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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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Using Serially Collected Specimens to Investigate the Potential Population Genetic Consequences of Reported Declines in Eastern Woodland Salamanders
ABSTRACT Biodiversity is facing global change at an unprecedented rate. Understanding how populations have responded to accelerated change over the last century is key to informing effective conservation policies. Serially collected specimens from natural history repositories can provide a window into how populations change over time and highlight further vulnerabilities in remaining populations. Changes in observed population abundance during field surveys suggest that somePlethodonsalamander populations experienced declines since the 1960s, but the potential population genetic consequences of these declines remain unstudied. Thanks to decades of sustained collection‐based efforts,Plethodonsalamanders serve as a model to test the utility of historical DNA to identify shifts in genetic diversity at recent time scales. Here, we investigate demographic change in sixPlethodonspecies through time using DNA from formalin‐fixed museum specimens (1960s–1970s), historic frozen blood (1980s–1990s), and contemporary sampling. We generated several reduced representation SNP datasets using a target‐capture approach to investigate two sites in the Appalachian Range: one with documented declines (Indian Grave Gap) and one without (Skull's Gap). We quantify the impact of bioinformatic choices on estimates of genetic diversity, quantify demographic shifts, and trace changes in allele frequencies in immune‐related loci to explore the potential impact of pathogens on putative declines. We found consistent patterns of genetic diversity change across datasets and filtering regimes. At Skull's Gap, our results suggest that populations were stable or expanding, while at Indian Grave Gap, our results suggest contraction in one species and mixed signals of contraction and expansion in the others. Analyses of immune loci suggest that balancing selection is maintaining shared polymorphism through time in all but one species. Our study outlines important considerations for leveraging historical DNA in time series collections to quantify the genomic effects of localized population declines.
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- Award ID(s):
- 2131060
- PAR ID:
- 10664281
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 16
- Issue:
- 1
- ISSN:
- 2045-7758
- Subject(s) / Keyword(s):
- genetic diversity historical DNA museum genomics Plethodon salamanders population declines time series analysis
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.1002/ece3.72805
