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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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Inferring the demographic history of coppery titi monkeys (Plecturocebus cupreus) from high-quality, whole-genome, population-level data
Abstract Despite being an important biomedical model species for social behavior, the natural population history of the coppery titi monkey (Plecturocebus cupreus) remains largely uncharacterized, in part due to the scarcity of genomic resources available for the species. Apart from the inherent interest in the demographic dynamics of this abundant platyrrhine native to the Amazon forest of Brazil and Peru, this quantification will also serve as a central component of future genotype-to-phenotype studies, given the ability of historical population size change and structure to generate genetic associations. In this study, we deep-sequenced the genomes of six unrelated individuals and inferred a baseline demographic model based on observed levels and patterns of variation in the non-coding regions of the genome. In characterizing these demographic dynamics, we found that estimated population size changes correspond well to previously described speciation times as well as to large-scale climatic changes relating to glaciation patterns.
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- Award ID(s):
- 2045343
- PAR ID:
- 10660987
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract How individuals use space and, thus, the rate and the nature of their interactions with others are shaped by their environment. Exogenous changes that alter aggregation patterns, such as resource pulses, can therefore have a significant impact on seemingly unrelated processes like disease spread. White-tailed deer (Odocoileus virginianus) aggregate in oak forests during mast events, and chronic wasting disease (CWD) transmission patterns vary with deer density, so we hypothesize a link between the masting cycle and CWD dynamics. We investigate various possible effects of masting on deer, including shifts to more frequency-dependent CWD transmission due to aggregation, as well as elevated fecundity and decreased mortality of deer in response to the resource pulse, using a simplified compartment model of CWD spread. When masting affects epidemiological parameters, including the strength of frequency dependence in CWD transmission, disease spread during masting events significantly reduces the size of deer populations but, paradoxically, without any change in the proportion of the population in the CWD-diseased state. In contrast, demographic parameters were found in principle to be capable of altering both population size and disease incidence, though the observed effects were very small. While our quantitative findings should be validated using more detailed models of CWD transmission before they are taken as specific predictions about this system, our fundamental qualitative result appears to be quite general. That is, our conclusion that epidemiological rates only influence population size, but demographic rates may affect both population size and disease incidence, can be derived not only from the model we studied but also from classical epidemiological models as well. Our work extends the understanding of the far-reaching impacts of resource pulses through ecological communities by highlighting the vastly different consequences of the same resource pulse acting in different ways.more » « less
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Accepted Manuscript
- Posted Content:
- https://doi.org/10.64898/2026.01.09.698678
