Detection of signatures of selection using FST

Methods in Molecular Biology

Volumn 1019, Issue , 2013, Pages 423-436

  Porto Neto, Laercio R ^a,b   Lee, Seung Hwan ^c   Lee, Hak Kyo ^d   Gondro, Cedric ^a  

^a UNIVERSITY OF NEW ENGLAND   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c National Institute of Animal Science   (South Korea)

^d Hankyong National University   (South Korea)

Author keywords

Adaptation; Divergence; Evolution; F statistics; Population genetics; R statistics; SNP; Speciation

Indexed keywords

ARTICLE; EVOLUTION; GENE FREQUENCY; GENETIC ANALYSIS; GENOME; HUMAN; NATURAL SELECTION; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TAXONOMY;

ANIMALIA;

EID: 84883142550     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-447-0_19     Document Type: Article

References (23)

1. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES (2006) Positive natural selection in the human lineage. Science 312:1614-1620
2. Bigham A, Bauchet M, Pinto D, Mao XY, Akey JM, Mei R, Scherer SW, Julian CG,Wilson MJ, Herraez DL, Brutsaert T, Parra EJ, Moore LG, Shriver MD (2010) Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genet 6
3. Kijas J, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, Servin B, McCulloch R, Whan V, Gietzen K, Paiva S, Barendse W, Ciani E, Raadsma H, McEwan J, Dalrymple B, The International Sheep Genomics Consortium (2012) Genome wide analysis of the World's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 10(2):e1001258
4. Akey JM, Ruhe AL, Akey DT, Wong AK, Connelly CF, Madeoy J, Nicholas TJ, Neff MW (2010) Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci USA 107:1160-1165
5. Flori L, Fritz S, Jaffrezic F, Boussaha M, Gut I, Heath S, Foulley JL, Gautier M (2009) The genome response to artificial selection: A case study in dairy cattle. PLoS One 4:e6595
6. Gautier M, Naves M (2011) Footprints of selection in the ancestral admixture of a New World Creole cattle breed. Mol Ecol 20:3128-3143
7. Holsinger KE, Weir BS (2009) Fundamental Concepts in Genetics.Genetics in geographically structured populations: Defining, estimating and interpreting FST. Nat Rev Genet 10:639-650
8. Wright S (1951) The genetical structure of populations. Ann Eugen 15:323-354
9. Weir BS, Cockerham CC (1984) Estimating Fstatistics for the analysis of populationstructure. Evolution 38:1358-1370
10. Nicholson G, Smith AV, Jonsson F, Gustafsson O, Stefansson K, Donnelly P (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J Royal Stat Soc Series B-Stat Methodol 64:695-715
11. Excoffier L (2001) Analysis of population subdivision. In: Balding DJ, Bishop M, Cannings C (eds) Handbook of statistical genetics. Wiley, Chichester, pp 271-307
12. Robert CP (2001) The Bayesian choice: From decision-theoretic foundations to computational implementation, 2nd edn. Springer, New York, NY
13. Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837
14. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, HuangW, Chu X, He Y, Jin L, Liu Y, SunW, Wang H, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Jamieson R, Stewart J (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-918
15. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72
16. Tang K, Thornton KR, Stoneking M (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 5:1587-1602
17. Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883-886
18. Nicholson G, Smith AV, Jonsson F, Gustafsson O, Stefansson K, Donnelly P (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. Annual meeting of the Royal-Statistical-Society, London, England, pp 695-715
19. Gasser T, Kneip A, Kohler W (1991) A flexible and fast method for automatic smoothing. J Am Stat Assoc 86:643-652
20. van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, de Jesus Sanchez Gonzalez J, Ross-Ibarra J (2011) Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc Natl Acad Sci USA 108:1088-1092
21. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559-575
22. R Development Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
23. VanRaden P (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91:4414-4423