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

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 (N
circe). Contrary to common perceptions, increasing the number of loci does
not increase the magnitude of linkage. Although we show it is possible to
identify some pairs of loci that produce unusually large r2 values, simply
removing large r2 values is not a reliable way to eliminate bias.
Fortunately, the magnitude of bias in N circe is strongly and negatively
correlated with the process of recombination, including the number of
chromosomes and their length, and this relationship provides a general way
to adjust for bias. Additionally, we show that with thousands of loci,
precision of N circe is much lower than expected based on the assumption
that each pair of loci provides completely independent information.