Page dedicated to our recent study on Neanderthal demography and ancient admxture with modern humans
Ancient gene flow from modern humans into Siberian Neanderthals .
Kuhlwilm M*, Gronau I*, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Z, Gusic I, Marques-Bonet T, Andres AM, Viola B, Paabo S, Meyer M, Siepel A, Castellano S.   (2016)   Nature 530, 429-433         PubMed         ReadCube public view
Population history of Neanderthals
In this paper, we re-examine the population history of Neanderthals and other archaic humans (Denisovans) by applying sophisticated computational methods to two published high quality genomes as well as chromosome 21 sequence data from two additional European Neanderthals. Despite the extensive analysis that these data have already undergone, a unified model for the demographic history of these individuals / populations has not been explicitly inferred before. We thus started out this project with a fairly modest goal of producing accurate estimates of demographic parameters for these populations, including effective populaiton sizes (Ne), population divergence times, and rates of gene flow. A summary of our estimates for populations sizes and divergence times inferred by using G-PhoCS can be seen here to the right.
Gene flow from early modern humans
However, as the study progressed, one finding stood out as especially intreguing. Our inference of migration rates showed signs of gene flow from the ancestors of present-day Africans to the ancsetors of the Siberian Neanderthal (for which we had a complete genome sequence). This finding was intreguing, because previous analysis of these genomes did not find similar signals, and at first glance it did not seem to fall in line with what we know about the population history of modern humans and Neanderthal. Interbreeding of modern humans and Neanderthals was already well established when we started our study, but all previously reported instances of this gene flow appeared to be a consequence of the expansion of modern humans in Europe and Asia, starting 65,000 years ago (see Figure). Interbreeding that would explain the signals that we found would have had to be significantly older and not orinigating from a population closely related to present-day non-Africans (highlighted arrow in Figure). Much of the second part of our study and the paper is devoted to this finding. One of the highlights of the paper is the use of a recently developed method for probabilistic inference of patterns of relatedness along the genome (ARGweaver) to find evidence of long segments in the Neanderthal genome that likely have modern human origins.
This finding suggests that our evolution and that of Neanderthal humans might be more intertwined than we previously thought. However, it also raises a very big question: who were these early populaitons that contributed modern human genetic segments to Neanderthals? One hypothesis points out to early modern humans inhabiting the middle east as early as 100,000 years ago. Archaeological evidence of such populations can be found in various places, including here in Israel. Their genetic contribution to present-day humans is unclear and they are currently thought to be a genetic dead-end. However, it is possible that these early modern humans served a bridge between our ansectors in Africa and Neanderthals in Eurasia. Unfortunately, with the current state of the data we can do little to resolve the origin question, whether it is from a specific population, or more continuous gene flow throughout time. We look forward to examining this exciting question with more more Neanderthal genomic data.
- Compressed bed file with 13,573 putative neutral loci used for demographic inference
sequence file containing sequence alignments of analyzed genomes in the putative neutral loci.
File contains alignments of the chimpanzee genome, four archaic individuals, ten present-day humans used in the study, and six additional present-day humans not used in the study.
- New York Times (US): In Neanderthals' DNA, Ancient Humans May Have Left Genetic Mark
- Science Daily (US): Neanderthals mated with modern humans much earlier than previously thought, study finds
- Discover (US): Were Humans and Neanderthals Swapping DNA Earlier Than We Thought?
- The telegraph (UK): Neanderthals and modern humans mated 100,000 years ago
- Haaretz (Israel): A prehistoric love story between Homo Sapiens and Neandethals (Hebrew)
- Haaretz (Israel): An Early Homo Sapiens Left Africa, Mated With Neanderthals and Went Extinct (English)
- Times of Israel (Israel): Israeli scholar helps rewrite humanity's timeline
- Lecture on Neanderthal genome analysis: The Neanderthal genome as a window to human prehistory - part of Scientific Discoveries lecture series at the Technion (Hebrew)
- Hezliya IDC research blog (Israel): Fascinating discovey about ancient Neanderthals
This study was covered by various outlets in the media, with surprisingly sensibility (some pop sci coverage can be quite bad). Below are some of the better pieces written about the study. We also participated in a Q&A session on Reddit, which was fun and insightful. If you're looking for tabloid-like headlines, see this one by the Huffington Post.