Estimating effective population size using RADseq: Effects of SNP selection and sample size.

ABSTRACT: Effective population size (Ne ) is a key parameter of population genetics. However, N e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site-associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Ne esti

SUBMITTER: Marandel F 

PROVIDER: S-EPMC7042749 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature