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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Biogeographical role of the Kuroshio Current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data
TL;DR: A potential colonization origin from the South China Sea was consistently inferred by different clues, including the populations' coalescence times, the ancestral haplotype distribution, the number of private haplotypes and species/genetic diversity.
Journal ArticleDOI
Genomic Analyses of Three Malaria Vectors Reveals Extensive Shared Polymorphism but Contrasting Population Histories.
Samantha M. O’Loughlin,Stephen M. Magesa,Charles Mbogo,Charles Mbogo,Franklin W. Mosha,Janet Midega,Janet Midega,Susan Lomas,Austin Burt +8 more
TL;DR: Analysis of genome-wide RADseq data in three Anopheles gambiae s.l. species collected from East Africa shows extensive shared polymorphism, particularly between A. gambiae and A. arabiensis, supporting a recent new phylogeny based on chromosomal inversions.
Journal ArticleDOI
Drift, not selection, shapes toll-like receptor variation among oceanic island populations
Catalina Gonzalez-Quevedo,Catalina Gonzalez-Quevedo,Lewis G. Spurgin,Juan Carlos Illera,David S. Richardson +4 more
TL;DR: This study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales.
Journal ArticleDOI
Population genetic structure of reared and wild gilthead sea bream (Sparus aurata) in the Adriatic Sea inferred with microsatellite loci
Tanja Šegvić-Bubić,Ivana Lepen,Željka Trumbić,Jelena Ljubković,Davorka Sutlović,Sanja Matić-Skoko,Leon Grubišić,Branko Glamuzina,Ivona Mladineo +8 more
TL;DR: Results imply that farmed escapees are involved in genetic pollution of adjacent wild populations showing lower differentiation among themselves, which strongly encourages strengthening of routine aquaculture practice in the Adriatic through development of genetic-based management for broodstock, fingerlings and farmed fish, as well as better zootechnological protocol related to maintenance of nets and cages.
Journal ArticleDOI
First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis).
TL;DR: Overall diversity of limnetic nematodes has been so far drastically underestimated and challenges the assumed ubiquitous distribution of other, single freshwater nematode morphospecies.
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.
Journal ArticleDOI
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.