Evolution of DNA Methylation in Papio Baboons.

TitleEvolution of DNA Methylation in Papio Baboons.
Publication TypeJournal Article
Year of Publication2019
AuthorsVilgalys, TP, Rogers, J, Jolly, CJ, Mukherjee, S, Tung, J
JournalMol Biol Evol
Volume36
Issue3
Pagination527-540
Date Published2019 Mar 01
ISSN1537-1719
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 in blood samples 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 timescales (0.380-1.4 My). 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.

DOI10.1093/molbev/msy227
Alternate JournalMol. Biol. Evol.
PubMed ID30521003
PubMed Central IDPMC6389319
Grant ListP51 OD011132 / OD / NIH HHS / United States
UL1 TR001117 / TR / NCATS NIH HHS / United States