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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.

Chronic diarrheal disease (CDD) is a critical problem for breeders of captive rhesus macaque (Macaca mulatta), as it results in significant levels of morbidity and death annually. As with other inflammatory disorders, CDD is thought to be caused by environmental and/or genetic factors. Although correspondence between the characters defined as Mendelian by pedigree or segregation analysis and functional genes is difficult to establish, such analyses provide essential entry points into understanding CDD in captive bred rhesus macaques. To investigate the familial aggregation of CDD in captive rhesus macaque, we performed pedigree, segregation and heritability analyses on genealogical data from 55 severely affected individuals (probands) through whom relatives with a history of CDD were ascertained from routine computerized colony records comprising vital and demographic statistics of 10,814 rhesus macaques. We identified 175 rhesus macaques with CDD and estimated its incidence as approximately 2% in the colony. The disease strongly clustered in eight multi-generation pedigrees. Inspection of the pedigrees, segregation analysis and heritability estimate of CDD suggest that susceptibility to the disease is under strong genetic control. Identification of the locations of susceptibility genes in the rhesus macaque genome could facilitate the reduction of their frequency in captive breeding facilities., (© 2013 Wiley Periodicals, Inc.)

Some breeding facilities in the United States have crossbred Chinese and Indian rhesus macaque (Macaca mulatta) founders either purposefully or inadvertently. Genetic variation that reflects geographic origins among research subjects has the potential to influence experimental outcomes. The use of animals from different geographic regions, their hybrids, and animals of varying degrees of kinship in an experiment can obscure treatment effects under study because high interanimal genetic variance can increase phenotypic variance among the research subjects. The intent of this study, based on a broad genomic analysis of 2,808 single nucleotide polymorphisms (SNPs), is to ensure that only animals estimated to be of pure Indian or Chinese ancestry, based on both demographic and genetic information, are used as sources of infants for derivation and expansion of the California National Primate Research Center's (CNPRC) super-Specific Pathogen Free (SSPF) rhesus macaque colony. Studies of short tandem repeats (STRs) in Indian and Chinese rhesus macaques have reported that heterozygosity of STRs is higher in Chinese rhesus macaques than in Indian rhesus macaques. The present study shows that heterozygosity of SNPs is actually higher in Indian than in Chinese rhesus macaques and that the Chinese SSPF rhesus macaque colony is far less differentiated from their founders compared to the Indian-origin animals. The results also reveal no evidence of recent gene flow from long-tailed and pig-tailed macaques into the source populations of the SSPF rhesus macaques. This study indicates that many of the long-tailed macaques held in the CNPRC are closely related individuals. Most polymorphisms shared among the captive rhesus, long-tailed, and pig-tailed macaques likely predate the divergence among these groups., (© 2012 Wiley Periodicals, Inc.)

The California National Primate Research Center (CNPRC) houses more than 1,000 rhesus macaques (Macaca mulatta) of mixed Chinese-Indian ancestry. Most of these animals are kept in outdoor field cages, the colony's long term breeding resource. Since 2001, hybrids comprised between 4 and 49% of the field cage populations, but in most cases have represented a maximum of 10% of those populations. The increasing prevalence of hybrids is partly due to management efforts to distribute genetic diversity effectively and minimize genetic subdivisions. However, other factors may also contribute to the spread of hybrids within the colony, most notably variance in socio-sexual behaviors and physical attributes. It is known that hybrids of some species exhibit heterosis, such as early maturation, that can enhance reproductive success, and anecdotal observations of mixed groups of hybrid, Indian and Chinese animals at the CNPRC suggest that hybrids are more sexually active. To determine whether hybrids experienced a reproductive advantage, a study was conducted using birth records of 5,611 offspring born in the CNPRC colony between 2003 and 2009. We found that while the degree of Chinese ancestry (DCA) appeared to influence the maturational schedule of both males and females (maturation was inversely related to proportion of Chinese ancestry), DCA had no independent effect on either male or female RS or rank. Therefore, we have found no evidence that a hybrid phenotype confers an absolute reproductive advantage in our colony., (© 2011 Wiley-Liss, Inc.)

Aim: To describe and assess the scientific and technical aspects of animal forensic testing at the University of California, Davis. The findings and recommendations contained in this report are designed to assess the past, evaluate the present, and recommend reforms that will assist the animal forensic science community in providing the best possible services that comply with court standards and bear judicial scrutiny., Methods: A batch of 32 closed files of domestic dog DNA cases processed at the University of California, Davis, between August 2003 and July 2005 were reviewed in this study. The case files comprised copies of all original paperwork, copies of the cover letter or final report, laboratory notes, notes on analyses, submission forms, internal chains of custody, printed images and photocopies of evidence, as well as the administrative and technical reviews of those cases., Results: While the fundamental aspects of animal DNA testing may be reliable and acceptable, the scientific basis for forensic testing animal DNA needs to be improved substantially. In addition to a lack of standardized and validated genetic testing protocols, improvements are needed in a wide range of topics including quality assurance and quality control measures, sample handling, evidence testing, statistical analysis, and reporting., Conclusion: This review implies that although a standardized panel of short tandem repeat and mitochondrial DNA markers and publicly accessible genetic databases for canine forensic DNA analysis are already available, the persistent lack of supporting resources, including standardized quality assurance and quality control programs, still plagues the animal forensic community. This report focuses on closed cases from the period 2003-2005, but extends its scope more widely to include other animal DNA forensic testing services.

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.

A study based on 14 STRs was conducted to understand intergenerational genetic changes that have occurred within the California National Primate Research Center's (CNPRC) regular specific pathogen-free (SPF) and super-SPF captive rhesus macaque populations relative to their conventional founders. Intergenerational genetic drift has caused age cohorts of each study population, especially within the conventional population, to become increasingly differentiated from each other and from their founders. Although there is still only minimal stratification between the conventional population and either of the two SPF populations, separate derivation of the regular and super-SPF animals from their conventional founders has caused the two SPF populations to remain marginally different from each other. The regular SPF and, especially, the super-SPF populations have been influenced by the effects of differential ancestry, sampling, and lost rare alleles, causing a substantial degree of genetic divergence between these subpopulations. The country of origin of founders is the principal determinant of the MHC haplotype composition of the SPF stocks at the CNPRC. Selection of SPF colony breeders bearing desired genotypes of Mamu-A*01 or -B*01 has not affected the overall genetic heterogeneity of the conventional and the SPF research stocks.Because misclassifying the ancestry of research stocks can undermine experimental outcomes by excluding animals with regional-specific genotypes or phenotypes of importance, understanding founder/descendent genetic relationships is crucial for investigating candidate genes with distinct geographic origins. Together with demographic management, population genetic assessments of SPF colonies can curtail excessive phenotypic variation among the study stocks and facilitate successful production goals., ((c) 2010 Wiley-Liss, Inc.)