The results of an international research project lasting over five years and involving some 56 scientists led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology and Richard E. Green of UC Santa Cruz have just been published in the journal Science, and they suggest that many modern humans have some Neanderthal ancestry. While Edward M. Rubin, the director of the US Department of Energy's Joint Genome Institute, said the project was 'a terrific piece of work and a monumental endeavor', many experts are surprised at the results, which contradict previous evidence for little or no Neanderthal genetic inheritance.
     The researchers sequenced DNA from three bones from the Vindija cave site in Croatia that belonged to three female Neanderthals who died more than 40,000 years ago. Recovering high quality genetic material for analysis was difficult because the DNA breaks down into short segments over time and becomes chemically altered, and remains also become contaminated by DNA from bacteria and fungi. However, because the chemical changes were predictable, the team were able to write software to compensate. Some 4 billion units of Neanderthal DNA were analyzed, although this was only 60 percent of the Neanderthal genome. Nevertheless, Pääbo stated that this was 'a very good statistical sample of the entire genome.'
     Using high-throughput technology to process many sequences simultaneously, the team then compared the draft Neanderthal sequence with samples from modern humans from France, Papua New Guinea, China, and southern and northern Africa. "The comparison of these two genetic sequences enables us to find out where our genome differs from that of our closest relative" Pääbo explained. While modern humans and chimpanzees share about 98 percent of their genes, modern humans and Neanderthals are 99.5 percent identical. Between one and four percent of modern Eurasian human genes seem to come from Neanderthals.
     Green stated that the results seem to provide 'compelling' evidence of interbreeding. "It seemed like it was likely to be possible, but I am surprised by the amount. I really was not expecting it to be as high as four percent..." said John Hawks, associate professor of anthropology at the University of Wisconsin-Madison, "They're us. We're them".
     The team identified over 70 gene changes unique to modern humans, associated with physiology, and the development of the brain, skin and bone. It is likely that behavioral differences also may have given an advantage to modern humans. Hawks stated that "any traits [Neanderthals] had that might have been useful in later populations should still be here," but, "when we see their anatomies are gone, this isn't just chance. Those things that made the Neanderthals distinct to us as a population - those things didn't work. They're gone because they didn't work in the context of our population."  
     The results also offer support to the Out of Africa hypothesis, in which the ancestors of modern humans evolved in Africa some 200,000 years ago and populations migrated out between 50,000 and 60,000 years ago, although they contradict the most conservative model in which all archaic populations were simply replaced by modern humans. The greatest similarities between genomes were found between the European, Chinese and Papuan samples, which suggests that there was limited mating or gene flow between Neanderthals and the ancestors of modern Eurasians. While scientists previously thought Europe, where Neanderthal and modern human populations co-existed for 10,000 years the most likely venue for any interbreeding, this may have taken place in North Africa, the Levant, or the Arabian Peninsula, when a pioneering population of modern humans was leaving Africa.
     However, Stanford archaeologist Richard G. Klein, noted for his work on the fossil record which suggests that modern humans replaced Neanderthals, has reservations about the results of the study. The Pääbo report "contradicts everything we know about the archaeological record. Their evidence is really wobbly and it bothers me a lot. But it's very important stuff if it's right - and I really do hope it's right."

Sources: BBC News (6 May 2010), SFGate.com (7 May 2010)