Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes

We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes.Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes.     

Population subdivision and gene flow among wild orangutans

Genetic variability among populations of orangutans from Borneo and Sumatra was assessed using seven SSR loci. Most SSR loci were highly polymorphic and their allele frequencies exhibited substantial variation across subpopulations. While significant genetic subdivision was observed among the island populations, genetic distance did not increase with geographic distance and sufficient gene flow persists to prevent marked genetic subdivision. Since it is unlikely that the Bornean Orangutans dispersed naturally among locations separated by such formidable geographic barriers, human assistance might already have altered their genetic structure. Our data suggests that there may be at least two subspecific clades of orangutans within Borneo while Central Kalimantan animals may have become more genetically related to animals in Sumatra due to human intervention.     

Use of microsatellite polymorphisms for paternity exclusion in rhesus macaques (Macaca multatta)

A total of 224 infant rhesus macaques and their dams and potential sires in 11 multimale groups in 2 different specific pathogen free breeding colonies were screened for up to 6 different microsatellite polymorphism using cross-species PCR amplification. Observed and expected success of paternity exclusion analysis (based on gene frequencies of sires and dams in each colony) were computed by individual locus and cumulatively. Greater or less success of PEA than expected was observed at most loci due to the nonrandom distribution of genotypes between sires and dams and among breeding groups at each colony and because genotypes at different loci did not provide completely independent information about parentage. The combined success of PEA using all loci, however, was slightly greater than predicted both with and without assuming knowledge of one parent's (i.e. the dam's) genotype and was far greater than that based on protein coding loci or DNA restriction fragment length polymorphisms.     

A genetic comparison of two alleged subspecies of Philippine cynomolgus macaques

Two subspecies of cynomolgus macaques (Macaca fascicularis) are alleged to co‐exist in the Philippines, M. f. philippensis in the north and M. f. fascicularis in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies M. f. fascicularis to warrant the subspecies distinction M. f. philippensis. Am J Phys Anthropol 155:136–148, 2014. © 2014 Wiley Periodicals, Inc.     

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

Background 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. Methods Twelve rhesus and longtail macaque populations were analyzed using single nucleotide polymorphic (SNP) loci. Results There is 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 in 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 were detected among the 245 genic SNPs assayed. Conclusion The implications of this inter‐specific admixture for the use of Chinese rhesus and mainland longtail in biomedical research should be considered.     

Identification of Country of Origin and Admixture Between Indian and Chinese Rhesus Macaques

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 origin, 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. A sample comprising 392 of these rhesus macaques was genotyped for 24 nuclear microsatellite (STR) loci. Principal coordinates analysis confirmed marked genetic similarity of regional populations within each country but a substantial difference between 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 rhesus 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 robabilities of Chinese and Indian ancestry to hybrids that closely corresponded with the proportions of alleles in that sample drawn from unmixed Chinese and Indian rhesus macaques.     

Genetic characterization of wild and captive rhesus macaques in China

The genetic structures of wild and captive rhesus macaque populations within China were compared by analyzing the mtDNA sequences of 203 captive-bred Chinese rhesus macaques with 77 GenBank sequences from wild-caught animals trapped throughout China. The genotypes of 22 microsatellites of captive Chinese rhesus macaques were also compared with those of captive Indian animals. The Chinese population is significantly differentiated from the Indian population and is more heterogeneous. Thus, compared with Indian rhesus macaques the phenotypic variance of traits with high heritability will be inflated in Chinese animals. Our data suggest that the western Chinese provinces have more subdivided populations than the eastern and southern Chinese provinces. The southern Chinese populations are the least structured and might have been more recently established. Human-mediated interbreeding among captive Chinese populations has occurred, implying that Chinese breeding strategies can influence the interpretation of biomedical research in the USA.     

Evaluating the genetic status of a closed colony of titi monkeys (Callicebus cupreus) using multigenerational pedigrees

Pedigree metrics are essential for investigating colony genetic structure. The genetic structure of a closed Callicebus cupreus colony was examined using multigenerational pedigrees. Inbreeding was low, but genetic drift caused the loss of founder genome representation. Pedigrees can be used to detect founder representation and prevent bottlenecks and allele loss.     

Reconstruction of Parentage in a Band of Captive Hamadryas Baboons

The male leaders of free-ranging harem groups of hamadryas baboons are believed to mate exclusively with the female members of their harems, which typically contain no more than 2–3 females. Using no-parent parentage exclusion analysis (PEA) we identified the paternity of 25 offspring born in a captive band of hamadryas baboons (Papio hamadryas hamadryas) containing five adult males, each with a stable harem of about five females. Nine of 13 microsatellite (SSR) loci known to be highly polymorphic in rhesus macaques (Macaca mulatta) were successful in identifying the sires of all but two offspring without knowledge of the dams' genotypes, and we were able to determine the sires of all offspring when the dams' genotypes were considered. Mating success of the males ranged between 2 and 7 offspring and bore no clear relationship to the males' ages, ranks or the number of females in their harems. The males sired 7 of the 25 offspring with females outside their own harems, with higher-ranking males exhibiting greater success monopolizing access to females in their harem than lower-ranking males did. More surprisingly, the females assigned as the dams of 14 of the 25 offspring could be unequivocally excluded from parentage. The identity of the true dam could be determined for each of these 14 offspring using single-parent PEA and was uncorrelated with the ranks of these offsprings' sires and whether the offspring were born to dams outside the sires' harem groups. The combined effect of this extraharem mating and kidnapping was that only 12 of the 25 offspring were raised within their sires' harem groups. A second group of hamadryas baboons of identical structure exhibited the same high incidences of infant kidnapping and mating outside the harem group. It is unclear whether these behaviors provide an adaptive advantage or represent aberrant behavior resulting from captivity or other circumstances.