rank and order evaluating the performance of snps for individual assignment in a non-model organism评估的性能等级和秩序snp对个人分配在non-model有机体.pdfVIP

Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism 1 1 1 2 1 Caroline G. Storer , Carita E. Pascal , Steven B. Roberts , William D. Templin , Lisa W. Seeb , James E. Seeb1* 1 School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America, 2 Gene Conservation Laboratory, Alaska Department of Fish and Game, Anchorage, Alaska, United States of America Abstract Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F , informativeness (I ), average ST n contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 9