CCB Seminar: From genomes to genealogies: mapping the history of humans and their genetic variation using ancient and modern genomes

Dr. Simon Myers, Professor, Department of Statistics, Oxford University
Abstract:
Genetic variation is shaped through evolutionary processes acting on our genomes over hundreds of millennia, including past migrations, isolation by distance, population bottlenecks, and natural selection. Such events are reflected in the genealogical trees that relate individuals back in time. We have developed an approach, Relate, to reconstruct such genealogies from genetic variation data for many thousands of individuals. Application of Relate to human data provides evidence of directional impacts of natural selection on many human traits, for example towards increased Type II diabetes risk in some populations, and of mutation processes through time, while simultaneously inferring demographic histories by estimating coalescence rates among different lineages through time.
Ancient genomes can provide a direct snapshot of historical genetic variation, and so add substantial information. We will discuss an extension to the Relate algorithm for incorporating such samples, which we use to reconstruct joint genealogies of the Simon’s Genome Diversity Project dataset and previously published high-coverage ancient humans. For low-coverage genomes, which cannot yet be incorporated fully into genealogies, we instead developed a fast and scalable method, Colate, enabling inference of historical coalescence rates based on a reference Relate genealogy. Together, these tools allow us to build joint population histories of hundreds of previously published ancient samples dating back thousands of years, and modern samples. We characterize how these ancients relate to modern human groups through time, alongside wide-spread recent relatedness for both ancient and some modern samples.