This study analyzed the genetic composition of 3382 genetically characterized and pedigreed animals currently maintained under 3 different housing configurations at the California National Primate Research Center, including the indoor colony, outdoor 'corn cribs,' and half-acre field cages. Summary statistics based on 15 short tandem repeats strongly suggest significant effects of genetic drift, including the loss of allele diversity, among the enclosures within the housing facilities even though gene flow among the different housing units is actively promoted by colony management. Management methods of selectively harvesting female macaques to prevent overrepresentation of one or only a few matrilines and cross-fostering 1-wk-old infants among breeding cages and corn cribs have been insufficient to prevent genetic subdivisions among the cages and corn cribs and to evenly distribute genetic diversity throughout the colony. In addition to promoting several colony management strategies recommended herein to effectively curb inbreeding and genetic differentiation, current attempts of infant cross-fostering and minimizing matriline fragmentation should be expanded. The inclusion of inbred or highly genetically homogeneous animals with diminished allele diversity in linkage and association studies will likely compromise the potential for identifying allele-disease associations, whereas the inclusion of macaques from different geographic origins or their hybrids (or both) in experimental research confounds interpretations of phenotypic differences, due to inflation of the genetic contribution to phenotypic variance.
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