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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Quaternary refugia in southwestern Iran: insights from two sympatric moth species (Insecta, Lepidoptera)
Hossein Rajaei Sh.,Dennis Rödder,Alexander M. Weigand,Johannes Dambach,Michael J. Raupach,J. Wolfgang Wägele +5 more
TL;DR: The effects of past climate change on the evolutionary history of two sympatric moth species and their host plants were inferred and indicated a shared refugium for the southwestern Zagros Mountains and potential species-specific refugial areas in the southern Caucasus and the Kope-Dagh Mountains.
Journal ArticleDOI
Analysis of ancestry informative markers in three main ethnic groups from Ecuador supports a trihybrid origin of Ecuadorians
Roberta Santangelo,Roberta Santangelo,Fabricio González-Andrade,Claus Børsting,Antonio Torroni,Vania Pereira,Niels Morling +6 more
TL;DR: The data generated in this work represent one important step to assess the application of ancestry inference in admixed populations in a forensic context and highlighted the sex-biased admixture process in the Ecuadorian Mestizo.
Journal ArticleDOI
Conservation and management of peripheral populations: Spatial and temporal influences on the genetic structure of wood frog (Rana sylvatica) populations
TL;DR: It is hypothesized that the lack of gene flow among wood frog populations in east-central Missouri is due to the absence of available fishless breeding habitats outside of protected, managed lands, and recommended that future management efforts of the wood frog include increasing population connectivity at the landscape scale via the creation and maintenance of fishless aquatic breeding habitat.
Journal ArticleDOI
Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex
TL;DR: Diploid, tetraPloid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.
Journal ArticleDOI
Historic Late Blight Outbreaks Caused by a Widespread Dominant Lineage of Phytophthora infestans (Mont.) de Bary.
TL;DR: The FAM-1 SSR lineage survived for almost 100 years in the US, was geographically widespread, and was displaced first in the mid-20th century by the US-1 lineage and then by distinct new aggressive lineages that migrated from Mexico.
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.