Primate colony management: part genes, part environment

When someone thinks of nonhuman primate (NHP) management, genetics might not be the first thing that comes to mind. But perhaps it should be. And unlike animals such as rodents—that are usually maintained as specific genetic strains—NHPs are often bred for diversity (1).

Genetic diversity, indeed, has long been considered a valuable rubric for evaluating animal populations. Inbreeding depression is a phenomenon well-known in biology, where individuals—especially in small populations—can suffer from reduced survival, growth, or fertility due to frequent mating amongst close relatives (2). This presents a challenge to institutions such as the National Primate Research Centers (NPRCs), which must select breeding animals from the limited numbers already in their ranks.

The NPRCs have proved up for the task. In addition to longstanding procedures such as pedigree analyses, NPRC geneticists have developed novel genetic assays to help standardize methods of ancestry estimation, parentage, and population fitness (3). This includes cooperation between centers in archiving and sharing of NHP genetic information, with the ultimate goal of managing NPRC resources as a unified whole. This is similar to the way stud books function at participating zoos, albeit with increased technical focus and precision.

Examples of NPRC application of genetic data to primate management questions are legion, but several recent applications will serve for purposes of illustration. California NPRC scientists have utilized short-tandem repeat (STR) markers to identify genetic locations (loci) of particular usefulness for estimating parentage in titi monkeys, a common species in behavioral studies, and furthermore clarified the genetic diversity of their population before and after an outbreak of adenovirus (4). Workers at Tulane NPRC have utilized single nucleotide polymorphisms (SNPs) to compare genetic diversity between rhesus monkeys—both historically and currently, a crucial model for human health—of Chinese and Indian-origin, and between those conventionally-bred and those bred to be Specific Pathogen Free (SPF) (5). And geneticists at Southwest NPRC utilized 100 high-coverage whole genome baboon sequences to clarify the influence of parental genetics on infant survival, to provide information on geographical ancestry, and to additionally help correct errors in colony records (6).

NHP management requires many things, not least of which is a profound knowledge of, and love for, natural history and animal behavior. But genetics has been, and will continue to be, a vital component of the toolkit.


Charlesworth D, and Charlesworth B. 1987. Inbreeding depression and its evolutionary consequences. Annual Review of Ecology and Systematics 18:237-268.

Hedrick PW, and Garcia-Dorado A. 2016. Understanding inbreeding depression, purging, and genetic rescue. Trends in Ecology & Evolution 31:940-952.

Kanthaswamy S, Capitanio JP, Dubay CJ, Ferguson B, Folks T, Ha JC, Hotchkiss CE, Johnson ZP, Katze MG, and Kean LS. 2009. Resources for genetic management and genomics research on non‐human primates at the National Primate Research Centers (NPRCs). Journal of Medical Primatology 38:17-23.

Kanthaswamy S, Ng J, Oldt RF, Phillippi‐Falkenstein K, and Kubisch HM. 2018. SNP‐based genetic characterization of the Tulane National Primate Research Center's conventional and specific pathogen‐free rhesus macaque (Macaca mulatta) populations. Journal of Medical Primatology 47:29-34.

Mendoza A, Ng J, Bales KL, Mendoza SP, George DA, Smith DG, and Kanthaswamy S. 2015. Population genetics of the California National Primate Research Center’s (CNPRC) captive Callicebus cupreus colony. Primates 56:37-44.

Robinson JA, Belsare S, Birnbaum S, Newman DE, Chan J, Glenn JP, Ferguson B, Cox LA, and Wall JD. 2019. Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony. Genome Research 29:848-856.


1. This holds for both laboratories and zoos. For the former, exceptions include breeding for specialized traits especially interesting to investigators, especially those that are health-relevant. For example, certain Major Histocompatibility Complex (MHC) allele combinations are favored for some types of AIDS-related work.

2. Charlesworth & Charlesworth 1987; Hendrick & Garcia-Dorado 2016

3. Kanthaswamy et al. 2009

4. Mendoza et al. 2015

5. Kanthaswamy et al. 2017

6. Robinson et al. 2019