Genome-wide distribution of linkage disequilibrium in the population of Palau and its implications for gene flow in Remote Oceania

Linkage disequilibrium (LD) between alleles on the same human chromosome re sults from various evolutionary processes and is thus telling about the his tory of populations. Recently, LD has garnered substantial interest for its value to map and fine-map disease genes. We examine the distribution of LD between short tandem repeat alleles on autosomes and sex chromosomes in th e Remote Oceanic population of Palau to evaluate whether the data are consi stent with a recent hypothesis about the origins of genetic variation in Pa lau, specifically that the population experienced extensive male-biased gen e flow following initial settlement. Consistent with evolutionary theory ba sed on effective population size, LD between X-linked alleles is stochastic ally greater than LD between autosomal alleles, however, small but detectab le LD occurs for autosomal markers separated by substantial distances. By c ontrast, while Y-linked alleles experience only one-third the effective pop ulation size of X-linked alleles, their mean value for pairwise LD is only slightly larger than X-linked alleles. For a small population known to expe rience at least two extreme bottlenecks, 56 six-locus Y haplotypes exhibit remarkable diversity (0.96), comparable to Y diversity of Europeans, howeve r, autosomal and X-linked markers display significantly less diversity, as measured by heterozygosity (4.1 % less). Palauan Y haplotypes also fall int o distinct clusters, again unlike that of Europe. We argue these data are c onsistent with waves of male-biased gene flow.