International Journal of Primatology, Vol. 27, No. 3, June 2006 ( C  2006) DOI: 10.1007/s10764-006-9026-3 Identification of Country of Origin and Admixture Between Indian and Chinese Rhesus Macaques David Glenn Smith, 1,2,3 Debra George, 1 Sreetharan Kanthaswamy, 1,2 and John McDonough 2 Received November 29, 2004; revision January 26, 2005; accepted February 6, 2005; Published Online June 6, 2006 We describe a restriction analysis that distinguishes between rhesus macaques of unmixed Indian and Chinese ancestry and between western and eastern Chinese ancestry. We amplified a 254-bp fragment of mitochondrial DNA (mtDNA) that contains restriction sites hypothesized to be diagnostic of country of origin for samples from 534 and 567 individuals alleged to be of solely Indian or solely Chinese ancestry, respectively. After digestion with the MaeIII, SmlI, and BccI restriction enzymes, the polymerase chain reaction (PCR) products of only 3 of the 1101 samples exhibited restriction patterns uncharacteristic of their alleged country of origin. We genotyped a sample comprising 392 of these rhesus macaques for 24 nuclear microsatellite (STR) loci. Principal coordinates analysis confirmed marked genetic similarity of regional populations within each country but a substantial difference be- tween Indian and Chinese rhesus macaques. Using STRUCTURE (Pritchard and Wen, 2003),we assigned probabilities of Chinese and Indian ancestry to each sample based on its STR genotypes. We assigned all the unmixed rhe- sus macaques to their correct countries of origin with probabilities >0.95. We constructed an artificial sample of 1st-generation hybrid Indian/Chinese rhesus macaques by randomly sampling from the genotypes of Indian and Chinese individuals. STRUCTURE assigned probabilities of Chinese and Indian ancestry to hybrids that closely corresponded with the proportions 1 Department of Anthropology, Davis, California. 2 California National Primate Research Center, Davis, California. 3 To whom correspondence should be addressed; e-mail: dgsmith@ucdavis.edu. 881 0164-0291/06/0600-0881/0 C  2006 Springer Science+Business Media, Inc.