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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Connectivity and population subdivision at the fringe of a large brown bear ( Ursus arctos ) population in North Western Europe
Alexander Kopatz,Hans Geir Eiken,Snorre B. Hagen,Minna Ruokonen,Rodrigo Esparza-Salas,Julia Schregel,Ilpo Kojola,Martin E. Smith,Ingvild Wartiainen,Paul Eric Aspholm,Steinar Wikan,Alexander M. Rykov,Olga Makarova,Natalia Polikarpova,Konstantin Tirronen,Pjotr Danilov,Jouni Aspi +16 more
TL;DR: Despite of a substantial influence of IBD on the genetic structure in the region, it is detected considerable variation in connectivity among the identified clusters that could not be explained solely by the distance between them.
Journal ArticleDOI
Phylogeography of Quercus glauca (Fagaceae), a dominant tree of East Asian subtropical evergreen forests, based on three chloroplast DNA interspace sequences
TL;DR: Haplotype spatial distribution, ENM, mismatch distribution, and neutrality tests suggest that Q. glauca in Southeast China experiences expansion, and the current distribution in region III might be shaped by southward expansion from regions I and II after last glacial maximum (LGM).
Journal ArticleDOI
Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia
Yong-Xin Zhao,Ji Yang,Feng-Hua Lv,Xiaoju Hu,Xing-Long Xie,Min Zhang,Min Zhang,Wen-Rong Li,Ming-Jun Liu,Yu-Tao Wang,Jin-Quan Li,Yong-Gang Liu,Yan-Ling Ren,Feng Wang,EEr Hehua,Juha Kantanen,Johannes A. Lenstra,Jian-Liin Han,Jian-Liin Han,Meng-Hua Li +19 more
TL;DR: Signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China are revealed.
Journal ArticleDOI
High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program
Xiao-Yang Zhou,Fa-Ming Zhu,Jianping Li,Wei Mao,De-Mei Zhang,Meng-Li Liu,Ai-Lian Hei,Da-Peng Dai,Ping Jiang,Xiao-Yan Shan,Bo-Wei Zhang,Chuan-Fu Zhu,Jie Shen,Zhihui Deng,Zheng-Lei Wang,Wei-Jian Yu,Qiang Chen,Yan-Hui Qiao,Xiang-Ming Zhu,Rong Lv,Guo-Ying Li,Guo Liang Li,Heng-Cong Li,Xu Zhang,Bin Pei,Li-Xin Jiao,Gang Shen,Ying Liu,Zhi Hui Feng,Yu-Ping Su,Zhao-Xia Xu,Wen-Ying Di,Yao-Qin Jiang,Hong-Lei Fu,Xiang-Jun Liu,Xiang Liu,Mei-Zhen Zhou,Dan Du,Qi Liu,Ying Han,Zhi-Xin Zhang,Jian-Ping Cai +41 more
TL;DR: This is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities and believes it might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies.
Journal ArticleDOI
Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika
Jason L. Brown,L. Lacey Knowles +1 more
TL;DR: The results support that the inclusion of a spatiotemporal dynamic is an important factor when studying the impact of distributional shifts on patterns of genetic data and demonstrate the utility of SDMs to generate species‐specific predictions about patterns of Genetic variation that account for varying degrees of habitat specialization and life history characteristics of taxa.
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.