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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 2 - 100 Archaic Genomes (Genome sequences from extinct hominins)

Teaser

Summary

At the beginning of this project, a single high-coverage Neandertal genome and a single high-coverage Denisovan genome had been generated. Although several novel insights have emerged from the analysis of these genomes, our knowledge about the extent of genetic variation among Neandertals is still limited. In addition, DNA retrieval has so far been restricted to late Neandertals. The amount of information about Denisovans is even more limited, being restricted to a single cave site in southern Siberia and a tentative find in China. The project aims at extending the knowledge about genetic variation among Neandertals, Denisovans and their ancestors across time and space. It will also attempt to generate genomic data from older hominins.

Work performed

We have more than doubled the number of Neandertals for which genome sequences are available. Analyses of these data show that Neandertals carried fewer differences among them than present-day humans, suggesting that Neandertal populations were of small size. Genetic similarity among late Neandertals is well predicted by their geographical location and a population turnover is likely to have occurred towards the end of Neandertal history.
The bulk of Neandertal gene flow into early modern humans originated from one or more Neandertal populations that were more closely related to the Neandertals we have sequenced in this project than the previously sequenced Neandertal from Siberia. This allows us to identify 10 to 20% more Neandertal DNA in present-day humans, including variants involved in medically significant traits such as low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
One technical breakthrough has been the demonstration that it is possible to retrieve hominin DNA from archaeological sediments at cave sites. This opens the possibility to demonstrate that Neandertals and Denisovans have been present at a site even when no recognizable physical remains of these groups are found at a site.

Final results

We have extended the knowledge about genetic variation in Neandertals and to some extent Denisovans. We have also developed methods that will allow us to work with older and less well preserved remains of hominins.
We will now apply these technical developments to older Neandertal remains with the aim of reconstructing their deeper population history. We will continue to look for hominin remains in Asia. We will generate genome-wide data from a large number of Neandertals, and wherever possible generate high quality genomes. If possible, we will study sites where several individuals who are likely to be contemporaneous with each other are found to elucidate relationships within Neandertal groups.