Reconstructing the Genetic History of Late Neandertals

Abstract

Although it is known that Neandertals contributed DNA to modern humans 1, 2, not much is known about the genetic diversity of Neandertals or the relationship between late Neandertal populations at the time when their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neandertal individuals has been limited by poor preservation of endogenous DNA 3 and large amounts of microbial and present-day human DNA that contaminate Neandertal skeletal remains 3– 5. Here we use hypochlorite treatment 6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five 39,000- to 47,000-year-old Neandertals ( i.e. late Neandertals), thereby doubling the number of Neandertals for which genome sequences are available. Genetic similarity among late Neandertals is well predicted by their geographical location, and comparison to the genome of an older Neandertal from the Caucasus 2, 7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neandertal history. We find that the bulk of Neandertal gene flow into early modern humans originated from one or more source populations that diverged from the Neandertals studied here at least 70,000 years ago, but after they split from a previously sequenced Neandertal from Siberia 2 ~150,000 years ago. Although four of these Neandertals post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.