ERC grant 310763: GeneFlow
The goal of the project is to investigate the importance of nuclear gene flow between populations for the evolution of Pleistocene mammalian species. To achieve this, we need to obtain genomic data from ancient DNA samples, which is generally hampered by the low quality and quantity of ancient DNA. So far, we were able, due to a combination of published and self-developed approaches, to establish an analysis pipeline that makes it possible to obtain not only genomic data but entire nuclear genomes at affordable costs from fossil specimens. Our investigations also showed that each step during the analysis process has a major influence not only on the quantity of DNA recovered, but also on qualitative measures such as average read length and read length distribution. We also found, together with collaborators, that the petrous part of the temporal bone contains substantially higher percentages of endogenous DNA than any other part of the mammalian skeleton. We have used these technical advances to obtain genome sequences from several ancient cave bears, an ancient brown bear and several modern brown bears. The analysis of these data showed that the nuclear genome tree for cave bears differs in topology from the mitochondrial genome tree. It is not yet clear whether this discrepancy is due to incomplete lineage sorting or massive male-mediated gene flow. We also found that the Pleistocene brown bear falls basal in a phylogenomic tree to all investigated modern Eurasian brown bears suggesting major population turnovers at the Pleistocene-Holocene boundary. We are now applying the technical approaches developed in our work on cave and brown bears to further samples from these species as well as to mammoths, cave hyenas and wolves to investigate which role nuclear gene flow played in the evolutionary history of these species.