A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers

Journal of Evolutionary Biology

Volumn 25, Issue 7, 2012, Pages 1364-1376

  Vilas, A ^a   Perez Figueroa A ^a   Caballero, A ^a  

^a UNIVERSITY OF VIGO   (Spain)

Author keywords

Genome scan; Linkage; Outliers; QTL; Recombination

Indexed keywords

CHROMOSOME; DIVERGENCE; GENETIC MARKER; GENOME; NUMERICAL MODEL; OUTLIER; POPULATION MIGRATION; RECOMBINATION; SUBPOPULATION;

EID: 85027952514     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/j.1420-9101.2012.02526.x     Document Type: Article

References (50)

1. Antao, T. & Beaumont, M.A. 2011. Mcheza: a workbench to detect selection using dominant markers. Bioinformatics 27: 1717-1718.
2. Antao, T., Lopes, A., Lopes, R., Beja-Pereira, A. & Luikart, G. 2008. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323.
3. Arias, J.A., Keehan, M., Fisher, P., Coppieters, W. & Spelman, R. 2009. A high density linkage map of the bovine genome. BMC Genet. 10: 18.
4. Barton, N.H. 2000. Genetic hitchhiking. Philos. Trans. R. Soc. Lond. B 355: 1553-1562.
5. Beaumont, M.A. & Balding, D.J. 2004. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 13: 969-980.
6. Beaumont, M.A. & Nichols, R.A. 1996. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B 263: 1619-1626.
7. Benjamini, Y. & Hochberg, Y. 1995. Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B Met. 57: 289-300.
8. Bierne, N. 2010. The distinctive footprint of local hitchhiking in a varied environment and global hitchhiking in a subdivided population. Evolution 64-11: 3254-3272.
9. Bonhomme, M., Chevalet, C., Servin, B., Boitard, S., Abdallah, J.M., Blott, S. et al. 2010. Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics 186: 241-262.
10. Butlin, R.K. 2010. Population genomics and speciation. Genetica 138: 409-418.
11. Caballero, A., Quesada, H. & Rolán-Alvarez, E. 2008. Impact of AFLP fragment size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179: 539-554.
12. Carvajal-Rodríguez, A., de Uña-Alvarez, J. & Rolán-Alvarez, E. 2009. A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. BMC Bioinformatics 10: 209.
13. Charlesworth, B., Nordborg, M. & Charlesworth, D. 1997. The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations. Genet. Res. 70: 155-174.
14. De Kovel, C.G.F. 2006. The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations. Genet. Sel. Evol. 38: 3-23.
15. Excoffier, L. & Lischer, H.E.L. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10: 564-567.
16. Excoffier, L., Hofer, T. & Foll, M. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103: 285-298.
17. Feder, J.L. & Nosil, P. 2010. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution 64-6: 1729-1747.
18. Foll, M. & Gaggiotti, O. 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180: 977-995.
19. Haldane, J.B.S. 1954. The measurement of natural selection. In: Proceedings of the 9th International Congress of Genetics (Caryologia, Supplement to Volume 6) 1: 480-487.
20. Hawthorne, D.J. & Via, S. 2001. Genetic linkage of ecological specialization and reproductive isolation in pea aphids. Nature 412: 904-907.
21. Hohenlohe, P.A., Bassham, S., Etter, P.D., Stiffler, N., Johnson, E.A. & Cresko, W.A. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 6: e1000862.
22. Hohenlohe, P.A., Bassham, S., Currey, M. & Cresko, W.A. 2012. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philos. Trans. R. Soc. B 367: 395-408.
23. Le Corre, V. & Kremer, A. 2012. The genetic differentiation at quantitative trait loci under local adaptation. Mol. Ecol. 21: 1548-1566.
24. Lewontin, R. & Krakauer, J. 1973. Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics 74: 175-195.
25. Merilä, J. & Crnokrak, P. 2001. Comparison of genetic differentiation at marker loci and quantitative traits. J. Evol. Biol. 14: 892-903.
26. ST outlier tests for SNP loci under selection. Mol. Ecol. Resour. 11(Suppl 1): 184-194.
27. Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
28. Nosil, P. & Feder, J.L. 2012. Genomic divergence during speciation: causes and consequences. Philos. Trans. R. Soc. B 367: 332-342.
29. Nosil, P., Funk, D.J. & Ortiz-Barrientos, D. 2009. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 18: 375-402.
30. Pardo-Manuel de Villena, F. & Sapienza, C. 2001. Recombination is proportional to the number of chromosome arms in mammals. Mamm. Genome 12: 318-322.
31. Pérez-Figueroa, A., García-Pereira, M.J., Saura, M., Rolán-Alvarez, E. & Caballero, A. 2010. Comparing three different methods to detect selective loci using dominant markers. J. Evol. Biol. 23: 2267-2276.
32. Przeworski, M. 2002. The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
33. Renaut, S., Maillet, N., Normandeau, E., Sauvage, C., Derome, N., Rogers, S.M. et al. 2012. Genome-wide patterns of divergence during speciation: the lake whitefish case study. Philos. Trans. R. Soc. B 367: 454-463.
34. Rogers, S.M. & Bernatchez, L. 2005. Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis). Mol. Ecol. 14: 351-361.
35. Santiago, E. & Caballero, A. 2005. Variations after a selective sweep in a subdivided population. Genetics 169: 475-483.
36. Smadja, C., Galindo, J. & Butlin, R.K. 2008. Hitching a lift on the road to speciation. Mol. Ecol. 17: 4177-4180.
37. Stinchcombe, J.R. & Hoekstra, H.E. 2008. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100: 158-170.
38. Storz, J.F. 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 14: 671-688.
39. Teshima, K.M., Coop, G. & Przeworski, M. 2006. How reliable are empirical genomic scans for selective sweeps? Genome Res. 16: 702-712.
40. Turelli, M. 1984. Heritable genetic variation via mutation-selection balance: Lerch′s zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138-193.
41. Turner, T.L., Hahn, M.W. & Nuzhdin, S.V. 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3: 1572-1578.
42. Via, S. 2009. Natural selection in action during speciation. Proc. Natl Acad. Sci. USA 106: 9939-9946.
43. Via, S. 2012. Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philos. Trans. R. Soc. B 367: 451-460.
44. Via, S. & Hawthorne, D.J. 2001. Genetic architecture of ecological specialization and incipient speciation in divergent races of pea aphids. Am. Nat. 159: S47-S60.
45. Via, S. & West, J. 2008. The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Mol. Ecol. 17: 4334-4345.
46. Vitalis, R., Dawson, K. & Boursot, P. 2001. Interpretation of variation across marker loci as evidence of selection. Genetics 158: 1811-1823.
47. Vitalis, R., Dawson, K., Boursot, P. & Belkhir, K. 2003. Computer Note: DetSel 1.0: a computer program to detect markers responding to selection. J. Hered. 94: 429-431.
48. Weir, B.S. & Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
49. Wright, S. 1969. Evolution and the Genetics of Populations. Vol. 2, The Theory of Gene Frequencies. The University of Chicago Press, Chicago, USA.
50. Zhivotovsky, L.A. 1999. Estimating population structure in diploids with multilocus dominant DNA markers. Mol. Ecol. 8: 907-913.