A Comparative Analysis of the Genetic Structures of Rhesus Macaques (Macaca mulatta) Kept in Enclosure-Based Systems and Semi-Natural Settings

This study compares 2 rhesus macaque populations, one captive (the California National Primate Research Center [CNPRC]) and one seminatural (the Cayo Santiago [CS] population), to evaluate the impact of colony management on genetic structure. While the CNPRC houses its 4,000-plus animals in different housing enclosures, CS has a seminatural, free-ranging population of ∼1,900 individuals. Pedigrees of 3,679 animals at the CNPRC and 2,147 animals at CS were analyzed to assess cross-generational genome uniqueness (GU), inbreeding coefficients, mean kinship (MK), founder equivalents, and founder genome equivalents. An estimated 30% of the 409 CS founders contributed to the present population, compared with <10% of the 2,980 founders and subsequently introduced animals at the CNPRC. Differences in pedigree structure and potential inbreeding risk, particularly at the CNPRC, indicate a more genetically subdivided population there than at CS. The CNPRC also exhibited a lower GU than CS, whereas the MK of both colonies showed a similar upward trend over the study period (2000-2024). Also revealed are significant differences in reproductive activity, lifespan, and the number of families per individual between the 2 colonies. There are challenges in maintaining captive-bred colonies, such as the CNPRC, where restricted gene flow and inbreeding lead to dramatic declines in genetic variability. Strategies such as equalizing reproductive success, implementing cross-fostering programs for infants, and introducing new animals are insufficient to combat inbreeding, genetic subdivisions, and the loss of founder representation. Findings highlight the need for ongoing monitoring of inbreeding coefficients, GU, and MK to safeguard genetic integrity and ensure the long-term viability of captive-bred colonies. The analysis also offers insights for managing these colonies, highlighting MK as a key metric for preserving genetic diversity because it integrates founder representation, drift, and inbreeding into a colony-wide measure that directly informs colony management decisions.