations at greatest risk. Clearly, environmental factors play a role in this disorder, but the ethnic predilection suggests a significant genetic component. Type 2 DM is a condition not well understood on a genetic basis. Familial clustering and ethnic variation have been documented. The populations of Africans living in diverse environments provide a unique opportunity to study type 2 DM as the mechanism is becoming more clear.

  16. 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...

  17. Classification of hyperspectral remote sensing images based on simulated annealing genetic algorithm and multiple instance learning

    Institute of Scientific and Technical Information of China (English)

    高红民; 周惠; 徐立中; 石爱业

    2014-01-01

    A hybrid feature selection and classification strategy was proposed based on the simulated annealing genetic algorithm and multiple instance learning (MIL). The band selection method was proposed from subspace decomposition, which combines the simulated annealing algorithm with the genetic algorithm in choosing different cross-over and mutation probabilities, as well as mutation individuals. Then MIL was combined with image segmentation, clustering and support vector machine algorithms to classify hyperspectral image. The experimental results show that this proposed method can get high classification accuracy of 93.13%at small training samples and the weaknesses of the conventional methods are overcome.

  18. Dynamic Change of Genetic Diversity in Conserved Populations with Different Initial Genetic Architectures

    Institute of Scientific and Technical Information of China (English)

    LU Yun-feng; LI Hong-wei; WU Ke-liang; WU Chang-xin

    2013-01-01

    Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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 (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.

  6. Genetic structure in dwarf bamboo (Bashania fangiana clonal populations with different genet ages.

    Directory of Open Access Journals (Sweden)

    Qing-qing Ma

    Full Text Available Amplified fragment length polymorphism (AFLP fingerprints were used to reveal genotypic diversity of dwarf bamboo (Bashania fangiana clonal populations with two different genet ages (≤30 years versus >70 years at Wolong National Natural Reserve, Sichuan province, China. We generated AFLP fingerprints for 96 leaf samples, collected at 30 m intervals in the two populations, using ten selective primer pairs. A total of 92 genotypes were identified from the both populations. The mean proportion of distinguishable genotypes (G/N was 0.9583 (0.9375 to 0.9792 and Simpson's index of diversity (D was 0.9982 (0.9973 to 0.9991. So, two B. fangiana populations were multiclonal and highly diverse. The largest single clone may occur over a distance of about 30 m. Our results demonstrated that the genotypic diversity and genet density of B. fangiana clonal population did not change significantly (47 versus 45 with genet aging and low partitioned genetic differentiation was between the two populations (Gst = 0.0571. The analysis of molecular variance consistently showed that a large proportion of the genetic variation (87.79% existed among the individuals within populations, whereas only 12.21% were found among populations. In addition, the high level of genotypic diversity in the two populations implies that the further works were needed to investigate the reasons for the poor seed set in B. fangiana after flowering.

  7. 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....

  8. Genetic structure and phylogeography of European catfish (Silurus glanis) populations.

    Science.gov (United States)

    Triantafyllidis, A; Krieg, F; Cottin, C; Abatzopoulos, T J; Triantaphyllidis, C; Guyomard, R

    2002-06-01

    The genetic structure of Silurus glanis (Europe's largest freshwater fish species) across most of its natural distribution was investigated using 10 microsatellite loci. The revealed levels of genetic diversity were much higher than previous allozyme and restriction fragment length polymorphism mitochondrial DNA analyses had shown; relative levels of variability among populations were however, in good agreement with the previous studies. Populations from large basins (Volga and Danube rivers) were the most polymorphic, while samples from the smaller Greek rivers, which are more prone to genetic bottleneck, exhibited the lowest levels of genetic diversity. Microsatellite multilocus genotyping permitted the assignment of individual fish to their population of origin with a score as high as 98.3%. Despite the great genetic differentiation of S. glanis populations, no consistent pattern of geographical structuring was revealed, in contrast to previous studies of European freshwater fish species. A model of isolation by distance seems more probable and a hypothesis of recent dispersion from only one glacial refugium is proposed. The discovery of the highest levels of microsatellite and mitochondrial diversity in the Volga sample and the presence of river connections, during the Pleistocene, between this area and all major areas of the present catfish distribution, place this refugium around the Ponto-Caspian region. Combining these data with those from previous studies, a number of markers are now available to monitor wild and hatchery populations even at the individual level.

  9. Population and genomic lessons from genetic analysis of two Indian populations.

    Science.gov (United States)

    Juyal, Garima; Mondal, Mayukh; Luisi, Pierre; Laayouni, Hafid; Sood, Ajit; Midha, Vandana; Heutink, Peter; Bertranpetit, Jaume; Thelma, B K; Casals, Ferran

    2014-10-01

    Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.

  10. Population connectivity and genetic structure of burbot (Lota lota) populations in the Wind River Basin, Wyoming

    Science.gov (United States)

    Underwood, Zachary E.; Mandeville, Elizabeth G.; Walters, Annika W.

    2016-01-01

    Burbot (Lota lota) occur in the Wind River Basin in central Wyoming, USA, at the southwestern extreme of the species’ native range in North America. The most stable and successful of these populations occur in six glacially carved mountain lakes on three different tributary streams and one large main stem impoundment (Boysen Reservoir) downstream from the tributary populations. Burbot are rarely found in connecting streams and rivers, which are relatively small and high gradient, with a variety of potential barriers to upstream movement of fish. We used high-throughput genomic sequence data for 11,197 SNPs to characterize the genetic diversity, population structure, and connectivity among burbot populations on the Wind River system. Fish from Boysen Reservoir and lower basin tributary populations were genetically differentiated from those in the upper basin tributary populations. In addition, fish within the same tributary streams fell within the same genetic clusters, suggesting there is movement of fish between lakes on the same tributaries but that populations within each tributary system are isolated and genetically distinct from other populations. Observed genetic differentiation corresponded to natural and anthropogenic barriers, highlighting the importance of barriers to fish population connectivity and gene flow in human-altered linked lake-stream habitats.

  11. Population structure and genetic diversity in natural populations of Theobroma speciosum Willd. Ex Spreng (Malvaceae).

    Science.gov (United States)

    Giustina, L D; Luz, L N; Vieira, F S; Rossi, F S; Soares-Lopes, C R A; Pereira, T N S; Rossi, A A B

    2014-02-14

    The genus Theobroma found in the Amazon region is composed of 22 species, including Theobroma speciosum, better known as cacauí. These species are constantly threatened by forest fragmentation caused by human activities and require conservation strategies and management aimed at preserving them in their natural environments. The main objective of this study was to analyze the population structure and genetic diversity within and between natural populations of T. speciosum by using ISSR molecular markers to understand the population structure of the species. Four natural populations belonging to the Amazon rainforest (BAC, CRO, FLA, and PNA), located in the State of Mato Grosso, were selected. Amplification reactions were performed using 15 ISSR primers. A total of 101 loci were found, of which 54.46% were polymorphic at the species level. The BAC population showed higher genetic diversity (H=0.095 and I=0.144) and higher percentage of polymorphism (28.71%). The populations showed an FST value of 0.604, indicating marked genetic differentiation. The highest genetic variation was found between populations. Gene flow was low between populations, indicating genetic isolation between populations.

  12. 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.

  13. Population genetic structure of a colonising, triploid weed, Hieracium lepidulum.

    Science.gov (United States)

    Chapman, H; Robson, B; Pearson, M L

    2004-03-01

    Understanding the breeding system and population genetic structure of invasive weed species is important for biocontrol, and contributes to our understanding of the evolutionary processes associated with invasions. Hieracium lepidulum is an invasive weed in New Zealand, colonising a diverse range of habitats including native Nothofagus forest, pine plantations, scrubland and tussock grassland. It is competing with native subalpine and alpine grassland and herbfield vegetation. H. lepidulum is a triploid, diplosporous apomict, so theoretically all seed is clonal, and there is limited potential for the creation of variation through recombination. We used intersimple sequence repeats (ISSRs) to determine the population genetic structure of New Zealand populations of H. lepidulum. ISSR analysis of five populations from two regions in the South Island demonstrated high intrapopulation genotypic diversity, and high interpopulation genetic structuring; PhiST = 0.54 over all five populations. No private alleles were found in any of the five populations, and allelic differentiation was correlated to geographic distance. Cladistic compatibility analysis indicated that both recombination and mutation were important in the creation of genotypic diversity. Our data will contribute to any biocontrol program developed for H. lepidulum. It will also be a baseline data set for future comparisons of genetic structure during the course of H. lepidulum invasions.

  14. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

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

    2008-10-01

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

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

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    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

  16. gPGA: GPU Accelerated Population Genetics Analyses.

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    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.

  17. Quasispecies theory in the context of population genetics

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    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.

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

    DEFF Research Database (Denmark)

    Fumagalli, Matteo; Vieira, Filipe G.; 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 da...... individuals, suggesting that employing this new method is useful for investigating the genetic relationships of populations sampled at low coverage....... 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...... 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...

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

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    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,

  20. [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.

  1. Nosology and classification of genetic skeletal disorders: 2015 revision.

    Science.gov (United States)

    Bonafe, Luisa; Cormier-Daire, Valerie; Hall, Christine; Lachman, Ralph; Mortier, Geert; Mundlos, Stefan; Nishimura, Gen; Sangiorgi, Luca; Savarirayan, Ravi; Sillence, David; Spranger, Jürgen; Superti-Furga, Andrea; Warman, Matthew; Unger, Sheila

    2015-12-01

    The purpose of the nosology is to serve as a "master" list of the genetic disorders of the skeleton to facilitate diagnosis and to help delineate variant or newly recognized conditions. This is the 9th edition of the nosology and in comparison with its predecessor there are fewer conditions but many new genes. In previous editions, diagnoses that were phenotypically indistinguishable but genetically heterogenous were listed separately but we felt this was an unnecessary distinction. Thus the overall number of disorders has decreased from 456 to 436 but the number of groups has increased to 42 and the number of genes to 364. The nosology may become increasingly important today and tomorrow in the era of big data when the question for the geneticist is often whether a mutation identified by next generation sequencing technology in a particular gene can explain the clinical and radiological phenotype of their patient. This can be particularly difficult to answer conclusively in the prenatal setting. Personalized medicine emphasizes the importance of tailoring diagnosis and therapy to the individual but for our patients with rare skeletal disorders, the importance of tapping into a resource where genetic data can be centralized and made available should not be forgotten or underestimated. The nosology can also serve as a reference for the creation of locus-specific databases that are expected to help in delineating genotype-phenotype correlations and to harbor the information that will be gained by combining clinical observations and next generation sequencing results.

  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 m......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...

  3. Genetic population structure of local populations of the endangered saltmarsh sesarmid crab Clistocoeloma sinense in Japan.

    Science.gov (United States)

    Yuhara, Takeshi; Kawane, Masako; Furota, Toshio

    2014-01-01

    During recent decades, over 40% of Japanese estuarine tidal flats have been lost due to coastal developments. Local populations of the saltmarsh sesarmid crab Clistocoeloma sinense, designated as an endangered species due to the limited suitable saltmarsh habitat available, have decreased accordingly, being now represented as small remnant populations. Several such populations in Tokyo Bay, have been recognised as representing distributional limits of the species. To clarify the genetic diversity and connectivity among local coastal populations of Japanese Clistocoeloma sinense, including those in Tokyo Bay, mitochondrial DNA analyses were conducted in the hope of providing fundamental information for future conservation studies and an understanding of metapopulation dynamics through larval dispersal among local populations. All of the populations sampled indicated low levels of genetic diversity, which may have resulted from recent population bottlenecks or founder events. However, the results also revealed clear genetic differentiation between two enclosed-water populations in Tokyo Bay and Ise-Mikawa Bay, suggesting the existence of a barrier to larval transport between these two water bodies. Since the maintenance of genetic connectivity is a requirement of local population stability, the preservation of extant habitats and restoration of saltmarshes along the coast of Japan may be the most effective measures for conservation of this endangered species.

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

    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 Fls-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 Tangiiahe 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].

  5. Genetic hitchhiking in a subdivided population of Mytilus edulis

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    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

  6. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.

  7. 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

    geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels...... 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...

  8. Can small wildlife conservancies maintain genetically stable populations of large mammals? Evidence for increased genetic drift in geographically restricted populations of Cape buffalo in East Africa

    DEFF Research Database (Denmark)

    Heller, R; Okello, J B A; Siegismund, H

    2010-01-01

    populations, the level of genetic differentiation found here is comparable to that among pan-African populations. Overall, correlations between conservancy area and indices of genetic diversity suggest buffalo populations inhabiting small parks are showing signs of genetic erosion, stressing the need for more...

  9. Genetic substructure of Kuwaiti population reveals migration history.

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    Osama Alsmadi

    Full Text Available The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP data to understand admixtures in each group reveals the following: the first group (Kuwait P is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait's population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait's geographical location at the nexus

  10. Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus.

    Science.gov (United States)

    Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

    2012-04-01

    Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.

  11. Community structure and population genetics of Eastern Mediterranean polychaetes

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    Giorgos eChatzigeorgiou

    2014-10-01

    Full Text Available Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1776 during two successive years at two locations in northern Crete (Aegean Sea and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community.

  12. Rapid genetic erosion in pollutant-exposed experimental chironomid populations

    Energy Technology Data Exchange (ETDEWEB)

    Nowak, Carsten [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: cnowak@senckenberg.de; Vogt, Christian [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: vogt@bio.uni-frankfurt.de; Pfenninger, Markus [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: pfenninger@bio.uni-frankfurt.de; Schwenk, Klaus [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: k.schwenk@bio.uni-frankfurt.de; Oehlmann, Joerg [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: oehlmann@bio.uni-frankfurt.de; Streit, Bruno [Abteilung Okologie und Evolution, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: streit@bio.uni-frankfurt.de; Oetken, Matthias [Abteilung Aquatische Okotoxikologie, Institut fuer Okologie, Evolution und Diversitaet, J. W. Goethe-Universitaet Frankfurt am Main, Siesmayerstrasse 70, 60054 Frankfurt am Main (Germany)], E-mail: oetken@bio.uni-frankfurt.de

    2009-03-15

    Few studies have evaluated how effectively environmental contamination may reduce genetic diversity of a population. Here, we chose a laboratory approach in order to test if tributyltin (TBT) exposure at environmentally relevant concentrations leads to reduced genetic variation in the midge Chironomus riparius. Two TBT-exposed and two unexposed experimental populations were reared simultaneously in the laboratory for 12 generations. We recorded several life-history traits in each generation and monitored genetic variation over time using five variable microsatellite markers. TBT-exposed strains showed increased larval mortality (treatments: 43.8%; controls: 27.8%), slightly reduced reproductive output, and delayed larval development. Reduction of genetic variation was strongest and only significant in the TBT-exposed strains (treatments: -45.9%, controls: -24.4% of initial heterozygosity) after 12 generations. Our findings document that chemical pollution may lead to a rapid decrease in genetic diversity, which has important implications for conservation strategies and ecological management in polluted environments. - Chronic TBT exposure reduces allelic variation at five variable microsatellite loci in experimental populations of Chironomus riparius.

  13. The genetic population structure of northern Sweden and its implications for mapping genetic diseases.

    Science.gov (United States)

    Einarsdottir, Elisabet; Egerbladh, Inez; Beckman, Lars; Holmberg, Dan; Escher, Stefan A

    2007-11-01

    The northern Swedish population has a history of admixture of three ethnic groups and a dramatic population growth from a relatively small founder population. This has resulted in founder effects that together with unique resources for genealogical analyses provide excellent conditions for genetic mapping of monogenic diseases. Several recent examples of successful mapping of genetic factors underlying susceptibility to complex diseases have suggested that the population of northern Sweden may also be an important tool for efficient mapping of more complex phenotypes. A potential factor contributing to these effects may be population sub-isolates within the large river valleys, constituting a central geographic characteristic of this region. We here provide evidence that marriage patterns as well as the distribution of gene frequencies in a set of marker loci are compatible with this notion. The possible implications of this population structure on linkage- and association based strategies for identifying genes contributing risk to complex diseases are discussed.

  14. Beluga whale (Delphinapterus leucas) vocalizations and call classification from the eastern Beaufort Sea population.

    Science.gov (United States)

    Garland, Ellen C; Castellote, Manuel; Berchok, Catherine L

    2015-06-01

    Beluga whales, Delphinapterus leucas, have a graded call system; call types exist on a continuum making classification challenging. A description of vocalizations from the eastern Beaufort Sea beluga population during its spring migration are presented here, using both a non-parametric classification tree analysis (CART), and a Random Forest analysis. Twelve frequency and duration measurements were made on 1019 calls recorded over 14 days off Icy Cape, Alaska, resulting in 34 identifiable call types with 83% agreement in classification for both CART and Random Forest analyses. This high level of agreement in classification, with an initial subjective classification of calls into 36 categories, demonstrates that the methods applied here provide a quantitative analysis of a graded call dataset. Further, as calls cannot be attributed to individuals using single sensor passive acoustic monitoring efforts, these methods provide a comprehensive analysis of data where the influence of pseudo-replication of calls from individuals is unknown. This study is the first to describe the vocal repertoire of a beluga population using a robust and repeatable methodology. A baseline eastern Beaufort Sea beluga population repertoire is presented here, against which the call repertoire of other seasonally sympatric Alaskan beluga populations can be compared.

  15. Genetic and Metabolite Diversity of Sardinian Populations of Helichrysum italicum

    Science.gov (United States)

    Melito, Sara; Sias, Angela; Petretto, Giacomo L.; Chessa, Mario; Pintore, Giorgio; Porceddu, Andrea

    2013-01-01

    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. PMID:24260149

  16. 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.

  17. Population genetic structure in the Holstein breed in Brazil.

    Science.gov (United States)

    Magalhães Araújo da Silva, Mário Henrique; Malhado, Carlos Henrique Mendes; Costa, José Lauro; Cobuci, Jaime Araujo; Costa, Claudio Napolis; Carneiro, Paulo Luiz Souza

    2016-02-01

    We evaluated the population genetic structure of the Holstein breed in Brazil through pedigree analysis with the aim of supporting genetic management of extant herds. We used data from genealogical records of 204,511 animals in farms from south and southeast Brazil. Pedigree records between 1943 and 2005 were divided into seven periods of 8 years to estimate the effective population size (N e ). N e varied during the study periods, ranging from 0.19 to 3016.25. There was an increase in the percentage of inbred animals over time, from 0.18 to 5.0 %. However, this figure may be an underestimate due to the low completeness of pedigree, primarily related to paternal pedigree. The effective number of founders (fe) was 473 animals and ancestors (fa) was 471. The genetic contribution of 260 ancestors (founders or not) accounted for 50 % of the genetic variability in the population. The average relatedness coefficient (AR) and inbreeding coefficient indicate that the Holstein breed in Brazil is being effectively managed, despite a moderate founder effect and the low number of animals that are responsible for the population variance.

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

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    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.

  19. The impact of clonality on parasite population genetic structure

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    Prugnolle F.

    2008-09-01

    Full Text Available In this paper, we briefly review the consequences of clonal reproduction on the apportionment of genetic diversity in parasite populations. We distinguish three kinds of parasite life-cycle where clonal reproduction occurs. The consequences of this mode of reproduction for the different kinds of parasite life-cycles are described. We here particularly focus on clonal diploids.

  20. Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

    Science.gov (United States)

    Clowers, Katie J; Heilberger, Justin; Piotrowski, Jeff S; Will, Jessica L; Gasch, Audrey P

    2015-09-01

    How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1, a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.

  1. Accurate crop classification using hierarchical genetic fuzzy rule-based systems

    Science.gov (United States)

    Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

    2014-10-01

    This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

  2. Genetic ancestry, social classification, and racial inequalities in blood pressure in Southeastern Puerto Rico.

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    Clarence C Gravlee

    Full Text Available BACKGROUND: The role of race in human genetics and biomedical research is among the most contested issues in science. Much debate centers on the relative importance of genetic versus sociocultural factors in explaining racial inequalities in health. However, few studies integrate genetic and sociocultural data to test competing explanations directly. METHODOLOGY/PRINCIPAL FINDINGS: We draw on ethnographic, epidemiologic, and genetic data collected in Southeastern Puerto Rico to isolate two distinct variables for which race is often used as a proxy: genetic ancestry versus social classification. We show that color, an aspect of social classification based on the culturally defined meaning of race in Puerto Rico, better predicts blood pressure than does a genetic-based estimate of continental ancestry. We also find that incorporating sociocultural variables reveals a new and significant association between a candidate gene polymorphism for hypertension (alpha(2C adrenergic receptor deletion and blood pressure. CONCLUSIONS/SIGNIFICANCE: This study addresses the recognized need to measure both genetic and sociocultural factors in research on racial inequalities in health. Our preliminary results provide the most direct evidence to date that previously reported associations between genetic ancestry and health may be attributable to sociocultural factors related to race and racism, rather than to functional genetic differences between racially defined groups. Our results also imply that including sociocultural variables in future research may improve our ability to detect significant allele-phenotype associations. Thus, measuring sociocultural factors related to race may both empower future genetic association studies and help to clarify the biological consequences of social inequalities.

  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. Genetic variation of cowslip (Primula veris L. populations (West Poland

    Directory of Open Access Journals (Sweden)

    Maria Morozowska

    2011-04-01

    Full Text Available Genetic variation of twelve Polish populations of Primula veris L. from western Poland was investigated in respect of six enzyme systems: 6-phosphogluconate dehydrogenase (6PGD, diaphorase (DIA, menadione reductase (MNR, formate dehydrogenase (FDH, isocitrate dehydrogenase (IDH and glutamate oxaloacetate transaminase (GOT. Only two of them (6PGD and DIA were polymorphic and all populations were compared according to four loci and eight alleles. For 6PGD only one out of the two detected loci (locus 6PGD-2 was polymorphic and consisted of three alleles a, b and c. For DIA each of two detected loci had two alleles. For 6PGD-2 one population was monomorphic and four populations were monomorphic for DIA-1 and DIA-2. The rest of the populations were polymorphic with low frequency of heterozygotes. The low heterozygosity level, found in the examined populations, was confirmed by high values of the fixation index (F. The level of genetic differentiation among GST populations specified for each polymorphic loci, was equal to 0.045 for 6PGD-2 and had the value of 0.078 for DIA-2 and 0.186 for DIA-1. Nm value for polymorphic loci was 1.10 for DIA-1 and 2.94 for DIA-2, and for 6PGD-2 was 5.33, what indicates some gene flow between the examined populations. The dendrogram constructed on the basis of genotype frequencies showed that the populations were divided into two groups, however the most southern population No. 2 was clearly similar to the northern population No. 8.

  5. Population structure and genetic diversity of moose in Alaska.

    Science.gov (United States)

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P moose in Alaska with population expansion from interior Alaska westward toward the coast.

  6. 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.

  7. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.

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    Wolfram Möbius

    2015-12-01

    Full Text Available As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the

  8. 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.

  9. Population genetics of venous thromboembolism. A narrative review.

    Science.gov (United States)

    Margaglione, Maurizio; Grandone, Elvira

    2011-02-01

    Results from epidemiological studies are consistent with the hypothesis that disparities in venous thromboembolism (VTE) burden are attributable to differences in genetic structure among populations from different genetic backgrounds. To that end, recent genetic studies have demonstrated not only potential associations between certain alleles and VTE but also clear differences in the distribution of these alleles in patients stratified by ancestry. There are a number of notable clinical and pathophysiological questions that arise from these findings. First at all is defining the precise variant(s) that alter disease susceptibility. The comparatively lower rates of VTE recorded among Asians would imply that risk profile is devoid of many risk factors on comparison to Caucasian or African counterparts or that a putative protective factor is advocated in the former population. Identification of these variants provided specific insight into VTE disease in selected populations and also shed lights on the biology of the disease. The association observed between ancestry and VTE is likely to be multifactorial, possibly reflecting, in addition to genetic variation, also socioeconomic differences. Acknowledgment of this may provide useful information in biomedical contexts and help to identify individual risk factors for VTE.

  10. 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.

  11. Genetic affinities of the central Indian tribal populations.

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    Gunjan Sharma

    Full Text Available BACKGROUND: The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic. There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. METHODOLOGY/PRINCIPAL FINDINGS: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe with the Austroasiatic (Munda group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. CONCLUSIONS/SIGNIFICANCE: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.

  12. 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.

  13. 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.

  14. Performance Analyses on Population Seeding Techniques for Genetic Algorithms

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    P. Victer Paul

    2013-06-01

    Full Text Available In Genetic Algorithm (GA, the fitness or quality of individual solutions in the initial population plays a significant part in determining the final optimal solution. The traditional GA withrandom population seeding technique is simple and proficient however the generated population may contain poor fitness individuals, which take long time to converge to the optimal solution. On the otherhand, the hybrid population seeding techniques, which have the benefits of generating good fitness individuals and fast convergence to the optimal solution. Researchers have proposed several populationseeding techniques using the background knowledge on the problem taken to solve. In this paper, we analyse the performance of different population seeding techniques for the permutation coded genetic algorithm based on the quality of the individuals generated. Experiments are carried out using the famous Travelling Salesman Problem (TSP benchmark instances obtained from the TSPLIB, which isthe standard library for TSP problems. The experimental results show the order of performance of different population seeding techniques in terms of Convergence Rate (% and Error Rate (%.

  15. 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.

  16. A modified decision tree algorithm based on genetic algorithm for mobile user classification problem.

    Science.gov (United States)

    Liu, Dong-sheng; Fan, Shu-jiang

    2014-01-01

    In order to offer mobile customers better service, we should classify the mobile user firstly. Aimed at the limitations of previous classification methods, this paper puts forward a modified decision tree algorithm for mobile user classification, which introduced genetic algorithm to optimize the results of the decision tree algorithm. We also take the context information as a classification attributes for the mobile user and we classify the context into public context and private context classes. Then we analyze the processes and operators of the algorithm. At last, we make an experiment on the mobile user with the algorithm, we can classify the mobile user into Basic service user, E-service user, Plus service user, and Total service user classes and we can also get some rules about the mobile user. Compared to C4.5 decision tree algorithm and SVM algorithm, the algorithm we proposed in this paper has higher accuracy and more simplicity.

  17. 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.

  18. Genetic Diversity and Genetic Structure of Different Types of Natural Populations in Osmanthus fragrans Lour. and the Relationships with Sex Ratio, Population Structure, and Geographic Isolation

    Directory of Open Access Journals (Sweden)

    Shaoqing Hu

    2014-01-01

    Full Text Available Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites, once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of Ne, He, and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity.

  19. Genetic diversity and genetic structure of different types of natural populations in Osmanthus fragrans Lour. and the relationships with sex ratio, population structure, and geographic isolation.

    Science.gov (United States)

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhao, Hongbo; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of N e , H e , and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity.

  20. 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.

  1. Hitchhiker's guide to genetic diversity in socially structured populations

    Institute of Scientific and Technical Information of China (English)

    L.S.PREMO

    2012-01-01

    When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking.A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration.Under conditions in which genetic and cultural variants are transmitted symmetrically,neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking.Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity,and it may be applicable to humans as well.This paper provides a critical review of recent models of both types of hitchhiking in socially structured populations.The models' assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species,and vice versa [Current Zoology 58 (1):287-297,2012].

  2. [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.

  3. Genetic Algorithm Optimized Back Propagation Neural Network for Knee Osteoarthritis Classification

    Directory of Open Access Journals (Sweden)

    Jian WeiKoh

    2014-10-01

    Full Text Available Osteoarthritis (OA is the most common form of arthritis that caused by degeneration of articular cartilage, which function as shock absorption cushion in our joint. The most common joints that infected by osteoarthritis are hand, hip, spine and knee. Knee osteoarthritis is the focus in this study. These days, Magnetic Resonance Imaging (MRI technique is widely applied in diagnosis the progression of osteoarthritis due to the ability to display the contrast between bone and cartilage. Traditionally, interpretation of MR image is done manually by physicians who are very inconsistent and time consuming. Hence, automated classifier is needed for minimize the processing time of classification. In this study, genetic algorithm optimized neural network technique is used for the knee osteoarthritis classification. This classifier consists of 4 stages, which are feature extraction by Discrete Wavelet Transform (DWT, training stage of neural network, testing stage of neural network and optimization stage by Genetic Algorithm (GA. This technique obtained 98.5% of classification accuracy when training and 94.67% on testing stage. Besides, classification time is reduced by 17.24% after optimization of the neural network.

  4. A Novel Training Algorithm of Genetic Neural Networks and Its Application to Classification

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    First of all, this paper discusses the drawbacks of multilayer perceptron (MLP), which is trained by the traditional back propagation (BP) algorithm and used in a special classification problem. A new training algorithm for neural networks based on genetic algorithm and BP algorithm is developed. The difference between the new training algorithm and BP algorithm in the ability of nonlinear approaching is expressed through an example, and the application foreground is illustrated by an example.

  5. Classification

    Science.gov (United States)

    Clary, Renee; Wandersee, James

    2013-01-01

    In this article, Renee Clary and James Wandersee describe the beginnings of "Classification," which lies at the very heart of science and depends upon pattern recognition. Clary and Wandersee approach patterns by first telling the story of the "Linnaean classification system," introduced by Carl Linnacus (1707-1778), who is…

  6. Estimation of recombination frequency in bi-parental genetic populations.

    Science.gov (United States)

    Sun, Ziqi; Li, Huihui; Zhang, Luyan; Wang, Jiankang

    2012-06-01

    Summary Linkage analysis plays an important role in genetic studies. In linkage analysis, accurate estimation of recombination frequency is essential. Many bi-parental populations have been used, and determining an appropriate population is of great importance in precise recombination frequency. In this study, we investigated the estimation efficiency of recombination frequency in 12 bi-parental populations. The criteria that we used for comparison were LOD score in testing linkage relationship, deviation between estimated and real recombination frequency, standard error (SE) of estimates and the least theoretical population size (PS) required to observe at least one recombinant and to declare the statistically significant linkage relationship. Theoretical and simulation results indicated that larger PS and smaller recombination frequency resulted in higher LOD score and smaller deviation. Lower LOD score, higher deviation and higher SE for estimating the recombination frequency in the advanced backcrossing and selfing populations are larger than those in backcross and F2 populations, respectively. For advanced backcrossing and selfing populations, larger populations were needed in order to observe at least one recombinant and to declare significant linkage. In comparison, in F2 and F3 populations higher LOD score, lower deviation and SE were observed for co-dominant markers. A much larger population was needed to observe at least one recombinant and to detect loose linkage for dominant and recessive markers. Therefore, advanced backcrossing and selfing populations had lower precision in estimating the recombination frequency. F2 and F3 populations together with co-dominant markers represent the ideal situation for linkage analysis and linkage map construction.

  7. Genetic structure of West Greenland populations of lumpfish Cyclopterus lumpus

    DEFF Research Database (Denmark)

    Mayoral, Elsa Garcia; Olsen, M.; Hedeholm, R.

    2016-01-01

    In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identifica......In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow...... for identification of origin of C. lumpus in Greenlandic waters, genetic assignment analysis was performed for 86 C. lumpus sampled on a feeding migration. Significant structuring with isolation by distance was observed in the West Greenland samples and two major subpopulations, north and south, were suggested...

  8. 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.

  9. Genetically distinct coelacanth population off the northern Tanzanian coast.

    Science.gov (United States)

    Nikaido, Masato; Sasaki, Takeshi; Emerson, J J; Aibara, Mitsuto; Mzighani, Semvua I; Budeba, Yohana L; Ngatunga, Benjamin P; Iwata, Masamitsu; Abe, Yoshitaka; Li, Wen-Hsiung; Okada, Norihiro

    2011-11-01

    Since the sensational discovery of a living coelacanth off the east coast of South Africa, the geographic distribution of viable coelacanth populations has been a subject of debate. In the past, the coelacanths off the African mainland were thought to be strays from the Comoros because most coelacanths captured were caught in the waters surrounding the Comoros archipelagos. However, in recent years, a large number of coelacanths were captured off the coast of Tanzania, including nine living specimens observed in a remotely operated vehicles survey. Thus, it is possible that there is a reproducing population inhabiting waters off the Tanzania coast. We have sequenced the complete mitochondrial genomes of 21 Tanzanian and 2 Comoran coelacanths and analyzed these sequences together with two additional full mitochondrial genomes and 47 d-loop sequences from the literature. We found that the coelacanth population off the northern Tanzanian coast is genetically differentiated from those of the southern Tanzania coast and the Comoros, whereas no significant genetic differentiation occurs between the latter two localities. The differentiation between the northern and southern Tanzanian coast populations is consistent with the hypothesis that the existence of northward-flowing ocean current along the Tanzanian coast may reduce or prevent gene flow from the northern to the southern population. Finally, we estimated that the population localized to the southern Tanzanian coast and the Comoros diverged from other coelacanths at least 200,000 y ago. These results indicate that the coelacanths off the northern Tanzania coast are not strays but a genetically distinct group. Our study provides important information for the conservation of this threatened "living fossil."

  10. Genetics in population health science: strategies and opportunities.

    Science.gov (United States)

    Belsky, Daniel W; Moffitt, Terrie E; Caspi, Avshalom

    2013-10-01

    Translational research is needed to leverage discoveries from the frontiers of genome science to improve public health. So far, public health researchers have largely ignored genetic discoveries, and geneticists have ignored important aspects of population health science. This mutual neglect should end. In this article, we discuss 3 areas where public health researchers can help to advance translation: (1) risk assessment: investigate genetic profiles as components in composite risk assessments; (2) targeted intervention: conduct life-course longitudinal studies to understand when genetic risks manifest in development and whether intervention during sensitive periods can have lasting effects; and (3) improved understanding of environmental causation: collaborate with geneticists on gene-environment interaction research. We illustrate with examples from our own research on obesity and smoking.

  11. 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”.

  12. 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.

  13. Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey.

    Science.gov (United States)

    Akhan, Suleyman; Bektas, Yusuf; Berber, Selcuk; Kalayci, Gokhan

    2014-10-01

    The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19-6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96-3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H d = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.

  14. Reconstructing the population genetic history of the Caribbean.

    Directory of Open Access Journals (Sweden)

    Andrés Moreno-Estrada

    2013-11-01

    Full Text Available 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

  15. 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

  16. Genetic variation of phytate and ionorganic phosphorus in maize population

    OpenAIRE

    2009-01-01

    Analysis of 60 maize populations was conducted to identify genotypes that had either low or high concentration of phytate. Genetic variability in seed phytate content was observed, with values ranging from 1,147 to 4, 13 g kg-1. Inorganic phosphorus (Pi) concentrations were between 0, 35 and 1, 29 and averaged 0, 65 g kg-1. Three groups of populations were identified as having low, intermediate and high phytate content. The low phytate concentration was measured in eight, intermediate in 25 a...

  17. 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.

  18. 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.

  19. Complex genetic origin of Indian populations and its implications

    Indian Academy of Sciences (India)

    Rakesh Tamang; Lalji Singh; Kumarasamy Thangaraj

    2012-11-01

    Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.

  20. Genetic variation and population structure of interleukin genes among seven ethnic populations from Karnataka, India

    Indian Academy of Sciences (India)

    Srilakshmi M. Raj; Diddahally R. Govindaraju; Ranajit Chakraborty

    2007-12-01

    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 interleukin gene cluster. Allele frequencies varied by threefold among these populations, which also differed for gene diversity and heterozygosity levels. The average degree of population subdivision among these castes was low ($F_{ST} = 0.02$). However, pair-wise interpopulation differentiation ranged from 0–7%, indicating no detectable differentiation to moderate differentiation between specific populations. The results of phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data on these ethnic groups. Variation in the allele frequencies, as well as differentiation, may be attributed to differential selection and demographic factors including consanguinity among the ethnic groups. Information on the distribution of functionally relevant polymorphisms among ethnic populations may be important towards developing community medicine and public health policies.

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

    Population genefc 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: Fsr = 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.

  2. 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

    in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number...

  3. Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation.

    Science.gov (United States)

    Holmes, Christopher J; Pantel, Jelena H; Schulz, Kimberly L; Cáceres, Carla E

    2016-07-01

    When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination ('high' clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher-quality and lower-quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with 'high' clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.

  4. Behavior genetics of personality disorders: informing classification and conceptualization in DSM-5.

    Science.gov (United States)

    South, Susan C; DeYoung, Nathaniel J

    2013-07-01

    Personality pathology is currently captured in the Diagnostic and Statistical Manual through 10 categorical personality disorder (PD) diagnoses grouped into three descriptive clusters. This classification system has been criticized by many for using discrete categories and arbitrary thresholds when making clinical decisions. To address these critiques, the DSM-5 Personality and Personality Disorders Work Group has put forth a proposal that significantly alters the structure and content of the DSM-IV PD section. If this DSM-5 Work Group has conducted its own systematic review of the empirical literature, this review has not been released or made widely available. As such, it is up to the psychology community at large to determine how well the suggested changes align with findings from extant PD research. The current article joins this effort by addressing the contribution of behavior genetic findings to the revision process for classification of PDs in DSM-5. First, we provide a brief review of the history of PD classification in the DSM. Next, we present an overview and rationale for each of the five major suggested changes to PD diagnoses. For each suggested change, we outline the available evidence from behavior genetics and interpretations of these findings. Finally, we offer a summary of considerations for PD classification as the DSM-5 moves forward. Review of the behavior genetics literature suggests that several features of the DSM-5 proposal, including the elimination of 4 PDs, merging clinical disorders and PDs on a single axis, and the implementation of a trait rating system, require significantly greater explication before a product is finalized.

  5. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    Science.gov (United States)

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.

  6. Difference in MSA phenotype distribution between populations: genetics or environment?

    Science.gov (United States)

    Ozawa, Tetsutaro; Revesz, Tamas; Paviour, Dominic; Lees, Andrew J; Quinn, Niall; Tada, Mari; Kakita, Akiyoshi; Onodera, Osamu; Wakabayashi, Koichi; Takahashi, Hitoshi; Nishizawa, Masatoyo; Holton, Janice L

    2012-01-01

    The reasons for the differences in emphasis on striatonigral or olivopontocerebellar involvement in multiple system atrophy (MSA) remain to be determined. Semi-quantitative pathological analyses carried out in the United Kingdom and Japan demonstrated that olivopontocerebellar-predominant pathology was more frequent in Japanese MSA than British MSA. This observation provides evidence for a difference in phenotype distribution between British and Japanese patients with definite MSA. Studies of the natural history and epidemiology of MSA carried out in various populations have revealed that the relative prevalences of clinical subtypes of MSA probably differ among populations; the majority of MSA patients diagnosed in Europe have predominant parkinsonism (MSA-P), while the majority of MSA patients diagnosed in Asia have predominant cerebellar ataxia (MSA-C). Although potential drawbacks to the published frequencies of clinical subtypes and pathological subtypes should be considered because of selection biases, the difference demonstrated in pathological subtype is also consistent with the differences in clinical subtype of MSA demonstrated between Europe and Asia. Modest alterations in susceptibility factors may contribute to the difference in MSA phenotype distribution between populations. Synergistic interactions between genetic risk variants and environmental toxins responsible for parkinsonism or cerebellar dysfunction should therefore be explored. Further investigations are needed to determine the environmental, genetic, and epigenetic factors that account for the differences in clinicopathological phenotype of MSA among different populations.

  7. Population Bottlenecks Increase Additive Genetic Variance But Do Not Break a Selection Limit in Rainforest Drosophila

    DEFF Research Database (Denmark)

    van Heerwaarden, Belinda; Willi, Yvonne; Kristensen, Torsten N;

    2008-01-01

    According to neutral quantitative genetic theory, population bottlenecks are expected to decrease standing levels of additive genetic variance of quantitative traits. However, some empirical and theoretical results suggest that, if nonadditive genetic effects influence the trait, bottlenecks may ...

  8. Detecting populations in the 'ambiguous' zone : kinship-based estimation of population structure at low genetic divergence

    NARCIS (Netherlands)

    Palsboll, Per J.; Peery, M. Zachariah; Berube, Martine

    2010-01-01

    Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Iss

  9. 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

  10. Population genetic analysis among five Indian population groups using six microsatellite markers.

    Science.gov (United States)

    Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

    2003-04-01

    Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

  11. Local genetic structure in a white-bearded manakin population.

    Science.gov (United States)

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present.

  12. Population Genetics of Plasmodium vivax in the Peruvian Amazon.

    Directory of Open Access Journals (Sweden)

    Christopher Delgado-Ratto

    2016-01-01

    Full Text Available Characterizing the parasite dynamics and population structure provides useful information to understand the dynamic of transmission and to better target control interventions. Despite considerable efforts for its control, vivax malaria remains a major health problem in Peru. In this study, we have explored the population genetics of Plasmodium vivax isolates from Iquitos, the main city in the Peruvian Amazon, and 25 neighbouring peri-urban as well as rural villages along the Iquitos-Nauta Road.From April to December 2008, 292 P. vivax isolates were collected and successfully genotyped using 14 neutral microsatellites. Analysis of the molecular data revealed a similar proportion of monoclonal and polyclonal infections in urban areas, while in rural areas monoclonal infections were predominant (p = 0.002. Multiplicity of infection was higher in urban (MOI = 1.5-2 compared to rural areas (MOI = 1 (p = 0.003. The level of genetic diversity was similar in all areas (He = 0.66-0.76, p = 0.32 though genetic differentiation between areas was substantial (PHIPT = 0.17, p<0.0001. Principal coordinate analysis showed a marked differentiation between parasites from urban and rural areas. Linkage disequilibrium was detected in all the areas ([Formula: see text] = 0.08-0.49, for all p<0.0001. Gene flow among the areas was stablished through Bayesian analysis of migration models. Recent bottleneck events were detected in 4 areas and a recent parasite expansion in one of the isolated areas. In total, 87 unique haplotypes grouped in 2 or 3 genetic clusters described a sub-structured parasite population.Our study shows a sub-structured parasite population with clonal propagation, with most of its components recently affected by bottleneck events. Iquitos city is the main source of parasite spreading for all the peripheral study areas. The routes of transmission and gene flow and the reduction of the parasite population described are important from the public

  13. Feature Selection and Classification of Electroencephalographic Signals: An Artificial Neural Network and Genetic Algorithm Based Approach.

    Science.gov (United States)

    Erguzel, Turker Tekin; Ozekes, Serhat; Tan, Oguz; Gultekin, Selahattin

    2015-10-01

    Feature selection is an important step in many pattern recognition systems aiming to overcome the so-called curse of dimensionality. In this study, an optimized classification method was tested in 147 patients with major depressive disorder (MDD) treated with repetitive transcranial magnetic stimulation (rTMS). The performance of the combination of a genetic algorithm (GA) and a back-propagation (BP) neural network (BPNN) was evaluated using 6-channel pre-rTMS electroencephalographic (EEG) patterns of theta and delta frequency bands. The GA was first used to eliminate the redundant and less discriminant features to maximize classification performance. The BPNN was then applied to test the performance of the feature subset. Finally, classification performance using the subset was evaluated using 6-fold cross-validation. Although the slow bands of the frontal electrodes are widely used to collect EEG data for patients with MDD and provide quite satisfactory classification results, the outcomes of the proposed approach indicate noticeably increased overall accuracy of 89.12% and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.904 using the reduced feature set.

  14. Feasibility of Genetic Algorithm for Textile Defect Classification Using Neural Network

    Directory of Open Access Journals (Sweden)

    Md. Tarek Habib

    2012-07-01

    Full Text Available The global market for textile industry is highly competitive nowadays. Quality control in production process in textile industry has been a key factor for retaining existence in such competitive market. Automated textile inspection systems are very useful in this respect, because manual inspection is time consuming and not accurate enough. Hence, automated textile inspection systems have been drawing plenty of attention of the researchers of different countries in order to replace manual inspection. Defect detection and defect classification are the two major problems that are posed by the research of automated textile inspection systems. In this paper, we perform an extensive investigation on the applicability of genetic algorithm (GA in the context of textile defect classification using neural network (NN. We observe the effect of tuning different network parameters and explain the reasons. We empirically find a suitable NN model in the context of textile defect classification. We compare the performance of this model with that of the classification models implemented by others.

  15. The genetic basis of population fecundity prediction across multiple field populations of Nilaparvata lugens.

    Science.gov (United States)

    Sun, Zhong Xiang; Zhai, Yi Fan; Zhang, Jian Qing; Kang, Kui; Cai, Jing Heng; Fu, Yonggui; Qiu, Jie Qi; Shen, Jia Wei; Zhang, Wen Qing

    2015-02-01

    Identifying the molecular markers for complex quantitative traits in natural populations promises to provide novel insight into genetic mechanisms of adaptation and to aid in forecasting population dynamics. In this study, we investigated single nucleotide polymorphisms (SNPs) using candidate gene approach from high- and low-fecundity populations of the brown planthopper (BPH) Nilaparvata lugens Stål (Hemiptera: Delphacidae) divergently selected for fecundity. We also tested whether the population fecundity can be predicted by a few SNPs. Seven genes (ACE, fizzy, HMGCR, LpR, Sxl, Vg and VgR) were inspected for SNPs in N. lugens, which is a serious insect pest of rice. By direct sequencing of the complementary DNA and promoter sequences of these candidate genes, 1033 SNPs were discovered within high- and low-fecundity BPH populations. A panel of 121 candidate SNPs were selected and genotyped in 215 individuals from 2 laboratory populations (HFP and LFP) and 3 field populations (GZP, SGP and ZSP). Prior to association tests, population structure and linkage disequilibrium (LD) among the 3 field populations were analysed. The association results showed that 7 SNPs were significantly associated with population fecundity in BPH. These significant SNPs were used for constructing general liner models with stepwise regression. The best predictive model was composed of 2 SNPs (ACE-862 and VgR-816 ) with very good fitting degree. We found that 29% of the phenotypic variation in fecundity could be accounted for by only two markers. Using two laboratory populations and a complete independent field population, the predictive accuracy was 84.35-92.39%. The predictive model provides an efficient molecular method to predict BPH fecundity of field populations and provides novel insights for insect population management.

  16. Molecular Genetic Variation in a Clonal Plant Population of Leymus chinensis (Trin.) Tzvel.

    Institute of Scientific and Technical Information of China (English)

    Yu-Sheng WANG; Li-Ming ZHAO; Hua WANG; Jie WANG; Da-Ming HUANG; Rui-Min HONG; Xiao-Hua TENG; Nakamura MIKI

    2005-01-01

    Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the genetic variation among populations, between populations, and within populations, relationships between genetic distance and geographic distance, and the molecular variation and population size. The effects of geographic and genetic distances, as well as of genetic differentiation and population size, on genetic variations of Leymus chinensis (Trin.) Tzvel. are discussed. The present study showed that there was significant RAPD variation between the Baicheng region population and the Daqing region population, with a molecular variance of 6.35% (P < 0.04), and for differentiation among area populations of the Daqing region, with a molecular variance of 8.78% (P < 0.002). A 21.06% RAPD variation among all 16 populations among two regions was found (P < 0.001), as well as 72.59% variation within populations (P < 0.001). Molecular variation within populations was significantly different among 16 populations.

  17. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    Directory of Open Access Journals (Sweden)

    Khulekhani Sedwell Khanyile

    2015-02-01

    Full Text Available Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146, Malawi (n =30 and Zimbabwe (n =136 were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK and 0.24 (VD at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population

  18. Sex change and effective population size: implications for population genetic studies in marine fish.

    Science.gov (United States)

    Coscia, I; Chopelet, J; Waples, R S; Mann, B Q; Mariani, S

    2016-10-01

    Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.

  19. 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

  20. Beluga whale (Delphinapterus leucas) vocalizations and call classification from the eastern Beaufort Sea population

    OpenAIRE

    2015-01-01

    Funding was provided by the Bureau of Ocean Energy Management under InterAgency Agreement M09PG00016. E.C.G. was supported by a National Research Council (National Academy of Sciences) Postdoctoral Fellowship. Beluga whales, Delphinapterus leucas, have a graded call system; call types exist on a continuum making classification challenging. A description of vocalizations from the eastern Beaufort Sea beluga population during its spring migration are presented here, using both a non-parametr...

  1. Genetic Bee Colony (GBC) algorithm: A new gene selection method for microarray cancer classification.

    Science.gov (United States)

    Alshamlan, Hala M; Badr, Ghada H; Alohali, Yousef A

    2015-06-01

    Naturally inspired evolutionary algorithms prove effectiveness when used for solving feature selection and classification problems. Artificial Bee Colony (ABC) is a relatively new swarm intelligence method. In this paper, we propose a new hybrid gene selection method, namely Genetic Bee Colony (GBC) algorithm. The proposed algorithm combines the used of a Genetic Algorithm (GA) along with Artificial Bee Colony (ABC) algorithm. The goal is to integrate the advantages of both algorithms. The proposed algorithm is applied to a microarray gene expression profile in order to select the most predictive and informative genes for cancer classification. In order to test the accuracy performance of the proposed algorithm, extensive experiments were conducted. Three binary microarray datasets are use, which include: colon, leukemia, and lung. In addition, another three multi-class microarray datasets are used, which are: SRBCT, lymphoma, and leukemia. Results of the GBC algorithm are compared with our recently proposed technique: mRMR when combined with the Artificial Bee Colony algorithm (mRMR-ABC). We also compared the combination of mRMR with GA (mRMR-GA) and Particle Swarm Optimization (mRMR-PSO) algorithms. In addition, we compared the GBC algorithm with other related algorithms that have been recently published in the literature, using all benchmark datasets. The GBC algorithm shows superior performance as it achieved the highest classification accuracy along with the lowest average number of selected genes. This proves that the GBC algorithm is a promising approach for solving the gene selection problem in both binary and multi-class cancer classification.

  2. The molecular genetics and morphometry-based Endometrial Intraepithelial Neoplasia classification system predicts disease progression in Endometrial hyperplasia more accurately than the 1994 World Health Organization classification system

    NARCIS (Netherlands)

    Baak, JP; Mutter, GL; Robboy, S; van Diest, PJ; Uyterlinde, AM; Orbo, A; Palazzo, J; Fiane, B; Lovslett, K; Burger, C; Voorhorst, F; Verheijen, RH

    2005-01-01

    BACKGROUND. The objective of this study was to compare the accuracy of disease progression prediction of the molecular genetics and morphometry-based Endometrial Intraepithelial Neoplasia (EIN) and World Health Organization 1994 (WHO94) classification systems in patients with endometrial hyperplasia

  3. Initial founders of captive populations are genetically representative of natural populations in critically endangered dusky gopher frogs, Lithobates sevosus.

    Science.gov (United States)

    Hinkson, Kristin M; Henry, Natochia L; Hensley, Nina M; Richter, Stephen C

    2016-09-01

    The rapid rate of decline in amphibian populations has urged many researchers and conservationists to establish captive, or ex situ, populations. Such populations are guarded against effects of habitat loss and degradation, and if actively managed, can serve as a reservoir for rare alleles that might be lost in the wild. Without proper management, ex situ population sizes can dwindle and will no longer perform this function. The dusky gopher frog, Lithobates sevosus, is a critically endangered species, imperiled by habitat loss and population isolation. To assist in recovery of the species and prevent further genetic erosion, a captive breeding program was initiated. We investigated how well natural genetic variation was captured within the ex situ population and determined relatedness within each ex situ population. We genotyped individuals from two natural populations and two founding, captive populations to compare metrics of genetic variation and relatedness. The data show the initial founder populations are genetically representative of the natural populations, although variation is low in each, and that relatedness values are similar. Therefore, founding captive populations were successful at capturing genetic variation in the wild. Future research should continue to compare genetic variation of captive and natural populations to monitor efficacy of their management programs. Zoo Biol. 35:378-384, 2016. © 2016 Wiley Periodicals, Inc.

  4. 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

  5. Reference benchmarks relating to great groups of genetic soil classification of China with soil taxonomy

    Institute of Scientific and Technical Information of China (English)

    SHI Xuezheng; YU Dongsheng; SUN Weixia; WANG Hongjie; ZHAO Qiguo; GONG Zitong

    2004-01-01

    Soil classification forms the basis for the exchange and extension of research findings in soil science and for the modernization of management of soil resources. This paper systematically reviews the compatibility of the genetic soil classification of China (GSCC) and soil taxonomy (ST).This includes a study of the evolution and consummation of the GSCC and assessment of the databases and methods of the study. Using the "Soil Species of China (six volumes)"and some provincial soil species as the basic material, the authors gathered information from 2540 soil species. Based on the key described in ST, the 2540 soil species were taxonomically classified into corresponding soil orders, suborders,great groups and subgroups and then matched with corresponding map units in the 1: 1000000 digital soil map of China. Using the high-level classification units of the two soil classification systems, and the attributes of each soil species,the sizes of distribution areas were mapped. The soil distribution results were analyzed and compared statistically. The reference compatibility between the great groups used in GSCC system and the soil orders of the ST is discussed. It is believed that 20 great groups display maximum referencibility >95% and 15 great groups depict maximum referencibility in the range of 70%-95%, which can be cited as reference benchmarks. The remaining 25 great groups are less compatible (with maximum referencibility <70%) and need further study, or require referencing at lower classification levels or at a regional level to help to improve the accuracy of the reference.

  6. Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.

    Science.gov (United States)

    Kovi, Mallikarjuna Rao; Fjellheim, Siri; Sandve, Simen R; Larsen, Arild; Rudi, Heidi; Asp, Torben; Kent, Matthew Peter; Rognli, Odd Arne

    2015-01-01

    Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L.), and freezing tolerance is a complex trait of major agronomical importance in northern and central Europe. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. The plant material investigated in this study was an experimental synthetic population derived from pair-crosses among five European perennial ryegrass genotypes, representing adaptations to a range of climatic conditions across Europe. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF], and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected (US) control population were genotyped using 278 genome-wide SNPs derived from perennial ryegrass transcriptome sequences. Our studies investigated the genetic diversity among the three experimental populations by analysis of molecular variance and population structure, and determined that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two F st outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN, both detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation, and abiotic stress. These six candidate loci under directional selection for freezing tolerance might be potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  7. Genetic similarity of island populations of tent caterpillars during successive outbreaks.

    Directory of Open Access Journals (Sweden)

    Michelle T Franklin

    Full Text Available Cyclic or fluctuating populations experience regular periods of low population density. Genetic bottlenecks during these periods could give rise to temporal or spatial genetic differentiation of populations. High levels of movement among increasing populations, however, could ameliorate any differences and could also synchronize the dynamics of geographically separated populations. We use microsatellite markers to investigate the genetic differentiation of four island and one mainland population of western tent caterpillars, Malacosoma californicum pluviale, in two periods of peak or pre-peak density separated by 8 years. Populations showed high levels of genetic variation and little genetic differentiation either temporally between peaks or spatially among sites. Mitochondrial haplotypes were also shared between one island population and one mainland population in the two years studied. An isolation-by-distance analysis showed the FST values of the two geographically closest populations to have the highest level of differentiation in both years. We conclude that high levels of dispersal among populations maintain both synchrony of population dynamics and override potential genetic differentiation that might occur during population troughs. As far we are aware, this is the first time that genetic similarity between temporally separated population outbreaks in insects has been investigated. A review of genetic data for both vertebrate and invertebrate species of cyclic animals shows that a lack of spatial genetic differentiation is typical, and may result from high levels of dispersal associated with fluctuating dynamics.

  8. Genetic similarity of island populations of tent caterpillars during successive outbreaks.

    Science.gov (United States)

    Franklin, Michelle T; Myers, Judith H; Cory, Jenny S

    2014-01-01

    Cyclic or fluctuating populations experience regular periods of low population density. Genetic bottlenecks during these periods could give rise to temporal or spatial genetic differentiation of populations. High levels of movement among increasing populations, however, could ameliorate any differences and could also synchronize the dynamics of geographically separated populations. We use microsatellite markers to investigate the genetic differentiation of four island and one mainland population of western tent caterpillars, Malacosoma californicum pluviale, in two periods of peak or pre-peak density separated by 8 years. Populations showed high levels of genetic variation and little genetic differentiation either temporally between peaks or spatially among sites. Mitochondrial haplotypes were also shared between one island population and one mainland population in the two years studied. An isolation-by-distance analysis showed the FST values of the two geographically closest populations to have the highest level of differentiation in both years. We conclude that high levels of dispersal among populations maintain both synchrony of population dynamics and override potential genetic differentiation that might occur during population troughs. As far we are aware, this is the first time that genetic similarity between temporally separated population outbreaks in insects has been investigated. A review of genetic data for both vertebrate and invertebrate species of cyclic animals shows that a lack of spatial genetic differentiation is typical, and may result from high levels of dispersal associated with fluctuating dynamics.

  9. Genetic diversity of microsatellite loci in hierarchically structured populations.

    Science.gov (United States)

    Song, Seongho; Dey, Dipak K; Holsinger, Kent E

    2011-08-01

    Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are small. Using the exact expressions for F(ST) and R(ST), our numerical results show that, when the migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to F(ST) depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, R(ST) is relatively insensitive to the mutation rates and mutational models. The differing behaviors of R(ST) and F(ST) suggest that properties of the among-population distribution of allele frequencies may allow the roles of mutation and migration in producing patterns of diversity to be distinguished, a topic of continuing investigation.

  10. Reappraisal of phylogenetic status and genetic diversity analysis of Asian population of Lentinula edodes

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Phylogenetic relationship within the Lentinula genus is constructed based on the sequenced ITS fragments of the 60Chinese wild L. edodes isolates and the sequence data of 48 isolates of different species from other districts downloaded from the GenBank. The 108 isolates of Lentinula genus are divided into two branches and seven groups, one branch and two groups in the New World, and the other branch and five groups in the Old World, and the isolates clustering of different groups corresponds obviously with the classification of the morphological species. Asian isolates are partitioned in group Ⅰ and Ⅴ, two of the five groups of the Old World,by which the germplasm resources status represented is of great importance shown by the phylogenetic analysis. Group V which fills up the blank of geographic distribution has become one of the mainstream groups with an increased isolate number, while group Ⅰ has a tendency to dissimilate into two subgroups (Ia and Ib) with a huge isolate quantity and a coverage of most tested districts, suggesting that China (or Asia) is an important genetic diversity center of the natural population of Lentinula genus. Genetic analysis of Asian isolates based on groups Ia, Ib and group V indicates that the diversity of the east coastal-land, northwestern highland and southwestern China and Himalayas districts is the most plentiful, which is the three priorities in diversity protection of Asian Lentinula population.

  11. Extracting classification rules from an informatic security incidents repository by genetic programming

    Directory of Open Access Journals (Sweden)

    Carlos Javier Carvajal Montealegre

    2015-04-01

    Full Text Available This paper describes the data mining process to obtain classification rules over an information security incident data collection, explaining in detail the use of genetic programming as a mean to model the incidents behavior and representing such rules as decision trees. The described mining process includes several tasks, such as the GP (Genetic Programming approach evaluation, the individual's representation and the algorithm parameters tuning to upgrade the performance. The paper concludes with the result analysis and the description of the rules obtained, suggesting measures to avoid the occurrence of new informatics attacks. This paper is a part of the thesis work degree: Information Security Incident Analytics by Data Mining for Behavioral Modeling and Pattern Recognition (Carvajal, 2012.

  12. 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.

  13. 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.

  14. Genetic diversity of Leishmania infantum field populations from Brazil

    Directory of Open Access Journals (Sweden)

    Marcela Segatto

    2012-02-01

    Full Text Available Leishmania infantum (syn. Leishmania chagasi is the etiological agent of visceral leishmaniasis (VL in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT, random amplification of polymorphic DNA (RAPD and simple sequence repeats-polymerase chain reaction (SSR-PCR, were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.

  15. 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.

  16. Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians

    Directory of Open Access Journals (Sweden)

    Alicia S. Goicoechea

    2000-09-01

    Full Text Available Fertility, mortality and migration data from four Mapuche Indian communities located along a 215-km NE-SW linear area in the Province of Río Negro, Argentina, were collated with genetic information furnished by nine blood group systems and by mtDNA haplogroups. The demographic and genetic data indicated a clear dichotomy, which split the four populations into two groups of two. Differing degrees of non-Indian exchanges was probably the main determining factor for this separation. Total genetic variability was very similar in all groups, and the interpopulational variability accounted for only 10% of the total variability. A low prevalence of the Diego(a antigen among the Mapuche was confirmed. The fact that significant genetic heterogeneity and population clusters were found in such a small territorial region attests to the sensitivity of demographic and genetic approaches in unraveling human history.Dados relativos a fertilidade, mortalidade e migração de quatro comunidades de índios Mapuche localizadas em uma área linear na direção nordeste-sudoeste com 215 km de extensão na Província de Rio Negro, Argentina, foram associados com a informação genética fornecida por nove sistemas de grupos sangüíneos e os haplogrupos do DNA mitocondrial. Ambos os tipos de informação apontam claramente para uma dicotomia, as quatro populações sendo divididas em grupos de duas. O principal fator responsável por esta separação é provavelmente graus diferentes de mistura com não-índios. A variabilidade genética total foi muito similar em todos os grupos, aquela entre populações sendo de apenas 10% deste valor. Foi confirmada a baixa prevalência do antígeno Diego(a entre os Mapuche. O fato de que heterogeneidade genética significativa e conjuntos populacionais diversos foram observados em uma região territorial tão pequena demonstra a sensibilidade dos enfoques demográfico e genético no esclarecimento da história humana.

  17. 基于粗集分类和遗传算法的知识库集成方法%The Methods of Knowledge Database Integration Based on the Rough Set Classification and Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    郭平; 程代杰

    2003-01-01

    As the base of intelligent system, it is very important to guarantee the consistency and non-redundancy of knowledge in knowledge database. Since the variety of knowledge sources, it is necessary to dispose knowledge with redundancy, inclusion and even contradiction during the integration of knowledge database. This paper researches the integration method based on the multi-knowledge database. Firstly, it finds out the inconsistent knowledge sets between the knowledge databases by rough set classification and presents one method eliminating the inconsistency by test data. Then, it regards consistent knowledge sets as the initial population of genetic calculation and constructs a genetic adaptive function based on accuracy, practicability and spreadability of knowledge representation to carry on the genetic calculation. Lastly, classifying the results of genetic calculation reduces the knowledge redundancy of knowledge database. This paper also presents a frameworkfor knowledge database integration based on the rough set classification and genetic algorithm.

  18. Population genetics of drifting (Calanus spp.) and resident (Acartia clausi) plankton in Norwegian fjords

    Digital Repository Service at National Institute of Oceanography (India)

    Bucklin, A.; Kaartvedt, S.; Guarnieri, M.; Goswami, U.

    rRNA, population genetic diversity and structure in drifting populations of Calanus spp. with that of resident populations of Acartia clausi is contrasted. With the exception of Sorfjorden (where Calanus spp. were rare), two or three species...

  19. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa.

    Science.gov (United States)

    Khanyile, Khulekani S; Dzomba, Edgar F; Muchadeyi, Farai C

    2015-01-01

    Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective

  20. Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae

    Directory of Open Access Journals (Sweden)

    Nitz Barbara

    2010-03-01

    Full Text Available Abstract Background Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex, examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae. Results AFLP demonstrated a significant population structure (Bayesian θB = 0.22. Lower differentiation between allopatric (θB = 0.028 than sympatric (0.063-0.083 populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. Conclusions While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises

  1. Vascular bone tumors: a proposal of a classification based on clinicopathological, radiographic and genetic features

    Energy Technology Data Exchange (ETDEWEB)

    Errani, Costantino [Istituto Ortopedico Rizzoli, Ortopedia Generale, Orthopaedic Service, Bagheria (Italy); Struttura Complessa Ortopedia Generale, Dipartimento Rizzoli-Sicilia, Bagheria, PA (Italy); Vanel, Daniel; Gambarotti, Marco; Alberghini, Marco [Istituto Ortopedico Rizzoli, Pathology Service, Bologna (Italy); Picci, Piero [Istituto Ortopedico Rizzoli, Laboratory for Cancer Research, Bologna (Italy); Faldini, Cesare [Istituto Ortopedico Rizzoli, Ortopedia Generale, Orthopaedic Service, Bagheria (Italy)

    2012-12-15

    The classification of vascular bone tumors remains challenging, with considerable morphological overlap spanning across benign to malignant categories. The vast majority of both benign and malignant vascular tumors are readily diagnosed based on their characteristic histological features, such as the formation of vascular spaces and the expression of endothelial markers. However, some vascular tumors have atypical histological features, such as a solid growth pattern, epithelioid change, or spindle cell morphology, which complicates their diagnosis. Pathologically, these tumors are remarkably similar, which makes differentiating them from each other very difficult. For this rare subset of vascular bone tumors, there remains considerable controversy with regard to the terminology and the classification that should be used. Moreover, one of the most confusing issues related to vascular bone tumors is the myriad of names that are used to describe them. Because the clinical behavior and, consequently, treatment and prognosis of vascular bone tumors can vary significantly, it is important to effectively and accurately distinguish them from each other. Upon review of the nomenclature and the characteristic clinicopathological, radiographic and genetic features of vascular bone tumors, we propose a classification scheme that includes hemangioma, hemangioendothelioma, angiosarcoma, and their epithelioid variants. (orig.)

  2. Evolving Neural Network Using Variable String Genetic Algorithm for Color Infrared Aerial Image Classification

    Institute of Scientific and Technical Information of China (English)

    FU Xiaoyang; P E R Dale; ZHANG Shuqing

    2008-01-01

    Coastal wetlands are characterized by complex patterns both in their geomorphic and ecological features.Besides field observations,it is necessary to analyze the land cover of wetlands through the color infrared (CIR) aerial photography or remote sensing image.In this paper,we designed an evolving neural network classifier using variable string genetic algorithm (VGA) for the land cover classification of CIR aerial image.With the VGA,the classifier that we designed is able to evolve automatically the appropriate number of hidden nodes for modeling the neural network topology optimally and to find a near-optimal set of connection weights globally.Then,with backpropagation algorithm (BP),it can find the best connection weights.The VGA-BP classifier,which is derived from hybrid algorithms mentioned above,is demonstrated on CIR images classification effectively.Compared with standard classifiers,such as Bayes maximum-likelihood classifier,VGA classifier and BP-MLP (multi-layer perception) classifier,it has shown that the VGA-BP classifier can have better performance on highly resolution land cover classification.

  3. Genetic algorithm for the optimization of features and neural networks in ECG signals classification

    Science.gov (United States)

    Li, Hongqiang; Yuan, Danyang; Ma, Xiangdong; Cui, Dianyin; Cao, Lu

    2017-01-01

    Feature extraction and classification of electrocardiogram (ECG) signals are necessary for the automatic diagnosis of cardiac diseases. In this study, a novel method based on genetic algorithm-back propagation neural network (GA-BPNN) for classifying ECG signals with feature extraction using wavelet packet decomposition (WPD) is proposed. WPD combined with the statistical method is utilized to extract the effective features of ECG signals. The statistical features of the wavelet packet coefficients are calculated as the feature sets. GA is employed to decrease the dimensions of the feature sets and to optimize the weights and biases of the back propagation neural network (BPNN). Thereafter, the optimized BPNN classifier is applied to classify six types of ECG signals. In addition, an experimental platform is constructed for ECG signal acquisition to supply the ECG data for verifying the effectiveness of the proposed method. The GA-BPNN method with the MIT-BIH arrhythmia database achieved a dimension reduction of nearly 50% and produced good classification results with an accuracy of 97.78%. The experimental results based on the established acquisition platform indicated that the GA-BPNN method achieved a high classification accuracy of 99.33% and could be efficiently applied in the automatic identification of cardiac arrhythmias.

  4. Effective Rule Based Classifier using Multivariate Filter and Genetic Miner for Mammographic Image Classification

    Directory of Open Access Journals (Sweden)

    Nirase Fathima Abubacker

    2015-06-01

    Full Text Available Mammography is an important examination in the early detection of breast abnormalities. Automatic classifications of mammogram images into normal, benign or malignant would help the radiologists in diagnosis of breast cancer cases. This study investigates the effectiveness of using rule-based classifiers with multivariate filter and genetic miner to classify mammogram images. The method discovers association rules with the classes as the consequence and classifies the images based on the Highest Average Confidence of the association rules (HAvC matched for the classes. In the association rules mining stage, Correlation based Feature Selection (CFS plays an enormous significance to reduce the complexity of image mining process is used in this study as a feature selection method and a modified genetic association rule mining technique, the GARM, is used to discover the rules. The method is evaluated on mammogram image dataset with 240 images taken from DDSM. The performance of the method is compared against other classifiers such as SMO; Naïve Bayes and J48. The performance of the proposed method is promising with 88% accuracy and outperforms other classifiers in the context of mammogram image classification.

  5. Does local adaptation to resources explain genetic differentiation among Daphnia populations?

    Science.gov (United States)

    Allen, Michael R; Thum, Ryan A; Cáceres, Carla E

    2010-08-01

    Substantial genetic differentiation is frequently observed among populations of cyclically parthenogenetic zooplankton despite their high dispersal capabilities and potential for gene flow. Local adaptation has been invoked to explain population genetic differentiation despite high dispersal, but several neutral models that account for basic life history features also predict high genetic differentiation. Here, we study genetic differentiation among four populations of Daphnia pulex in east central Illinois. As with other studies of Daphnia, we demonstrate substantial population genetic differentiation despite close geographic proximity (explain genetic differentiation among these Daphnia populations and that other factors related to extinction/colonization dynamics, a long approach to equilibrium F(ST) or substantial genetic drift due to a low number of individuals hatching from the egg bank each season may explain genetic differentiation.

  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......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...

  7. Heterogeneous Ensemble Combination Search Using Genetic Algorithm for Class Imbalanced Data Classification.

    Science.gov (United States)

    Haque, Mohammad Nazmul; Noman, Nasimul; Berretta, Regina; Moscato, Pablo

    2016-01-01

    Classification of datasets with imbalanced sample distributions has always been a challenge. In general, a popular approach for enhancing classification performance is the construction of an ensemble of classifiers. However, the performance of an ensemble is dependent on the choice of constituent base classifiers. Therefore, we propose a genetic algorithm-based search method for finding the optimum combination from a pool of base classifiers to form a heterogeneous ensemble. The algorithm, called GA-EoC, utilises 10 fold-cross validation on training data for evaluating the quality of each candidate ensembles. In order to combine the base classifiers decision into ensemble's output, we used the simple and widely used majority voting approach. The proposed algorithm, along with the random sub-sampling approach to balance the class distribution, has been used for classifying class-imbalanced datasets. Additionally, if a feature set was not available, we used the (α, β) - k Feature Set method to select a better subset of features for classification. We have tested GA-EoC with three benchmarking datasets from the UCI-Machine Learning repository, one Alzheimer's disease dataset and a subset of the PubFig database of Columbia University. In general, the performance of the proposed method on the chosen datasets is robust and better than that of the constituent base classifiers and many other well-known ensembles. Based on our empirical study we claim that a genetic algorithm is a superior and reliable approach to heterogeneous ensemble construction and we expect that the proposed GA-EoC would perform consistently in other cases.

  8. A genetic classification of sinkholes illustrated from evaporite paleokarst exposures in Spain

    Science.gov (United States)

    Gutiérrez, Francisco; Guerrero, Jesús; Lucha, Pedro

    2008-01-01

    This contribution analyses the processes involved in the generation of sinkholes from the study of paleokarst features exposed in four Spanish Tertiary basins. Bedrock strata are subhorizontal evaporites, and in three of the basins they include halite and glauberite in the subsurface. Our studies suggest that formation of dolines in these areas results from a wider range of subsidence processes than those included in the most recently published sinkhole classifications; a new genetic classification of sinkholes applicable to both carbonate and evaporite karst areas is thus proposed. With the exception of solution dolines, it defines the main sinkhole types by use of two terms that refer to the material affected by downward gravitational movements (cover, bedrock or caprock) and the main type of process involved (collapse, suffosion or sagging). Sinkholes that result from the combination of several subsidence processes and affect more than one type of material are described by combinations of the different terms with the dominant material or process followed by the secondary one (e.g. bedrock sagging and collapse sinkhole). The mechanism of collapse includes any brittle gravitational deformation of cover and bedrock material, such as upward stoping of cavities by roof failure, development of well-defined failure planes and rock brecciation. Suffosion is the downward migration of cover deposits through dissolutional conduits accompanied with ductile settling. Sagging is the ductile flexure of sediments caused by differential corrosional lowering of the rockhead or interstratal karstification of the soluble bedrock. The paleokarsts we analysed suggest that the sagging mechanism (not included in previous genetic classifications) plays an important role in the generation of sinkholes in evaporites. Moreover, collapse processes are more significant in extent and rate in areas underlain by evaporites than in carbonate karst, primarily due to the greater solubility of the

  9. The impact of genomics on population genetics of parasitic diseases.

    Science.gov (United States)

    Hupalo, Daniel N; Bradic, Martina; Carlton, Jane M

    2015-02-01

    Parasites, defined as eukaryotic microbes and parasitic worms that cause global diseases of human and veterinary importance, span many lineages in the eukaryotic Tree of Life. Historically challenging to study due to their complicated life-cycles and association with impoverished settings, their inherent complexities are now being elucidated by genome sequencing. Over the course of the last decade, projects in large sequencing centers, and increasingly frequently in individual research labs, have sequenced dozens of parasite reference genomes and field isolates from patient populations. This 'tsunami' of genomic data is answering questions about parasite genetic diversity, signatures of evolution orchestrated through anti-parasitic drug and host immune pressure, and the characteristics of populations. This brief review focuses on the state of the art of parasitic protist genomics, how the peculiar genomes of parasites are driving creative methods for their sequencing, and the impact that next-generation sequencing is having on our understanding of parasite population genomics and control of the diseases they cause.

  10. Cytochrome P450 genetic polymorphisms of Mexican indigenous populations.

    Science.gov (United States)

    Sosa-Macías, Martha; Llerena, Adrián

    2013-01-01

    This review focuses on the genetic polymorphisms of the cytochrome P450 (CYP) genes in Mexican indigenous populations, who are a part of the wide ethnic diversity of this country. These native groups have a particular historical trajectory that is different from the Mexican Mestizos. This variability may be reflected in the frequency distribution of polymorphisms in the CYP genes that encode enzymes involved in the metabolism of drugs and other xenobiotics. Therefore, these polymorphisms may affect drug efficacy and safety in indigenous populations in Mexico. The present study aimed to analyze the prevalence of CYP polymorphisms in indigenous Mexicans and to compare the results with studies in Mexican Mestizos. Because the extrapolation of pharmacogenetic data from Mestizos is not applicable to the majority of indigenous groups, pharmacogenetic studies directed at indigenous populations need to be developed. The Amerindians analyzed in this study showed a low phenotypic (CYP2D6) and genotypic (CYP2D6, CYP2C9) diversity, unlike Mexican Mestizos. The frequency of polymorphisms in the CYP1A1, CYP2C19, CYP2E1, and CYP3A4 genes was more similar among the Amerindians and Mexican Mestizos, with the exception of the CYP1A2 gene, whose *1F variant frequency in Mexican Amerindians was the highest described to date.

  11. 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.

  12. Genetic Background and Population Genetics of Hungarian Brown Trout Populations Using PCR-RFLP and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    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

  13. The four-populations model: a new classification scheme for pre-planetesimal collisions

    CERN Document Server

    Geretshauser, Ralf J; Speith, Roland; Kley, WIlhelm

    2011-01-01

    Within the collision growth scenario for planetesimal formation, the growth step from centimetre sized pre-planetesimals to kilometre sized planetesimals is still unclear. The formation of larger objects from the highly porous pre-planetesimals may be halted by a combination of fragmentation in disruptive collisions and mutual rebound with compaction. However, the right amount of fragmentation is necessary to explain the observed dust features in late T Tauri discs. Therefore, detailed data on the outcome of pre-planetesimal collisions is required and has to be presented in a suitable and precise format. We propose and apply a new classification scheme for pre-planetesimal collisions based on the quantitative aspects of four fragment populations: the largest and second largest fragment, a power-law population, and a sub-resolution population. For the simulations of pre-planetesimal collisions, we adopt the SPH numerical scheme with extensions for the simulation of porous solid bodies. By means of laboratory b...

  14. Impact of founder population, drift and selection on the genetic diversity of a recently translocated tree population.

    Science.gov (United States)

    Lefèvre, F; Fady, B; Fallour-Rubio, D; Ghosn, D; Bariteau, M

    2004-12-01

    Recently established, temperate tree populations combine a high level of differentiation for adaptive traits, suggesting rapid genetic evolution, with a high level of genetic diversity within population, suggesting a limited impact of genetic drift and purifying selection. To study experimentally the evolutionary forces in a recently established population, we assessed the spatial and temporal patterns of genetic diversity within a disjunct population of Cedrus atlantica established 140 years ago in south-eastern France from a North African source. The population is expanding through natural regeneration. Three generations were sampled, including founder trees. We analysed 12 isozyme loci, three of which were previously found in tight association with selected genes, and quantitative traits. No bottleneck effect was detected in the founder generation, but a simple test of allelic association revealed an initial disequilibrium which disappeared in the following generations. The impact of genetic drift during secondary evolution was limited, as suggested by the weak temporal differentiation. The genetic load was not reduced after 3 generations, and the quantitative variation for adaptive traits did not change either. Thus, initial genetic changes first proceed from a rapid re-organisation of the diversity through mating and recombination, whereas genetic erosion through drift and selection is delayed due to temporal and spatial stochasticity. Two life-history traits of trees contribute to slowing down the processes of genetic erosion: perenniality and large spatial scale. Thus, one would expect recently established tree populations to have a higher diversity than older ones, which seems in accordance with experimental surveys.

  15. Genetic diversity in different populations of sloths assessed by DNA fingerprinting

    Directory of Open Access Journals (Sweden)

    N. MORAES

    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.

  16. Effect of population size on genetic variation levels in Capparis spinosa (Capparaceae detected by RAPDs

    Directory of Open Access Journals (Sweden)

    Houshang Nosrati

    2012-07-01

    Full Text Available Background: The population size of plants affects on population genetic variation. Materials and Methods: We studied the impact of population size on genetic variation in populations of Capparis spinosa (caper, Capparaceae using RAPDs in East Azerbaijan (Iran. Within-population genetic diversity was estimated based on Nei`s and Shanonn`s diversity using Popgen, and genetic similarity among the populations was studied from a UPGMA dendrogram based the matrix of Nei’s distances obtained through SHAN. Difference in the level genetic variation between small-sized and large-sized populations was tested using Mann-Whitney U test, and correlation between geographical and genetic distances among populations was examined by Pearson test (SPSS, 11.3. Total genetic variation was partitioned into within and among populations based on AMOVA using Arlequin. Results: The polymorphism levels of RAPDs bands among the populations ranged from 48.8% to 81.4%, and within-population Nei’s diversity varied from 0.1667 to 0.2630. Genetic variation in small-sized populations (0.1667 to 0.1809 was significantly lower than the variations in large-sized populations (0.2158 -0.2630 (N= 7, P0.674, Pearson correlation test. Conclusions: Population size has a dramatic impact on its genetic diversity. The results revealed that fragmentation of caper population in the study region has most likely occurred recently. The low genetic diversity revealed within caper populations indicates high risk of extinction and suggests that urgent conservation action is needed to recover diversity in these populations.

  17. Classification of ETM+ Remote Sensing Image Based on Hybrid Algorithm of Genetic Algorithm and Back Propagation Neural Network

    Directory of Open Access Journals (Sweden)

    Haisheng Song

    2013-01-01

    Full Text Available The back propagation neural network (BPNN algorithm can be used as a supervised classification in the processing of remote sensing image classification. But its defects are obvious: falling into the local minimum value easily, slow convergence speed, and being difficult to determine intermediate hidden layer nodes. Genetic algorithm (GA has the advantages of global optimization and being not easy to fall into local minimum value, but it has the disadvantage of poor local searching capability. This paper uses GA to generate the initial structure of BPNN. Then, the stable, efficient, and fast BP classification network is gotten through making fine adjustments on the improved BP algorithm. Finally, we use the hybrid algorithm to execute classification on remote sensing image and compare it with the improved BP algorithm and traditional maximum likelihood classification (MLC algorithm. Results of experiments show that the hybrid algorithm outperforms improved BP algorithm and MLC algorithm.

  18. 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.

  19. Diabetes mellitus in two genetically distinct populations in Jordan

    Science.gov (United States)

    Al-Eitan, Laith N.; Nassar, Ahmad M.; Dajani, Rana B.; Almomani, Basima A.; Saadeh, Nesreen A.

    2017-01-01

    Objectives: To compare clinical, anthropometric, and laboratory characteristics in diabetes type 2 patients of 2 genetically-distinct ethnicities living in Jordan, Arabs and Circassians/Chechens. Methods: This cross sectional ethnic comparison study was conducted in King Abdullah University Hospital, Irbid and The National Center for Diabetes, Endocrinology, and Genetics, Amman, Jordan between June 2013 and February 2014. A sample of 347 (237 Arab and 110 Circassian/Chechen) people living with diabetes were included in the study. Data were collected through direct interviews with the participants. Clinical data were collected using a questionnaire and anthropometric measurements. Laboratory data were extracted from the patients’ medical records. Results: More Arabs with diabetes had hypertension as a comorbidity than Circassians/Chechens with diabetes. Arabs living with diabetes were generally more obese, whereas Circassians/Chechens living with diabetes had worse lipid control. Arabs with diabetes had higher means of glycated haemoglobin (HbA1c) and fasting blood sugar, and more Arabs with diabetes had unsatisfactory glycemic control (60.6%) than Circassians/Chechens with diabetes (38.2%) (HbA1c ≥7.0%). Most participants (88.8%) had at least one lipid abnormality (dyslipidemia). Conclusion: Multiple discrepancies among the 2 ethnic diabetic populations were found. New diabetes management recommendations and policies should be used when treating people living with diabetes of those ethnicities, particularly in areas of glycemic control, lipid control, and obesity. PMID:28133689

  20. Genetic consequences of population subdivision: the marsupial Micoureus paraguayanus (Mammalia: Didelphimorphia as a case study

    Directory of Open Access Journals (Sweden)

    Daniel Brito

    2009-12-01

    Full Text Available Habitat fragmentation may cause population subdivision, affecting genetic variation, leading to heterozygosity loss and increased inbreeding, and contributing to population extinction. However, some genetic models have shown that under some conditions, population subdivision can favor heterozygosity and allelic diversity, and small populations may adapt to inbreeding. Here I investigate the relationship between population subdivision and genetic diversity for the marsupial Micoureus paraguayanus (Tate, 1931 using the program Vortex. Hypothetical populations of 100 and 2000 individuals were partitioned into 1, 2, 5 or 10 populations that were linked by varying rates of dispersal and also by sex-biased dispersal. Results suggested that heterozygosity and allelic diversity declined rapidly when a population was subdivided. Genetic and demographic stochasticity diminished the effectiveness of selection against recessive lethal alleles. Dispersal partly reversed the impacts of population subdivision. However, even high rates of dispersal did not eliminate demographic fluctuations or prevent extinction. Although gene flow largely prevented genetic divergence between populations, dispersal did not prevent heterozygosity from being lost more rapidly in subdivided populations than in single populations of equivalent total size. The dynamics of small, fragmented populations were critically dependent on interactions between demographic and genetic processes. Populations of M. paraguayanus may have to be relatively large and continuous to avoid significant losses of genetic diversity.

  1. 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.

  2. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation.

    Science.gov (United States)

    Hoffmann, Gunther Sebastian; Johannesen, Jes; Griebeler, Eva Maria

    2016-05-01

    Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods (F ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population.

  3. Genetic sub-structure in western Mediterranean populations revealed by 12 Y-chromosome STR loci

    DEFF Research Database (Denmark)

    Rodríguez, V; Tomas Mas, Carmen; Sánchez, J J;

    2008-01-01

    .9988 +/- 0.0002. These Y-STRs markers showed a low capacity of discrimination (56.3%) in the Ibiza population probably due to genetic drift. Comparisons between the populations studied and other neighbouring populations showed a clear genetic sub-structure in the western Mediterranean area....

  4. Designs and Methods for Association Studies and Population Size Inference in Statistical Genetics

    DEFF Research Database (Denmark)

    Waltoft, Berit Lindum

    2016-01-01

    . Population genetics In population genetics two methods concerning the inference of the population size back in time are described. Both methods are based on the site iii iv frequency spectrum (SFS), and the fact that the expected SFS only depends on the time between coalescent events back in time. The rst...

  5. 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 micr

  6. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers.

    Science.gov (United States)

    Edea, Zewdu; Dadi, Hailu; Kim, Sang-Wook; Dessie, Tadelle; Lee, Taeheon; Kim, Heebal; Kim, Jong-Joo; Kim, Kwan-Suk

    2013-01-01

    In total, 166 individuals from five indigenous Ethiopian cattle populations - Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) - were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (F ST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, F ST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (F ST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed.

  7. Experimental separation of genetic and demographic factors on extinction risk in wild populations.

    Science.gov (United States)

    Wootton, J Timothy; Pfister, Catherine A

    2013-10-01

    When populations reach small size, an extinction risk vortex may arise from genetic (inbreeding depression, genetic drift) and ecological (demographic stochasticity, Allee effects, environmental fluctuation) processes. The relative contribution of these processes to extinction in wild populations is unknown, but important for conserving endangered species. In experimental field populations of a harvested kelp (Postelsia palmaeformis), in which we independently varied initial genetic diversity (completely inbred, control, outbred) and population size, ecological processes dominated the risk of extinction, whereas the contribution of genetic diversity was slight. Our results match theoretical predictions that demographic processes will generally doom small populations to extinction before genetic effects act strongly, prioritize detailed ecological analysis over descriptions of genetic structure in assessing conservation of at-risk species, and highlight the need for field experiments manipulating both demographics and genetic structure on long-term extinction risk.

  8. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  9. Genealogical data in population medical genetics: field guidelines

    Directory of Open Access Journals (Sweden)

    Fernando A. Poletta

    2014-01-01

    Full Text Available This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources.

  10. The Druze: a population genetic refugium of the Near East.

    Directory of Open Access Journals (Sweden)

    Liran I Shlush

    Full Text Available BACKGROUND: Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization. PRINCIPAL FINDINGS: We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations. CONCLUSIONS: These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age.

  11. Genetic evidence for two founding populations of the Americas

    Science.gov (United States)

    Skoglund, Pontus; Mallick, Swapan; Bortolini, Maria Cátira; Chennagiri, Niru; Hünemeier, Tábita; Petzl-Erler, Maria Luiza; Salzano, Francisco Mauro; Patterson, Nick; Reich, David

    2015-01-01

    Genetic studies have been consistent with a single common origin of Native American groups from Central and South America1-4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island southeast Asia)5-8. Here we analyze genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent or at all in present-day Northern and Central Americans or a ~12,600 year old Clovis genome, suggesting a more diverse set of founding populations of the Americas than previously accepted. PMID:26196601

  12. Genealogical data in population medical genetics: Field guidelines

    Science.gov (United States)

    Poletta, Fernando A.; Orioli, Ieda M.; Castilla, Eduardo E.

    2014-01-01

    This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources. PMID:24764752

  13. Mongolians in the Genetic Landscape of Central Asia: Exploring the Genetic Relations among Mongolians and Other World Populations.

    Science.gov (United States)

    Brissenden, Jane E; Kidd, Judith R; Evsanaa, Baigalmaa; Togtokh, Ariunaa J; Pakstis, Andrew J; Friedlaender, Françoise; Kidd, Kenneth K; Roscoe, Janet M

    2015-04-01

    Genetic data on North and Central Asian populations are underrepresented in the literature, especially for autosomal markers. In the present study we used 812 single nucleotide polymorphisms (SNPs) distributed across all the human autosomes and extensively studied at Yale to examine the affinities of two recently collected samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations with each other and with a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single SNPs and multi-SNP haplotypes) studied in 57 populations representing all the major geographical regions of the world. We conclude that these North and Central Asian populations are genetically distinct from all other populations in our study and may be close to the ancestral lineage leading to the New World populations.

  14. Genetic evidence on the origins of Indian caste populations.

    Science.gov (United States)

    Bamshad, M; Kivisild, T; Watkins, W S; Dixon, M E; Ricker, C E; Rao, B B; Naidu, J M; Prasad, B V; Reddy, P G; Rasanayagam, A; Papiha, S S; Villems, R; Redd, A J; Hammer, M F; Nguyen, S V; Carroll, M L; Batzer, M A; Jorde, L B

    2001-06-01

    The origins and affinities of the approximately 1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in approximately 265 males from eight castes of different rank to approximately 750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%-30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Alu elements

  15. Sampling strategy for wild soybean (Glycine soja) populations based on their genetic diversity and fine-scale spatial genetic structure

    Institute of Scientific and Technical Information of China (English)

    ZHU Weiyue; ZHOU Taoying; ZHONG Ming; LU Baorong

    2007-01-01

    A total of 892 individuals sampled from a wild soybean population in a natural reserve near the Yellow River estuary located in Kenli of Shandong Province (China) were investigated.Seventeen SSR (simple sequence repeat) primer pairs from cultivated soybeans were used to estimate the genetic diversity of the population and its variation pattern versus changes of the sample size (sub-samples),in addition to investigating the fine-scale spatial genetic structure within the population.The results showed relatively high genetic diversity of the population with the mean value of allele number (A) being 2.88,expected heterozygosity (He) 0.431,Shannon diversity index (/) 0.699,and percentage of polymorphic loci (P) 100%.Sub-samples of different sizes (ten groups) were randomly drawn from the population and their genetic diversity was calculated by computer simulation.The regression model of the four diversity indexes with the change of sample sizes was computed.As a result,27-52 individuals can reach 95% of total genetic variability of the population.Spatial autocorrelation analysis revealed that the genetic patch size of this wild soybean population is about 18 m.The study provided a scientific basis for the sampling strategy of wild soybean populations.

  16. Population genetics of Phytophthora infestans in Denmark reveals dominantly clonal populations and specific alleles linked to metalaxyl-M resistance

    DEFF Research Database (Denmark)

    Montes, Melanie Sarah; Nielsen, B.J.; Schmidt, S.G.;

    2016-01-01

    population of P. infestans was characterized over the course of the 2013 growing season, as was the population genetic structure, using simple sequence repeat (SSR) genotypes and single nucleotide polymorphism (SNP)-based mitochondrial haplotyping of over 80 isolates. Both mating types A1 and A2 were present......Control of the potato late blight pathogen Phytophthora infestans relies heavily on chemicals. The fungicide metalaxyl-M (Mefenoxam) has played an important role in controlling the disease, but insensitivity to the fungicide in certain isolates is now of major concern. A genetic basis...... for resistance to metalaxyl suggests the possibility for linking resistance phenotypes to specific population genetic markers, but in order to do this, the population genetic structure and mode of reproduction in a population must first be well described. The dynamics of metalaxyl-M resistance in the Danish...

  17. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Hanwoo breeds using SNP markers

    Directory of Open Access Journals (Sweden)

    Zewdu eEdea

    2013-03-01

    Full Text Available In total, 166 individuals from 5 indigenous Ethiopian cattle populations—Ambo (n = 27, Borana (n = 35, Arsi (n = 30, Horro (n = 36, and Danakil (n = 38—were genotyped for 8773 single nucleotide polymorphism (SNP markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40 were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs ≥ 0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥ 0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST (1% in Ethiopian cattle revealed that within-individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine and Ethiopian cattle populations. The low estimate of genetic differentiation (FST among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, PCA, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed

  18. Genetic differentiation of Puccinia triticina populations in the Middle East and genetic similarity with populations in Central Asia.

    Science.gov (United States)

    Kolmer, J A; Ordoñez, M E; Manisterski, J; Anikster, Y

    2011-07-01

    Leaf rust of wheat, caused by Puccinia triticina, is a common and widespread disease in the Middle East. The objective of this study was to determine whether genetically differentiated groups of P. triticina are present in the Middle East region and to compare the population from the Middle East with the previously characterized population from Central Asia to determine whether genetically similar groups of isolates are found in the two regions. In total, 118 isolates of P. triticina collected from common wheat and durum wheat in Egypt, Israel, Turkey, Ethiopia, and Kenya were tested for virulence on 20 lines of wheat with single genes for leaf rust resistance and for molecular genotypes with 23 simple-sequence repeat (SSR) markers. After removal of isolates with identical virulence and SSR genotype in each country, 103 isolates were retained for further analysis. Clustering of SSR genotypes based on two-dimensional principal coordinates and virulence to wheat differential lines grouped the isolates into four Middle East (ME) groups. The two largest ME groups had virulence phenotypes typical of isolates collected from common wheat and two smaller ME groups had virulence typical of isolates collected from durum wheat. All pairs of ME groups were significantly differentiated for SSR genotype based on R(ST) and F(ST) statistics, and for virulence phenotype based on Φ(PT). All ME groups had observed values of heterozygosity greater than expected and significant fixation indices that indicated the clonal reproduction of urediniospores in the overall population. Linkage disequilibria for SSR genotypes was high across the entire population. The overall values of R(ST) and F(ST) were lower when isolates were grouped by country of origin that indicated the likely migration of isolates within the region. Although the two ME groups with virulence typical of isolates from common wheat were not differentiated for SSR genotype from groups of isolates from Central Asia based on

  19. Classification of Atrial Septal Defect and Ventricular Septal Defect with Documented Hemodynamic Parameters via Cardiac Catheterization by Genetic Algorithms and Multi-Layered Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Mustafa Yıldız

    2012-08-01

    Full Text Available Introduction: We aimed to develop a classification method to discriminate ventricular septal defect and atrial septal defect by using severalhemodynamic parameters.Patients and Methods: Forty three patients (30 atrial septal defect, 13 ventricular septal defect; 26 female, 17 male with documentedhemodynamic parameters via cardiac catheterization are included to study. Such parameters as blood pressure values of different areas,gender, age and Qp/Qs ratios are used for classification. Parameters, we used in classification are determined by divergence analysismethod. Those parameters are; i pulmonary artery diastolic pressure, ii Qp/Qs ratio, iii right atrium pressure, iv age, v pulmonary arterysystolic pressure, vi left ventricular sistolic pressure, vii aorta mean pressure, viii left ventricular diastolic pressure, ix aorta diastolicpressure, x aorta systolic pressure. Those parameters detected from our study population, are uploaded to multi-layered artificial neuralnetwork and the network was trained by genetic algorithm.Results: Trained cluster consists of 14 factors (7 atrial septal defect and 7 ventricular septal defect. Overall success ratio is 79.2%, andwith a proper instruction of artificial neural network this ratio increases up to 89%.Conclusion: Parameters, belonging to artificial neural network, which are needed to be detected by the investigator in classical methods,can easily be detected with the help of genetic algorithms. During the instruction of artificial neural network by genetic algorithms, boththe topology of network and factors of network can be determined. During the test stage, elements, not included in instruction cluster, areassumed as in test cluster, and as a result of this study, we observed that multi-layered artificial neural network can be instructed properly,and neural network is a successful method for aimed classification.

  20. Alu repeats as markers for human population genetics

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  1. Population genetics of the sugarcane borer Diatraea saccharalis (Fabr.) (Lepidoptera: Crambidae)

    OpenAIRE

    Denise Alves Lopes; Liriana Belizário Cantagalli; Ana Lucia Paz Barateiro Stuchi; Claudete Aparecida Mangolin; Maria Claudia Colla Ruvolo-Takasusuki

    2014-01-01

    Diatraea saccharalis is the principal pest of sugarcane in Brazil and is found throughout the sugarcane crop. Information about its population genetics is scarce, but population genetic analysis is of particular importance as a basis for a successful pest control program. Pest control requires a constant evaluation of genetic variability so that appropriate strategies can be employed. In this study, the structure of D. saccharalis populations in sugarcane crops was analyzed with PCR-RAPD (Pol...

  2. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

    Science.gov (United States)

    Raghavan, Maanasa; Steinrücken, Matthias; Harris, Kelley; Schiffels, Stephan; Rasmussen, Simon; DeGiorgio, Michael; Albrechtsen, Anders; Valdiosera, Cristina; Ávila-Arcos, María C; Malaspinas, Anna-Sapfo; Eriksson, Anders; Moltke, Ida; Metspalu, Mait; Homburger, Julian R; Wall, Jeff; Cornejo, Omar E; Moreno-Mayar, J Víctor; Korneliussen, Thorfinn S; Pierre, Tracey; Rasmussen, Morten; Campos, Paula F; Damgaard, Peter de Barros; Allentoft, Morten E; Lindo, John; Metspalu, Ene; Rodríguez-Varela, Ricardo; Mansilla, Josefina; Henrickson, Celeste; Seguin-Orlando, Andaine; Malmström, Helena; Stafford, Thomas; Shringarpure, Suyash S; Moreno-Estrada, Andrés; Karmin, Monika; Tambets, Kristiina; Bergström, Anders; Xue, Yali; Warmuth, Vera; Friend, Andrew D; Singarayer, Joy; Valdes, Paul; Balloux, Francois; Leboreiro, Ilán; Vera, Jose Luis; Rangel-Villalobos, Hector; Pettener, Davide; Luiselli, Donata; Davis, Loren G; Heyer, Evelyne; Zollikofer, Christoph P E; Ponce de León, Marcia S; Smith, Colin I; Grimes, Vaughan; Pike, Kelly-Anne; Deal, Michael; Fuller, Benjamin T; Arriaza, Bernardo; Standen, Vivien; Luz, Maria F; Ricaut, Francois; Guidon, Niede; Osipova, Ludmila; Voevoda, Mikhail I; Posukh, Olga L; Balanovsky, Oleg; Lavryashina, Maria; Bogunov, Yuri; Khusnutdinova, Elza; Gubina, Marina; Balanovska, Elena; Fedorova, Sardana; Litvinov, Sergey; Malyarchuk, Boris; Derenko, Miroslava; Mosher, M J; Archer, David; Cybulski, Jerome; Petzelt, Barbara; Mitchell, Joycelynn; Worl, Rosita; Norman, Paul J; Parham, Peter; Kemp, Brian M; Kivisild, Toomas; Tyler-Smith, Chris; Sandhu, Manjinder S; Crawford, Michael; Villems, Richard; Smith, David Glenn; Waters, Michael R; Goebel, Ted; Johnson, John R; Malhi, Ripan S; Jakobsson, Mattias; Meltzer, David J; Manica, Andrea; Durbin, Richard; Bustamante, Carlos D; Song, Yun S; Nielsen, Rasmus; Willerslev, Eske

    2015-08-21

    How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

  3. Genetic Algorithms and Classification Trees in Feature Discovery: Diabetes and the NHANES database

    Energy Technology Data Exchange (ETDEWEB)

    Heredia-Langner, Alejandro; Jarman, Kristin H.; Amidan, Brett G.; Pounds, Joel G.

    2013-09-01

    This paper presents a feature selection methodology that can be applied to datasets containing a mixture of continuous and categorical variables. Using a Genetic Algorithm (GA), this method explores a dataset and selects a small set of features relevant for the prediction of a binary (1/0) response. Binary classification trees and an objective function based on conditional probabilities are used to measure the fitness of a given subset of features. The method is applied to health data in order to find factors useful for the prediction of diabetes. Results show that our algorithm is capable of narrowing down the set of predictors to around 8 factors that can be validated using reputable medical and public health resources.

  4. Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers.

    Science.gov (United States)

    Matsumoto, Asako; Uchida, Kohji; Taguchi, Yuriko; Tani, Naoki; Tsumura, Yoshihiko

    2010-09-01

    The genetic diversity and population structure of hinoki (Chamaecyparis obtusa) in Japan were investigated by examining the distribution of alleles at 13 microsatellite loci in 25 natural populations from Iwaki in northern Japan to Yakushima Island in southern Japan. On average, 26.9 alleles per locus were identified across all populations and 4.0% of the genetic variation was retained among populations (G(ST) = 0.040). According to linkage disequilibrium analysis, estimates of effective population size and detected evidence of bottleneck events, the genetic diversity of some populations may have declined as a result of fragmentation and/or over-exploitation. The central populations located in the Chubu district appear to have relatively large effective population sizes, while marginal populations, such as the Yakushima, Kobayashi and Iwaki populations, have smaller effective population sizes and are isolated from the other populations. Microsatellite analysis revealed the genetic uniqueness of the Yakushima population. Although genetic differentiation between populations was low, we detected a gradual cline in the genetic structure and found that locus Cos2619 may be non-neutral with respect to natural selection.

  5. Genetic variation and structure in remnant population of critically endangered Melicope zahlbruckneri

    Science.gov (United States)

    Raji, J. A.; Atkinson, Carter T.

    2016-01-01

    The distribution and amount of genetic variation within and between populations of plant species are important for their adaptability to future habitat changes and also critical for their restoration and overall management. This study was initiated to assess the genetic status of the remnant population of Melicope zahlbruckneri–a critically endangered species in Hawaii, and determine the extent of genetic variation and diversity in order to propose valuable conservation approaches. Estimated genetic structure of individuals based on molecular marker allele frequencies identified genetic groups with low overall differentiation but identified the most genetically diverse individuals within the population. Analysis of Amplified Fragment Length Polymorphic (AFLP) marker loci in the population based on Bayesian model and multivariate statistics classified the population into four subgroups. We inferred a mixed species population structure based on Bayesian clustering and frequency of unique alleles. The percentage of Polymorphic Fragment (PPF) ranged from 18.8 to 64.6% for all marker loci with an average of 54.9% within the population. Inclusion of all surviving M. zahlbruckneri trees in future restorative planting at new sites are suggested, and approaches for longer term maintenance of genetic variability are discussed. To our knowledge, this study represents the first report of molecular genetic analysis of the remaining population of M. zahlbruckneri and also illustrates the importance of genetic variability for conservation of a small endangered population.

  6. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    Science.gov (United States)

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.

  7. Genetic Diversity and Structure of Brazilian Populations of Diatraea saccharalis (Lepidoptera: Crambidae): Implications for Pest Management.

    Science.gov (United States)

    Silva-Brandão, Karina L; Santos, Thiago V; Cônsoli, Fernando L; Omoto, Celso

    2015-02-01

    The sugarcane borer, Diatraea saccharalis (F.), is the main pest of sugarcane in Brazil. Genetic variability and gene flow among 13 Brazilian populations of the species were evaluated based on mitochondrial DNA sequences to estimate the exchange of genetic information within and among populations. We found high genetic structure among sampled localities (ΦST=0.50923), and pairwise genetic distances were significantly correlated to geographic distances. Demographic analysis and genealogical network of mitochondrial sequences indicate population growth and admixture of D. saccharalis populations, events likely related to the sequential expansion of the corn and sugarcane crops in Brazil. The implications of these findings for pest management are discussed.

  8. Binary Image Classification: A Genetic Programming Approach to the Problem of Limited Training Instances.

    Science.gov (United States)

    Al-Sahaf, Harith; Zhang, Mengjie; Johnston, Mark

    2016-01-01

    In the computer vision and pattern recognition fields, image classification represents an important yet difficult task. It is a challenge to build effective computer models to replicate the remarkable ability of the human visual system, which relies on only one or a few instances to learn a completely new class or an object of a class. Recently we proposed two genetic programming (GP) methods, one-shot GP and compound-GP, that aim to evolve a program for the task of binary classification in images. The two methods are designed to use only one or a few instances per class to evolve the model. In this study, we investigate these two methods in terms of performance, robustness, and complexity of the evolved programs. We use ten data sets that vary in difficulty to evaluate these two methods. We also compare them with two other GP and six non-GP methods. The results show that one-shot GP and compound-GP outperform or achieve results comparable to competitor methods. Moreover, the features extracted by these two methods improve the performance of other classifiers with handcrafted features and those extracted by a recently developed GP-based method in most cases.

  9. Comparative population genetic analysis of brackish- and freshwater populations of Eurasian perch (Perca fluviatilis L.: implication for fish forensics.

    Directory of Open Access Journals (Sweden)

    Lilian Pukk

    2015-11-01

    Full Text Available Understanding the genetic population structure of commercially important fish species is crucial for developing biologically sound management and conservation strategies. Genetic information can be also useful for fighting against illegal fishing and fish trade. Here, we studied commercially important brackish and freshwater populations of Eurasian perch (Perca fluviatilis L. in Estonia, to describe the genetic divergence among populations and evaluate the power of 16 microsatellite markers to assign individual fish and group of fish to their population of origin. To do so, a total of 785 individuals caught from 13 different sites in the Baltic Sea and four locations in Lake Peipus were analyzed. We found significant differences in genetic diversity between brackish and freshwater populations with Baltic Sea samples showing slightly lower allelic richness and heterozygosity compared to Lake Peipus. We also observed moderate genetic differentiation among populations (overall FST=0.034. Individual self-assignment tests assigned large proportion of individuals correctly back to freshwater or coastal origin (Lake Peipus: 87.1%; Baltic Sea: 89.4%. Also, when evaluating the origin of group of individuals, it was possible to identify the origin of the brackish and freshwater fish groups with very high confidence (log 10 LR > 2 when sample size was larger than 15. Our results demonstrate the power of highly variable genetic markers separating two commercially most important Eurasian perch stocks in Estonia and the usefulness of assignment tests to successfully identify the genetic origin of fish.

  10. Genetic structure of Indian populations based on fifteen autosomal microsatellite loci

    Directory of Open Access Journals (Sweden)

    Bindu G Hima

    2006-05-01

    Full Text Available Abstract Background Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers. Results The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively. Conclusion Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.

  11. Genetic genealogy comes of age: perspectives on the use of deep-rooted pedigrees in human population genetics.

    Science.gov (United States)

    Larmuseau, M H D; Van Geystelen, A; van Oven, M; Decorte, R

    2013-04-01

    In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies.

  12. Correlation analysis of genetic diversity and population structure of Houttuynia cordata Thunb with regard to environment.

    Science.gov (United States)

    Zhong, J; Wu, F-C; Qiu, P; Dai, L-J

    2016-01-01

    To study the levels of genetic diversity, and population structure, of Houttuynia cordata Thunb, the genetic background and relationships of populations were analyzed in terms of environmental factors. The genetic diversity and population structure of H. cordata were investigated using sequence-related amplified polymorphisms and correlation with environmental factors was analyzed using the SPSS software. Two thousand one hundred sixty-three sites were amplified from 41 pairs of primers, 1825 of which were polymorphic, and the percentage of polymorphic loci was 84.37%; the percentage of polymorphic sites was 72.14 and 67.77% at the species and population level, respectively. The observed number of alleles was 1.52 and 1.30 at species and population level, respectively. The effective number of alleles was 1.38 and 1.24 at species and population level, respectively. The Nei's diversity was 0.26 and 0.15 at species and population level, respectively. The Shannon's information index was 0.87 and 0.63 at species and population level, respectively. The genetic differentiation coefficient of populations was 0.51, and 12 populations were divided into three classes based on D = 0.20; the genetic diversities of different populations are correlated at different significance levels (P Genetic differentiation existed among populations and the populations exhibited heteroplasmy.

  13. Comparison of genetic population structure of the large blue butterflies Maculinea nausithous and M. teleius

    DEFF Research Database (Denmark)

    Figurny-Puchalska, Edyta; Gadeberg, Rebekka M.E.; Boomsma, Jacobus Jan

    2000-01-01

    We investigated the genetic population structure of two rare myrmecophilous lycaenid butterflies, Maculinea nausithous and M. teleius, which often live sympatrically and have similar biology. In Europe, both species occur in highly fragmented populations and are vulnerable to local extinction...

  14. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  15. Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation.

    Science.gov (United States)

    Tsumura, Y; Matsumoto, A; Tani, N; Ujino-Ihara, T; Kado, T; Iwata, H; Uchida, K

    2007-08-01

    We investigated 25 natural populations of Chamaecyparis obtusa using 51 cleaved amplified polymorphic sequence (CAPS) markers, which were developed using information on sequence-tagged sites (STS) in Cryptomeria japonica. Most CAPS markers have codominant expression patterns, and are suitable for population studies because of their robustness and convenience. We estimated various genetic diversity parameters, including average heterozygosity (H(e)) and allelic richness and found that the more peripheral populations tended to have lower genetic diversity than central populations, in agreement with a previous theoretical study. The overall genetic differentiation between populations was low, but statistically significant (G(ST)=0.039), and similar to the level reported in a previous allozyme study. We attempted to detect non-neutral loci associated with local adaptation to clarify the relationship between the fixation index (F(ST)) and H(e) values for each locus and found seven candidates non-neutral loci. Phylogenetic tree analysis of the populations and Bayesian clustering analysis revealed a pattern of gradually increasing isolation of populations with increasing geographical distance. Three populations had a high degree of linkage disequilibrium, which we attribute to severe bottlenecks due to human disturbance or competition with other species during their migration from refugia after the most recent glaciation. We concluded that the small populations in western Japan and in Kanto district are more important, from a conservation perspective, than the populations in central Japan, due to their genetic divergence, relatively small sizes and restricted areas.

  16. Genetic variability and population structure of endangered Panax ginseng in the Russian Primorye

    Directory of Open Access Journals (Sweden)

    Muzarok Tamara I

    2010-06-01

    Full Text Available Abstract Background The natural habitat of wild P. ginseng is currently found only in the Russian Primorye and the populations are extremely exhausted and require restoration. Analysis of the genetic diversity and population structure of an endangered species is a prerequisite for conservation. The present study aims to investigate the patterns and levels of genetic polymorphism and population structures of wild P. ginseng with the AFLP method to (1 estimate the level of genetic diversity in the P. ginseng populations in the Russian Primorsky Krai, (2 calculate the distribution of variability within a population and among populations and (3 examine the genetic relationship between the populations. Methods Genetic variability and population structure of ten P. ginseng populations were investigated with Amplified Fragment Length Polymorphism (AFLP markers. The genetic relationships among P. ginseng plants and populations were delineated. Results The mean genetic variability within populations was high. The mean level of polymorphisms was 55.68% at the population level and 99.65% at the species level. The Shannon's index ranged between 0.1602 and 0.3222 with an average of 0.2626 at the population level and 0.3967 at the species level. The analysis of molecular variances (AMOVA showed a significant population structure in P. ginseng. The partition of genetic diversity with AMOVA suggested that the majority of the genetic variation (64.5% was within populations of P. ginseng. The inter-population variability was approximately 36% of the total variability. The genetic relationships among P. ginseng plants and populations were reconstructed by Minimum Spanning tree (MS-tree on the basis of Euclidean distances with ARLEQUIN and NTSYS, respectively. The MS-trees suggest that the southern Uss, Part and Nad populations may have promoted P. ginseng distribution throughout the Russian Primorye. Conclusion The P. ginseng populations in the Russian Primorye

  17. Quantitative measurement of retinal ganglion cell populations via histology-based random forest classification.

    Science.gov (United States)

    Hedberg-Buenz, Adam; Christopher, Mark A; Lewis, Carly J; Fernandes, Kimberly A; Dutca, Laura M; Wang, Kai; Scheetz, Todd E; Abràmoff, Michael D; Libby, Richard T; Garvin, Mona K; Anderson, Michael G

    2016-05-01

    The inner surface of the retina contains a complex mixture of neurons, glia, and vasculature, including retinal ganglion cells (RGCs), the final output neurons of the retina and primary neurons that are damaged in several blinding diseases. The goal of the current work was two-fold: to assess the feasibility of using computer-assisted detection of nuclei and random forest classification to automate the quantification of RGCs in hematoxylin/eosin (H&E)-stained retinal whole-mounts; and if possible, to use the approach to examine how nuclear size influences disease susceptibility among RGC populations. To achieve this, data from RetFM-J, a semi-automated ImageJ-based module that detects, counts, and collects quantitative data on nuclei of H&E-stained whole-mounted retinas, were used in conjunction with a manually curated set of images to train a random forest classifier. To test performance, computer-derived outputs were compared to previously published features of several well-characterized mouse models of ophthalmic disease and their controls: normal C57BL/6J mice; Jun-sufficient and Jun-deficient mice subjected to controlled optic nerve crush (CONC); and DBA/2J mice with naturally occurring glaucoma. The result of these efforts was development of RetFM-Class, a command-line-based tool that uses data output from RetFM-J to perform random forest classification of cell type. Comparative testing revealed that manual and automated classifications by RetFM-Class correlated well, with 83.2% classification accuracy for RGCs. Automated characterization of C57BL/6J retinas predicted 54,642 RGCs per normal retina, and identified a 48.3% Jun-dependent loss of cells at 35 days post CONC and a 71.2% loss of RGCs among 16-month-old DBA/2J mice with glaucoma. Output from automated analyses was used to compare nuclear area among large numbers of RGCs from DBA/2J mice (n = 127,361). In aged DBA/2J mice with glaucoma, RetFM-Class detected a decrease in median and mean nucleus size

  18. 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 ...

  19. A risk-based classification scheme for genetically modified foods. I: Conceptual development.

    Science.gov (United States)

    Chao, Eunice; Krewski, Daniel

    2008-12-01

    The predominant paradigm for the premarket assessment of genetically modified (GM) foods reflects heightened public concern by focusing on foods modified by recombinant deoxyribonucleic acid (rDNA) techniques, while foods modified by other methods of genetic modification are generally not assessed for safety. To determine whether a GM product requires less or more regulatory oversight and testing, we developed and evaluated a risk-based classification scheme (RBCS) for crop-derived GM foods. The results of this research are presented in three papers. This paper describes the conceptual development of the proposed RBCS that focuses on two categories of adverse health effects: (1) toxic and antinutritional effects, and (2) allergenic effects. The factors that may affect the level of potential health risks of GM foods are identified. For each factor identified, criteria for differentiating health risk potential are developed. The extent to which a GM food satisfies applicable criteria for each factor is rated separately. A concern level for each category of health effects is then determined by aggregating the ratings for the factors using predetermined aggregation rules. An overview of the proposed scheme is presented, as well as the application of the scheme to a hypothetical GM food.

  20. Constructivisms from a genetic point of view: a critical classification of current tendencies.

    Science.gov (United States)

    Sánchez, José Carlos; Loredo, José Carlos

    2009-12-01

    In this paper, we propose a critical classification of contemporary constructivist orientations. Our fundamental theoretical reference is the notion of genesis, understood as the construction of reality in a way that is neither relativist nor positivist-realist. We identify a nucleus of classic, genetic constructivism that revolves around the ideas of Baldwin, Piaget and Vygotsky and discuss two tendencies that distort the spirit of that nucleus: objectivism and subjectivism. Objectivism rules out the psychological, constructive activity of the subject, subordinating (or just reducing) it to objective structures either from nature (like genetic endowment or neural functioning), or from culture (like language or social practices). Subjectivism completely detaches the objectivity of knowledge from its construction on the part of the subject, reducing it to the mere product of individual interest, view, or irrationality. Thus, subjectivism is the non-constructive way to conceive the subject. Then, we attempt to show the dialectics that exists between these two tendencies and the scope of our criteria by analysing a representative (non exhaustive) group of authors who are defined as constructivists or who bring important elements to the debate about constructivism.

  1. Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei).

    Science.gov (United States)

    Hausdorf, Bernhard; Wilkens, Horst; Strecker, Ulrike

    2011-07-01

    Astyanax has become an important model system for evolutionary studies of cave animals. We investigated correlations of population genetic patterns revealed by microsatellite data and phylogeographic patterns shown by mitochondrial DNA sequences in Mexican cave and surface fish of the genus Astyanax (Characidae, Teleostei) to improve the understanding of the colonization history of this neotropical fish in Central and North America and to assess a recent taxonomic classification. The distribution of nuclear genotypes is not congruent with that of the mitochondrial clades. Admixture analyses suggest there has been nuclear gene flow between populations defined by different mitochondrial clades. The microsatellite data indicate that there was mitochondrial capture of a cave population from adjacent populations. Furthermore, gene flow also occurred between populations belonging to different nuclear genotypic clusters. This indicates that neither the nuclear genotypic clusters nor the mitochondrial clades represent independent evolutionary units, although the mitochondrial divergences are high and in a range usually characteristic for different fish species. This conclusion is supported by the presence of morphologically intermediate forms. Our analyses show that the Trans-Mexican Volcanic Belt limited gene flow, but has been crossed by Astyanax several times. In Yucatán, where obvious geographic barriers are missing, the incongruence between the distribution of nuclear and mitochondrial markers reflects random colonization events caused by inundations or marine transgressions resulting in random phylogeographic breaks. Thus, conclusions about the phylogeographic history and even more about the delimitation of species should not be based on single genetic markers.

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

    Science.gov (United States)

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

    2016-08-12

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

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Surname distribution in population genetics and in statistical physics

    Science.gov (United States)

    Rossi, Paolo

    2013-12-01

    Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from genetists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents.

  5. Population genetics provides evidence for recombination in Giardia.

    Science.gov (United States)

    Cooper, Margarethe A; Adam, Rodney D; Worobey, Michael; Sterling, Charles R

    2007-11-20

    Giardia lamblia (syn. Giardia intestinalis, Giardia duodenalis) is an enteric protozoan parasite with two nuclei, and it might be one of the earliest branching eukaryotes. However, the discovery of at least rudimentary forms of certain features, such as Golgi and mitochondria, has refuted the proposal that its emergence from the eukaryotic lineage predated the development of certain eukaryotic features. The recent recognition of many of the genes known to be required for meiosis in the genome has also cast doubt on the idea that Giardia is primitively asexual, but so far there has been no direct evidence of sexual reproduction in Giardia, and population data have suggested clonal reproduction. We did a multilocus sequence evaluation of the genotype A2 reference strain, JH, and five genotype A2 isolates from a highly endemic area in Peru. Loci from different chromosomes yielded significantly different phylogenetic trees, indicating that they do not share the same evolutionary history; within individual loci, tests for recombination yielded significant statistical support for meiotic recombination. These observations provide genetic data supportive of sexual reproduction in Giardia.

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

    Science.gov (United States)

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

    2008-01-01

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

  7. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  8. Population genetic structure of an endangered Utah endemic, Astragalus ampullarioides (Fabaceae).

    Science.gov (United States)

    Breinholt, Jesse W; Van Buren, Renee; Kopp, Olga R; Stephen, Catherine L

    2009-03-01

    The endangered Shivwits milkvetch, Astragalus ampullarioides, is a perennial, herbaceous plant. This Utah endemic was federally listed as endangered in 2001 because of its high habitat specificity and low numbers of individuals and populations. All habitat currently occupied by A. ampullarioides was designated as critical by the U.S. Fish and Wildlife Service in 2006 as a result of conservation litigation. We used AFLP markers to assess genetic differentiation among the seven extant populations and quantified genetic diversity in each. Six different AFLP markers resulted in 217 unambiguous polymorphic loci. We used multiple methods to examine any changes in population genetic structure in this species over time. Results indicate that A. ampullarioides had much higher gene flow among populations in the past, but has since fragmented into regional genetic units. These regions further fragmented genetically, and extant populations have differentiated through genetic drift. Populations had low levels of gene flow, even between geographically close populations. Rapid urban development reduces gene flow among regions and encroaches on populations of A. ampullarioides and remaining patches of unoccupied habitat. The genetic makeup of each of the extant populations should be carefully considered in management decisions such as population establishment or augmentation.

  9. Gene flow and genetic diversity of a broadcast-spawning coral in northern peripheral populations.

    Directory of Open Access Journals (Sweden)

    Yuichi Nakajima

    Full Text Available Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (F(ST < or = 0.033 although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained.

  10. Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

    Science.gov (United States)

    Yao, Hong-Bing; Wang, Chuan-Chao; Wang, Jiang; Tao, Xiaolan; Shang, Lei; Wen, Shao-Qing; Du, Qiajun; Deng, Qiongying; Xu, Bingying; Huang, Ying; Wang, Hong-Dan; Li, Shujin; Bin Cong; Ma, Liying; Jin, Li; Krause, Johannes; Li, Hui

    2017-01-01

    The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China. PMID:28112227

  11. Population genetics of Y-chromosome STRs in a population of Northern Greeks.

    Science.gov (United States)

    Kovatsi, Leda; Saunier, Jessica L; Irwin, Jodi A

    2009-12-01

    Seventeen Y STR loci were typed in a population sample of 191 unrelated male individuals from Northern Greece. Haplotypes are presented for the following loci: DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448. The overall haplotype diversity was 0.9992. This database study provides significant additional information for the application of Y-chromosomal STRs to forensic identification efforts in Greece by nearly doubling both the number of individuals and the number of Y-loci typed from Greek populations. These samples have been previously typed for autosomal STRs [L. Kovatsi, T.J. Parsons, R.S. Just, J.A. Irwin, Genetic variation for 15 autosomal STR loci (PowerPlex 16) in a population sample from northern Greece, Forensic Sci. Int. 159 (2006) 61-63] and the mitochondrial DNA control region [J. Irwin, J. Saunier, K. Strouss, C. Paintner, T. Diegoli, K. Sturk, L. Kovatsi, A. Brandstatter, M.A. Cariolou, W. Parson, T.J. Parsons, Mitochondrial control region sequences from northern Greece and Greek Cypriots, Int. J. Legal Med. 122 (2008) 87-89].

  12. Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

    Science.gov (United States)

    Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

    2016-04-01

    While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients.

  13. Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral.

    Science.gov (United States)

    Nunes, F; Norris, R D; Knowlton, N

    2009-10-01

    Limited dispersal and connectivity in marine organisms can have negative fitness effects in populations that are small and isolated, but reduced genetic exchange may also promote the potential for local adaptation. Here, we compare the levels of genetic diversity and connectivity in the coral Montastraea cavernosa among both central and peripheral populations throughout its range in the Atlantic. Genetic data from one mitochondrial and two nuclear loci in 191 individuals show that M. cavernosa is subdivided into three genetically distinct regions in the Atlantic: Caribbean-North Atlantic, Western South Atlantic (Brazil) and Eastern Tropical Atlantic (West Africa). Within each region, populations have similar allele frequencies and levels of genetic diversity; indeed, no significant differentiation was found between populations separated by as much as 3000 km, suggesting that this coral species has the ability to disperse over large distances. Gene flow within regions does not, however, translate into connectivity across the entire Atlantic. Instead, substantial differences in allele frequencies across regions suggest that genetic exchange is infrequent between the Caribbean, Brazil and West Africa. Furthermore, markedly lower levels of genetic diversity are observed in the Brazilian and West African populations. Genetic diversity and connectivity may contribute to the resilience of a coral population to disturbance. Isolated peripheral populations may be more vulnerable to human impacts, disease or climate change relative to those in the genetically diverse Caribbean-North Atlantic region.

  14. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    Science.gov (United States)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  15. Genetic polymorphism of blood proteins in a population of Shetland ponies

    NARCIS (Netherlands)

    Buis, R.C.

    1976-01-01

    Genetic variation of proteins (protein polymorphism) is widespread among many animal species. The biological significance of protein polymorphism has been the subject of many studies. This variation has a supporting function for population genetic studies as a source of genetic markers. In farm anim

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

    Science.gov (United States)

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

    2016-02-01

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

  17. Developing educational resources for population genetics in R: An open and collaborative approach

    Science.gov (United States)

    The R computing and statistical language community has developed a myriad of resources for conducting populations genetic analyses. However, resources for learning how to carry out population genetic analyses in R are scattered and often incomplete, which can make acquiring this skill unnecessarily ...

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

    Science.gov (United States)

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

    1997-01-01

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

  19. Attitudes toward genetic testing among the general population and relatives of patients with a severe genetic disease

    DEFF Research Database (Denmark)

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

    1995-01-01

    In the present study we explore the attitudes of the Finnish population toward genetic testing by conducting a questionnaire study of a stratified sample of the population as well as of family members of patients with a severe hereditary disease, aspartylglucosaminuria (AGU). The questionnaire...... members of AGU patients have a favorable attitude toward genetic testing. However, a commonly expressed reason against testing was that test results might lead to discrimination in employment or insurance policies. Based on the responses, we predict that future genetic testing programs will most probably...

  20. 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, Sifa

    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.

  1. Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research.

    Science.gov (United States)

    Chesler, Elissa J

    2014-02-01

    The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.

  2. Genetic Structure of Native Sheep Populations in East and South Asia

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Variations of structural loci among 4 sheep populations in China were examined by the method of multiloci electrophoresis, and similar data from 11 sheep populations were taken as basic references to analyze the genetic structure of the native sheep populations in East and South Asia. The results showed that the average heterozygosity and effective number of alleles among 15 populations were 0.2746 and 1.559, respectively. Mongolian sheep possessed the largest average heterozygosity and effective number of alleles. Genetic diversity of sheep populations in Mongolia, China, Vietnam,Bangladesh and Nepal was reduced in this order. The coefficients of genetic differentiation were between 0.0126 and 0.3083, with the average of 0.148, demonstrating that genetic variations lay mainly in populations with 85.2% of the total variations. There exists no correlation between geographical distances and genetic distances. Gene flow was smooth among most populations, which led to inconsistency between geographical distances and genetic distances. The 15 native sheep populations in East and South Asia could be divided into two groups: One group included part populations of China and Mongolia, and the other included Yunnan populations of China, and part populations of Nepal and Bangladesh.Other populations did not cluster together and divide into the above-mentioned two groups. This study indicated genetic differentiation of the 15 native sheep populations in East and South Asia was relatively low, geographical isolation was not the main reason affecting genetic differentiation, and the fifteen sheep populations could be divided into two groups according to phylogenetic relationships.

  3. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Institute of Scientific and Technical Information of China (English)

    QIAO Hongjin; LIU Xiangquan; ZHANG Xijia; JIANG Haibin; WANG Jiying; ZHANG Limin

    2013-01-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa,Rhizostomatidae).One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations.The polymorphic ratio,Shannon's diversity index and average heterozygosity were 70.3%,0.346 and 0.228 for the white hatchery population,74.3%,0.313,and 0.201 for the red hatchery population,79.3%,0.349,and 0.224 for the Jiangsu wild population,and 74.9%,0.328 and 0.210 for the Penglai wild population,respectively.Thus,all populations had a relatively high level of genetic diversity.A specific band was identified that could separate the white from the red hatchery population.There was 84.85% genetic differentiation within populations.Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided.For the hatchery populations,the white and red populations clustered separately; however,for the wild populations,Penglai and Jiangsu populations clustered together.The genetic diversity at the clone level was also determined.Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations,which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing.These findings will benefit the artificial seeding and conservation of the germplasm resources.

  4. Human genetic variation database, a reference database of genetic variations in the Japanese population

    Science.gov (United States)

    Higasa, Koichiro; Miyake, Noriko; Yoshimura, Jun; Okamura, Kohji; Niihori, Tetsuya; Saitsu, Hirotomo; Doi, Koichiro; Shimizu, Masakazu; Nakabayashi, Kazuhiko; Aoki, Yoko; Tsurusaki, Yoshinori; Morishita, Shinichi; Kawaguchi, Takahisa; Migita, Osuke; Nakayama, Keiko; Nakashima, Mitsuko; Mitsui, Jun; Narahara, Maiko; Hayashi, Keiko; Funayama, Ryo; Yamaguchi, Daisuke; Ishiura, Hiroyuki; Ko, Wen-Ya; Hata, Kenichiro; Nagashima, Takeshi; Yamada, Ryo; Matsubara, Yoichi; Umezawa, Akihiro; Tsuji, Shoji; Matsumoto, Naomichi; Matsuda, Fumihiko

    2016-01-01

    Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/. PMID:26911352

  5. Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

    Science.gov (United States)

    Duc, N M; Duy, V D; Xuan, B T T; Thang, B V; Ha, N T H; Tam, N M

    2016-10-24

    Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (NA = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise FST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising

  6. Phylogenetics, phylogeography and population genetics of North American sea ducks (tribe: Mergini)

    Science.gov (United States)

    Talbot, Sandra; Sonsthagen, Sarah A.; Pearce, John M.; Scribner, Kim T.

    2015-01-01

    Many environments occupied by North American sea ducks are remote and difficult to access, and as a result, detailed information about life history characteristics that drive population dynamics within and across species is limited. Nevertheless, progress on this front during the past several decades has benefited by the application of genetic technologies, and for several species, these technologies have allowed for concomitant tracking of population trends and genetic diversity, delineation of populations, assessment of gene flow among metapopulations, and understanding of migratory connectivity between breeding and wintering grounds. This chapter provides an overview of phylogenetic, phylogeographic, and population genetics studies of North American sea duck species, many of which have sought to understand the major and minor genetic divisions within and among sea duck species, and most of which have been conducted with the understanding that the maintenance of genetic variation in wild sea duck populations is fundamental to the group’s long-term persistence.

  7. Population genetic differentiation of height and body mass index across Europe

    DEFF Research Database (Denmark)

    Robinson, Matthew R.; Hemani, Gibran; Medina-Gomez, Carolina;

    2015-01-01

    Across-nation differences in the mean values for complex traits are common(1-8), but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European coun...... for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P Europe masked genetic differentiation for BMI (P

  8. Population genetics of Agave cocui: evidence for low genetic diversity at the southern geographic limit of genus Agave.

    Science.gov (United States)

    Figueredo, Carmen J; Nassar, Jafet M

    2011-01-01

    The Agave genus embraces many species with outstanding ecological and economic importance in the arid regions of the Americas. Even though this genus covers a broad geographic distribution, our knowledge on the population genetics of species is concentrated in taxa located in North America. Recently, it has been demonstrated that plant domestication decreases levels of genetic diversity in managed populations and increases population structure with respect to wild populations. We examined levels of allozyme diversity (N = 17 loci) and population structure of Agave cocui, the species at the southern limit of distribution of the genus. We sampled 7 wild populations (N = 30-35 individuals per population) representative of the geographic distribution of the species in Venezuela. Among the agaves studied, A. cocui has some of the lowest estimates of genetic diversity (H(e)[species] = 0.059, H(e)[population] = 0.054) reported until present. We propose that this condition is probably linked to the recent origin of this species in arid and semiarid regions of Colombia and Venezuela, probably through one or a few founder events. The lowest estimates of genetic diversity were associated with small populations in very restricted arid patches; but also with overexploitation of rosettes for production of fermented drinks and fibers. Santa Cruz de Pecaya, one of the 2 centers of economic use of agaves in northwestern Venezuela presented one of the lowest values of genetic variability, a sign suggesting that human impact represents a significant threat to the available genetic pool that this species possesses in the region.

  9. Population genetics and the effects of a severe bottleneck in an ex situ population of critically endangered Hawaiian tree snails.

    Science.gov (United States)

    Price, Melissa R; Hadfield, Michael G

    2014-01-01

    As wild populations decline, ex situ propagation provides a potential bank of genetic diversity and a hedge against extinction. These programs are unlikely to succeed if captive populations do not recover from the severe bottleneck imposed when they are founded with a limited number of individuals from remnant populations. In small captive populations allelic richness may be lost due to genetic drift, leading to a decline in fitness. Wild populations of the Hawaiian tree snail Achatinella lila, a hermaphroditic snail with a long life history, have declined precipitously due to introduced predators and other human impacts. A captive population initially thrived after its founding with seven snails, exceeding 600 captive individuals in 2009, but drastically declined in the last five years. Measures of fitness were examined from 2,018 captive snails that died between 1998 and 2012, and compared with genotypic data for six microsatellite loci from a subset of these deceased snails (N = 335), as well as live captive snails (N = 198) and wild snails (N = 92). Surprisingly, the inbreeding coefficient (Fis) declined over time in the captive population, and is now approaching values observed in the 2013 wild population, despite a significant decrease in allelic richness. However, adult annual survival and fecundity significantly declined in the second generation. These measures of fitness were positively correlated with heterozygosity. Snails with higher measures of heterozygosity had more offspring, and third generation offspring with higher measures of heterozygosity were more likely to reach maturity. These results highlight the importance of maintaining genetic diversity in captive populations, particularly those initiated with a small number of individuals from wild remnant populations. Genetic rescue may allow for an increase in genetic diversity in the captive population, as measures of heterozygosity and rarified allelic richness were higher in wild tree

  10. Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

    Science.gov (United States)

    Lesser, M R; Parchman, T L; Jackson, S T

    2013-05-01

    Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.

  11. Population genetic structure of rare and endangered plants using molecular markers

    Science.gov (United States)

    Raji, Jennifer; Atkinson, Carter T.

    2013-01-01

    This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

  12. Effect of domestication on the genetic diversity and structure of Saccharina japonica populations in China

    Science.gov (United States)

    Zhang, Jie; Wang, Xiuliang; Yao, Jianting; Li, Qiuying; Liu, Fuli; Yotsukura, Norishige; Krupnova, Tatiana N.; Duan, Delin

    2017-01-01

    Saccharina japonica is a commercially and ecologically important seaweed and is an excellent system for understanding the effects of domestication on marine crops. In this study, we used 19 selected simple sequence repeat (SSR) markers to investigate the influence of domestication on the genetic diversity and structure of S. japonica populations. Wild kelp populations exhibited higher genetic diversity than cultivated populations based on total NA, HE, HO, NP and AR. Discriminant analysis of principal components (DAPC), a neighbour-joining (NJ) tree and STRUCTURE analyses indicated that S. japonica populations could be divided into two groups (a cultivated/introduced group and a wild indigenous group) with significant genetic differentiation (P < 0.0001). Divergent selection, continuous inbreeding and inter-specific hybridization have caused the divergence of these two genetically separate gene pools. The significant genetic differentiation between northern and southern cultivated populations appears to be due to inter-specific hybridization and wild germplasm introduction during the domestication process. In addition, the cultivation of S. japonica has not resulted in any serious genetic disturbance of wild introduced S. japonica populations. An understanding of the genetic diversity and genetic structure of domesticated S. japonica will be necessary for further genetic improvement and effective use of germplasm. PMID:28176848

  13. Inbreeding and loss of genetic variation in a reintroduced population of Mauritius Kestrel.

    Science.gov (United States)

    Ewing, Steven R; Nager, Ruedi G; Nicoll, Malcolm A C; Aumjaud, Aurelien; Jones, Carl G; Keller, Lukas F

    2008-04-01

    Many populations have recovered from severe bottlenecks either naturally or through intensive conservation management. In the past, however, few conservation programs have monitored the genetic health of recovering populations. We conducted a conservation genetic assessment of a small, reintroduced population of Mauritius Kestrel (Falco punctatus) to determine whether genetic deterioration has occurred since its reintroduction. We used pedigree analysis that partially accounted for individuals of unknown origin to document that (1) inbreeding occurred frequently (2.6% increase per generation; N(eI)= 18.9), (2) 25% of breeding pairs were composed of either closely or moderately related individuals, (3) genetic diversity has been lost from the population (1.6% loss per generation; N(eV)= 32.1) less rapidly than the corresponding increase in inbreeding, and (4) ignoring the contribution of unknown individuals to a pedigree will bias the metrics derived from that pedigree, ultimately obscuring the prevailing genetic dynamics. The rates of inbreeding and loss of genetic variation in the subpopulation of Mauritius Kestrel we examined were extreme and among the highest yet documented in a wild vertebrate population. Thus, genetic deterioration may affect this population's long-term viability. Remedial conservation strategies are needed to reduce the impact of inbreeding and loss of genetic variation in this species. We suggest that schemes to monitor genetic variation after reintroduction should be an integral component of endangered species recovery programs.

  14. Novel synthetic Medea selfish genetic elements drive population replacement in Drosophila; a theoretical exploration of Medea-dependent population suppression.

    Science.gov (United States)

    Akbari, Omar S; Chen, Chun-Hong; Marshall, John M; Huang, Haixia; Antoshechkin, Igor; Hay, Bruce A

    2014-12-19

    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 replacement in Drosophila. These elements use microRNA-mediated silencing of myd88, a maternally expressed gene required for embryonic dorso-ventral pattern formation, coupled with early zygotic expression of a rescuing transgene, to bring about gene drive. Medea elements that work through additional mechanisms are needed in order to be able to carry out cycles of population replacement and/or remove existing transgenes from the population, using second-generation elements that spread while driving first-generation elements out of the population. Here we report the synthesis and population genetic behavior of two new synthetic Medea elements that drive population replacement through manipulation of signaling pathways involved in cellular blastoderm formation or Notch signaling, demonstrating that in Drosophila Medea elements can be generated through manipulation of diverse signaling pathways. We also describe the mRNA and small RNA changes in ovaries and early embryos associated from Medea-bearing females. Finally, we use modeling to illustrate how Medea elements carrying genes that result in diapause-dependent female lethality could be used to bring about population suppression.

  15. Population genetic data of 38 insertion-deletion markers in six populations of the northern fringe of the Iberian Peninsula.

    Science.gov (United States)

    Cardoso, Sergio; Sevillano, Rubén; Gamarra, David; Santurtún, Ana; Martínez-Jarreta, Begoña; de Pancorbo, Marian M

    2017-03-01

    Insertion-deletions have been reported very useful markers for forensic purposes. To further deepen in this matter, 38 non-coding bi-allelic autosomal indels were analyzed in 575 individuals representing six populations from the northern fringe of the Iberian Peninsula. Autochthonous populations from the Basque Country, northern Navarre, the Pas Valley in Cantabria and Aragon were analyzed, together with non-autochthonous populations from the Basque Country and northern Navarre. At the intra-population level, all loci analyzed were in Hardy-Weinberg equilibrium except for marker rs33917182 in autochthonous Basques. Linkage disequilibrium (LD) test did not reveal statistically significant allelic association between the different loci pairs in all six populations. Forensic parameters proved to be highly informative in the six populations analyzed, even if a scenario with population substructure and local inbreeding was considered for match probability calculations, and the potential of this indels set to be used in combination with other genetic markers is remarkable. As for inter-population analyses, in general terms the six populations showed low but statistically significant genetic distances. However, though this indels set efficiently differentiate between main ancestries, it does not allow an accurate separation at a local level and, for the time being, their combination with other informative markers is needed to maximize the power to accurately differentiate populations with close genetic ancestry.

  16. Genetic Distance and Genetic Identity between Hindu and Muslim populations of Barak Valley for ABO and Rh genes

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-09-01

    Full Text Available A genetic study was carried out in two endogamous populations namely Hindus and Muslims in the Barak Valley Zone of Assam in India. Nei�s genetic distance and genetic identity between two populations were calculated on the basis of estimated allele frequencies of ABO and Rh blood group genes. The genetic distance between Hindus and Muslims was 0.12% for ABO gene and 0.10% for Rh gene. The genetic identity between two populations was estimated as 99.88% for ABO gene and 99.90% for Rh gene suggesting very high genetic similarity between these two populations. Observed heterozygosity estimate was higher in Hindus (0.5598 for ABO gene and 0.2822 for Rh gene than Muslims (0.5346 for ABO gene and 0.2408 for Rh gene indicating lesser inbreeding in Hindus than Muslims. Fixation index was lower in Hindus (16.02% for ABO gene and 43.56% for Rh gene than Muslims (19.80% for ABO gene and 51.84% for Rh gene. Panmictic index was higher in Hindus than Muslims for both the genes. Fixation and panmictic indices revealed that during evolutionary process the Hindus maintained more outbreeding feature than the Muslims in the valley. In this study, the concepts of genetic load of a population and genotype fitness were extended to alleles to estimate the magnitude of allele genetic load (GL and allele fitness for 3 alleles in ABO gene and for 2 alleles in Rh gene in two populations. The genetic load for O, A and B alleles were lower in Hindus than Muslims. Similar results for genetic load were found for the alleles of Rh gene in the comparison of two populations. The fitness estimates of O, A and B alleles for ABO gene and D and d alleles for Rh gene were higher in Hindus than Muslims. A population with low allele genetic load (GL and high allele fitness (AF might have greater survival advantage in nature in the absence of heterozygote advantage and higher adaptive value of the allele with increased frequency.

  17. Patterns of genetic diversity in southern and southeastern Araucaria angustifolia (Bert.) O. Kuntze relict populations

    Science.gov (United States)

    2009-01-01

    Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five “genetic clusters” (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three “genetic clusters”. These results are in agreement with the pattern of geographic distribution of the studied populations. PMID:21637518

  18. Genetic variation and population structure of the mushroom Pleurotusferulae in China inferred from nuclear DNA analysis

    Institute of Scientific and Technical Information of China (English)

    ZHAO Meng-ran; HUANG Chen-yang; WU Xiang-li; CHEN Qiang; QU Ji-bin; LI Yan-chun; GAO Wei; ZHANG Jin-xia

    2016-01-01

    To investigate the genetic diversity of an edible fungusPleurotus ferulae, a total of 89 wild samples colected from six geographical locations in the Xinjiang Uygur Autonomous Region of China and two geographical locations in Italy, were analyzed using three DNA fragments including the translation elongation factor (EF1α), the second largest subunit of the RNA polymerase II (RPB2) and the largest subunit of the RNA polymerase II (RPB1). The results indicated relatively abundant genetic variability in the wild resources ofP.ferulae.The analysis of molecular variance (AMOVA) showed that the vast majority of the genetic variation was found within geographical populations. Both the Chinese populations and the Italian populations ofP. ferulaedisplayed a limited genetic differentiation. The degree of differentiation between the Chinese populations and the Italian populations was obviously higher than that between the populations from the same region, and moreover the genetic differentiation among al the tested populations was correlated to the geographical dis-tance. The phylogeny analyses conifrmed that samples from China and Italy belonged to another genetic group separated fromPleurotus eryngi. They were closely related to each other but were clustered according to their geographical origins, which implied the Chinese populations were highly differentiated from the Italian populations because of distance isolation, and the two populations from different regions might be stil in the process of alopatric divergence.

  19. Assessing genetic diversity of wild populations of Japanese flounder using AFLP markers

    Institute of Scientific and Technical Information of China (English)

    XU Xiaofei; ZHANG Quanqi; WANG Zhigang; QI Jie; ZHANG Zhifeng; BAO Zhenmin; Heisuke Nakagawa

    2006-01-01

    Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic diversity of four wild geographical populations of Japanese flounder (Paralichthys olivaceus). A total of 775 loci (58.32% of which was polymorphic) in the range between 100 and 1 300 base pairs were detected from 110 individuals using seven primer combinations. The percentage of polymorphic loci detected by single primer combination for each population was calculated, ranging from 19.59% to 53.33%. Genetic similarities within and among the populations were calculated from the binary matrices of presence - absence. Phylogenetic tree of four populations was constructed by using the UPGMA method using PHYLIP Version 3.5. According to intrapopulation genetic similarities, CW population displayed the highest genetic diversity value and KY population had the lowest genetic diversity value.The distance between CW and CF populations was the farthest, which was possibly resulted from the farthest distance of Weihai of Shandong and Fujian of China compared with the geographical distance between other locations of populations. The subpopulation differentiation value ( Gst ) is 0.356 5, showing a certain extent of differentiation among the four geographical populations. AFLP technology was confirmed to be an effective tool to assess within- and among-population genetic diversity of Japanese flounder. The present survey provided significant insights for research in the Japanese flounder breeding program.

  20. Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis.

    Science.gov (United States)

    Whitehouse, A M; Harley, E H

    2001-09-01

    Widespread hunting had fragmented and severely reduced elephant populations in South Africa by 1900. Elephant numbers increased during the 1900s, although rates of recovery of individual populations varied. The Kruger National Park elephant population increased rapidly, to more than 6000 by 1967, with recruitment boosted by immigration from Mozambique. The Addo Elephant National Park population was reduced to 11 elephants in 1931 and remains relatively small (n = 325). Loss of genetic variation is expected to occur whenever a population goes through a bottleneck, especially when post-bottleneck recovery is slow. Variation at nine polymorphic microsatellite loci was analysed for Kruger and Addo elephants, as well as museum specimens of Addo elephants shot prior to the population bottleneck. Significantly reduced genetic variation and heterozygosity were observed in Addo in comparison to Kruger (mean alleles/locus and H(E): Addo 1.89, 0.18; Kruger 3.89, 0.44). Two alleles not present in the current Addo population were observed in the museum specimens. Addo elephants represent a genetic subset of the Kruger population, with high levels of genetic differentiation resulting from rapid genetic drift. The Kruger population is low in genetic diversity in comparison to East African elephants, confirming this population also suffered an appreciable bottleneck.

  1. Population Genetic Structure of a Widespread Bat-Pollinated Columnar Cactus.

    Science.gov (United States)

    Bustamante, Enriquena; Búrquez, Alberto; Scheinvar, Enrique; Eguiarte, Luis Enrique

    2016-01-01

    Bats are the main pollinators and seed dispersers of Stenocereus thurberi, a xenogamous columnar cactus of northwestern Mexico and a good model to illustrate spatial dynamics of gene flow in long-lived species. Previous studies in this cactus showed differences among populations in the type and abundance of pollinators, and in the timing of flowering and fruiting. In this study we analyzed genetic variability and population differentiation among populations. We used three primers of ISSR to analyze within and among populations genetic variation from eight widely separated populations of S. thurberi in Sonora, Mexico. Sixty-six out of 99 of the ISSR bands (P = 66.7%) were polymorphic. Total heterozygosity for all populations sampled revealed high genetic diversity (Hsp = 0.207, HBT = 0.224). The AMOVA showed that most of the genetic variation was within populations (80.5%). At the species level, estimates of population differentiation, θ = 0.175 and θB = 0.194, indicated moderate gene flow among populations. The absence of a significant correlation between genetic and geographic distances indicated little isolation by geographic distance. The large genetic variation and diversity found in S. thurberi is consistent with its open reproductive system and the high mobility of bats, a major pollinator. However, small changes in number or kind of pollinators and seed dispersal agents, in the directionality of migratory routes, and/or in the timing of flowering and fruiting among populations, can critically affect gene flow dynamics.

  2. [Molecular genetic analysis of wild soybean (Glycine soja Sieb. & Zucc.) population structure in anthropogenic and natural landscapes of Primorskii krai].

    Science.gov (United States)

    Nedoluzhko, A V; Tikhonov, A V; Dorokhov, D B

    2008-08-01

    The data are presented on genetic population structure of wild soybean growing in natural and anthropogenically disturbed landscapes of Primorskii krai of the Russian Federation. Comparative analysis showed that wild soybean populations exposed to anthropogenic influence exhibited lower genetic diversity than natural populations. Recommendations on conservation of the wild plant gene pools using comparative data on population genetic structures are made.

  3. 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.

  4. Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India

    Science.gov (United States)

    Mawkhlieng, Bandapkuper; Misra, A. K.; Pattanayak, A.; Harish, G. D.; Singh, S. K.; Ngachan, S. V.; Bansal, K. C.

    2015-01-01

    The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, chakhao rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice

  5. Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L. Landraces from North-Eastern India.

    Directory of Open Access Journals (Sweden)

    Somnath Roy

    Full Text Available The North-eastern (NE India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, aromatic rice accessions from Nagaland; and P3, chakhao rice germplasm from Manipur [corrected]. Pair-wise FST between three groups varied from 0.223 (P1 vs P2 to 0.453 (P2 vs P3. With reference to the global classification of rice cultivars, two major groups (Indica and Japonica were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of

  6. Reductions in genetic diversity of Schistosoma mansoni populations under chemotherapeutic pressure: the effect of sampling approach and parasite population definition.

    Science.gov (United States)

    French, Michael D; Churcher, Thomas S; Basáñez, María-Gloria; Norton, Alice J; Lwambo, Nicholas J S; Webster, Joanne P

    2013-11-01

    Detecting potential changes in genetic diversity in schistosome populations following chemotherapy with praziquantel (PZQ) is crucial if we are to fully understand the impact of such chemotherapy with respect to the potential emergence of resistance and/or other evolutionary outcomes of interventions. Doing so by implementing effective, and cost-efficient sampling protocols will help to optimise time and financial resources, particularly relevant to a disease such as schistosomiasis currently reliant on a single available drug. Here we explore the effect on measures of parasite genetic diversity of applying various field sampling approaches, both in terms of the number of (human) hosts sampled and the number of transmission stages (miracidia) sampled per host for a Schistosoma mansoni population in Tanzania pre- and post-treatment with PZQ. In addition, we explore population structuring within and between hosts by comparing the estimates of genetic diversity obtained assuming a 'component population' approach with those using an 'infrapopulation' approach. We found that increasing the number of hosts sampled, rather than the number of miracidia per host, gives more robust estimates of genetic diversity. We also found statistically significant population structuring (using Wright's F-statistics) and significant differences in the measures of genetic diversity depending on the parasite population definition. The relative advantages, disadvantages and, hence, subsequent reliability of these metrics for parasites with complex life-cycles are discussed, both for the specific epidemiological and ecological scenario under study here and for their future application to other areas and schistosome species.

  7. Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

    Directory of Open Access Journals (Sweden)

    Reim Stefanie

    2016-06-01

    Full Text Available In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR and chloroplast single nucleotide polymorphism (cpSNP. In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA. The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

  8. Genetic Diversity of Three Aristichthys nobilis Populations and One Inbreeding Stock

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Genetic diversity of three Aristichthys nobilis populations and one inbreeding stock was studied using random amplified polymorphic DNA(RAPD)method. Materials of natural populations were collected from two counties of Guangxi Province, Hengxian (NH) and Shanglin (NS) and one city of Hubei Province, Wuhan city.(NW). Shanglin and Hengxian's river system respectively belongs to Qianjiang and Yujiang River, two tributaries confluencing to Xunjiang River, main tributary of Xijiang River, which is the biggest tributary of the Zhujiang River system, and Wuhan's water system belongs to the Yangtse River system. The inbreeding stock (RS) was the more than 10 generation descendant by brother-sister mating system whose parents were collected from Shanglin. The results showed that the genetic variety of individuals of RS was very low (0.105 4), whereas that of natural populations was relatively high,which from high to low was 0.158 1 (NW), 0.132 0 (NH) and 0.110 5 (NS). As an index for genetic distance pair-wise populations, the genetic variety between populations was studied, which characterized the genetic distance between populations. The genetic distance of NW and NH, NW and NS, NW and RS were respectively high, whereas that of NH and NS, NS and RS, NH and RS was low. Chi-test(χ2) and the analysis of the genetic variety pair-wise populations was taken as efficient approach for studying population difference.

  9. Population genetic differences along a latitudinal cline between original and recently colonized habitat in a butterfly.

    Directory of Open Access Journals (Sweden)

    Sofie Vandewoestijne

    Full Text Available BACKGROUND: Past and current range or spatial expansions have important consequences on population genetic structure. Habitat-use expansion, i.e. changing habitat associations, may also influence genetic population parameters, but has been less studied. Here we examined the genetic population structure of a Palaeartic woodland butterfly Pararge aegeria (Nymphalidae which has recently colonized agricultural landscapes in NW-Europe. Butterflies from woodland and agricultural landscapes differ in several phenotypic traits (including morphology, behavior and life history. We investigated whether phenotypic divergence is accompanied by genetic divergence between populations of different landscapes along a 700 km latitudinal gradient. METHODOLOGY/PRINCIPAL FINDINGS: Populations (23 along the latitudinal gradient in both landscape types were analyzed using microsatellite and allozyme markers. A general decrease in genetic diversity with latitude was detected, likely due to post-glacial colonization effects. Contrary to expectations, agricultural landscapes were not less diverse and no significant bottlenecks were detected. Nonetheless, a genetic signature of recent colonization is reflected in the absence of clinal genetic differentiation within the agricultural landscape, significantly lower gene flow between agricultural populations (3.494 than between woodland populations (4.183, and significantly higher genetic differentiation between agricultural (0.050 than woodland (0.034 pairwise comparisons, likely due to multiple founder events. Globally, the genetic data suggest multiple long distance dispersal/colonization events and subsequent high intra- and inter-landscape gene flow in this species. Phosphoglucomutase deviated from other enzymes and microsatellite markers, and hence may be under selection along the latitudinal gradient but not between landscape types. Phenotypic divergence was greater than genetic divergence, indicating directional

  10. A predictive relationship between population and genetic sex ratios in clonal species

    Science.gov (United States)

    McLetchie, D. Nicholas; García-Ramos, Gisela

    2017-04-01

    Sexual reproduction depends on mate availability that is reflected by local sex ratios. In species where both sexes can clonally expand, the population sex ratio describes the proportion of males, including clonally derived individuals (ramets) in addition to sexually produced individuals (genets). In contrast to population sex ratio that accounts for the overall abundance of the sexes, the genetic sex ratio reflects the relative abundance of genetically unique mates, which is critical in predicting effective population size but is difficult to estimate in the field. While an intuitive positive relationship between population (ramet) sex ratio and genetic (genet) sex ratio is expected, an explicit relationship is unknown. In this study, we determined a mathematical expression in the form of a hyperbola that encompasses a linear to a nonlinear positive relationship between ramet and genet sex ratios. As expected when both sexes clonally have equal number of ramets per genet both sex ratios are identical, and thus ramet sex ratio becomes a linear function of genet sex ratio. Conversely, if sex differences in ramet number occur, this mathematical relationship becomes nonlinear and a discrepancy between the sex ratios amplifies from extreme sex ratios values towards intermediate values. We evaluated our predictions with empirical data that simultaneously quantified ramet and genet sex ratios in populations of several species. We found that the data support the predicted positive nonlinear relationship, indicating sex differences in ramet number across populations. However, some data may also fit the null model, which suggests that sex differences in ramet number were not extensive, or the number of populations was too small to capture the curvature of the nonlinear relationship. Data with lack of fit suggest the presence of factors capable of weakening the positive relationship between the sex ratios. Advantages of this model include predicting genet sex ratio using

  11. Classification models for subthreshold generalized anxiety disorder in a college population: Implications for prevention.

    Science.gov (United States)

    Kanuri, Nitya; Taylor, C Barr; Cohen, Jeffrey M; Newman, Michelle G

    2015-08-01

    Generalized anxiety disorder (GAD) is one of the most common psychiatric disorders on college campuses and often goes unidentified and untreated. We propose a combined prevention and treatment model composed of evidence-based self-help (SH) and guided self-help (GSH) interventions to address this issue. To inform the development of this stepped-care model of intervention delivery, we evaluated results from a population-based anxiety screening of college students. A primary model was developed to illustrate how increasing levels of symptomatology could be linked to prevention/treatment interventions. We used screening data to propose four models of classification for populations at risk for GAD. We then explored the cost considerations of implementing this prevention/treatment stepped-care model. Among 2489 college students (mean age 19.1 years; 67% female), 8.0% (198/2489) met DSM-5 clinical criteria for GAD, in line with expected clinical rates for this population. At-risk Model 1 (subthreshold, but considerable symptoms of anxiety) identified 13.7% of students as potentially at risk for developing GAD. Model 2 (subthreshold, but high GAD symptom severity) identified 13.7%. Model 3 (subthreshold, but symptoms were distressing) identified 12.3%. Model 4 (subthreshold, but considerable worry) identified 17.4%. There was little overlap among these models, with a combined at-risk population of 39.4%. The efficiency of these models in identifying those truly at risk and the cost and efficacy of preventive interventions will determine if prevention is viable. Using Model 1 data and conservative cost estimates, we found that a preventive intervention effect size of even 0.2 could make a prevention/treatment model more cost-effective than existing models of "wait-and-treat."

  12. Genetic structure in insular and mainland populations of house sparrows (Passer domesticus) and their hemosporidian parasites

    Science.gov (United States)

    Bichet, Coraline; Moodley, Yoshan; Penn, Dustin J; Sorci, Gabriele; Garnier, Stéphane

    2015-01-01

    Small and isolated populations usually exhibit low levels of genetic variability, and thus, they are expected to have a lower capacity to adapt to changes in environmental conditions, such as exposure to pathogens and parasites. Comparing the genetic variability of selectively neutral versus functional loci allows one to assess the evolutionary history of populations and their future evolutionary potential. The genes of the major histocompatibility complex (MHC) control immune recognition of parasites, and their unusually high diversity is genes which is likely driven by parasite-mediated balancing selection. Here, we examined diversity and differentiation of neutral microsatellite loci and functional MHC class I genes in house sparrows (Passer domesticus), living in six insular and six mainland populations, and we aimed to determine whether their diversity or differentiation correlates with the diversity and the prevalence of infection of hemosporidian parasites. We found that island bird populations tended to have lower neutral genetic variability, whereas MHC variability gene was similar between island and mainland populations. Similarly, island populations tended to show greater genetic differentiation than mainland populations, especially at microsatellite markers. The maintenance of MHC genetic diversity and its less marked structure in the island populations could be attributed to balancing-selection. The greater MHC differentiation among populations was negatively correlated with similarity in blood parasites (prevalence and diversity of parasite strains) between populations. Even at low prevalence and small geographical scale, haemosporidian parasites might contribute to structure the variability of immune genes among populations of hosts. PMID:25937907

  13. Fine-scale genetic structure in Pinus clausa (Pinaceae) populations: effects of disturbance history.

    Science.gov (United States)

    Parker, K C; Hamrick, J L; Parker, A J; Nason, J D

    2001-07-01

    Spatial autocorrelation analyses of 12 allozyme loci were used to compare genetic structure within populations of two varieties of Pinus clausa. P. clausa var. immuginata populations tend to be uneven-aged, with continuous recruitment in small gaps created by wind damage, whereas P. clausa var. clausa populations are more even-aged, with recruitment postdating periodic canopy fires. Three var. immuginata populations and three matched pairs of var. clausa populations, including both a mature and a nearby recently burned population, were examined. Aggregation of multilocus genotypes at small distances was evident in all young var. clausa populations. Little inbreeding was apparent among juveniles or adults in these populations; their genetic structure is likely to have resulted from limited seed dispersal. Genotypes were not significantly spatially structured in nearby matched mature populations. Genetic structure was less evident in var. immuginata populations. Aggregated genotypes were only apparent in the population where patches included juveniles of similar ages; dense juvenile clumps in the other two var. immuginata populations comprised a variety of ages. Interannual variability in allele frequencies of surviving seedlings may account for the absence of genetic structure in these populations.

  14. Modeling of genetic algorithms with a finite population

    NARCIS (Netherlands)

    Kemenade, C.H.M. van

    1997-01-01

    Cross-competition between non-overlapping building blocks can strongly influence the performance of evolutionary algorithms. The choice of the selection scheme can have a strong influence on the performance of a genetic algorithm. This paper describes a number of different genetic algorithms, all in

  15. Optimization of genomic selection training populations with a genetic algorithm

    Science.gov (United States)

    In this article, we derive a computationally efficient statistic to measure the reliability of estimates of genetic breeding values for a fixed set of genotypes based on a given training set of genotypes and phenotypes. We adopt a genetic algorithm scheme to find a training set of certain size from ...

  16. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Directory of Open Access Journals (Sweden)

    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  17. Morphological, physiological, and genetic variation between metallicolous and nonmetallicolous populations of Dianthus carthusianorum.

    Science.gov (United States)

    Wójcik, Małgorzata; Dresler, Sławomir; Jawor, Emilia; Kowalczyk, Krzysztof; Tukiendorf, Anna

    2013-01-01

    Waste deposits produced by metal mining and smelting activities provide extremely difficult habitats for plant colonization and growth. Therefore, plants spontaneously colonizing such areas represent a very interesting system for studying evolution of plant adaptation and population differentiation between contaminated and noncontaminated environments. In this study, two populations of Dianthus carthusianorum, one originating from Zn-Pb waste deposit (a metallicolous population, M) and the other from unpolluted soil (a nonmetallicolous population, NM), were analyzed in respect of their morphological and physiological traits as well as genetic markers. It was found that the plants inhabiting the waste heap differed significantly from the NM plants in terms of leaf size and shape, and these differences were persistent between the first generation of the plants of both populations cultivated under uniform, controlled laboratory conditions. In contrast with the evident morphological differences, no significant differentiation between the populations regarding the physiological traits measured (accumulation of proline, anthocyanins, chlorophyll, carotenoids) was found. These traits can be regarded as neither population specific nor stress markers. The genetic variability was analyzed using 17 random amplified polymorphic DNA (RAPD) and four inter simple sequence repeat (ISSR) markers; this proved that the differentiation between the M and NM populations exists also at the genetic level. Analysis of molecular variance (AMOVA) showed that 24% of the total genetic diversity resided among populations, while 76% - within the populations. However, no significant differences in intrapopulation genetic diversity (Hj) between the M and NM populations of D. carthusianorum was found, which contradicts the theory that acquisition of adaptation mechanisms to adverse, isolated growth habitats is related to reduction in genetic diversity. Distinct genetic differences between the two

  18. Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae: effects of reproductive strategy.

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    Ting Wang

    Full Text Available BACKGROUND: Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation. METHODOLOGY/PRINCIPAL FINDINGS: Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations. CONCLUSIONS/SIGNIFICANCE: Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

  19. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    Science.gov (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pKenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya.

  20. Genetic structure analysis of Eufriesea violacea (Hymenoptera, Apidae populations from southern Brazilian Atlantic rainforest remnants

    Directory of Open Access Journals (Sweden)

    Silvia H. Sofia

    2005-09-01

    Full Text Available Random amplified polymorphic DNA (RAPD markers were used to analyze the genetic structure of Eufriesea violacea populations in three fragments (85.47, 832.58 and 2800 ha of Atlantic rainforest located in the north of the Brazilian state of Paraná. A total of twelve primers produced 206 loci, of which 129 were polymorphic (95% criterion. The proportions of polymorphic loci in each population ranged from 57.28% to 59.2%, revealing very similar levels of genetic variability in the groups of bees from each fragment. Unbiased genetic distances between groups ranged from 0.0171 to 0.0284, the smallest genetic distance occurring between bees from the two larger fragments. These results suggest that the E. violacea populations from the three fragments have maintained themselves genetically similar to native populations of this species originally present in northern Paraná.

  1. An investigation of the statistical power of neutrality tests based on comparative and population genetic data

    DEFF Research Database (Denmark)

    Zhai, Weiwei; Nielsen, Rasmus; Slatkin, Montgomery

    2009-01-01

    In this report, we investigate the statistical power of several tests of selective neutrality based on patterns of genetic diversity within and between species. The goal is to compare tests based solely on population genetic data with tests using comparative data or a combination of comparative...... and population genetic data. We show that in the presence of repeated selective sweeps on relatively neutral background, tests based on the d(N)/d(S) ratios in comparative data almost always have more power to detect selection than tests based on population genetic data, even if the overall level of divergence...... selection. The Hudson-Kreitman-Aguadé test is the most powerful test for detecting positive selection among the population genetic tests investigated, whereas McDonald-Kreitman test typically has more power to detect negative selection. We discuss our findings in the light of the discordant results obtained...

  2. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach

    Directory of Open Access Journals (Sweden)

    Amr T. M. Saeb

    2016-01-01

    Full Text Available Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

  3. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation.

    Science.gov (United States)

    Singh, Pradeep; Nag, Akshay; Parmar, Rajni; Ghosh, Sneha; Bhau, Brijmohan Singh; Sharma, Ram Kumar

    2015-12-01

    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. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  4. 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. PMID:28239386

  5. Genetic Instability in Gastric Epithelial Neoplasias Categorized by the Revised Vienna Classification

    Science.gov (United States)

    Chung, Woo Chul; Jung, Sung Hoon; Lee, Kang Moon; Paik, Chang Nyol; Kwak, Jae Wuk; Jung, Ji Han; Yoo, Jin Young; Lee, Min Kyoung

    2010-01-01

    Background/Aims The aim of this study was to determine the structural chromosomal aberrations, such as loss of heterozygosity (LOH) and microsatellite instability (MSI), at multiple tumor suppressor gene loci in gastric epithelial neoplasia categorized by the revised Vienna classification. Methods All tissue samples were excised by endoscopic mucosal resection. Sixty category 3 (low-grade adenoma) tissue samples and 51 category 4 samples (high-grade adenoma and intramucosal carcinoma with adenoma) were examined at the 7 sets of microsatellite loci linked to the tumor suppressor gene locus. Results For category 3 and 4 tissue samples, there were no differences in the frequencies of LOH-positive chromosomes or the extent of chromosomal loss. The Helicobacter-pylori (H. pylori)-positive rate was significantly higher in MSI-positive category 4 samples than in category 3 samples (p=0.04). The frequency of MSI positivity was significantly higher in category 4 samples than in category 3 samples (p=0.003). Conclusions H. pylori infection is associated with genetic instability of the premalignant lesion. MSI occurs in the early stages of gastric carcinogenesis and its occurrence increases during malignant transformation. Detection of MSI in premalignant gastric lesions may be a surveillant of risk of malignant transformation. PMID:20559519

  6. A risk-based classification scheme for genetically modified foods. II: Graded testing.

    Science.gov (United States)

    Chao, Eunice; Krewski, Daniel

    2008-12-01

    This paper presents a graded approach to the testing of crop-derived genetically modified (GM) foods based on concern levels in a proposed risk-based classification scheme (RBCS) and currently available testing methods. A graded approach offers the potential for more efficient use of testing resources by focusing less on lower concern GM foods, and more on higher concern foods. In this proposed approach to graded testing, products that are classified as Level I would have met baseline testing requirements that are comparable to what is widely applied to premarket assessment of GM foods at present. In most cases, Level I products would require no further testing, or very limited confirmatory analyses. For products classified as Level II or higher, additional testing would be required, depending on the type of the substance, prior dietary history, estimated exposure level, prior knowledge of toxicity of the substance, and the nature of the concern related to unintended changes in the modified food. Level III testing applies only to the assessment of toxic and antinutritional effects from intended changes and is tailored to the nature of the substance in question. Since appropriate test methods are not currently available for all effects of concern, future research to strengthen the testing of GM foods is discussed.

  7. A Population Classification Evolution Algorithm for the Parameter Extraction of Solar Cell Models

    Directory of Open Access Journals (Sweden)

    Yiqun Zhang

    2016-01-01

    Full Text Available To quickly and precisely extract the parameters for solar cell models, inspired by simplified bird mating optimizer (SBMO, a new optimization technology referred to as population classification evolution (PCE is proposed. PCE divides the population into two groups, elite and ordinary, to reach a better compromise between exploitation and exploration. For the evolution of elite individuals, we adopt the idea of parthenogenesis in nature to afford a fast exploitation. For the evolution of ordinary individuals, we adopt an effective differential evolution strategy and a random movement of small probability is added to strengthen the ability to jump out of a local optimum, which affords a fast exploration. The proposed PCE is first estimated on 13 classic benchmark functions. The experimental results demonstrate that PCE yields the best results on 11 functions by comparing it with six evolutional algorithms. Then, PCE is applied to extract the parameters for solar cell models, that is, the single diode and the double diode. The experimental analyses demonstrate that the proposed PCE is superior when comparing it with other optimization algorithms for parameter identification. Moreover, PCE is tested using three different sources of data with good accuracy.

  8. The population genetic structure of vectors and our understanding of disease epidemiology

    Directory of Open Access Journals (Sweden)

    McCoy K.D.

    2008-09-01

    Full Text Available Understanding and predicting disease epidemiology relies on clear knowledge about the basic biology of the organisms involved. Despite the key role that arthropod vectors play in disease dynamics and detailed mechanistic work on the vectorpathogen interface, little information is often available about how these populations function under natural conditions. Population genetic studies can help fill this void by providing information about the taxonomic status of species, the spatial limits of populations, and the nature of gene flow among populations. Here, I briefly review different types of population genetic structure and some recent examples of where this information has provided key elements for understanding pathogen transmission in tick-borne systems.

  9. Analysis of genetic distribution and population genetic structure of the MyoD gene in 10 pig breeds

    Institute of Scientific and Technical Information of China (English)

    Li ZHU; Xuewei LI; Surong SHUAI; Mingzhou LI; Fangqiong LI; Lei CHEN

    2008-01-01

    Restriction fragment length polymorphism (RFLP) data was applied to analyze the distribution of the MyoD gene in 10 pig breeds and pig breed crosses.The population genetic information about genetic distribution,variation,and heterozygosity of the MyoD gene in different breed populations were analyzed.Based on the allele frequency,genetic distance and evolution distance among each breed populations were calculated and Unweighted Pair Group Method with Arithmetic mean (UPGMA) phylogenetic tree was gained based on the evolution distances between populations.The results indicated that the distribution of the MyoD genotype kept in Hardy-Weinberg equilibrium in most tested groups but not in Duroc (D) and Duroc × (Landrance × Yorkshire)(DLY) population.Generally,the genetic diversity of the MyoD gene was abundant and these tested breed populations had high genetic variations.The evolution of the MyoD gene was under natural selection pressure.On the phylogenetic tree,10 pig breeds were divided into 4 clusters.The first cluster consisted of four breeds developed from Landrace.The second cluster was two indigenous Chinese pig breeds.The third cluster was three breeds developed from Duroc.The fourth cluster was a Tibetan pig breed.The constitution of the topology of the phylogenetic tree was consistent with the breeding history of each pig breed.From this experiment,we can conclude that some RFLP data obtained from functional gene can be used in the genetic deviation research between some closely related species or between different populations in certain species.

  10. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.

  11. Population genetics of the understory fishtail palm Chamaedorea ernesti-augusti in Belize: high genetic connectivity with local differentiation

    Directory of Open Access Journals (Sweden)

    Thomas Meredith M

    2009-10-01

    Full Text Available Abstract Background Developing a greater understanding of population genetic structure in lowland tropical plant species is highly relevant to our knowledge of increasingly fragmented forests and to the conservation of threatened species. Specific studies are particularly needed for taxa whose population dynamics are further impacted by human harvesting practices. One such case is the fishtail or xaté palm (Chamaedorea ernesti-augusti of Central America, whose wild-collected leaves are becoming progressively more important to the global ornamental industry. We use microsatellite markers to describe the population genetics of this species in Belize and test the effects of climate change and deforestation on its recent and historical effective population size. Results We found high levels of inbreeding coupled with moderate or high allelic diversity within populations. Overall high gene flow was observed, with a north and south gradient and ongoing differentiation at smaller spatial scales. Immigration rates among populations were more difficult to discern, with minimal evidence for isolation by distance. We infer a tenfold reduction in effective population size ca. 10,000 years ago, but fail to detect changes attributable to Mayan or contemporary deforestation. Conclusion Populations of C. ernesti-augusti are genetically heterogeneous demes at a local spatial scale, but are widely connected at a regional level in Belize. We suggest that the inferred patterns in population genetic structure are the result of the colonization of this species into Belize following expansion of humid forests in combination with demographic and mating patterns. Within populations, we hypothesize that low aggregated population density over large areas, short distance pollen dispersal via thrips, low adult survival, and low fruiting combined with early flowering may contribute towards local inbreeding via genetic drift. Relatively high levels of regional connectivity

  12. Genetic variation in native and introduced populations of Taeniatherum caput-medusae (Poaceae)

    Science.gov (United States)

    Genetic analysis of both native and introduced populations of invasive species can be used to examine population origins and spread. Accurate delineation of an invasive species’ source populations can contribute to the search for specific and effective biological control agents. Medusahead, Taenia...

  13. Genetic variation and differentiation in parent-descendant cattle and bison populations

    Science.gov (United States)

    Genetic variation and differentiation at 32 microsatellite DNA loci is quantified for parent-descendant cattle populations and parent-descendant bison (Bison bison) populations. Heterozygosity (Ho) and numbers of alleles/locus (AR) are less in the Line 1 Hereford inbred cattle population than in t...

  14. Business Analysis and Decision Making Through Unsupervised Classification of Mixed Data Type of Attributes Through Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Rohit Rastogi

    2014-01-01

    Full Text Available Grouping or unsupervised classification has variety of demands in which the major one is the capability of the chosen clustering approach to deal with scalability and to handle the mixed variety of data set. There are variety of data sets like categorical/nominal, ordinal, binary (symmetric or asymmetric, ratio and interval scaled variables. In the present scenario, latest approaches of unsupervised classification are Swarm Optimization based, Customer Segmentation based, Soft Computing methods like Fuzzy Based and GA based, Entropy Based methods and hierarchical approaches. These approaches have two serious bottlenecks…Either they are hybrid mathematical techniques or large computation demanding which increases their complexity and hence compromises with accuracy. It is very easy to compare and analyze that unsupervised classification by Genetic Algorithm is feasible, suitable and efficient for high-dimensional data sets with mixed data values that are obtained from real life results, events and happenings.

  15. Molecular insights of genetic variation in Erianthus arundinaceus populations native to China.

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    Jianbo Zhang

    Full Text Available BACKGROUND: E. arundinaceus (Retz. Jeswiet is a warm-season, tall-growing perennial species native to much southern portion in China. The grass has been extensively used in sugarcane breeding and is recently targeted as a bioenergy feedstock crop. However, information on the genetic structure of the Chinese wild germplasm is limited. Knowledge of genetic variation within and among populations is essential for breeding new cultivars in the species. The major objective of this study was to quantify the magnitude of genetic variation among and within natural populations in China. METHODOLOGY/PRINCIPAL FINDINGS: In this experiment, we analyzed genetic variation of 164 individuals of 18 populations collected from natural habitats in six Chinese provinces using 20 sequence-related amplified polymorphism (SRAP primer pairs generating 277 polymorphic bands. Among and within the populations, the percentage of polymorphic bands (PPB was 80.00% and 27.07%, genetic diversity (HE was 0.245 and 0.099, effective number of alleles (NE was 1.350 and 1.170, and Shannon's information index (I was 0.340 and 0.147, respectively. The populations were clustered into six groups exhibiting a high level of genetic differentiation, which was highly associated with geographic origins of respective germplasm populations, but was not significantly associated with geographic distances between the populations. CONCLUSIONS/SIGNIFICANCE: This is the first report indicating that large genetic variation exists in the Chinese E. arundinaceus germplasm based on the SRAP molecular marker analysis of native populations. The genetic structure of populations in the species has been substantially affected by geographic landforms and environments. The diverse collection will be highly valuable in genetic improvement in the species per se and likely in sugarcane.

  16. Genetic Polymorphisms of Nine X-STR Loci in Four Population Groups from Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Qiao-Fang Hou; Bin Yu; Sheng-Bin Li

    2007-01-01

    Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance betweent Mongol and Han (Xi'an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.

  17. Low levels of genetic divergence across geographically and linguistically diverse populations from India.

    Directory of Open Access Journals (Sweden)

    Noah A Rosenberg

    2006-12-01

    Full Text Available Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States-sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans than might be expected for such a geographically and linguistically diverse subset of the human population.

  18. Low levels of genetic divergence across geographically and linguistically diverse populations from India.

    Science.gov (United States)

    Rosenberg, Noah A; Mahajan, Saurabh; Gonzalez-Quevedo, Catalina; Blum, Michael G B; Nino-Rosales, Laura; Ninis, Vasiliki; Das, Parimal; Hegde, Madhuri; Molinari, Laura; Zapata, Gladys; Weber, James L; Belmont, John W; Patel, Pragna I

    2006-12-01

    Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States-sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.

  19. Genetic variation of 15 autosomal microsatellite loci in a Nayarit population (Mexico).

    Science.gov (United States)

    Alvarez-Cubero, M J; Martinez-Gonzalez, L J; Virgen-Ponce, D; Delgado-Najar, E A; Moscoso-Caloca, G H; Alvarez, J C; Lorente, J A

    2011-11-01

    Fifteen STRs are studied to determine the allele frequencies' distribution and to evaluate the homogeneity of Nayarit populations. This study allows the identification of forensic efficiency parameters to be used in forensic genetics and to explore the genetic similarities between Nayarit and the neighboring countries such as Mexico, Brazil, Puerto Rico, Guatemala, Honduras, Bolivia and Costa Rica. The Hardy-Weinberg equilibrium, expected heterozygosity, matching probability, and power of discrimination, were calculated in the Nayarit population. We found that with respect to the studied markers, Nayarit genetic structure is homogeneous. In this study, it is established that Nayarit is genetically similar to the South American Mestizo population. The distribution of a set of these 15 STRs was analyzed with other South American populations as well as in the extensive set of neighboring populations from the literature (USA, Europe and Africa). We found significant differences exist between the isolated populations (Huastecos, Otomi from Sierra Madre and from Ixmiquilpan Valley) and Mestizo populations. Statistical analysis supports that Americans actual inhabitants and Europeans are genetically similar, while Africans and isolated populations from South America have more genetic differences.

  20. Conservation genetics of American crocodile, Crocodylus acutus, populations in Pacific Costa Rica

    Science.gov (United States)

    Mauger, Laurie A.; Velez, Elizabeth; Cherkiss, Michael S.; Brien, Matthew L.; Mazzotti, Frank J.; Spotila, James R.

    2017-01-01

    Maintaining genetic diversity is crucial for the survival and management of threatened and endangered species. In this study, we analyzed genetic diversity and population genetic structure at neutral loci in American crocodiles, Crocodylus acutus, from several areas (Parque Nacional Marino Las Baulas, Parque Nacional Santa Rosa, Parque Nacional Palo Verde, Rio Tarcoles, and Osa Conservation Area) in Pacific Costa Rica. We genotyped 184 individuals at nine microsatellite loci to describe the genetic diversity and conservation genetics between and among populations. No population was at Hardy-Weinberg Equilibrium (HWE) over all loci tested and a small to moderate amount of inbreeding was present. Populations along the Pacific coast had an average heterozygosity of 0.572 across all loci. All populations were significantly differentiated from each other with both FST and RST measures of population differentiation with a greater degree of molecular variance (81%) found within populations. Our results suggest C. acutus populations in Pacific Costa Rica were not panmictic with moderate levels of genetic diversity. An effective management plan that maintains the connectivity between clusters is critical to the success of C. acutus in Pacific Costa Rica.

  1. Dental functional status in a southern vietnamese adult population-a combined quantitative and qualitative classification system analysis

    NARCIS (Netherlands)

    Nguyen, T.C.; Witter, D.J.; Bronkhorst, E.M.; Pham, L.H.; Creugers, N.H.J.

    2011-01-01

    PURPOSE: The aim of this study was to explore the dental functional status of a Southern Vietnamese adult population using a new quantitative- and qualitative-based classification system. MATERIALS AND METHODS: The sample consisted of 2,809 dentate subjects aged =/> 20 years from urban and rural

  2. Interobserver Agreement of the Gross Motor Function Classification System in an Ambulant Population of Children with Cerebral Palsy

    Science.gov (United States)

    McDowell, Brona C.; Kerr, Claire; Parkes, Jackie

    2007-01-01

    Gross Motor Function Classification System (GMFCS) level was reported by three independent assessors in a population of children with cerebral palsy (CP) aged between 4 and 18 years (n=184; 112 males, 72 females; mean age 10y 10mo [SD 3y 7mo]). A software algorithm also provided a computed GMFCS level from a regional CP registry. Participants had…

  3. Genetic variability and relationships for populations of Cerastoderma edule and of the C. Glaucum complex

    Science.gov (United States)

    Hummel, H.; Wolowicz, M.; Bogaards, R. H.

    Genetic variability and relationships of populations of the cockles Cerastoderma edule and of the C. glaucum complex in Europe were determined by means of isoenzyme electrophoresis. Distinct isoenzyme markers allowed a clear distinction between these two taxa. C edule showed a higher genetic intra-population variability than the other cockle species. The imbalance of the genotypes within popuulation and the inter-population differentiation of the C. glaucum complex are stronger than in C. edule. The genetic variability is related to the different habitats of the species, the members of the C. glaucum complex living in more isolated areas and having more limited gene flow.

  4. Preliminary Report on Seaside Sparrow Population Genetics Project

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a preliminary report on a genetic variation study that was conducted at St. Vincent National Wildlife Refuge. Blood samples were taken from 57 Seaside...

  5. A Hybrid Machine Learning Method for Fusing fMRI and Genetic Data: Combining both Improves Classification of Schizophrenia

    Directory of Open Access Journals (Sweden)

    Honghui Yang

    2010-10-01

    Full Text Available We demonstrate a hybrid machine learning method to classify schizophrenia patients and healthy controls, using functional magnetic resonance imaging (fMRI and single nucleotide polymorphism (SNP data. The method consists of four stages: (1 SNPs with the most discriminating information between the healthy controls and schizophrenia patients are selected to construct a support vector machine ensemble (SNP-SVME. (2 Voxels in the fMRI map contributing to classification are selected to build another SVME (Voxel-SVME. (3 Components of fMRI activation obtained with independent component analysis (ICA are used to construct a single SVM classifier (ICA-SVMC. (4 The above three models are combined into a single module using a majority voting approach to make a final decision (Combined SNP-fMRI. The method was evaluated by a fully-validated leave-one-out method using 40 subjects (20 patients and 20 controls. The classification accuracy was: 0.74 for SNP-SVME, 0.82 for Voxel-SVME, 0.83 for ICA-SVMC, and 0.87 for Combined SNP-fMRI. Experimental results show that better classification accuracy was achieved by combining genetic and fMRI data than using either alone, indicating that genetic and brain function representing different, but partially complementary aspects, of schizophrenia etiopathology. This study suggests an effective way to reassess biological classification of individuals with schizophrenia, which is also potentially useful for identifying diagnostically important markers for the disorder.

  6. Facial asymmetry and genetic ancestry in Latin American admixed populations

    OpenAIRE

    Quinto Sanchez, Mirsha; Adhikari, Kaustubh; Acunã Alonzo, Víctor; Cintas, Célia; de Cerqueira, Caio Cesar Silva; Ramallo, Virgínia; Castillo, Lucia; Farrera, Alodi; Jaramillo, Claudia; Arias, Williams; Fuentes, Macarena; Everardo, Paola; Avila, Francisco de; Jorge A. Gómez Valdés; Hunemeier, Tábita

    2015-01-01

    Fluctuating and directional asymmetry are aspects of morphological variation widely used to infer environmental and genetic factors affecting facial phenotypes. However, the genetic basis and environmental determinants of both asymmetry types is far from being completely known. The analysis of facial asymmetries in admixed individuais can be of help to characterize the impact of a genome's heterozygosity on the deveiopmental basis of both fl.uctuating and directional asymmetries. Here we char...

  7. Colonization and persistence of urban ant populations as revealed by joint estimation of kinship and population genetic parameters.

    Science.gov (United States)

    Yamamoto, Junpei; Uchida, Kei; Takami, Yasuoki

    2013-01-01

    The decrease in biodiversity due to increasing urbanization has been well documented, but the processes of colonization and maintenance of wildlife populations in urban areas remain poorly understood. We address this issue using 462 individuals from 10 urban populations of the ant Formica japonica in Kobe City, Japan. We sampled workers regardless of colony identity, genotyped them using 6 microsatellite loci, and estimated allele frequencies and genotypes of reproductive individuals, together with other population genetic parameters, by estimating kinship structure using a likelihood method. Estimated genetic diversity and effective size of populations were not associated with environmental parameters, suggesting that populations are unaffected by urbanization. However, effective population sizes were small, and frequent population bottlenecks were detected. These results suggest that urban F. japonica populations are unstable, and the possibility of frequent extinctions and recolonizations in urban habitats. Populations were moderately differentiated without isolation by distance, suggesting a strong dispersal ability that enables colonization of urban habitats. Dispersal was male biased. Collectively, F. japonica was regarded as an urban adapter, which can colonize urban habitats by virtue of its preference for open ground and high dispersal ability but can persist in urban populations for only a short time, showing a tendency as a temporary urban inhabitant.

  8. Genetic Variation among 11 Abies concolor Populations Based on Allozyme Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhang Jin-feng; Li Hui; Dong Jian-sheng; Wang Jun-hui

    2005-01-01

    In order to obtain information on the genetic structure of Abies concolor and the genetic variation among 11 populations introduced from America to China, allozyme analysis based on starch gel electrophoresis technology was used. 24 loci of 10allozyme systems were mensurated, and the genetic structure and genetic diversity of the 11 populations of A. concolor evaluated.The results show that the genetic variation among is significant, and the genetic variation within A. concolor populations is more important. In contrast with other conifers, the variation of A. concolor is above the average level of conifers, and higher than the same level ofAbies. The percentage of polymorphic loci (P) was 62.5%, the number of alleles per locus (A) 2.08, the number of effective alleles per locus (Ae) was 1.37, the expected heterozygosity (H) 0.204, and the Shannon information index (I) 0.351 7. There is a short genetic distance (D=0.061) and a low gene flow (Nm=0.839 4) among the 11 introduced populations of A. concolor with high genetic variation. The genetic differentiation coefficient (Gst) was 0.229 5, which is higher than that of the mean in Abies or Pinus.

  9. Allozyme Genetic Diversity and Conservation Strategy of Ten Natural Populations of Pinus bungeana Zuuc. ex Endl

    Institute of Scientific and Technical Information of China (English)

    Li Bin; Gu Wanchun; Chen Xiaoyang

    2003-01-01

    Pinus bungeana is a three-needle pine with typical fragmented distribution in central and northwestern China. Its natural resources are gradually decreasing and need to be conserved. For conserving genetic diversity of P. bungeana, the authors sampled 10 natural populations in its distribution areas and conducted the analysis of isozymes. Thirty one loci with 53 alleles on the basis of 16 enzyme systems were assayed. The parameters of genetic diversity at species and population level are respectively as follows: As= 1.742, Ae[s] = 1.49, Ps= 54.8%, He[s] = 0.162, Ap= 1.39, Ae[p]= 1.30, Pp= 34.85, He[p] = 0.0986. In comparison with other pines, P. bungeana possesses a slightly low amount of genetic variation especially at the population level. By contrast, the level of population genetic differentiation (GST = 0.135) is higher compared to other pines. All ten populations are divided into three groups according to Nei's genetic identity (I). There is a slight relation (r = 0.31) between genetic distance and geographical distance.Some populations are obviously deviate from Hardy-Weinberg equilibrium but the total population is basically accordant with Hardy-Weinberg equilibrium. The correlation analysis between allele frequencies and ecological factors showed that the alleles at loci of Idh and Pgi-2 had gradient variation trends of their frequencies. The sample capturing curves' analysis indicated that the captured alleles increased when the number of sampled populations increased and 99% out of whole allele pool of ten populations would be captured when five populations were randomly selected. At last,. the population genetic structure of P. bungeana and its conservation strategy were discussed.

  10. Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution.

    Directory of Open Access Journals (Sweden)

    Yoshi Kawamoto

    Full Text Available Bonobos (Pan paniscus inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species' range. In 136 effective samples from different individuals (range: 7-37 per population, we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D, which included a newly identified clade (D. MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.

  11. [Genetic effects in populations of plants growing in the zone of Kyshtym and Chernobyl accidents].

    Science.gov (United States)

    Shevchenko, V A; Kal'chenko, V A; Abramov, V I; Rubanovich, A V; Shevchenko, V V; Grinikh, L I

    1999-01-01

    Studies to analyze the genetic processes in natural populations of plants were started on the territory of the East-Ural Radioactive Trace (EURT) in 1962 and in the zone of the Chernobyl accident in May 1986. The main directions of the genetic studies in both radioactive areas were similar: 1) study of the mutation process intensity depending on the dose and dose rate and analysis of dose-effect relationships for different genetic changes (point mutations, chromosome aberrations in mitosis and meiosis) in irradiated plant populations; 2) study of the mutation process dynamics in generations of chronically (prolongly) irradiated populations of plants; 3) analysis of microevolutionary processes in irradiated plant populations. The report presents an analysis of observed dose-effect relationships under the action of radiation on populations of Arabidopsis thaliana, Pinus sylvestris and a number of other plant species. Analysis of the mutation processes dynamics in 8 Arabidopsis populations growing in the zone of the Chernobyl catastrophe has demonstrated that the level of the embryo lethal mutations 10 years after the accident in the irradiated populations significantly exceeds the control level. The following phenomena observed in chronically irradiated populations have also been considered: increased radioresistance of irradiated populations (radioadaptation), the appearance of abnormal karyotypes and selective markers upon chronic irradiation. The authors call attention to the high importance of monitoring of genetic processes in irradiated plant populations for understanding of the action of radiation on human populations.

  12. Individual organisms as units of analysis: Bayesian-clustering alternatives in population genetics.

    Science.gov (United States)

    Mank, Judith E; Avise, John C

    2004-12-01

    Population genetic analyses traditionally focus on the frequencies of alleles or genotypes in 'populations' that are delimited a priori. However, there are potential drawbacks of amalgamating genetic data into such composite attributes of assemblages of specimens: genetic information on individual specimens is lost or submerged as an inherent part of the analysis. A potential also exists for circular reasoning when a population's initial identification and subsequent genetic characterization are coupled. In principle, these problems are circumvented by some newer methods of population identification and individual assignment based on statistical clustering of specimen genotypes. Here we evaluate a recent method in this genre--Bayesian clustering--using four genotypic data sets involving different types of molecular markers in non-model organisms from nature. As expected, measures of population genetic structure (F(ST) and phiST) tended to be significantly greater in Bayesian a posteriori data treatments than in analyses where populations were delimited a priori. In the four biological contexts examined, which involved both geographic population structures and hybrid zones, Bayesian clustering was able to recover differentiated populations, and Bayesian assignments were able to identify likely population sources of specific individuals.

  13. Comparative population genetics of the German shepherd dog in South Africa

    Directory of Open Access Journals (Sweden)

    N. J. Coutts

    2010-01-01

    Full Text Available Modern breeding practices strive to achieve distinctive phenotypic uniformity in breeds of dogs, but these strategies are associated with the inevitable loss of genetic diversity. Thus, in parallel with the morphological variation displayed by breeds, purebred dogs commonly express genetic defects as a result of the inbreeding associated with artificial selection and the reduction of selection against disease phenotypes. Microsatellite marker analyses of 15 polymorphic canine loci were used to investigate measures of genetic diversity and population differentiation within and between German-bred and South African-bred German shepherd dogs. These data were quantified by comparison with typically outbred mongrel or crossbred dogs. Both the imported and locally-bred German shepherd dogs exhibited similar levels of genetic diversity. The breed is characterised by only a moderate loss of genetic diversity relative to outbred dogs, despite originating from a single founding sire and experiencing extensive levels of inbreeding throughout the history of the breed. Non-significant population differentiation between the ancestral German and derived South African populations indicates sufficient contemporary gene flow between these populations, suggesting that migration resulting from the importation of breeding stock has mitigated the effects of random genetic drift and a population bottleneck caused by the original founder event in South Africa. Significant differentiation between the combined German shepherd dog population and the outbred dogs illustrates the effects of selection and genetic drift on the breed since its establishment just over 100 years ago.

  14. Population differentiation in Pacific salmon: local adaptation, genetic drift, or the environment?

    Science.gov (United States)

    Adkison, M.D.

    1995-01-01

    Morphological, behavioral, and life-history differences between Pacific salmon (Oncorhynchus spp.) populations are commonly thought to reflect local adaptation, and it is likewise common to assume that salmon populations separated by small distances are locally adapted. Two alternatives to local adaptation exist: random genetic differentiation owing to genetic drift and founder events, and genetic homogeneity among populations, in which differences reflect differential trait expression in differing environments. Population genetics theory and simulations suggest that both alternatives are possible. With selectively neutral alleles, genetic drift can result in random differentiation despite many strays per generation. Even weak selection can prevent genetic drift in stable populations; however, founder effects can result in random differentiation despite selective pressures. Overlapping generations reduce the potential for random differentiation. Genetic homogeneity can occur despite differences in selective regimes when straying rates are high. In sum, localized differences in selection should not always result in local adaptation. Local adaptation is favored when population sizes are large and stable, selection is consistent over large areas, selective diffeentials are large, and straying rates are neither too high nor too low. Consideration of alternatives to local adaptation would improve both biological research and salmon conservation efforts.

  15. Genetic differentiation between conspecific populations of Merodon avidus A (Diptera, Syrphidae

    Directory of Open Access Journals (Sweden)

    Milankov Vesna R.

    2004-01-01

    Full Text Available Allozyme variability of populations of Merodon avidus A (M i l a n - k o v et al., 2001 from Dubašnica Mountain (Serbia, Morinj Bay (Montenegro and Pindos Mountain (Greece was analysed. The influence of gene flow on genetic differentiation among populations from the three biogeographical regions was also investigated. Genetic differentiaiton quantified by the Fst value, which is an inverse function of gene flow between populations, seemed to be correlated to both geographic and genetic distance (D, N e i, 1978, Namely in the population pairs Morinj - Dubašnica (253 km air distance, Morinj - Pindos (390km air distance genetic differentiation and genetic distance increased with the geographic distance (Fst = 0.133, D = 0.022 and Fst = 0.309, D = 0.052, respectively. The exception was the population pair Dubašnica - Pindos (500 km air distance, where a lower degree of genetic differentiation was observed (Fst = 0.266; D = 0.047 than was expected based solely on the geographic distance. Results of this study suggest that that genetic differentiation among conspecific populations depends not only on the number of migrants (i. e. gene flow, but also on different selection pressure in different habits.

  16. Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

    Directory of Open Access Journals (Sweden)

    Monika Sharma

    Full Text Available The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA. Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes. Further the nucleotide sequences (retrieved from GenBank for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia, indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

  17. ORAI1 genetic polymorphisms associated with the susceptibility of atopic dermatitis in Japanese and Taiwanese populations.

    Directory of Open Access Journals (Sweden)

    Wei-Chiao Chang

    Full Text Available Atopic dermatitis is a chronic inflammatory skin disease. Multiple genetic and environmental factors are thought to be responsible for susceptibility to AD. In this study, we collected 2,478 DNA samples including 209 AD patients and 729 control subjects from Taiwanese population and 513 AD patients and 1027 control subject from Japanese population for sequencing and genotyping ORAI1. A total of 14 genetic variants including 3 novel single-nucleotide polymorphisms (SNPs in the ORAI1 gene were identified. Our results indicated that a non-synonymous SNP (rs3741596, Ser218Gly associated with the susceptibility of AD in the Japanese population but not in the Taiwanese population. However, there is another SNP of ORAI1 (rs3741595 associated with the risk of AD in the Taiwanese population but not in the Japanese population. Taken together, our results indicated that genetic polymorphisms of ORAI1 are very likely to be involved in the susceptibility of AD.

  18. ORAI1 genetic polymorphisms associated with the susceptibility of atopic dermatitis in Japanese and Taiwanese populations.

    Science.gov (United States)

    Chang, Wei-Chiao; Lee, Chih-Hung; Hirota, Tomomitsu; Wang, Li-Fang; Doi, Satoru; Miyatake, Akihiko; Enomoto, Tadao; Tomita, Kaori; Sakashita, Masafumi; Yamada, Takechiyo; Fujieda, Shigeharu; Ebe, Koji; Saeki, Hidehisa; Takeuchi, Satoshi; Furue, Masutaka; Chen, Wei-Chiao; Chiu, Yi-Ching; Chang, Wei Pin; Hong, Chien-Hui; Hsi, Edward; Juo, Suh-Hang Hank; Yu, Hsin-Su; Nakamura, Yusuke; Tamari, Mayumi

    2012-01-01

    Atopic dermatitis is a chronic inflammatory skin disease. Multiple genetic and environmental factors are thought to be responsible for susceptibility to AD. In this study, we collected 2,478 DNA samples including 209 AD patients and 729 control subjects from Taiwanese population and 513 AD patients and 1027 control subject from Japanese population for sequencing and genotyping ORAI1. A total of 14 genetic variants including 3 novel single-nucleotide polymorphisms (SNPs) in the ORAI1 gene were identified. Our results indicated that a non-synonymous SNP (rs3741596, Ser218Gly) associated with the susceptibility of AD in the Japanese population but not in the Taiwanese population. However, there is another SNP of ORAI1 (rs3741595) associated with the risk of AD in the Taiwanese population but not in the Japanese population. Taken together, our results indicated that genetic polymorphisms of ORAI1 are very likely to be involved in the susceptibility of AD.

  19. Population isolates in South Tyrol and their value for genetic dissection of complex diseases.

    Science.gov (United States)

    Marroni, F; Pichler, I; De Grandi, A; Volpato, C Beu; Vogl, F D; Pinggera, G K; Bailey-Wilson, J E; Pramstaller, P P

    2006-11-01

    The study of genetic isolates is a promising approach for the study of complex genetic traits. The small and constant population size, lack of migration, and multiple relationships between individuals in the isolate population could reduce the genetic diversity, and lead to increased levels of linkage disequilibrium (LD). We studied the extent of LD on Xq13 in six population isolates from South Tyrol in the Eastern Italian Alps. We found different levels of LD in our study samples, probably reflecting their degrees of isolation and their demographic histories. The highest values were obtained in Val Gardena (ranking among the highest levels of LD in Europe) and in Stelvio, which qualified as a microisolate according to historical information, and biodemographic and genealogical criteria. Phylogenetic analysis revealed that the two Ladin-speaking populations are genetically distant from each other, and from their German-speaking neighbours, and are characterized by a smaller effective population size than the neighbouring valleys. These peculiar characteristics suggest that South Tyrol could be a unique resource for the study of complex diseases, showing all the characteristics of isolated populations with the advantage of including, in a fairly homogeneous environment, two genetically differentiated sub-populations. This could allow investigators to gain an insight into the contribution of genetic heterogeneity in complex diseases.

  20. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Cardoso Márcio Z

    2011-01-01

    Full Text Available Abstract Background Brazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of two Heliconius butterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on population connectivity in butterflies with home-range behavior. Results We generated microsatellite, AFLP and mtDNA sequence data for 136 Heliconius erato specimens from eight collecting locations and 146 H. melpomene specimens from seven locations. Population genetic analyses of the data revealed high levels of genetic diversity in H. erato relative to H. melpomene, widespread genetic differentiation among populations of both species, and no evidence for isolation-by-distance. Conclusions These results are consistent with the hypothesis that the extensive habitat fragmentation along Brazil's Atlantic Forest has reduced dispersal of Heliconius butterflies among neighboring habitat patches. The results also lend support to the observation that fine-scale population genetic structure may be common in Heliconius. If such population structure also exists independent of human activity, and has been common over the evolutionary history of Heliconius butterflies, it may have contributed to the evolution of wing pattern diversity in the genus.

  1. Canine Cutaneous Leishmaniasis: Dissemination and Tissue Tropism of Genetically Distinct Leishmania (Viannia braziliensis Populations

    Directory of Open Access Journals (Sweden)

    Guilherme Marx de Oliveira

    2013-01-01

    Full Text Available Little is known regarding the internal dissemination of initial cutaneous lesions and tissue tropism of Leishmania (Viannia braziliensis populations in naturally infected dogs. The aim of this study was to investigate genetic polymorphisms of L. (V. braziliensis populations in different anatomic sites of naturally infected dogs by using polymerase chain reaction (PCR and low-stringency single specific primer-PCR (LSSP-PCR techniques. The amplified products were analyzed by LSSP-PCR to investigate the genetic variability of the parasite populations present in different anatomical sites. Twenty-three out of the 52 samples gave PCR-positive results. The existence of L. (V. braziliensis strains that remained restricted to cutaneous lesions and others showing characteristics of dissemination to internal organs and healthy skin was observed. LSSP-PCR and numerical analyses revealed that parasite populations that do not disseminate were genetically similar and belonged to a separate phenetic cluster. In contrast, populations that showed spreading to internal organs displayed a more polymorphic genetic profile. Despite the heterogeneity, L. (V. braziliensis populations with identical genetic profiles were observed in popliteal and cervical lymph nodes of the same animal. Our results indicate that infection in dogs can be manifested by dissemination and tissue tropism of genetically distinct populations of L. (V. braziliensis.

  2. Population genetic structure of moose (Alces Alces) of South-central Alaska.

    Science.gov (United States)

    Wilson, Robert E.; McDonough, John T.; Barboza, Perry S.; Talbot, Sandra L.; Farley, Sean D.

    2015-01-01

    The location of a population can influence its genetic structure and diversity by impacting the degree of isolation and connectivity to other populations. Populations at range margins areoften thought to have less genetic variation and increased genetic structure, and a reduction in genetic diversity can have negative impacts on the health of a population. We explored the genetic diversity and connectivity between 3 peripheral populations of moose (Alces alces) with differing potential for connectivity to other areas within interior Alaska. Populations on the Kenai Peninsula and from the Anchorage region were found to be significantly differentiated (FST= 0.071, P < 0.0001) with lower levels of genetic diversity observed within the Kenai population. Bayesian analyses employing assignment methodologies uncovered little evidence of contemporary gene flow between Anchorage and Kenai, suggesting regional isolation. Although gene flow outside the peninsula is restricted, high levels of gene flow were detected within the Kenai that is explained by male-biased dispersal. Furthermore, gene flow estimates differed across time scales on the Kenai Peninsula which may have been influenced by demographic fluctuations correlated, at least in part, with habitat change.

  3. Genetic diversity of high-elevation populations of an endangered medicinal plant.

    Science.gov (United States)

    Nag, Akshay; Ahuja, Paramvir Singh; Sharma, Ram Kumar

    2014-11-21

    Intraspecific genetic variation in natural populations governs their potential to overcome challenging ecological and environmental conditions. In addition, knowledge of this variation is critical for the conservation and management of endangered plant taxa. Found in the Himalayas, Podophyllum hexandrum is an endangered high-elevation plant species that has great medicinal importance. Here we report on the genetic diversity analysis of 24 P. hexandrum populations (209 individuals), representing the whole of the Indian Himalayas. In the present study, seven amplified fragment length polymorphism (AFLP) primer pairs generated 1677 fragments, of which 866 were found to be polymorphic. Neighbour joining clustering, principal coordinate analysis and STRUCTURE analysis clustered 209 individuals from 24 populations of the Indian Himalayan mountains into two major groups with a significant amount of gene flow (Nm = 2.13) and moderate genetic differentiation Fst(0.196), G'st(0.20). This suggests that, regardless of geographical location, all of the populations from the Indian Himalayas are intermixed and are composed broadly of two types of genetic populations. High variance partitioned within populations (80 %) suggests that most of the diversity is restricted to the within-population level. These results suggest two possibilities about the ancient population structure of P. hexandrum: either all of the populations in the geographical region of the Indian Himalayas are remnants of a once-widespread ancient population, or they originated from two types of genetic populations, which coexisted a long time ago, but subsequently separated as a result of long-distance dispersal and natural selection. High variance partitioned within the populations indicates that these populations have evolved in response to their respective environments over time, but low levels of heterozygosity suggest the presence of historical population bottlenecks.

  4. Genetic diversity of alfalfa domesticated varietal populations from Libyan genbank revealed by RAPD markers

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    Ahsyee Salem R.

    2013-01-01

    Full Text Available Alfalfa (Medicago sativa L. is an important forage legume in Libya. The genetic diversity of nine alfalfa domesticated varietal populations was studied using thirteen RAPD primer combinations. The number of polymorphic fragments detected per primer combination ranged from 8 to 46 bands with an average of 24 bands. The number of polymorphic bands detected was from 6 (Atalia population to 37 (Gabsia population. The lowest genetic distance was 0.058 and the highest was 0.655. The average genetic distance was (0.356. The dendrogram based on Ward’s minimum variance clustering method grouped the nine populations into the two main clusters. The first group included Fazania, Atalia, Masratia, Zawia, Denamo Ferade and Arezona. The second group was composed of Tagoria, Gabsia and Wade Alrabeh. The simplicity of RAPD assays for detection of genetic polymorphisms is confirmed in our study, and results can be utilized in breeding practice.

  5. Population genetics provides an efficient tool to quantify fragmentation impact in forest ecosystems

    Directory of Open Access Journals (Sweden)

    2005-01-01

    Full Text Available A method in population genetics (Dutech et al., Am. J. Bot. 92 (2, 252-261, February 2005 is described and discussed as an interesting tool for investigating the effects of fragmentation in forest ecosystems.

  6. Genetic diversity in populations of Acrocomia aculeata (Arecaceae) in the northern region of Minas Gerais, Brazil.

    Science.gov (United States)

    Oliveira, D A; Melo Júnior, A F; Brandão, M M; Rodrigues, L A; Menezes, E V; Ferreira, P R B

    2012-03-08

    Macaúba (Acrocomia aculeata) is a palm of economic importance, widely distributed in natural forests from Mexico to Uruguay. We analyzed the genetic diversity of populations of macaúba (A. aculeata) in the northern region of the State of Minas Gerais, Brazil. Young leaves from 10 macaúba individuals encompassing 49 genotypes of macaúba were collected from Montes Claros, Itacambira, Brasília de Minas, Mirabela, and Grão Mogol. After extraction and amplification of samples, the amplified fragments were separated by electrophoresis. We found high levels of genetic diversity within the populations. Genetic diversity indices were high, except in the Itacambira and Mirabela populations. Results show that Mirabela and Itacambira populations can require conservation strategies because they present lower values of genetic diversity.

  7. Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

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    Toraj KHABIRI

    2013-02-01

    Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  8. Subpopulation genetic structure of a plant panmictic population of Castanea sequinii as revealed by microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    WANG Ying; KANG Ming; HUANG Hongwen

    2007-01-01

    Castanea squinii Dode,an endemic tree widely distributed in China,plays an important role both in chestnut breeding and forest ecosystem function.The spatial genetic structure within and among populations is an important part of the evolutionary and ecological genetic dynamics of natural populations,and can provide insights into effective conservation of genetic resources.In the present study,the spatial genetic structure of a panmictic natural population of C.sequinii in the Dabie Mountain region was investigated using microsatellite markers.Nine prescreened microsatellite loci generated 29-33 alleles each,and were used for spatial autocorrelation analysis.Based on Moran's I coefficient,a panmictic population of C.sequinii in the Dabie Mountain region was found to be lacking a spatial genetic structure.These results suggest that a high pollen-mediated gene flow among subpopulations counteract genetic drift and/or genetic differentiation and plays an important role in maintaining a random and panmictic population structure in C.sequinii populations.Further,a spatial genetic structure was detected in each subpopulation's scale (0.228 km),with all three subpopulations showing significant fine-scale structure.The genetic variation was found to be nonrandomly distributed within 61 m in each subpopulation (Moran's I positive values).Although Moran's I values varied among the different subpopulations,Moran's I in all the three subpopulations reached the expected values with an increase in distances,suggesting a generally patchy distribution in the subpopulations.The fine-scale structure seems to reflect restricted seed dispersal and microenvironment selection in C.sequinii.These results have important implications for understanding the evolutionary history and ecological process of the natural population of C.sequinii and provide baseline data for formulating a conservation strategy of Castanea species.

  9. Genetic diversity in introduced golden mussel populations corresponds to vector activity.

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    Sara Ghabooli

    Full Text Available We explored possible links between vector activity and genetic diversity in introduced populations of Limnoperna fortunei by characterizing the genetic structure in native and introduced ranges in Asia and South America. We surveyed 24 populations: ten in Asia and 14 in South America using the mitochondrial cytochrome c oxidase subunit I (COI gene, as well as eight polymorphic microsatellite markers. We performed population genetics and phylogenetic analyses to investigate population genetic structure across native and introduced regions. Introduced populations in Asia exhibit higher genetic diversity (H(E = 0.667-0.746 than those in South America (H(E =  0.519-0.575, suggesting higher introduction effort for the former populations. We observed pronounced geographical structuring in introduced regions, as indicated by both mitochondrial and nuclear markers based on multiple genetic analyses including pairwise Ф(ST, F(ST, bayesian clustering method, and three-dimensional factorial correspondence analyses. Pairwise F(ST values within both Asia (F(ST = 0.017-0.126, P = 0.000-0.009 and South America (F(ST =0.004-0.107, P = 0.000-0.721 were lower than those between continents (F(ST = 0.180-0.319, P = 0.000. Fine-scale genetic structuring was also apparent among introduced populations in both Asia and South America, suggesting either multiple introductions of distinct propagules or strong post-introduction selection and demographic stochasticity. Higher genetic diversity in Asia as compared to South America is likely due to more frequent propagule transfers associated with higher shipping activities between source and donor regions within Asia. This study suggests that the intensity of human-mediated introduction vectors influences patterns of genetic diversity in non-indigenous species.

  10. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    Science.gov (United States)

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-04-05

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  11. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

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    Wan Isa Hatin

    Full Text Available Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis. To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  12. The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis.

    Science.gov (United States)

    Rodríguez-Ramilo, Silvia T; Wang, Jinliang

    2012-09-01

    The inference of population genetic structures is essential in many research areas in population genetics, conservation biology and evolutionary biology. Recently, unsupervised Bayesian clustering algorithms have been developed to detect a hidden population structure from genotypic data, assuming among others that individuals taken from the population are unrelated. Under this assumption, markers in a sample taken from a subpopulation can be considered to be in Hardy-Weinberg and linkage equilibrium. However, close relatives might be sampled from the same subpopulation, and consequently, might cause Hardy-Weinberg and linkage disequilibrium and thus bias a population genetic structure analysis. In this study, we used simulated and real data to investigate the impact of close relatives in a sample on Bayesian population structure analysis. We also showed that, when close relatives were identified by a pedigree reconstruction approach and removed, the accuracy of a population genetic structure analysis can be greatly improved. The results indicate that unsupervised Bayesian clustering algorithms cannot be used blindly to detect genetic structure in a sample with closely related individuals. Rather, when closely related individuals are suspected to be frequent in a sample, these individuals should be first identified and removed before conducting a population structure analysis.

  13. Population Genetic Diversity and Fitness in Multiple Environments(BMCEB)

    Science.gov (United States)

    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 p...

  14. Analyzing Population Genetics Using the Mitochondrial Control Region and Bioinformatics

    Science.gov (United States)

    Sato, Takumi; Phillips, Bonnie; Latourelle, Sandra M.; Elwess, Nancy L.

    2010-01-01

    The 14-base pair hypervariable region in mitochondrial DNA (mtDNA) of Asian populations, specifically Japanese and Chinese students at Plattsburgh State University, was examined. Previous research on this 14-base pair region showed it to be susceptible to mutations and as a result indicated direct correlation with specific ethnic populations.…

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

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    Sitthi-amorn Chitr

    2009-07-01

    Full Text Available Abstract Background The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites. Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. Methods The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. Results A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 ± 0.17, where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai

  16. Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis

    Institute of Scientific and Technical Information of China (English)

    LIU Yunguo; LI Junfeng; YE Naihao

    2011-01-01

    The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%,50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH,QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands,average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations,while the LZ population was the lowest among the wild populations. Compared with the wild populations,the hatchery population showed a low genetic viability.

  17. Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora

    Science.gov (United States)

    Galindo, Rene; Wilson, Wade; Caldwell, Colleen A.

    2016-01-01

    In the southwestern United States (US), the Rio Grande chub (Gila pandora) is state-listed as a fish species of greatest conservation need and federally listed as sensitive due to habitat alterations and competition with non-native fishes. Characterizing genetic diversity, genetic population structure, and effective number of breeders will assist with conservation efforts by providing a baseline of genetic metrics. Genetic relatedness within and among G. pandora populations throughout New Mexico was characterized using 11 microsatellite loci among 15 populations in three drainage basins (Rio Grande, Pecos, Canadian). Observed heterozygosity (HO) ranged from 0.71–0.87 and was similar to expected heterozygosity (0.75–0.87). Rio Ojo Caliente (Rio Grande) had the highest allelic richness (AR = 15.09), while Upper Rio Bonito (Pecos) had the lowest allelic richness (AR = 6.75). Genetic differentiation existed among all populations with the lowest genetic variation occurring within the Pecos drainage. STRUCTURE analysis revealed seven genetic clusters. Populations of G. pandora within the upper Rio Grande drainage (Rio Ojo Caliente, Rio Vallecitos, Rio Pueblo de Taos) had high levels of admixture with Q-values ranging from 0.30–0.50. In contrast, populations within the Pecos drainage (Pecos River and Upper Rio Bonito) had low levels of admixture (Q = 0.94 and 0.87, respectively). Estimates of effective number of breeders (N b ) varied from 6.1 (Pecos: Upper Rio Bonito) to 109.7 (Rio Grande: Rio Peñasco) indicating that populations in the Pecos drainage are at risk of extirpation. In the event that management actions are deemed necessary to preserve or increase genetic diversity of G. pandora, consideration must be given as to which populations are selected for translocation.

  18. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

    OpenAIRE

    Cardoso Márcio Z; Quek Swee-Peck; Albuquerque de Moura Priscila; Kronforst Marcus R

    2011-01-01

    Abstract Background Brazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of two Heliconius butterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on po...

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

    Science.gov (United States)

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

    2014-04-01

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

  20. Genetic traits in the bivalve Mytilus from Europe, with an emphasis on Arctic populations

    NARCIS (Netherlands)

    Hummel, H.; Colucci, P.; Bogaards, R.H.; Strelkov, P.P.

    2001-01-01

    Genetic and some ecophysiological traits of mussels collected in the European Arctic, up to their northeastern distribution limit in the Barents Sea, were studied and compared with traits of mussels from the Mediterranean, Atlantic and Baltic. The genetic traits of these populations we-re analysed b

  1. Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

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    Ilga Porth

    2014-04-01

    Full Text Available Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

  2. Genetic structure in a dynamic baboon hybrid zone corroborates behavioural observations in a hybrid population

    NARCIS (Netherlands)

    Charpentier, M J E; Fontaine, M C; Cherel, E; Renoult, J P; Jenkins, T; Benoit, L; Barthès, N; Alberts, S C; Tung, J

    2012-01-01

    Behaviour and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behaviour of the hybridizing taxa can also impact

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

    NARCIS (Netherlands)

    Piotti, A.; Leonardi, S.; Heuertz, M.; Buiteveld, J.; Geburek, T.; Gerber, S.; Kramer, K.; Vettori, C.; Vendramin, G.G.

    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

  4. Genetic variation in Danish populations of Erysiphe graminis f.sp. hordei: estimation of gene diversity and effective population size using RFLP data

    DEFF Research Database (Denmark)

    Damgaard, C.; Giese, Nanna Henriette

    1996-01-01

    Genetic variation of the barley powdery mildew fungus (Erysiphe graminis f.sp. hordei) was estimated in three Danish local populations. Genetic variation was estimated from the variation amongst clones of Egh, and was therefore an estimate of the maximum genetic variation in the local populations...

  5. The influence of admixture and consanguinity on population genetic diversity in Middle East.

    Science.gov (United States)

    Yang, Xiong; Al-Bustan, Suzanne; Feng, Qidi; Guo, Wei; Ma, Zhiming; Marafie, Makia; Jacob, Sindhu; Al-Mulla, Fahd; Xu, Shuhua

    2014-11-01

    The Middle East (ME) is an important crossroad where modern humans migrated 'out of Africa' and spread into Europe and Asia. After the initial peopling and long-term isolation leading to well-differentiated populations, the ME also had a crucial role in subsequent human migrations among Africa, Europe and Asia; thus, recent population admixture has been common in the ME. On the other hand, consanguinity, a well-known practice in the ME, often reduces genetic diversity and works in opposition to admixture. Here, we explored the degree to which admixture and consanguinity jointly affected genetic diversity in ME populations. Genome-wide single-nucleotide polymorphism data were generated in two representative ME populations (Arabian and Iranian), with comparisons made with populations worldwide. Our results revealed an overall higher genetic diversity in both ME populations relative to other non-African populations. We identified a much larger number of long runs of homozygosity in ME populations than in any other populations, which was most likely attributed to high levels of consanguineous marriages that significantly decreased both individual and population heterozygosity. Additionally, we were able to distinguish African, European and Asian ancestries in ME populations and quantify the impact of admixture and consanguinity with statistical approaches. Interestingly, genomic regions with significantly excessive ancestry from individual source populations are functionally enriched in olfactory pathways, which were suspected to be under natural selection. Our findings suggest that genetic admixture, consanguinity and natural selection have collectively shaped the genetic diversity of ME populations, which has important implications in both evolutionary studies and medical practices.

  6. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR loci

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    Babiker Hiba MA

    2011-05-01

    Full Text Available Abstract Background There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. Result We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. Conclusion We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  7. Population genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis across multiple spatial scales.

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    Shem D Unger

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

  8. Genetic diversity and population structure of begomoviruses infecting sweet potato

    Science.gov (United States)

    Begomoviruses infecting sweet potatoes (Ipomoea batatas) exhibit high genetic diversity, and approximately eight species including Sweet potato leaf curl virus (SPLCV) have been described from different regions around the world. In this study, the complete genomic sequences of 17 geographically dist...

  9. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    NARCIS (Netherlands)

    Lv, J.; Qi, J.; Shi, Q.; Shen, D.; Zhang, S.; Shao, G.; Li, H.; Sun, Z.; Weng, Y.; Shang, Y.; Gu, X.; Li, X.; Zhu, X.; Zhang, J.; Treuren, van R.; Dooijeweert, van W.; Zhang, Z.; Huang, S.

    2012-01-01

    Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also incl

  10. The statistics of genetic diversity in rapidly adapting populations.

    Science.gov (United States)

    Desai, Michael

    2013-03-01

    Evolutionary adaptation is driven by the accumulation of beneficial mutations, but the sequence-level dynamics of this process are poorly understood. The traditional view is that adaptation is dominated by rare beneficial ``driver'' mutations that occur sporadically and then rapidly increase in frequency until they fix (a ``selective sweep''). Yet in microbial populations, multiple beneficial mutations are often present simultaneously. Selection cannot act on each mutation independently, but only on linked combinations. This means that the fate of any mutation depends on a complex interplay between its own fitness effect, the genomic background in which it arises, and the rest of the sequence variation in the population. The balance between these factors determines which mutations fix, the patterns of sequence diversity within populations, and the degree to which evolution in replicate populations will follow parallel (or divergent) trajectories at the sequence level. Earlier work has uncovered signatures of these effects, but the dynamics of genomic sequence evolution in adapting microbial populations have not yet been directly observed. In this talk, I will describe how full-genome whole-population sequencing can be used to provide a detailed view of these dynamics at high temporal resolution over 1000 generations in 40 adapting Saccharomyces cerevisiaepopulations. This data shows how patterns of sequence evolution are driven by a balance between chance interference and hitchhiking effects, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favors parallel solutions in replicate populations.

  11. Characterization of the genetic variation present in CYP3A4 in three South African populations

    Directory of Open Access Journals (Sweden)

    Britt Ingrid Drögemöller

    2013-02-01

    Full Text Available TThe CYP3A4 enzyme is the most abundant human cytochrome P450 and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of approximately 600 bp of the 5’-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4*12, CYP3A4*15, and the reportedly functional CYP3A4*1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.

  12. Modelling the loss of genetic diversity in vole populations in a spatially and temporally varying environment

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino

    2003-01-01

    to habitat availability and their influence on vole behaviour. Interaction between spatial and temporal dynamics altered the ratio of effective population size to census size. This indicates an altered reproductive potential, crucial in conservation biology applications. However, when the loss...... a genetically explicit individual-based model (IBM) coupled to a dynamic landscape model was used to obtain measures for the genetic status of simulated vole populations. The rate of loss of expected heterozygosity (He) was calculated for simulated populations using two levels of spatial and temporal...... heterogeneity. Results showed that both spatial and temporal heterogeneity exerted an influence on the rate of loss of genetic diversity, but the precise effect was a balance between the effects of population sub-structuring, the frequency of founder effects and population size. These were in turn related...

  13. Spatio-temporal population genetic survey of the Danish pine marten (Martes martes)

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Barker, J Stuart F; Madsen, Aksel Bo;

    2008-01-01

    samples indicates changes in the genetic compositions over time, and the higher FST values between the two recent samples, as compared with the two historical samples, indicates that the populations in Sealand and Jutland have drifted apart within a short time span. No deviation from Hardy......A spatio-temporal study of genetic variation in the Danish pine marten (Martes martes) populations from the Jutland peninsula and from the island of Sealand was performed using 11 microsatellite markers. Samples obtained from 1892 to 2003 were subdivided into historical (prior to 1970) and recent...... (from 1970) groups. As compared with the historical samples, there was a significant loss of genetic variation in the recent Jutland population, but not in Sealand. Effective population sizes were estimated using Bayesian-based software (TMVP). Historical effective population sizes were 5897 (90...

  14. Variation in palaeo-shorelines explains contemporary population genetic patterns of rocky shore species.

    Science.gov (United States)

    Toms, Jessica A; Compton, John S; Smale, Malcolm; von der Heyden, Sophie

    2014-06-01

    Processes driving and maintaining disjunct genetic populations in marine systems are poorly understood, owing to a lack of evidence of hard barriers that could have shaped patterns of extant population structure. Here, we map two genetically divergent lineages of an obligate rocky shore fish, Clinus cottoides, and model sea-level change during the last 110 000 years to provide the first evidence of a vicariant event along the southern coastline of Africa. Results reveal that lowered sea levels during glacial periods drastically reduced rocky intertidal habitat, which may have isolated populations in two refugia for at least 40 000 years. Contemporary coastal dynamics and oceanography explain secondary contact between lineages. This scenario provides an explanation for the origin of population genetic breaks despite a lack of obvious present-day geographical barriers and highlights the need for including palaeo-oceanography in unravelling extant population patterns.

  15. Spatio-temporal population genetics of the Danish pine marten (Martes martes)

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Barker, Stuart F; Madsen, Aksel Bo;

    2008-01-01

    A spatio-temporal study of genetic variation in the Danish pine marten (Martes martes) populations from the Jutland peninsula and from the island of Sealand was performed using 11 microsatellite markers. Samples obtained from 1892 to 2003 were subdivided into historical (prior to 1970) and recent...... (from 1970) groups. As compared with the historical samples, there was a significant loss of genetic variation in the recent Jutland population, but not in Sealand. Effective population sizes were estimated using Bayesian-based software (TMVP). Historical effective population sizes were 5897 (90...... samples indicates changes in the genetic compositions over time, and the higher FST values between the two recent samples, as compared with the two historical samples, indicates that the populations in Sealand and Jutland have drifted apart within a short time span. No deviation from Hardy...

  16. Integrating empirical data and population genetic simulations to study the genetic architecture of type 2 diabetes

    OpenAIRE

    Agarwala, Vineeta

    2013-01-01

    Most common diseases have substantial heritable components but are characterized by complex inheritance patterns implicating numerous genetic and environmental factors. A longstanding goal of human genetics research is to delineate the genetic architecture of these traits - the number, frequencies, and effect sizes of disease-causing alleles - to inform mapping studies, elucidate mechanisms of disease, and guide development of targeted clinical therapies and diagnostics. Although vast empir...

  17. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population

    Science.gov (United States)

    Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi- genetic background population that contained more than 8000 l...

  18. Meeting review. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics.

    Science.gov (United States)

    Joost, Stéphane; Vuilleumier, Séverine; Jensen, Jeffrey D; Schoville, Sean; Leempoel, Kevin; Stucki, Sylvie; Widmer, Ivo; Melodelima, Christelle; Rolland, Jonathan; Manel, Stéphanie

    2013-07-01

    A workshop recently held at the École Polytechnique Fédérale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.g. focus on populations as units, focus on hard selective sweeps, no hypothesis-based framework in the design of the statistical tests) reduce their capability of detecting adaptive genetic variation. In parallel, landscape genomics offers a solution to several of these problems and provides a number of advantages (e.g. fast computation, landscape heterogeneity integration). But the approach makes several implicit assumptions that should be carefully considered (e.g. selection has had enough time to create a functional relationship between the allele distribution and the environmental variable, or this functional relationship is assumed to be constant). To address the respective strengths and weaknesses mentioned above, the workshop brought together a panel of experts from both disciplines to present their work and discuss the relevance of combining these approaches, possibly resulting in a joint software solution in the future.

  19. Quantitative genetics of functional characters in Drosophila melanogaster populations subjected to laboratory selection

    Indian Academy of Sciences (India)

    Henrique Teotónio; Margarida Matos; Michael R. Rose

    2004-12-01

    What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantitative-genetic basis of divergence was characterized for outbred Drosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line-cross analysis using first-generation and second-generation hybrids from reciprocal crosses was conducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to starvation stress. The other type of cross was between the same set of ancestral-representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating single-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differentiation to adaptation.

  20. Intra and inter populational genetic variability in Maytenus ilicifolia Mart. ex Reiss. 1861, through RAPD markers

    Directory of Open Access Journals (Sweden)

    AJ. Mossi

    Full Text Available Maytenus ilicifolia is a medicinal plant largely used in the South Brazilian folk medicine. The aim of this study was to quantify the intra and inter populational genetic variability in three populations of M. ilicifolia, focusing on the genetic conservation of this species, which has been threatened by anthropic action. RAPD (Random Amplified Polymorphic DNA markers were used to analyze 30 plants of each of the three populations collected in the Alto Uruguai Gaúcho region. Fourteen selected primers generated a total of 158 bands, 71.5% of which were polymorphic. The comparison of Jaccard’s distances showed that the intra populational variation was higher than the inter populational variability, and cluster analysis allowed the separation of the three populations. Just 7.6% of the bands were specific of at least two populations. Data indicate that the analyzed M. ilicifolia populations represent a single genetic pool, and therefore any of the population thoroughly can represent the overall genetic variability of the species in the sampled region.

  1. Genetic diversity and differentiation of mud crab Scylla serrata populations from southeastern China

    Institute of Scientific and Technical Information of China (English)

    LI Zhongbao; LI Shaojing; WANG Guizhong

    2004-01-01

    The genetic diversity and differentiation of 6 mud crab Scylla serrata populations from southeastern China are investigated using allozyme electrophoresis. The mean number of alleles per locus population is 1.3 ± 0.1; the percentage of polymorphic loci per population is 27.3; the observed heterozygosity ranges from ( 0.195 ± 0.083)to ( 0.241 ± 0.090) and the expected heterozygosity ranges from ( 0.105 ± 0.043 ) to ( 0.131 ± 0.047 ). The coefficient of gene differentiation among populations is low (Fst =0.032), indicating that only 3.2 % of the total genetic diversity comes from inter-population, while the remaining 96.8 % comes from intra-population differences.The genetic distance among populations is 0.000~0.008 (the average is 0.002). Gene flow among the populations is large (Nm= 7.56).Genetic structure is very similar among 6 Scylla serrata populations.

  2. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy.