Debra George

Hybridization and Stratification of Nuclear Genetic Variation in Macaca mulatta and M. fascicularis

We used genotypes for 13 short tandem repeats (STRs) to assess the genetic diversity within and differentiation among populations of rhesus macaques (Macaca mulatta) from mainland Asia and long-tailed macaques (M. fascicularis) from mainland and insular Southeast Asia. The subjects were either recently captured in the wild or derived from wild-caught founders maintained in captivity for biomedical research. A large number of alleles are shared between the 2 macaque species but a significant genetic division between them persists. The distinction is more clear-cut among populations that are not, or are unlikely to have recently been, geographically contiguous. Our results suggest there has been significant interspecific nuclear gene flow between rhesus macaques and long-tailed macaques on the mainland. Comparisons of mainland and island populations of long-tailed macaques reflect marked genetic subdivisions due to barriers to migration. Geographic isolation has restricted gene flow, allowing island populations to become subdivided and genetically differentiated. Indonesian long-tailed macaques show evidence of long-term separation and genetic isolation from the mainland populations, whereas long-tailed macaques from the Philippines and Mauritius both display evidence of founder effects and subsequent isolation, with the impact from genetic drift being more profound in the latter.

The genetic composition of populations of cynomolgus macaques (Macaca fascicularis) used in biomedical research

The genetic composition of cynomolgus macaques used in biomedical research is not as well‐characterized as that of 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.

Development of a Chinese–Indian hybrid (Chindian) rhesus macaque colony at the California National Primate Research Center by introgression

Background  Fullbred Chinese and Indian rhesus macaques represent genetically distinct populations. The California National Primate Research Center introduced Chinese founders into its Indian‐derived rhesus colony in response to the 1978 Indian embargo on exportation of animals for research and the concern that loss of genetic variation in the closed colony would hamper research efforts. The resulting hybrid rhesus now number well over a thousand animals and represent a growing proportion of the animals in the colony.

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.

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.

Population and landscape genetics of an introduced species (M. fascicularis) on the Island of Mauritius.

The cynomolgus macaque, Macaca fascicularis, was introduced onto the island of Mauritius in the early 17th century. The species experienced explosive population growth, and currently exists at high population densities. Anecdotes collected from nonhuman primate trappers on the island of Mauritius allege that animals from the northern portion of the island are larger in body size than and superior in condition to their conspecifics in the south. Although previous genetic studies have reported Mauritian cynomolgus macaques to be panmictic, the individuals included in these studies were either from the southern/central or an unknown portion of the island. In this study, we sampled individuals broadly throughout the entire island of Mauritius and used spatial principle component analysis to measure the fine-scale correlation between geographic and genetic distance in this population. A stronger correlation between geographic and genetic distance was found among animals in the north than in those in the southern and central portions of the island. We found no difference in body weight between the two groups, despite anecdotal evidence to the contrary. We hypothesize that the increased genetic structure among populations in the north is related to a reduction in dispersal distance brought about by human habitation and tourist infrastructure, but too recent to have produced true genetic differentiation.

Mitochondrial DNA of Protohistoric Remains of an Arikara Population from South Dakota: Implications for the Macro-Siouan Language Hypothesis

Abstract Mitochondrial DNA (mtDNA) was extracted from skeletal remains excavated from three Arikara sites in South Dakota occupied between AD 1600 and 1832. The diagnostic markers of four mtDNA haplogroups to which most Native Americans belong (A, B, C, and D) were successfully identified in the extracts of 55 (87%) of the 63 samples studied. The frequencies of the four haplogroups were 42%, 29%, 22%, and 7%, respectively, and principal coordinates analysis and Fishers exact tests were conducted to compare these haplogroup frequencies with those from other populations. Both analyses showed closer similarity among the Mohawk, Arikara, and Sioux populations than between any of these three and any other of the comparison populations. Portions of the first hypervariable segment (HVSI) of the mitochondrial genome were successfully amplified and sequenced for 42 of these 55 samples, and haplotype networks were constructed for two of the four haplogroups. The sharing of highly derived lineages suggests that some recent admixture of the Arikara with Algonquian-speaking and Siouan-speaking groups has occurred. The Arikara shared more ancient lineages with both Siouan and Cherokee populations than with any other population, consistent with the Macro-Siouan language hypothesis that Iroquoian, Siouan, and Caddoan languages share a relatively recent common ancestry.

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

Regional populations of rhesus and long-tailed macaques exhibit fundamental differences in mitochondrial DNA, short tandem repeat and single nucleotide polymorphism variation between mainland and insular Southeast Asian populations. Some studies have revealed genetic admixture between these species due to natural hybridization and human-assisted intercrosses. A quantitative real-time PCR (qPCR) assay was developed to efficiently determine the species of origin of a macaque biological sample, and to quantify the species-specific template DNA. Prior knowledge of species identity and DNA concentrations are crucial for maintaining cost-effective methods and accurate DNA analysis. DNA from 109 regionally representative rhesus and long-tailed macaques was qPCR amplified to determine the species and template quantities. Of the 19 Vietnamese long-tailed macaques, 3 samples were discovered to be hybrids.

Population genetics of the California National Primate Research Center's (CNPRC) captive Callicebus cupreus colony.

Abstract The California National Primate Research Center maintains a small colony of titi monkeys (Callicebus cupreus) for behavioral studies. While short tandem repeat (STR) markers are critical for the genetic management of the center’s rhesus macaque (Macaca mulatta) breeding colony, STRs are not used for this purpose in the maintenance of the center’s titi monkey colony. Consequently, the genetic structure of this titi monkey population has not been characterized. A lack of highly informative genetic markers in titi monkeys has also resulted in scant knowledge of the species’ genetic variation in the wild. The purpose of this study was to develop a panel of highly polymorphic titi monkey STRs using a cross-species polymerase chain reaction (PCR) amplification protocol that could be used for the genetic management of the titi monkey colony. We screened 16 STR primer pairs and selected those that generated robust and reproducible polymorphic amplicons. Loci that were found to be highly polymorphic, very likely to be useful for parentage verification, pedigree assessment, and studying titi monkey population genetics, were validated using Hardy–Weinberg equilibrium and linkage disequilibrium analyses. The genetic data generated in this study were also used to assess directly the impact on the colony’s genetic diversity of a recent adenovirus outbreak. While the adenovirus epizootic disease caused significant mortality (19 deaths among the 65 colony animals), our results suggest that the disease exhibited little or no influence on the overall genetic diversity of the colony.