Detecting signatures of inter‐regional and inter‐specific hybridization among the Chinese rhesus macaque specific pathogen‐free (SPF) population using single nucleotide polymorphic (SNP) markers

Abstract

While rates of gene flow between rhesus and longtail macaque populations near their hybrid zone in Indochina have been quantified elsewhere, this study demonstrates that the inter-specific introgression is not limited to the Indochinese hybrid zone but is more geographically widespread. SNP analysis across the rhesus and longtail genomes shows evidence for inter-specific admixture between Chinese rhesus and mainland longtails, with implications for genetic diversity both in the Chinese super-SPF population at the California National Primate Research Center and other primate facilities. Eastern Chinese rhesus appeared more highly derived than western Chinese rhesus, and allele sharing between longtails and Chinese rhesus was not random with regard to geographic distance, but no significant nuclear genetic differences between eastern and western Chinese rhesus was detected among the 245 genic SNPs assayed. The implications of this inter-specific admixture for the use of Chinese rhesus and mainland longtail in biomedical research should be considered.

A Rapid Quantitative Real-Time PCR-Based DNA Quantification Assay Coupled with Species – Assignment Capabilities for Two Hybridizing Macaca Species

“…The same is true for geographically separated long-tailed macaques [Tosi and Coke, 2007]. Yet there is ample evidence that some of the animals, especially rhesus macaques of Chinese origin, which have been purchased and/or bred in captivity for biomedical experimentation in the US, exhibit recent and ancient genetic signatures of interspecific admixture [Kanthaswamy et al, 2010]. The same is true for long-tailed macaques [Kanthaswamy et al, 2008[Kanthaswamy et al, , 2010.…”

“…This study was conducted on 109 whole blood samples obtained from the facilities listed in Kanthaswamy et al [2008Kanthaswamy et al [ , 2010. Blood samples of long-tailed macaques from each of the following locations (and number of samples or n) were used ( fig.…”

“…Yet there is ample evidence that some of the animals, especially rhesus macaques of Chinese origin, which have been purchased and/or bred in captivity for biomedical experimentation in the US, exhibit recent and ancient genetic signatures of interspecific admixture [Kanthaswamy et al, 2010]. The same is true for long-tailed macaques [Kanthaswamy et al, 2008[Kanthaswamy et al, , 2010. Sixty-five percent of all long-tailed macaques imported into the US are from Chinese breeders, who in turn have obtained their wild-caught founder stocks from Indonesia, Malaysia, the Philippines and Indochina including Cambodia, Laos and Vietnam [AESOP Project, 2006].…”

“…Based on a study of Y chromosome and mitochondrial DNA (mtDNA) markers in long-tailed macaques, Tosi et al [2002] have proposed that introgression from male rhesus to female long-tailed macaques was one conduit for gene flow. Consequently, Indochinese long-tailed macaques exhibit much greater genetic diversity than long-tailed macaques from other geographic locations [Kanthaswamy et al, 2008[Kanthaswamy et al, , 2010. (1) India (rhesus macaques) (2) Burma (rhesus macaques) (3) China (rhesus macaques) (4) Vietnam (long-tailed macaques) (5) Indonesia (long-tailed macaques) (6) The Philippines (long-tailed macaques) (7) Mauritius (long-tailed macaques) Fig.…”

“…However, mtDNA is maternally inherited and can neither detect male-mediated gene flow [Kanthaswamy and Smith, 2004;Hajibabaei et al, 2007], nor be used to quantify the nuclear DNA on which most of the biomedically relevant protein-coding genes reside. Short tandem repeat (STR) Barr/Premasuthan/Satkoski/Smith/George/ Kanthaswamy [Ferguson et al, 2007] and single nucleotide polymorphism (SNP)-based procedures have been developed [Kanthaswamy et al, 2008[Kanthaswamy et al, , 2010 that ascertain evolutionary relationships among groups of animals from the same species or groups from different species among populations of rhesus and long-tail macaques. While these assays can provide the discriminatory power to separate species and detect intraspecies variation, they rely on complicated multiplex approaches that are cumbersome and costly.…”