Journal ArticleDOI
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
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TLDR
The main innovations of the new version of the Arlequin program include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans.Abstract:
We present here a new version of the Arlequin program available under three different forms: a Windows graphical version (Winarl35), a console version of Arlequin (arlecore), and a specific console version to compute summary statistics (arlsumstat). The command-line versions run under both Linux and Windows. The main innovations of the new version include enhanced outputs in XML format, the possibility to embed graphics displaying computation results directly into output files, and the implementation of a new method to detect loci under selection from genome scans. Command-line versions are designed to handle large series of files, and arlsumstat can be used to generate summary statistics from simulated data sets within an Approximate Bayesian Computation framework.read more
Citations
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Population Genetics of Ceratitis capitata in South Africa: Implications for Dispersal and Pest Management
TL;DR: Estimates of dispersal ability are provided in medfly from South Africa at three spatial scales using molecular approaches to suggest high levels of gene flow among sampling locations, and documented levels of high gene flow in the present study are likely the result of human-mediated dispersal or at least some form of long-distance jump dispersal.
Journal ArticleDOI
Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations
Pradiptajati Kusuma,Pradiptajati Kusuma,Murray P. Cox,Denis Pierron,Harilanto Razafindrazaka,Nicolas Brucato,Laure Tonasso,Helena Suryadi,Thierry Letellier,Herawati Sudoyo,Herawati Sudoyo,François-Xavier Ricaut +11 more
TL;DR: A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands.
Journal ArticleDOI
Climate and refugial origin influence the mitochondrial lineage distribution of weasels (Mustela nivalis) in a phylogeographic suture zone
TL;DR: Bayesian coalescent analysis revealed the importance of the Last Glacial Maximum and the Younger Dryas in the diversification of, and demographic changes in, identified mitochondrial lineages and strongly points to a Carpathian origin for one of the lineages.
Journal ArticleDOI
Sclerotinia sclerotiorum populations infecting canola from China and the United States are genetically and phenotypically distinct.
TL;DR: Isolates in the Chinese population were unique in several aspects and heritabilities of the phenotypic traits were similar for both populations, and significant correlations were found among five phenotyping traits.
Journal ArticleDOI
Human Neutral Genetic Variation and Forensic STR Data
TL;DR: The forensic genetic markers currently produced for the purpose of individual assignment and identification allow the detection of the patterns of neutral genetic structure that characterize the human population but they do underestimate the levels of this genetic structure compared to the datasets of STRs (or other kinds of markers) generated specifically to study the diversity of human populations.
References
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Journal ArticleDOI
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Journal ArticleDOI
Arlequin (version 3.0): An integrated software package for population genetics data analysis
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Journal ArticleDOI
Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
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Evaluating Loci for Use in the Genetic Analysis of Population Structure
TL;DR: It is suggested that genetic variation at a discrepant locus, Identified under these conditions, is likely to have been influenced by natural selection, either acting on the locus itself or at a closely linked locus.
Journal ArticleDOI
Detection of reduction in population size using data from microsatellite loci.
TL;DR: It is demonstrated that the mean ratio of the number of alleles to the range in allele size, which is calculated from a population sample of microsatellite loci, can be used to detect reductions in population size and that the value of M consistently predicts the reported demographic history for these populations.