Research
Detecting episodes of positive selection in complex histories
We have designed several model-based tests for selection that use patterns of allele frequency differentiation in a three-population tree to scan the genome for regions under ancient positive selection. One of these methods - called 3P-CLR - can serve to distinguish selective events that occurred before two populations split from each other from those that occurred after the split. A more recent method we developed - called Graph Aware Retrieval of Selective Sweeps (GRoSS) - can identify past episodes of positive selection events in arbitrarily complex admixture histories. Below is an example looking at genes under positive selection in the complex history of bovine breeds.
Archaic adaptive introgression
We have worked in several projects to detect regions of the genome that were beneficial to modern humans after being introduced into our gene pool via admixture from archaic human groups, like Neanderthals and Denisovans. A prime example of adaptive introgression is the TBX15/WARS2 region, which appears to have been introduced via introgression from a Denisovan-like hominin and may have allowed the ancestors of Native Americans and Greenlandic Inuits to survive the cold temperatures as they were crossing Beringia. Below is a haplotype network in the TBX15/WARS2 region, showing that the Native American haplotypes cluster closely to the Denisovan haplotype and distantly from other present-day haplotypes around the world.
Polygenic adaptation
We are also interested in more subtle modes of positive selection, namely polygenic adaptation, which generally occurs when a complex trait (like height) evolves towards a new optimum.
Archaic human demographic history
We have a broad interest in paleogenomics. Fernando was involved in the data processing and analysis of the first high-coverage Neanderthal and Denisova genomes (Meyer et al. 2012, Prüfer et al. 2014). One of these analyses consisted in elucidating a signal of super-archaic admixture into the Denisova genome, which is likely to have come from a hominin group that diverged before Neaderthals, Denisovans and modern humans diverged from each other (Prüfer et al. 2014).
Ancient DNA and modern human history
We have also worked in projects to elucidate the history of recent human population movements using ancient DNA. In 2018, I was a first co-author in a study of the peopling of southeast Asia in the past 8,000 years, which showed that the region has undergone multiple migration events since humans first colonized it.
