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ABSTRACT As a major model for biomedical research, the rhesus macaque (Macaca mulatta) is one of the most important and heavily studied nonhuman primates. Despite this importance, the level of population structure and subspecific division in this species remains relatively unclear; for example, the number of proposed subspecies in the literature ranges from one to six within China, with additional populations found across India. Motivated by an interest in comparing recombination rate landscapes between rhesus macaque subspecies, we re‐evaluated the demographic history of this group using a previously published data set from 79 wild‐born individuals sampled across 17 regions in China. In so doing, we found that previously published demographic models utilizing five subspecies did not well reproduce empirical levels or patterns of genomic variation. Thus, we re‐performed demographic inference, finding instead multiple lines of support for a single, interbreeding population (i.e., an absence of population structuring), as well as a population size‐change history linking periods of population growth and contraction to historical patterns of glaciation. Finally, utilizing this well‐fitting population history, we inferred a genome‐wide, fine‐scale recombination rate map for this population, finding mean rates consistent with those estimated in other closely related populations and species. However, we also observed notable difference in the fine‐scale landscape between rhesus macaques of Chinese and Indian origin – two populations widely used as models in biomedical research – highlighting the importance of accounting for population‐specific demographic history and recombination rate variation in future population genomic studies of this species.
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Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques ( Macaca mulatta )
Abstract Meiotic recombination landscapes differ greatly between distantly and closely related taxa, populations, individuals, sexes, and even within genomes; however, the factors driving this variation are yet to be well elucidated. Here, we directly estimate contemporary crossover rates and, for the first time, noncrossover rates in rhesus macaques (Macaca mulatta) from four three-generation pedigrees comprising 32 individuals. We further compare these results with historical, demography-aware, linkage disequilibrium–based recombination rate estimates. From paternal meioses in the pedigrees, 165 crossover events with a median resolution of 22.3 kb were observed, corresponding to a male autosomal map length of 2,357 cM—approximately 15% longer than an existing linkage map based on human microsatellite loci. In addition, 85 noncrossover events with a mean tract length of 155 bp were identified—similar to the tract lengths observed in the only other two primates in which noncrossovers have been studied to date, humans and baboons. Consistent with observations in other placental mammals with PRDM9-directed recombination, crossover (and to a lesser extent noncrossover) events in rhesus macaques clustered in intergenic regions and toward the chromosomal ends in males—a pattern in broad agreement with the historical, sex-averaged recombination rate estimates—and evidence of GC-biased gene conversion was observed at noncrossover sites.
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- PAR ID:
- 10487523
- Editor(s):
- Kosiol, Carolin
- Publisher / Repository:
- Oxford University Press on behalf of Society for Molecular Biology and Evolution
- Date Published:
- Journal Name:
- Genome Biology and Evolution
- Volume:
- 16
- Issue:
- 1
- ISSN:
- 1759-6653
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/gbe/evad223
