GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data

被引:8
作者
Adams, Richard H. [1 ]
Schield, Drew R. [1 ]
Card, Daren C. [1 ]
Blackmon, Heath [2 ]
Castoe, Todd A. [1 ]
机构
[1] Univ Texas Arlington, Dept Biol, Arlington, TX 76019 USA
[2] Univ Minnesota, Dept Ecol Evolut & Behav, St Paul, MN 55108 USA
基金
美国国家科学基金会;
关键词
PACKAGE; COALESCENT; GENETICS;
D O I
10.1093/bioinformatics/btw795
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We introduce GppFst, an open source R package that generates posterior predictive distributions of F-ST and d(x) under a neutral coalescent model to identify putative targets of selection from genomic data.
引用
收藏
页码:1414 / 1415
页数:2
相关论文
共 12 条
[1]   Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis [J].
Bryant, David ;
Bouckaert, Remco ;
Felsenstein, Joseph ;
Rosenberg, Noah A. ;
RoyChoudhury, Arindam .
MOLECULAR BIOLOGY AND EVOLUTION, 2012, 29 (08) :1917-1932
[2]   Arlequin (version 3.0): An integrated software package for population genetics data analysis [J].
Excoffier, Laurent ;
Laval, Guillaume ;
Schneider, Stefan .
EVOLUTIONARY BIOINFORMATICS, 2005, 1 :47-50
[3]  
Gelman A., 2004, Bayesian Data Analysis, V2
[4]   GENELAND: a computer package for landscape genetics [J].
Guillot, G ;
Mortier, F ;
Estoup, A .
MOLECULAR ECOLOGY NOTES, 2005, 5 (03) :712-715
[5]   The past, present and future of genomic scans for selection INTRODUCTION [J].
Jensen, Jeffrey D. ;
Foll, Matthieu ;
Bernatchez, Louis .
MOLECULAR ECOLOGY, 2016, 25 (01) :1-4
[6]   Phybase: an R package for species tree analysis [J].
Liu, Liang ;
Yu, Lili .
BIOINFORMATICS, 2010, 26 (07) :962-963
[7]   Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data [J].
Reid, Noah M. ;
Hird, Sarah M. ;
Brown, Jeremy M. ;
Pelletier, Tara A. ;
McVay, John D. ;
Satler, Jordan D. ;
Carstens, Bryan C. .
SYSTEMATIC BIOLOGY, 2014, 63 (03) :322-333
[8]   Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox) [J].
Schield, Drew R. ;
Card, Daren C. ;
Adams, Richard H. ;
Jezkova, Tereza ;
Reyes-Velasco, Jacobo ;
Proctor, F. Nicole ;
Spencer, Carol L. ;
Herrmann, Hans-Werner ;
Mackessy, Stephen P. ;
Castoe, Todd A. .
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2015, 83 :213-223
[9]   Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon [J].
Shapiro, Michael D. ;
Kronenberg, Zev ;
Li, Cai ;
Domyan, Eric T. ;
Pan, Hailin ;
Campbell, Michael ;
Tan, Hao ;
Huff, Chad D. ;
Hu, Haofu ;
Vickrey, Anna I. ;
Nielsen, Sandra C. A. ;
Stringham, Sydney A. ;
Hu, Hao ;
Willerslev, Eske ;
Gilbert, M. Thomas P. ;
Yandell, Mark ;
Zhang, Guojie ;
Wang, Jun .
SCIENCE, 2013, 339 (6123) :1063-1067
[10]  
TAKAHATA N, 1985, GENETICS, V110, P325