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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Journal ArticleDOI
Phylogeography of noble crayfish (Astacus astacus) reveals multiple refugia
Anne Schrimpf,Kathrin Theissinger,Jenifer Dahlem,Ivana Maguire,Lucian Pârvulescu,Holger K. Schulz,Ralf Schulz +6 more
TL;DR: The results suggest the existence of at least two refugial areas in south-eastern Europe, and the highest genetic diversity in the Black Sea basin and par-ticularly high differentiation between populations from the western Balkans and the remaining Black Sea populations.
Journal ArticleDOI
A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species
TL;DR: A multimarker phylogeographical survey is conducted to explore the evolutionary independence of these mitochondrial DNA lineages of the crested newt T. karelinii sensu lato and includes representatives of the other species to guide the interpretation of the results.
Journal ArticleDOI
The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents
Bernard Secher,Rosa Fregel,Rosa Fregel,José M. Larruga,Vicente M. Cabrera,Phillip Endicott,José Pestano,José Pestano,Ana M. González +8 more
TL;DR: The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands, leaving the specific sign of the colonizers origin.
Journal ArticleDOI
Long-term isolation of a highly mobile seabird on the Galapagos
Frank Hailer,E. A. Schreiber,Joshua M. Miller,Iris I. Levin,Patricia G. Parker,R. Terry Chesser,Robert C. Fleischer +6 more
TL;DR: Signs of extensive gene flow are found over most of the range of magnificent frigatebirds, even across the Isthmus of Panama, which is a major barrier to gene flow in other tropical seabirds.
Journal ArticleDOI
Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua).
Luciano B. Beheregaray,Lauren V. Pfeiffer,Catherine R. M. Attard,Jonathan Sandoval-Castillo,Fabricius M. C. B. Domingos,Leanne K. Faulks,Dean M. Gilligan,Peter J. Unmack +7 more
TL;DR: This work used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distribution across arid and semi-arid regions of Australia, and identified cases suggestive of anthropogenic hybridization between lineages.
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.