Noninvasive saliva collection for DNA analyses from free-ranging Tibetan macaques (Macaca thibetana).

Cryptic and endangered fauna, including many primate taxa, pose challenges for noninvasive collection of biomaterials. As a result, application of noninvasive genotyping to primates has been limited to the use of samples such as feces and hair for the extraction of PCR-amplifiable DNA. We present a method for noninvasive collection of saliva from habituated, free-ranging monkeys. The method utilizes a low-cost apparatus that controls for contamination and is usable with individual, free-ranging primates. Saliva samples were collected from 18 individuals in a population of Tibetan macaques (Macaca thibetana) in the Valley of Wild Monkeys in Huangshan, People's Republic of China. DNA was extracted from these samples and PCR-amplified for both mitochondrial and nuclear genes, Cytochrome B and MHC-DR Beta 1, respectively. These results indicate this is an effective technique for the noninvasive collection of saliva across age and sex class, and dominance rank in a free-ranging, terrestrial primate species. This device could have wide application for obtaining high-quality saliva samples from free-ranging primate populations for use in epidemiological studies, hormonal analyses of HPA axis function, pathogen screening, noninvasive genotyping, and behavioral genetics.

Early experience and serotonin transporter gene variation interact to influence primate CNS function.

Nonhuman primates offer unique opportunities to study the effects of genes, environments, and their interaction, on physiology and complex behavior. We examined genotype and early environment contributions to CNS function in a large sample of rhesus monkeys. In humans, length variation of the serotonin (5-HT) transporter (5-HTT) gene-linked polymorphic region (5-HTTLPR) that results in allelic variation in 5-HTT expression is associated with decreased serotonergic function and 5-HT-mediated psychopathology. We report that an analogous variation of the gene's regulatory region in monkeys interacts with early experience to affect central 5-HT functioning. Monkeys with deleterious early rearing experiences were differentiated by genotype in cerebrospinal fluid concentrations of the 5-HT metabolite, 5-hydroxyindoleacetic acid, while monkeys reared normally were not. These findings demonstrate an environment-dependent effect of the rh5-HTTLPR genotype on CNS 5-HT function and suggest nonhuman primates may provide an important avenue for investigating gene/environment interactions using candidate genes for physiological and behavioral traits.

Mamu-DQA1 allele and genotype frequencies in a randomly sampled breeding colony of rhesus macaques (Macaca mulatta).

We studied the allelic and genotypic distribution of the major histocompatibility class-II locus DQA1 observed in a random sample of Indian rhesus macaques (Macaca mulatta) from a major breeding facility in the United States. The DNA was isolated from whole blood samples collected between 1991 and 1994 from 65 Indian rhesus monkeys. Polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP), which involves use of specific amplification of DQA1 exon 2 and subsequent restriction digestion of the 242-base pair fragment, was used to genotype the animals for the 20 known macaque (Mamu)-DQA1 alleles. Frequencies for four alleles (DQA1*240x, *2502, *2503 and *0102) differed significantly from those reported in a smaller sample of rhesus macaques from the German Primate Center. The modest genetic survey of Mamu-DQA1 genotypes presented here will be particularly useful in designing epidemiologic studies that investigate associations between immunogenetic background and disease susceptibility in macaque models of human disease.

Rearing experiences and stress-induced plasma cortisol as early risk factors for excessive alcohol consumption in nonhuman primates.

BACKGROUND: The purpose of this study was to assess the impact of early rearing and stress-induced rise of plasma cortisol collected during infancy as a biological predictors of adult alcohol consumption in nonhuman primates. METHODS: Ninety-seven female and male rhesus macaques (Macaca mulatta) were investigated. They were reared for their first 6 months of life either without mothers or other adults but with constant access to same-aged peers (peer-reared), or as controls with their mothers (mother-reared). When subjects reached 6 months of age, they underwent a series of four sequential weeks of 4-day social separations. Blood was drawn 1 and 2 hr after initiation of the 4-day separation periods, and the plasma was assayed for plasma cortisol concentrations. When the subjects were young adults (approximately 50 months of age), they were tested for voluntary intake of alcohol for 1 hr per day, 4 days a week, during a period of 5 to 7 weeks under normal living conditions. RESULTS: The social separation challenge increased infant plasma cortisol concentrations, with peer-reared subjects exhibiting higher stress-induced cortisol concentrations than mother-reared animals. Subjects that responded to the social separation challenge with high cortisol levels consumed significantly more alcohol per kilogram of body weight as adults than subjects with a low cortisol response to the separation challenge, regardless of rearing condition. In addition, male and peer-reared subjects consumed significantly more alcohol than female and mother-reared subjects, respectively. CONCLUSIONS: These findings suggest that early rearing experiences, such as adult absence, and high plasma cortisol concentrations early in life after a social separation stressor, are useful psychobiological predictors of future high alcohol consumption among nonhuman primates.

Distribution of mtDNA haplogroup X among Native North Americans.

Mitochondrial DNA (mtDNA) samples of 70 Native Americans, most of whom had been found not to belong to any of the four common Native American haplogroups (A, B, C, and D), were analyzed for the presence of Dde I site losses at np 1715 and np 10394. These two mutations are characteristic of haplogroup X which might be of European origin. The first hypervariable segment (HVSI) of the non-coding control region (CR) of mtDNA of a representative selection of samples exhibiting these mutations was sequenced to confirm their assignment to haplogroup X. Thirty-two of the samples exhibited the restriction site losses characteristic of haplogroup X and, when sequenced, a representative selection (n = 11) of these exhibited the CR mutations commonly associated with haplogroup X, C --> T transitions at np 16278 and 16223, in addition to as many as three other HVSI mutations. The wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestor/descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups.

Distribution of sequence variation in the mtDNA control region of Native North Americans.

The distributions of mtDNA diversity within and/or among North American haplogroups, language groups, and tribes were used to characterize the process of tribalization that followed the colonization of the New World. Approximately 400 bp from the mtDNA control region of 1 Na-Dene and 33 Amerind individuals representing a wide variety of languages and geographic origins were sequenced. With the inclusion of data from previous studies, 225 native North American (284 bp) sequences representing 85 distinct mtDNA lineages were analyzed. Mean pairwise sequence differences between (and within) tribes and language groups were primarily due to differences in the distribution of three of the four major haplogroups that evolved before settlement of the New World. Pairwise sequence differences within each of these three haplogroups were more similar than previous studies based on restriction enzyme analysis have indicated. The mean of pairwise sequence differences between Amerind members of haplogroup A, the most common of the four haplogroups in North America, was only slightly higher than that for the Eskimo, providing no evidence of separate ancestry, but was about two-thirds higher than that for the Na-Dene. However, analysis of pairwise sequence divergence between only tribal-specific lineages, unweighted for sample size, suggests that random evolutionary processes have reduced sequence diversity within the Na-Dene and that members of all three language groups possess approximately equally diverse mtDNA lineages. Comparisons of diversity within and between specific ethnic groups with the largest sample size were also consistent with this outcome. These data are not consistent with the hypothesis that the New World was settled by more than a single migration. Because lineages tended not to cluster by tribe and because lineage sharing among linguistically unrelated groups was restricted to geographically proximate groups, the tribalization process probably did not occur soon after settlement of the New World, and/or considerable admixture has occurred among daughter populations.

Distribution of four founding mtDNA haplogroups among Native North Americans.

The mtDNA of most Native Americans has been shown to cluster into four lineages, or haplogroups. This study provides data on the haplogroup affiliation of nearly 500 Native North Americans including members of many tribal groups not previously studied. Phenetic cluster analysis shows a fundamental difference among 1) Eskimos and northern Na-Dene groups, which are almost exclusively mtDNA haplogroup A, 2) tribes of the Southwest and adjacent regions, predominantly Hokan and Uto-Aztecan speakers, which lack haplogroup A but exhibit high frequencies of haplogroup B, 3) tribes of the Southwest and Mexico lacking only haplogroup D, and 4) a geographically heterogeneous group of tribes which exhibit varying frequencies of all four haplogroups. There is some correspondence between language group affiliations and the frequencies of the mtDNA haplogroups in certain tribes, while geographic proximity appears responsible for the genetic similarity among other tribes. Other instances of similarity among tribes suggest hypotheses for testing with more detailed studies. This study also provides a context for understanding the relationships between ancient and modern populations of Native Americans.

Distribution of the 9-bp mitochondrial DNA region V deletion among North American Indians.

The deletion of a 9-bp segment from the intergenic region between the mtDNA cytochrome oxidase II gene and the lysine tRNA gene has been documented mainly in individuals of East Asian ancestry and in individuals from East Asian-derived populations (e.g., Polynesia). Among Native Americans the deletion is absent among Eskimos and northern Na-Dene populations and present among most Amerind populations [sensu Greenberg (1987); i.e., all Native Americans except Eskimo-Aleut and Na-Dene] that have been studied. To better characterize the frequency and distribution of the 9-bp deletion in North America, we surveyed more than 400 individuals from 59 tribes representing a variety of linguistic groups. The absence of the deletion among Eskimo and northern Na-Dene populations is confirmed. Among Amerind groups the deletion is present in all groups represented by more than six individuals. The geographic distribution of the frequencies of the deletion appears to be clinal in North America. The deletion is absent in the Artic and Subartic and reaches its highest frequency in the Southwest. This distribution is consistent with the hypothesis that the ancestors of the Amerinds and Na-Dene arrived in the New World by means of separate migrations. The presence of the 9-bp deletion in high frequencies in all the major linguistic groups in the Southwest suggests that migration among tribes was common.