Evolution of DNA methylation among Papio baboons
Evolutionary changes to DNA methylation likely contribute to the evolution of gene expression levels, and recent studies have provided a detailed picture of DNA methylation divergence between human populations and between humans and other great apes.
Here, I examine the relationship between genetic changes and divergence in DNA methylation using Papio baboons. Our results support the idea that divergence in DNA methylation is primarily explained by the nearby DNA sequence. Furthermore, unlike gene expression, DNA methylation appears to evolve most commonly via genetic drift rather than due to natural selection.
The results from this project have been published in Molecular Biology and Evolution and can be found here. During the course of this project, I also contributed to a review of methods to analyze DNA methylation data for ecological and evolutionary studies (available here).
Selection on gene regulatory traits following admixture
Admixture (the interbreeding of divergent, but related lineages) has been an important process in primate evolution. For example, admixture between modern humans and archaic hominins (such as Neanderthals and Denisovans) continues to affect genetic and phenotypic diversity among living people. Natural selection in humans is thought to have purged regions of the genome inherited from Neanderthals, especially when those regions strongly affected gene regulation (McCoy, et al. 2017). However, it is not possible to test this hypothesis in humans as admixture with archaic hominins ceases thousands of years ago.
To approach this question, I use a population of admixed baboons to test whether genetic ancestry affects DNA methylation and gene expression, and how introgressed regions have been affected by natural selection. This work will provide a living primate model for how admixture may have affected gene regulation in our own evolutionary history, and is supported by a NSF Doctoral Dissertation Research Improvement Grant and a Leakey Foundation Research Award.