The SPF breeding program at the Caribbean Primate Research Center supplies Indian-origin rhesus macaques of known genetic and virologic background for biomedical research. In this study, population genetic analyses using 14 short tandem-repeat sequences showed that the SPF colony has remained genetically homogenous over time, with sufficient amounts of heterozygosity and minimal stratification from its founders. Intergenerational studies indicated that an average of 7 alleles have been retained, inbreeding levels have remained low, and the degree of Indian ancestry is one of the highest among several national primate research centers. The relative low genetic diversity in the free-ranging population as well as in the captive SPF and conventional colonies when compared with that of other primate centers indicates that the free-ranging population, from which the captive-colony animals were derived, has experienced significant founder effects and genetic drift during the years after its establishment. This study supports the historical origin of the free-ranging population and confirms the high value of this resource for biomedical research. Current genetic diversity levels within the SPF colony can be ensured with the practice of colony management approaches such as equalizing male:female ratios in each SPF breeding group and increasing breeding group sizes. Introducing new Indian-origin macaques from other captive colonies might help to maximize the genetic diversity of the breeding stock. Furthermore, genetic estimates must be used to rank breeders according to their genetic value or their genome uniqueness to increase founder-genome representation and curb future genetic bottlenecks and allele loss.
We used the Affymetrix(®) Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.
The National Research Council recommends that genetic differentiation among subgroups of ethnic samples be lower than 3% of the total genetic differentiation within the ethnic sample to be used for estimating reliable random match probabilities for forensic use. Native American samples in the United States' Combined DNA Index System (CODIS) database represent four language families: Algonquian, Na-Dene, Eskimo-Aleut, and Salishan. However, a minimum of 27 Native American language families exists in the US, not including language isolates. Our goal was to ascertain whether genetic differences are correlated with language groupings and, if so, whether additional language families would provide a more accurate representation of current genetic diversity among tribal populations. The 21 short tandem repeat (STR) loci included in the Globalfiler® PCR Amplification Kit were used to characterize six indigenous language families, including three of the four represented in the CODIS database (i.e. Algonquian, Na-Dene, and Eskimo-Aleut), and two language isolates (Miwok and Seri) using major population genetic diversity metrics such as F statistics and Bayesian clustering analysis of genotype frequencies. Most of the genetic variation (97%) was found to be within language families instead of among them (3%). In contrast, when only the three of the four language families represented in both the CODIS database and the present study were considered, 4% of the genetic variation occurred among the language groups. Bayesian clustering resulted in a maximum posterior probability indicating three genetically distinct groups among the eight language families and isolates: (1) Eskimo, (2) Seri, and (3) all other language groups and isolates, thus confirming genetic subdivision among subgroups of the CODIS Native American database. This genetic structure indicates the need for an increased number of Native American populations based on language affiliation in the CODIS database as well as more robust sample sets for those language families. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1963088 .
Abstract Background Knowledge of major histocompatibility complex ( MHC ) composition and distribution in rhesus macaque colonies is critical for management strategies that maximize the utility of this model for biomedical research. Methods Variation within the Mamu‐A and Mamu‐B (class I) and DRB , DQA /B, and DPA /B (class II ) regions of 379 animals from the Caribbean Primate Research Center's (CPRC) specific pathogen free ( SPF ) colony was examined using massively parallel sequencing. Results Analyses of the 7 MHC loci revealed a background of Indian origin with high levels of variation despite past genetic bottlenecks. All loci exhibited mutual linkage disequilibria while conforming to Hardy–Weinberg expectations suggesting the achievement of mutation‐selection balance. Conclusion The CPRC's SPF colony is a significant resource for research on AIDS and other infectious agents. Characterizing colony‐wide MHC variability facilitates the breeding and selection of animals bearing desired haplotypes and increases the investigator's ability to understand the immune responses mounted by these animals.
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