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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Genetic structure of the reef grouper Epinephelus merra in the West Indian Ocean appears congruent with biogeographic and oceanographic boundaries
TL;DR: The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally and genetic analyses of the grouper Epinephelus merra are used to determine patterns of connectivity and to identify barriers to dispersal.
Journal ArticleDOI
Defining olive ridley turtle Lepidochelys olivacea management units in Australia and assessing the potential impact of mortality in ghost nets
Michael P. Jensen,Colin J. Limpus,Scott D. Whiting,Michael L. Guinea,Robert I. T. Prince,Kiki E. M. Dethmers,Ida Bagus Windia Adnyana,Rod Kennett,Nancy N. FitzSimmons +8 more
TL;DR: It is established that there are at least 2 independent manage- ment units (stocks) of olive ridley turtles nesting in Australia and the importance of conserving the genetically distinct small breeding population nesting along the western Cape York Peninsula is emphasised.
Journal ArticleDOI
Genetic diversity and biogeography of the south polar water bear Acutuncus antarcticus (Eutardigrada : Hypsibiidae) – evidence that it is a truly pan-Antarctic species
TL;DR: Morphological and molecular analyses show that A. antarcticus can still be considered a pan-Antarctic species, although the moderately high genetic diversity within Victoria Land indicates the potential for speciation events.
Journal ArticleDOI
The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach
TL;DR: Evidence that the autochthonous trout gene pools in the Tyrrhenian and Adriatic basins of the Italian peninsula started diverging very recently (most likely after the last glacial maximum) is provided.
Journal ArticleDOI
Trapped by climate: interglacial refuge and recent population expansion in the endemic Iberian adder Vipera seoanei
TL;DR: This study exemplifies how the combination of phylogeographic and ecological niche-based models is a powerful tool for inferring evolutionary scenarios and responses of species to Pleistocene climatic oscillations.
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.
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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.