Rank and Order Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism 英文参考文献.docVIP

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Rank and Order Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism 英文参考文献.doc

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Rank and Order Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism 英文参考文献

RankandOrder:EvaluatingthePerformanceofSNPsfor IndividualAssignmentinaNon-ModelOrganism CarolineG.Storer1,CaritaE.Pascal1,StevenB.Roberts1,WilliamD.Templin2,LisaW.Seeb1, JamesE.Seeb1* 1SchoolofAquaticandFisherySciences,UniversityofWashington,Seattle,Washington,UnitedStatesofAmerica,2GeneConservationLaboratory,AlaskaDepartmentof FishandGame,Anchorage,Alaska,UnitedStatesofAmerica Abstract Singlenucleotidepolymorphisms(SNPs)arevaluabletoolsforecologicalandevolutionarystudies.Innon-modelspecies, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technologycostshavefacilitatedthediscoveryofaconstantlyincreasingnumberofSNPs.Withhundredsorthousandsof SNPspotentiallyavailable,thereisinterestincomparinganddevelopingmethodsforevaluatingSNPstocreatepanelsof high-throughputassaysthatarecustomizedforperformance,researchquestions,andresources.Hereweusefivedifferent methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: FST, informativeness (In ), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performanceofthesedifferentrankingmethodsbycreating48-and96-SNPpanelsofthetop-rankedlociforeachmethod andusedempiricalandsimulateddatatoobtaintheprobabilityofassigningindividualstothecorrectpopulationusing eachpanel. All 96-SNP panels performed similarlyand better thanthe 48-SNP panels except for the 96-SNP BELS panel. Amongthe48-SNPpanels,panelscreatedfromFST,In,andLCranksperformedbetterthanpanelsformedusingthetop- rankedlocifromtheprogramsBELSandWHICHLOCI.Theapplicationofrankingmethodstooptimizepanelperformance willbecomemoreimportantasmorehigh-throughputassaysbecomeavailable. Citation:StorerCG,PascalCE,RobertsSB,TemplinWD,SeebLW,etal.(2012)RankandOrder:EvaluatingthePerformanceofSNPsforIndividualAssignmentina Non-ModelOrganism.PLoSONE7(11):e49018.doi:10.1371/journal.pone.0049018 Editor:FranciscoJose′ Esteban,UniversityofJae′n,Spai