Our work focuses on data-driven modeling of the patterns of genetic variation within and between populations and species. We study both humans and non-human species (such as the medically relevant rhesus macaque and domesticated species like cows and rice). We frequently employ detailed population genetic simulations to better understand the implications of interacting evolutionary forces. We currently have three main lines of research:

Population genetic modeling of human populations

In order to further understand the evolutionary forces that acted on our ancestors, we analyze large-scale sequencing data from populations throughout the world. In collaboration with the 1000 Genomes Project, we employ detailed population genetic models to better understand the implications of complex interactions among evolutionary forces on patterns of genetic variation within and between populations. One current focus is on the implications of a genome’s worth of deleterious mutations that are interacting in complex ways to drive systematic genomic patterns of variation. Using detailed simulations and models of background selection, we seek to learn more about our species’ history and to discover more of the functionally relevant regions of the genome.

Disease susceptibility in complex populations

Next-generation sequencing technologies are providing an unprecedented opportunity to learn about the genetic basis of disease. We strive to leverage evolutionary signals in patterns of genetic variation to uncover the meaningful associations with phenotypic variation. One primary focus is in a collaboration with Dr. Esteban Burchard, on the genetics of asthma in minority populations across the USA. By leveraging evolutionary signatures of natural selection and admixture patterns in trans-ethnic studies of Latino and African American populations, we will be able to gain insights into the genetics of this disease for the betterment of all populations.

Host-pathogen interactions

Populations do not evolve in isolation. Rather, they are constantly interacting with other species, both mutualistically (as in the human microbiome) as well as competitively (in the case of pathogens). We are developing tools to leverage patterns of genetic diversity within populations and divergence across phylogenies to learn more about the genetic targets of such interactions. In collaboration with Dr. Nevan Krogan, we are investigating interactions between mammals across the phylogenetic tree and their associated immunodeficiency viruses (e.g., HIV, SIV, FIV, etc). Using both phylogenetic and population genetic techniques, we are learning about the nature of these interactions, and addressing pressing questions about the conditions under which viruses jump species barriers.