A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers
Version of Record online: 3 MAY 2012
© 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology
Journal of Evolutionary Biology
Volume 25, Issue 7, pages 1364–1376, July 2012
How to Cite
VILAS, A., PÉREZ-FIGUEROA, A. and CABALLERO, A. (2012), A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers. Journal of Evolutionary Biology, 25: 1364–1376. doi: 10.1111/j.1420-9101.2012.02526.x
- Issue online: 12 JUN 2012
- Version of Record online: 3 MAY 2012
- Received 22 December 2011; revised 25 March 2012; accepted 27 March 2012
- 2011. Mcheza: a workbench to detect selection using dominant markers. Bioinformatics 27: 1717–1718. &
- 2008. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323. , , , &
- 2009. A high density linkage map of the bovine genome. BMC Genet. 10: 18. , , , &
- 2000. Genetic hitchhiking. Philos. Trans. R. Soc. Lond. B 355: 1553–1562.
- 2004. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 13: 969–980. &
- 1996. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B 263: 1619–1626. &
- 1995. Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B Met. 57: 289–300. &
- 2010. The distinctive footprint of local hitchhiking in a varied environment and global hitchhiking in a subdivided population. Evolution 64–11: 3254–3272.
- 2010. Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics 186: 241–262. , , , , , et al.
- 2010. Population genomics and speciation. Genetica 138: 409–418.
- 2008. Impact of AFLP fragment size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 179: 539–554. , &
- 2009. A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. BMC Bioinformatics 10: 209. , &
- 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. , &
- 2006. The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations. Genet. Sel. Evol. 38: 3–23.
- 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. &
- 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103: 285–298. , &
- 2010. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution 64–6: 1729–1747. &
- 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180: 977–995. &
- 1954. The measurement of natural selection. In: Proceedings of the 9th International Congress of Genetics (Caryologia, Supplement to Volume 6) 1: 480–487.
- 2001. Genetic linkage of ecological specialization and reproductive isolation in pea aphids. Nature 412: 904–907. &
- 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 6: e1000862. , , , , &
- 2012. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philos. Trans. R. Soc. B 367: 395–408. , , &
- 2012. The genetic differentiation at quantitative trait loci under local adaptation. Mol. Ecol. 21: 1548–1566. &
- 1973. Distribution of gene frequency as a test of theory of selective neutrality of polymorphisms. Genetics 74: 175–195. &
- 2001. Comparison of genetic differentiation at marker loci and quantitative traits. J. Evol. Biol. 14: 892–903. &
- 2011. Comparison of FST outlier tests for SNP loci under selection. Mol. Ecol. Resour. 11(Suppl 1): 184–194. &
- 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
- 2012. Genomic divergence during speciation: causes and consequences. Philos. Trans. R. Soc. B 367: 332–342. &
- 2009. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 18: 375–402. , &
- 2001. Recombination is proportional to the number of chromosome arms in mammals. Mamm. Genome 12: 318–322. &
- 2010. Comparing three different methods to detect selective loci using dominant markers. J. Evol. Biol. 23: 2267–2276. , , , &
- 2002. The signature of positive selection at randomly chosen loci. Genetics 160: 1179–1189.
- 2012. Genome-wide patterns of divergence during speciation: the lake whitefish case study. Philos. Trans. R. Soc. B 367: 454–463. , , , , , et al.
- 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. &
- 2005. Variations after a selective sweep in a subdivided population. Genetics 169: 475–483. &
- 2008. Hitching a lift on the road to speciation. Mol. Ecol. 17: 4177–4180. , &
- 2008. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100: 158–170. &
- 2005. Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 14: 671–688.
- 2006. How reliable are empirical genomic scans for selective sweeps? Genome Res. 16: 702–712. , &
- 1984. Heritable genetic variation via mutation-selection balance: Lerch′s zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138–193.
- 2005. Genomic islands of speciation in Anopheles gambiae. PLoS Biol. 3: 1572–1578. , &
- 2009. Natural selection in action during speciation. Proc. Natl Acad. Sci. USA 106: 9939–9946.
- 2012. Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philos. Trans. R. Soc. B 367: 451–460.
- 2001. Genetic architecture of ecological specialization and incipient speciation in divergent races of pea aphids. Am. Nat. 159: S47–S60. &
- 2008. The genetic mosaic suggests a new role for hitchhiking in ecological speciation. Mol. Ecol. 17: 4334–4345. &
- 2001. Interpretation of variation across marker loci as evidence of selection. Genetics 158: 1811–1823. , &
- 2003. Computer Note: DetSel 1.0: a computer program to detect markers responding to selection. J. Hered. 94: 429–431. , , &
- 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370. &
- 1969. Evolution and the Genetics of Populations. Vol. 2, The Theory of Gene Frequencies. The University of Chicago Press, Chicago, USA.
- 1999. Estimating population structure in diploids with multilocus dominant DNA markers. Mol. Ecol. 8: 907–913.