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

摘要: Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to selectively neutral and unlinked. This method has been commonly applied data sets containing 10-100 inform conservation study demography. Performance these Ne estimates could improved by incorporating from thousands loci. However, exist on a limited number chromosomes, ensuring that some fraction will physically linked. Linked have elevated LD due recombination, which if not accounted for cause downwardly biased. Here, we present results coalescent forward simulations designed evaluate the bias LD-based ([Ncirc ]e). Contrary common perceptions, increasing does increase magnitude linkage. Although show it is possible identify produce unusually large r(2) values, simply removing values reliable way eliminate bias. Fortunately, in [Ncirc ]e strongly negatively correlated with process including chromosomes their length, this relationship provides general adjust Additionally, loci, precision much lower than expected based assumption each pair completely independent information.