Domestication: Humans have been domesticating animals for over 10,000 years, and these species have been shaped through generations of natural selection. Given the close interaction between these species and humans for thousands of years, domestic animals can be used as a proxy for humans, to better understand human movements and demography.
Phylogeography: The geographic distribution and migration history of a species impacts its genetic diversity, and therefore the genetic diversity of modern populations can be analyzed to understand the demographic history of the species. Ancient and modern populations can also be compared to see how changes in the environment impacted the species.
Ancient DNA and Bioinformatics: Ancient DNA (aDNA) sequences are more challenging to analyze than DNA from modern sources, as they are fragmentary and low-coverage. Despite these problems, aDNA data is extremely valuable for examining past populations, and bioinformatics methods designed to cope with aDNA can be used to understand an ancient individual’s population history, or to compare them to modern individuals.
Ancient Dogs in the Americas: I am interested in how dogs migrated through the Americas, how different populations relate to one another, and how this relates to human movements in the Americas. More narrowly, I have been studying dogs from the region around Cahokia, a large mound city near present-day St. Louis. I have been using ancient dogs from multiple archaeological sites and time periods to examine how dog utilization and genetic diversity changed through time, and also to infer dietary changes in the human populations associated with them through the analysis of coprolites.
Macaque Phylogeography: A current research project, in collaboration with Dr. Lu Yao, is examining genetic diversity patterns in several populations of Macaca fascicularis (long-tailed macaques) distributed across multiple islands and the mainland of Southeast Asia, using low-coverage genomes extracted from museum specimens. We are interested in determining the migration history of this species, as well as how genetic diversity is distributed across these populations.
Archaic Admixture: I am examining how DNA from archaic humans (Neanderthals and Denisovans) impacts modern populations. I am currently examining the distribution of allele frequencies of these archaic variants across modern populations, to see how past bottlenecks and selective events have shaped the archaic variation in humans. I am also examining how admixture in modern humans affects the distribution of archaic variants across the genome.