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A Large‐Scale SNP ‐Based Genomic Admixture Analysis of the Captive Rhesus Macaque Colony at the C alifornia N ational P rimate R esearch C enter
Author(s) -
KANTHASWAMY SREETHARAN,
TRASK JESSICA SATKOSKI,
ROSS CODY T.,
KOU ALEX,
HOUGHTON PAUL,
SMITH DAVID G.,
LERCHE NICK
Publication year - 2012
Publication title -
american journal of primatology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.988
H-Index - 81
eISSN - 1098-2345
pISSN - 0275-2565
DOI - 10.1002/ajp.22025
Subject(s) - rhesus macaque , biology , macaque , loss of heterozygosity , genetics , snp , primate , genetic variation , evolutionary biology , single nucleotide polymorphism , genotype , allele , gene , ecology
Some breeding facilities in the U nited S tates have crossbred C hinese and I ndian rhesus macaque ( M acaca mulatta ) founders either purposefully or inadvertently. Genetic variation that reflects geographic origins among research subjects has the potential to influence experimental outcomes. The use of animals from different geographic regions, their hybrids, and animals of varying degrees of kinship in an experiment can obscure treatment effects under study because high interanimal genetic variance can increase phenotypic variance among the research subjects. The intent of this study, based on a broad genomic analysis of 2,808 single nucleotide polymorphisms ( SNP s), is to ensure that only animals estimated to be of pure I ndian or C hinese ancestry, based on both demographic and genetic information, are used as sources of infants for derivation and expansion of the C alifornia N ational P rimate R esearch C enter's ( CNPRC ) super‐Specific Pathogen Free (SSPF) rhesus macaque colony. Studies of short tandem repeats ( STR s) in I ndian and C hinese rhesus macaques have reported that heterozygosity of STR s is higher in C hinese rhesus macaques than in I ndian rhesus macaques. The present study shows that heterozygosity of SNP s is actually higher in I ndian than in C hinese rhesus macaques and that the C hinese SSPF rhesus macaque colony is far less differentiated from their founders compared to the I ndian‐origin animals. The results also reveal no evidence of recent gene flow from long‐tailed and pig‐tailed macaques into the source populations of the SSPF rhesus macaques. This study indicates that many of the long‐tailed macaques held in the CNPRC are closely related individuals. Most polymorphisms shared among the captive rhesus, long‐tailed, and pig‐tailed macaques likely predate the divergence among these groups. Am. J. Primatol. 74:747‐757, 2012. © 2012 Wiley Periodicals, Inc.