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Evolution of DNA methylation in Papio baboons

View ORCID ProfileTauras P Vilgalys, Jeffrey Rogers, Clifford Jolly, Baboon Genome Analysis Consortium, View ORCID ProfileSayan Mukherjee, View ORCID ProfileJenny Tung
doi: https://doi.org/10.1101/400093
Tauras P Vilgalys
Duke University;
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Jeffrey Rogers
Baylor College of Medicine;
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Clifford Jolly
New York University;
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Sayan Mukherjee
Duke University;
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Jenny Tung
Duke University;
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  • For correspondence: jenny.tung@duke.edu
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Abstract

Changes in gene regulation have long been thought to play an important role in primate evolution. However, although a number of studies have compared genome-wide gene expression patterns across primate species, fewer have investigated the gene regulatory mechanisms that underlie such patterns, or the relative contribution of drift versus selection. Here, we profiled genome-scale DNA methylation levels from five of the six extant species of the baboon genus Papio (4 - 14 individuals per species). This radiation presents the opportunity to investigate DNA methylation divergence at both shallow and deeper time scales (380,000 - 1.4 million years). In contrast to studies in human populations, but similar to studies in great apes, DNA methylation profiles clearly mirror genetic and geographic structure. Divergence in DNA methylation proceeds fastest in unannotated regions of the genome and slowest in regions of the genome that are likely more constrained at the sequence level (e.g., gene exons). Both heuristic approaches and Ornstein-Uhlenbeck models suggest that DNA methylation levels at a small set of sites have been affected by positive selection, and that this class is enriched in functionally relevant contexts, including promoters, enhancers, and CpG islands. Our results thus indicate that the rate and distribution of DNA methylation changes across the genome largely mirror genetic structure. However, at some CpG sites, DNA methylation levels themselves may have been a target of positive selection, pointing to loci that could be important in connecting sequence variation to fitness-related traits.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted August 25, 2018.
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Evolution of DNA methylation in Papio baboons
Tauras P Vilgalys, Jeffrey Rogers, Clifford Jolly, Baboon Genome Analysis Consortium, Sayan Mukherjee, Jenny Tung
bioRxiv 400093; doi: https://doi.org/10.1101/400093
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Evolution of DNA methylation in Papio baboons
Tauras P Vilgalys, Jeffrey Rogers, Clifford Jolly, Baboon Genome Analysis Consortium, Sayan Mukherjee, Jenny Tung
bioRxiv 400093; doi: https://doi.org/10.1101/400093

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