Gene Sampling Strategies for Multi-Locus Population Estimates of Genetic Diversity (θ) 英文参考文献.docVIP

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Gene Sampling Strategies for Multi-Locus Population Estimates of Genetic Diversity (θ) 英文参考文献.doc

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Gene Sampling Strategies for Multi-Locus Population Estimates of Genetic Diversity (θ) 英文参考文献

GeneSamplingStrategiesforMulti-LocusPopulation EstimatesofGeneticDiversity(h) MatthewD.Carling1,2*,RobbT.Brumfield1 1Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America, 2Department of Biological Sciences, LouisianaStateUniversity,BatonRouge,Louisiana,UnitedStatesofAmerica Background.Theoreticalworksuggeststhatdatafrommultiplenuclearlociprovidebetterestimatesofpopulationgenetic parametersthandosingleloci,butjusthowmanylociareneededandhowmuchsequenceisrequiredfromeachhasbeen little explored. Methodology/Principle Findings. To investigate how much data is required to estimate the population geneticparameterh(4Nem)accuratelyunderidealcircumstances,wesimulateddatasetsofDNAsequencesunderthreevalues of h persite (0.1,0.01, 0.001), varying inboth the total number ofbase pairssequenced per individual andthe number of equal-lengthloci.Fromthesedatasetsweestimatedhusingthemaximumlikelihoodcoalescentframeworkimplementedin the computer program MIGRATE. Our results corroborated the theoretical expectation that increasing the number of loci impactedtheaccuracyoftheestimatemorethanincreasingthesequencelengthatsingleloci.However,whenthevalueofh waslow(0.001),theper-locussequencelengthwasalsoimportantforestimatinghaccurately,somethingthathasnotbeen emphasized in previous work. Conclusions/Significance. Accurate estimation of h required data from at least 25 independently evolving loci. Beyond this, there was little added benefit in terms of decreasing the squared coefficient of variationofthecoalescentestimatesrelativetotheextraeffortrequiredtosamplemoreloci. Citation: CarlingMD,BrumfieldRT(2007)Gene SamplingStrategiesforMulti-LocusPopulationEstimatesofGeneticDiversity (h). PLoSONE2(1): e160.doi:10.1371/journal.pone.0000160 INTRODUCTION and how many base pairs from each locus? Until an analytical solutiontothisquestionisdeveloped,simulateddatacanprovide insightsintowhether,givenafixedamountofsequencingeffort,it ispreferab