Green and his colleagues demonstrated what scientists can do and what kind of information you can get by applying advanced genomic technology to study of Neanderthal remains, but at the same time, we have to remind ourselves that what the Neanderthal genome tell us is still limited and hypothetical, because of small amount of DNA preserved, possible contamination from modern DNA source, chemical damage on the nucleotides, small coverage of genome, and small sample size. Another reason why it is difficult to understand Neanderthal genome is that Neanderthals are genetically very similar to modern humans. Several places in the article, the authors say that the Neanderthals are not genetically very different from modern human.
Despite the similarity, from three way comparisons of Neanderthals, modern humans, and chimpanzee, they found many genetic changes occurred only among modern human including 78 nucleotide substitutions that change amino-acid sequence (see the list on Table 2 of the article) and substitutions at regulatory area. They also found 212 regions that could have changed significantly among modern humans through strong positive selection, or selective sweep. The top 20 candidate region that selective sweep affected are listed on Table 3 of the article. These regions include genes that are responsible for metabolism, cognition, and skeletal development. However, the list will probably change, as they have more Neanderthal genome sequencing coverage and more Neanderthal individual analyzed.
Based on the closer genetic similarity between non-Africans and Neanderthal compared to between modern Africans and Neanderthals that they observed, the authors proposed that gene flow between Neanderthal and ancestors of modern non-Africans occurred. They estimated the 1 to 4 % of modern human genome is from Neanderthal and according to the authors the most likely scenario is that gene flow between Neanderthals and anatomically modern human occurred possibly in the Middle East, before ancestors of non-Africans radiated from there (Scenario 3 of Fig. 6). However, the authors also point out that actually Neanderthal genetic contribution could be smaller, if there was surfing effect, or larger, but later migration events erased evidence of ancient admixture.
Alternatively to ancient admixture, the authors also suggest that ancient population structure within Africa can also cause to have closer genetic similarity between Eurasians and Neanderthal, if the population source of the out-of-Africa had a great amount of old genetic variation that Neanderthals and modern human shared.
Now, there are several important questions that need to be addressed. If anatomically modern humans mated with Neanderthals and other archaic humans, should we considered modern humans, Neanderthals, and other archaic humans as sub-species of a single species, Homo sapience, not different species? Then, Home Sapience once had a great genetic and morphological variation, but today they are lost somehow. Should we reconsider who these archaic humans were? Once anthropologists thought intellectually superior modern humans could not be a same species as Neanderthals that had more primitive culture. However, archaeological evidence suggests that Neanderthals were capable of more complex thoughts than we originally thought. How about other archaic humans? Were they capable of having more complex culture? Are we so biased and we tend to think we are so unique and Neanderthals and other archaic humans were so different? Just like the 19th century evolutionary anthropologists who tried to theorize that Europeans were intellectually superior based on the cultural traits that they observed.
For more information, read my post on Neanderthal genome (here and here) or go to my YouTube AnthroGenetics Channel. I have a playlist on Neanderthal DNA (here). You can find videos of Green, Krause, Briggs, and Paabo talking about Neanderthal Genome project.
