Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques

Abstract

To understand the demographic history of rhesus macaques ( Macaca mulatta ) and document the extent of linkage disequilibrium (LD) in the genome, we partially resequenced five Encyclopedia of DNA Elements regions in 9 Chinese and 38 captive-born Indian rhesus macaques. Population genetic analyses of the 1467 single-nucleotide polymorphisms discovered suggest that the two populations separated about 162,000 years ago, with the Chinese population tripling in size since then and the Indian population eventually shrinking by a factor of four. Using coalescent simulations, we confirmed that these inferred demographic events explain a much faster decay of LD in Chinese ( r 2 ≈ 0.15 at 10 kilobases) versus Indian ( r 2 ≈ 0.52 at 10 kilobases) macaque populations.