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Detection of Signatures of Selection Using F ST

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Genome-Wide Association Studies and Genomic Prediction

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1019))

Abstract

Natural selection has molded the evolution of species across all taxa. Much more recently, on an evolutionary scale, human-oriented selection started to play an important role in shaping organisms, markedly so after the domestication of animals and plants. These selection processes have left traceable marks in the genome. Following from the recent advances in molecular genetics technologies, a number of methods have been developed to detect such signals, termed genomic signatures of selection. In this chapter we discuss a straightforward protocol based on the F ST statistic to identify genomic regions that exhibit high variation in allelic frequency between groups, which is a characteristic of genomic regions that have gone through differential selection. How to define the borders of these regions and further explore its genetic content is then discussed.

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References

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  Google Scholar 

  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

    Article  PubMed  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  8. Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354

    Google Scholar 

  9. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population-structure. Evolution 38:1358–1370

    Article  Google Scholar 

  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

    Article  Google Scholar 

  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

    Google Scholar 

  12. Robert CP (2001) The Bayesian choice: from decision-theoretic foundations to computational implementation, 2nd edn. Springer, New York, NY

    Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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, Huang W, Chu X, He Y, Jin L, Liu Y, Sun W, 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, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe’er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Sham PC, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Yakub I, Birren BW, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L’Archeveque P, Bellemare G, Saeki K, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918

    Article  PubMed  CAS  Google Scholar 

  15. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72

    Article  PubMed  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Google Scholar 

  19. Gasser T, Kneip A, Kohler W (1991) A flexible and fast method for automatic smoothing. J Am Stat Assoc 86:643–652

    Article  Google Scholar 

  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

    Article  PubMed  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  22. R Development Core Team (2012) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria

    Google Scholar 

  23. VanRaden P (2008) Efficient methods to compute genomic predictions. J Dairy Sci 91:4414–4423

    Article  PubMed  CAS  Google Scholar 

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Acknowledgment

This work was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ008196), Rural Development Administration, Republic of Korea.

Author information

Authors and Affiliations

  1. School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia

    Laercio R. Porto-Neto

  2. School of Veterinary Science, The University of Queensland, St. Lucia, Brisbane, QLD, Australia

    Laercio R. Porto-Neto

  3. Hanwoo Experimental Station, National Institute of Animal Science, RDA, Pyongchang, Republic of Korea

    Seung Hwan Lee

  4. Department of Biotechnology, Hankyong National University, Ansung-City, Kyonggi-Do, Republic of Korea

    Hak Kyo Lee

  5. The Centre for Genetic Analysis and Applications, University of New England, Armidale, NSW, Australia

    Cedric Gondro

Authors
  1. Laercio R. Porto-Neto
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  2. Seung Hwan Lee
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  3. Hak Kyo Lee
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  4. Cedric Gondro
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Editor information

Editors and Affiliations

  1. , Ctr. Genetic Analysis and Applications, University of New England, Homestead Building 18, Armidale, 2351, New South Wales, Australia

    Cedric Gondro

  2. School of Environmental and Rural Scienc, Div. Animal Science, University of New England, Homestead Building 36, Armidale, 2351, New South Wales, Australia

    Julius van der Werf

  3. , Biosciences Research Division, Department of Primary Industries, Ring Road 5, Bundoora, 3083, Victoria, Australia

    Ben Hayes

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Porto-Neto, L.R., Lee, S.H., Lee, H.K., Gondro, C. (2013). Detection of Signatures of Selection Using F ST . In: Gondro, C., van der Werf, J., Hayes, B. (eds) Genome-Wide Association Studies and Genomic Prediction. Methods in Molecular Biology, vol 1019. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-447-0_19

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  • DOI: https://doi.org/10.1007/978-1-62703-447-0_19

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-446-3

  • Online ISBN: 978-1-62703-447-0

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