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
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Oxytocin and vasopressin receptor polymorphisms interact with circulating neuropeptides to predict human emotional reactions to stress
TL;DR: Evidence is provided that oxytocin and vasopressin receptor genes interact with levels of OT and AVP to predict sex-specific emotional stress responses, and women, but not men, with high levels of poststressor OT and the GG genotype of rs53576 felt the most positive affect after the stressor.
Journal ArticleDOI
Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™
Mayra Eduardoff,Theresa E. Gross,Carla Santos,M. de la Puente,David Ballard,Christina Strobl,Claus Børsting,Niels Morling,L. Fusco,Christian Hussing,Balázs Egyed,L. Souto,J. Uacyisrael,D. Syndercombe Court,Angel Carracedo,Angel Carracedo,M. V. Lareu,Peter M. Schneider,Walther Parson,Walther Parson,Christopher Phillips +20 more
TL;DR: The overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.
Journal ArticleDOI
Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring
Dorte Bekkevold,Sarah J. Helyar,Morten T. Limborg,Morten T. Limborg,Einar Eg Nielsen,Jakob Hemmer-Hansen,Lotte Worsøe Clausen,Gary R. Carvalho +7 more
TL;DR: The study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution, and reports novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea.
Journal ArticleDOI
Signatures of selection in the Iberian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms
Julio Chavez-Galarza,Dora Henriques,J. Spencer Johnston,João Azevedo,John C. Patton,Irene Muñoz,Pilar De la Rúa,M. Alice Pinto +7 more
TL;DR: This study enabled a more rigorous consideration of selection as the underlying cause of diversity patterns in Iberian honey bees, representing an important first step towards the identification of polymorphisms implicated in local adaptation and possibly in response to recent human‐mediated environmental changes.
Journal ArticleDOI
Geographical pattern of isolation and diversification in karst habitat islands: a case study in the Primulina eburnea complex
TL;DR: This study aimed to clarify species boundaries as well as phylogenetic relationships among species of the Primulina eburnea complex, a rapidly diversifying group of edaphic specialists confined to karst habitat islands in southern China.
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.