Journal ArticleDOI
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
Reads0
Chats0
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
More filters
Journal ArticleDOI
The distributions of HLA‐A, HLA‐B, HLA‐C, HLA‐DRB1 and HLA‐DQB1 allele and haplotype at high‐resolution level in Zhejiang Han population of China
Nanying Chen,Nanying Chen,Wei Wang,Fang Wang,L.-N. Dong,Shuoxian Zhao,Wei Zhang,Ji He,He Huang,Faming Zhu +9 more
TL;DR: The likelihood ratios test for the linkage disequilibrium of two loci haplotypes was revealed that the majority of the pairwise associations were statistically significant and will be useful for searching unrelated HLA‐matched donor, planning donor registry and for anthropology studies in China.
Journal ArticleDOI
Complete mtDNA genomes of Filipino ethnolinguistic groups: A melting pot of recent and ancient lineages in the Asia-Pacific region
Frederick S. Delfin,Albert Min-Shan Ko,Mingkun Li,Ellen Gunnarsdóttir,Kristina A. Tabbada,Jazelyn M. Salvador,Gayvelline C. Calacal,Minerva S. Sagum,Francisco A. Datar,Sabino G. Padilla,Maria Corazon A. De Ungria,Mark Stoneking +11 more
TL;DR: The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent.
Journal ArticleDOI
Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6
Juan Ángel Patiño-Galindo,Juan Ángel Patiño-Galindo,Karina Salvatierra,Karina Salvatierra,Fernando González-Candelas,Fernando González-Candelas,F. Xavier López-Labrador +6 more
TL;DR: It is shown that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations.
Journal ArticleDOI
Opsin clines in butterflies suggest novel roles for insect photopigments
Francesca D. Frentiu,Furong Yuan,Wesley K. Savage,Gary D. Bernard,Sean P. Mullen,Adriana D. Briscoe +5 more
TL;DR: The results suggest that opsin diversification in this butterfly is more consistent with natural selection unrelated to spectral tuning, and the possibility that insect opsins might have important, yet-to-be elucidated, adaptive functions in mediating animal responses to abiotic factors, such as temperature or photoperiod is discussed.
Journal ArticleDOI
Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L.
Kevin A. Bird,Hong An,Hong An,Elodie Gazave,Michael A. Gore,J. Chris Pires,Larry D. Robertson,Joanne A. Labate +7 more
TL;DR: Improved resolution is provided to the genetic and phylogenetic relationships of subspecies within the species B. rapa and there is found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. dichotoma) and turnips.
References
More filters
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.