Final Report Summary - GENEFLOW (The role of nuclear gene flow in the evolutionary history of Pleistocene mammals)
The goal of the project was to investigate the importance of nuclear gene flow between populations for the evolution of Pleistocene mammalian species. To achieve this, we obtained genomic data from ancient DNA samples, which is generally hampered by the low quality and quantity of ancient DNA. 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. This was helped by new technological developments in our group such as the use of CT-scanning to determine the optimal sampling site on a bone, which represents the first reliable screening technology in ancient DNA research. 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 ancient cave bears, ancient brown bears, mammoths, cave hyenas, ancient wolves and several other species including the extinct straight-tusked elephant as well as numerous samples from modern species for comparison. The analysis of these data showed, surprisingly, that gene flow has taken place between cave bears and brown bears. A detailed analysis of the temporal and geographical pattern of gene flow suggests that the direction was from cave bears into brown bears. While the genomic contribution of cave bears into the genome of brown bears is highest in the Pleistocene brown bear genome from Austria, the contribution is still measurable in European brown bears, showing that at least part of the cave bear genome has survived in the modern brown bear gene pool. Our analyses also 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. However, we found a variety of population scenarios, including nuclear gene flow in the light of mitochondrial DNA replacement, long-term isolation of geographically close populations of the same species and population continuity over half a million years, the later also representing the oldest ancient DNA outside the permafrost recovered to date. We also found that the Pleistocene brown bears were genetically substantially different to all investigated modern Eurasian brown bears suggesting major population turnovers at the Pleistocene-Holocene boundary. Wolves show a similar pattern, with higher genetic diversity of the Pleistocene population compared to the modern one and obviously a substantial genetic turnover at the turn of the Pleistocene to the Holocene. Altogether, these results indicate that there was substantial gene flow taking place between populations during the Pleistocene, while the Pleistocene/Holocene border seems to have been a major barrier to gene flow. In Eurasian brown bears, gene flow between Eastern and Western brown bears was already interrupted at the beginning of the cooling face during the late Pleistocene, since when these two populations followed different population trajectories. In cave and spotted hyenas we found clear evidence of an early divergence between African and Eurasian populations, that remained, however, connected by occasional gene flow events in both directions. Finally, we found that gene flow plays a key role in the evolution of a number of additional species, including the late Pleistocene Scimitar cat (Homotherium) population and the straight-tusked elephant, which is the first extinct species that could be shown to have been a hybrid species.