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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). 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 r(2) values, simply removing large r(2) values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in [Ncirc ]e 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 [Ncirc ]e is much lower than expected based on the assumption that each pair of loci provides completely independent information.

Coral reefs within the Coral Triangle (CT) are home to the greatest marine diversity on the globe and are an important supplier of marine resources to densely populated coastal regions. Many coral reefs within the CT and around the world are under threat from over-exploitation. Marine protected areas (MPAs) have been proven to be effective tools in restoring fish stocks. However, the role that MPAs play in promoting connectivity at greater distances through larval dispersal is still unknown. RADseq was used to discover 4253 SNPs from 81 individuals of the dusky parrotfish (Scarus niger) collected from three sites within the Philippines. A lack of population structure suggested a high rate of gene flow (F ST = 0.007). Estimates of Ne from linkage disequilibrium are relatively large, ranging from 1200 to 2000. A sibling analysis revealed one pair of well-supported full siblings (r = 0.773) and one pair of putative half siblings (r = 0.191) between sites separated by more than 500 km. The low F ST values indicate a high degree of gene flow between the reefs within the sampling area while the sibling analysis suggests demographic connectivity between the Sibuyan Sea and the Sulu Sea. The Mindoro–Panay throughflow is a likely vector by which larvae are transported between these sites, suggesting that reefs in Romblon are sources for reefs near Basay, 400 km to the south. Given the reliance of a vast majority of coral reef fishes on larval dispersal, this study reveals that MPAs established within the central Philippines can supply varying levels of larvae to overfished reefs.