Interbreeding with Neanderthals and Denisovans in the past introduced archaic DNA into modern human populations, an event often referred to as archaic introgression. Having access to Neanderthal and Denisovan genomes has enabled the quantification of the amount of archaic DNA present in individuals today, ranging from 0.1% to 7%. In my lab, we have discovered that some of this DNA has been useful in facilitating adaptations to diverse environments, which likely contributed to the expansion of humans into Europe, Asia, Oceania and the Americas. While there are some examples of how positive natural selection acted on archaic alleles, we still lack the full picture of how archaic variation evolved in modern human populations.
In this project, we will leverage the genomes of ancient humans spanning a wide geographical and temporal range to characterize how archaic variants have evolved over time and space in distinct modern human populations. This work also involves developing and benchmarking new methods to detect archaic ancestry in ancient genomes. By applying new methods and approaches to both ancient and modern genomic data sets, our analyses will provide a deeper understanding of the trajectories of archaic alleles over time. We will be able to determine what alleles have been purged, retained, and which ones have increased in frequency in the population. By looking at time-transects, we should also be able to observe the effects of population turnovers that have occurred in the history of modern humans. Moreover, examining the fragments of archaic DNA over time will enable inference of the timing of introgression and the timing of natural selection. Having this information will resolve details on the evolutionary processes that have affected the evolution of surviving archaic alleles. Our results will be important for determining the impact of archaic introgression in human evolution
