Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci.

ABSTRACT: Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause Ne estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based Ne estimates ([Ncirc ]e). C

SUBMITTER: Waples RK 

PROVIDER: S-EPMC5026758 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature