Rainforest hunter-gatherer small body size:
My main current project, for which I was awarded an NIH NRSA fellowship, examines the evolution of short stature in rainforest hunter-gatherers via population and functional genomics. Using comparative methods, I have identified population-specific and parallel selection in African and Asian populations with the “pygmy” phenotype, including subtle signatures of convergent polygenic positive selection on genes involved in growth factor binding and cardiac development (Bergey et al. 2018, PNAS; preprint, bioRxiv). We found that the growth hormone sub-responsiveness that may partly underlie the pygmy phenotype may have led to compensatory changes in cardiac pathways, in which growth hormone plays an essential role.
To further investigate the functional impact of this selected variation, we are exposing cell lines from rainforest hunter-gatherers to growth factors to observe gene expression changes. Future work includes deriving hepatocyte-like (liver-like cells) from induced pluripotent stem cells of the Batwa rainforest hunter-gatherers of Uganda to investigate synthesis of hormones that control growth.
Collaborators include: George Perry, Kathleen Grogan, Luis Barreiro, and Genelle Harrison.
Mosquito population structure and connectivity:
As part of my work on mosquitoes (genus Anopheles), I use population genomic-scale approaches to understand human-vector interactions. My main project investigates natural and human-assisted gene flow between islands on Lake Victoria in Uganda, which are similar to potential pilot sites for vector control initiatives involving genetically modified mosquitoes. I have identified loci—such as those that confer insecticide resistance or influence sensory perception—which are restricted to certain island populations and resistant to the homogenizing effects of gene flow, possibly indicative of local adaptation (Bergey et al. 2019, Evolutionary Applications; preprint, bioRxiv; Lukindu et al 2018, Parasites and Vectors; Wiltshire et al 2018, Malaria Journal). I also am leading a study of the ecological and anthropogenic influences on mosquito population structure in West Africa and their interaction with a major chromosomal inversion with known association to ecology, in particular aridity tolerance. Ultimately, this mosquito research will greatly increase our knowledge of the interaction between mosquitoes, malaria, and humans, and inform effective eradication strategies.
Collaborators include: Nora Besansky, Michael Fontaine, Jonathan Kayondo, Rachel Wiltshire, and Martin Lukindu.
Primate hybridization and phylogenetics:
Much of my work capitalizes on gene flow between populations or species for insight into the adaptive evolution of polygenic traits. Admixture between evolutionary lineages produces novel combinations of parental variation exposed to natural selection for the first time and can act as a conduit for genetic variation between lineages. For my dissertation, I studied a natural experiment in hybridization, in which two species of wild baboons produce fertile offspring in Ethiopia. I used genome-wide data to determine which regions of the genome are outliers in terms of either differentiation between parental species or the shapes of the clines of introgression. Using hundreds of samples collected since the 1970s, I found that regions of high differentiation between the species are more likely than expected to contain genes that are components of the dopamine receptor mediated signaling pathway, suggesting adaptive divergence between the two primates in brain regions involved in impulse control and linked to mating behavior (Bergey et al 2016, PNAS).
Ongoing primate projects focus on the dynamics of gene flow and selection from a phylogenomic perspective. Such projects include those funded by two NSF senior awards on which I am co-PI. The first investigates adaptive transfer of genetic material between members of a specious group of diverse African primates, the guenons. Despite differing in ecology and with pelage patterns hypothesized to reinforce species boundaries, we have found evidence of widespread hybridization. The second project investigates evolutionary conservation in anthropoid (monkey and ape) genomes and its application to distinguish false positives from causal variants in human disease association studies. Additional primate research includes work on ancient hybridization as part of the Baboon Genome Consortium (Rogers et al 2019, Science Advances) and development of methods for genomics from non-invasive sources, including museum specimens (Burrell, Disotell, and Bergey 2015; Journal of Human Evolution) and feces (Chiou and Bergey 2018; Scientific Reports).
Collaborators include: Clifford Jolly, Todd Disotell, Andrew Burrell, Anthony Tosi, Kenny Chiou, Jane Phillips-Conroy, Jeff Rogers.