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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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Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets ( Callithrix jacchus ) from High-Quality, Whole-Genome, Population-Level Data
Abstract As a species of considerable biomedical importance, characterizing the evolutionary genomics of the common marmoset (Callithrix jacchus) is of significance across multiple fields of research. However, at least 2 peculiarities of this species potentially preclude commonly utilized population genetic modeling and inference approaches: a high frequency of twin births and hematopoietic chimerism. We here investigate these effects within the context of demographic inference, demonstrating via simulation that neglecting these biological features results in significant mis-inference of the underlying population history. Based upon this result, we develop a novel approximate Bayesian inference approach accounting for both common twin births and chimeric sampling. In addition, we newly present population genomic data from 15 individuals sequenced to high coverage and utilize gene-level annotations to identify neutrally evolving intergenic regions appropriate for demographic inference. Applying our developed methodology, we estimate a well-fitting population history for this species, which suggests robust ancestral and current population sizes, as well as a size reduction roughly 7,000 years ago likely associated with a shift from arboreal to savanna vegetation in north-eastern Brazil during this period.
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- Award ID(s):
- 2045343
- PAR ID:
- 10660979
- Editor(s):
- Harris, Kelley
- Publisher / Repository:
- Mol. Biol. Evol.
- Date Published:
- Journal Name:
- Molecular Biology and Evolution
- Volume:
- 42
- Issue:
- 6
- ISSN:
- 0737-4038
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The common marmoset (Callithrix jacchus) is of considerable biomedical importance, yet there remains a need to characterize the evolutionary forces shaping empirically observed patterns of genomic variation in the species. However, two uncommon biological traits potentially prevent the use of standard population genetic approaches in this primate: a high frequency of twin births and the prevalence of hematopoietic chimerism. Here we characterize the impact of these biological features on the inference of natural selection, and directly model twinning and chimerism when performing inference of the distribution of fitness effects to characterize general selective dynamics as well as when scanning the genome for loci shaped by the action of episodic positive and balancing selection. Results suggest a generally increased degree of purifying selection relative to human populations, consistent with the larger estimated effective population size of common marmosets. Furthermore, genomic scans based on an appropriate evolutionary baseline model reveal a small number of genes related to immunity, sensory perception, and reproduction to be strong sweep candidates. Notably, two genes in the major histocompatibility complex were found to have strong evidence of being maintained by balancing selection, in agreement with observations in other primate species. Taken together, this work, presenting the first whole-genome characterization of selective dynamics in the common marmoset, thus provides important insights into the landscape of both persistent and episodic selective forces in this species.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1093/molbev/msaf119
