A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers - PubMed (original) (raw)
. 2012 Jul;25(7):1364-76.
doi: 10.1111/j.1420-9101.2012.02526.x. Epub 2012 May 3.
Affiliations
- PMID: 22551238
- DOI: 10.1111/j.1420-9101.2012.02526.x
Free article
A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers
A Vilas et al. J Evol Biol. 2012 Jul.
Free article
Abstract
We investigated the performance of two of the most popular differentiation-based methods to detect loci under selection (dfdist/fdist and bayescan) in order to ascertain the average chromosome map distance between the detected outlier markers and the nearest loci under selection. We used a model of neutral markers genetically linked to selected loci (QTL) controlling a quantitative trait subject to divergent selection in two subpopulations connected by migration. The results are not particularly encouraging because for chromosome lengths above 0.5 morgan, at least 30% of outliers detected were positioned in chromosomes where QTL were absent, clearly denoting false positives. Outliers linked to QTL were on average closer to the nearest QTL than randomly chosen markers, but the methods showed a substantial uncertainty about the genetic association between markers and selected loci, as this association could be shown significantly only in a moderate number of replicates for most scenarios. At equal conditions, bayescan seemed to perform somewhat more efficiently than dfdist/fdist, with little difference between results for dominant and codominant markers.
© 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.
Similar articles
- A population-based latent variable approach for association mapping of quantitative trait loci.
Wang T, Weir B, Zeng ZB. Wang T, et al. Ann Hum Genet. 2006 Jul;70(Pt 4):506-23. doi: 10.1111/j.1469-1809.2006.00264.x. Ann Hum Genet. 2006. PMID: 16759182 - Marker-assisted selection can reduce true as well as pedigree-estimated inbreeding.
Pedersen LD, Sørensen AC, Berg P. Pedersen LD, et al. J Dairy Sci. 2009 May;92(5):2214-23. doi: 10.3168/jds.2008-1616. J Dairy Sci. 2009. PMID: 19389980 - Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria).
Bonin A, Taberlet P, Miaud C, Pompanon F. Bonin A, et al. Mol Biol Evol. 2006 Apr;23(4):773-83. doi: 10.1093/molbev/msj087. Epub 2006 Jan 5. Mol Biol Evol. 2006. PMID: 16396915 - Divergent selection as revealed by P(ST) and QTL-based F(ST) in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient.
Raeymaekers JA, Van Houdt JK, Larmuseau MH, Geldof S, Volckaert FA. Raeymaekers JA, et al. Mol Ecol. 2007 Feb;16(4):891-905. doi: 10.1111/j.1365-294X.2006.03190.x. Mol Ecol. 2007. PMID: 17284219 - The genetic differentiation at quantitative trait loci under local adaptation.
Le Corre V, Kremer A. Le Corre V, et al. Mol Ecol. 2012 Apr;21(7):1548-66. doi: 10.1111/j.1365-294X.2012.05479.x. Epub 2012 Feb 14. Mol Ecol. 2012. PMID: 22332667 Review.
Cited by
- Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient.
Ninčević T, Jug-Dujaković M, Grdiša M, Liber Z, Varga F, Pljevljakušić D, Šatović Z. Ninčević T, et al. Sci Rep. 2021 Dec 21;11(1):24333. doi: 10.1038/s41598-021-03548-6. Sci Rep. 2021. PMID: 34934087 Free PMC article. - Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon.
Steane DA, Potts BM, McLean EH, Collins L, Holland BR, Prober SM, Stock WD, Vaillancourt RE, Byrne M. Steane DA, et al. Genome Biol Evol. 2017 Feb 1;9(2):253-265. doi: 10.1093/gbe/evw290. Genome Biol Evol. 2017. PMID: 28391293 Free PMC article. - Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe.
Brousseau L, Postolache D, Lascoux M, Drouzas AD, Källman T, Leonarduzzi C, Liepelt S, Piotti A, Popescu F, Roschanski AM, Zhelev P, Fady B, Vendramin GG. Brousseau L, et al. PLoS One. 2016 Jul 8;11(7):e0158216. doi: 10.1371/journal.pone.0158216. eCollection 2016. PLoS One. 2016. PMID: 27392065 Free PMC article. - Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae).
Picq S, McMillan WO, Puebla O. Picq S, et al. Ecol Evol. 2016 Feb 26;6(7):2109-24. doi: 10.1002/ece3.2028. eCollection 2016 Apr. Ecol Evol. 2016. PMID: 27099711 Free PMC article. - Detection of selection signatures in dairy and beef cattle using high-density genomic information.
Zhao F, McParland S, Kearney F, Du L, Berry DP. Zhao F, et al. Genet Sel Evol. 2015 Jun 19;47(1):49. doi: 10.1186/s12711-015-0127-3. Genet Sel Evol. 2015. PMID: 26089079 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources