Our Research

In our lab, we focus on mathematical and statistical approaches applied to genome-wide data, including ancient genome data.

In particular, we are interested in the genetic legacy of Neanderthals, Denisovans, and other archaic populations that contributed to our ancestry. What can we learn from genetics about how these species interacted, and how does their genetic legacy affect our lives and health? My lab develops theoretical, computational and data-driven approaches to address these questions.

Current research projects:

Understanding Neanderthal-human admixture events

The neutral coalescent framework allows for the study of population admixture, by looking at a collective of genealogies with various architectures. Each genealogy represents a possible relation between individuals, the abundance of a genealogy connecting two individuals from different populations representing both the probability and the frequency of admixture. Simulations under this framework are easy to understand, as the model has simple expectations. I use this approach to study the contribution of Neanderthals into the genomes of modern humans. Neanderthals and humans overlapped geographically for a period of over 30,000 years following human expansion out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that Eurasian populations have distinct levels of Neanderthal ancestry. I explored various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population. Using machine learning, the output from the simulations can compared to genomic data from the 1000 genomes project. This method was able to distinguish between various demographic models, and found that of the complex models, a model of multiple episodes of gene flow into both East Asian and European populations fits the data best. These findings suggest long-term, complex interaction between humans and Neanderthals.

Adaptive Introgression in American Populations

Indigenous American populations carry comparable levels of Neanderthal and Denisovan ancestry as Eurasian populations. Indigenous American populations also expanded through a vast continent, settling along numerous novel environments and becoming adapted to the challenges unique to each. Their Neanderthal and Denisovan ancestry provided a boost in genetic diversity which served as the bases for adaptation. In this project, we are exploring the unique Neanderthal and Denisovan ancestry in modern and ancient American individuals, and searching for signatures of adaptation. Because of the lasting consequences of the European colony, and the African slave trade, it is difficult to study the archaic genetic variation that was unique to the original Americans. For this reason, we supplement our research with ancient genomes, from individuals that lived long before European colonization. We have identified high levels of archaic ancestry, and signatures of selection across these ancient genomes. Our next goal is to understand how the dilution of archaic American ancestry and admixture with European and African populations have affected the adaptive archaic elements for individuals living today.