New Neanderthal genome indicates inbreeding and complex gene flow

The Altai Neanderthal had closely related parents, which could for example be a grandfather and granddaughter; Copyright: Neanderthal Museum

The Denisova cave in the Altai Mountains is known for the discovery of a finger bone, from which DNA was sequenced and related to a previous unknown species, the Denisovans. Now in an older layer in the same cave researchers found a toe bone, at least 50,000 years old. The complete genome of this toe bone was sequenced for DNA, providing the first high quality sequenced Neanderthal, and the results were published in Nature.

The genome of this Altai Neanderthal was compared to the Denisovan genome, 3 Neanderthal individuals from Vindija, the Mezmaiskaya Neanderthal and 25 present-day humans. The vast amount of data coming from these genomes can be assessed and compared from many different perspectives, resulting in 249 pages of supplementary information attached to the paper.

A first interesting point is that the authors were able to estimate the timing of the population splits. Modern humans and Neanderthals/Denisovans seem to have split between 550,000 and 765,000 years ago while the split between Neanderthals and Denisovans occurred around 380,000 and 473,000 years ago.

Secondly, the Altai Neanderthal genome contains several long runs of homozygosity, indicating that her parents were closely related, being for example half siblings, grandfather and granddaughter or uncle and niece. This indicates that the Altai Neanderthals were a rather isolated group, where mate choice was limited and hence incest was common. Further sequencing of additional Neanderthal genomes is needed to see if interbreeding was also common among Neanderthals elsewhere.

Thirdly, the comparisons between the different genomes indicated the common gene flow between different Late Pleistocene populations. Neanderthals contributed 1.5-2.1% to present-day populations outside of Africa and around 0.5% to Denisovans. Denisovans contributed 3-6% to present-day populations in Oceania. An unknown hominin also contributed 0.5-8.0% to the Denisovans. This unknown hominin is estimated to have split from the modern human lineage 0.9-1.4mya and is therefore speculated to be Homo erectus. Future work will further define these gene flow events and the real population history is likely to have been even more complex.

Using this high-quality Neandertal genome the authors also established a definitive genome-wide catalog of sites where present-day human genomes all carry the same nucleotide but differ from the Neandertal, Denisovan and great ape genomes. It is a catalog of the genetic features that sets all modern humans apart from all other organisms, living or extinct, and which will allow many new studies in the near future. These are exciting times for global Palaeolithic research!

Full reference: Prufer, K., et al. (2013). “The complete genome sequence of a Neanderthal from the Altai Mountains.” Nature.

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