[Plulpangepler]

From the paper everyone here refuses to read.

Average DNA divergence between Neandertals and humans. To estimate the DNA sequence divergence per base pair between the genomes of Neandertals and the reference human genome sequence, we generated three-way alignments between the Neandertal, human, and chimpanzee genomes, filtering out genomic regions that may be duplicated in either humans or chimpanzees (SOM Text 10) and using an inferred genome sequence of the common ancestor of humans and chimpanzees as a reference (51) to avoid potential biases (39). We then counted the number of substitutions specific to the Neandertal, the human, and the chimpanzee genomes (Fig. 2). The overall number of substitutions unique to the Neandertal genome is about 30 times as high as on the human lineage. Because these are largely due to transitions resulting from deamination of cytosine residues in the Neandertal DNA, we restricted the divergence estimates to transversions. We then observed four to six times as many on the Neandertal as on the human lineage, probably due to sequencing errors in the low-coverage Neandertal DNA sequences. The numbers of transversions on the human lineage, as well as those on the lineage from the Neandertal-human ancestor to the chimpanzee, were used to estimate the average divergence between DNA sequences in Neandertals and present-day humans, as a fraction of the lineage from the human reference genome to the common ancestor of Neandertals, humans, and chimpanzees. For autosomes, this was 12.7% for each of the three bones analyzed. For the X chromosome, it was 11.9 to 12.4% (table S26). Assuming an average DNA divergence of 6.5 million years between the human and chimpanzee genomes (52), this results in a point estimate for the average divergence of Neandertal and modern human autosomal DNA sequences of 825,000 years. We caution that this is only a rough estimate because of the uncertainty about the time of divergence of humans and chimpanzees.

Five present-day human genomes. To put the divergence of the Neandertal genomes into perspective with regard to present-day humans, we sequenced the genomes of one San from Southern Africa, one Yoruba from West Africa, one Papua New Guinean, one Han Chinese, and one French from Western Europe to 4- to 6-fold coverage on the Illumina GAII platform (SOM Text 9). These sequences were aligned to the chimpanzee and human reference genomes and analyzed using a similar approach to that used for the Neandertal data. Autosomal DNA sequences of these individuals diverged 8.2 to 10.3% back along the lineage leading to the human reference genome, considerably less than the 12.7% seen in Neandertals (SOM Text 10). We note that the divergence estimate for the Yoruba individual to the human genome sequence is ~14% greater than previous estimates for an African American individual (56) and similarly greater than the heterozygosity measured in another Yoruba individual (33). This may be due to differences in the alignment and filtering procedures between this and previous studies (SOM Text 9 and 10). Nevertheless, the divergence of the Neandertal genome to the human reference genome is greater than for any of the present-day human genomes analyzed.

Distributions of DNA divergences to humans. To explore the variation of DNA sequence divergence across the genome, we analyzed the divergence of the Neandertals and the five humans to the reference human genome in 100 kilobase windows for which at least 50 informative transversions were observed. The majority of the Neandertal divergences overlap with those of the humans (Fig. 3), reflecting the fact that Neandertals fall inside the variation of present-day humans. However, the overall divergence is greater for the three Neandertal genomes. For example, their modes are around divergences of ~11%, whereas for the San the mode is ~9% and for the other present-day humans ~8%. For the Neandertals, 13% of windows have a divergence above 20%, whereas this is the case for 2.5% to 3.7% of windows in the current humans.



Fig. 3 Divergence of Neandertal and human genomes. Distributions of divergence from the human genome reference sequence among segments of 100 kb are shown for three Neandertals and the five present-day humans.

Furthermore, whereas in the French, Han, and Papuan individuals, 9.8%, 7.8%, and 5.9% of windows, respectively, show between 0% and 2% divergence to the human reference genome, in the San and the Yoruba this is the case for 1.7% and 3.7%, respectively. For the three Neandertals, 2.2 to 2.5% of windows show 0% to 2% divergence to the reference genome.



Four possible scenarios of genetic mixture involving Neandertals. Scenario 1 represents gene flow into Neandertal from other archaic hominins, here collectively referred to as Homo erectus. This would manifest itself as segments of the Neandertal genome with unexpectedly high divergence from present-day humans. Scenario 2 represents gene flow between late Neandertals and early modern humans in Europe and/or western Asia. We see no evidence of this because Neandertals are equally distantly related to all non-Africans. However, such gene flow may have taken place without leaving traces in the present-day gene pool. Scenario 3 represents gene flow between Neandertals and the ancestors of all non-Africans. This is the most parsimonious explanation of our observation. Although we detect gene flow only from Neandertals into modern humans, gene flow in the reverse direction may also have occurred. Scenario 4 represents old substructure in Africa that persisted from the origin of Neandertals until the ancestors of non-Africans left Africa. This scenario is also compatible with the current data.

Better question.

What if they had a progenitor? Wouldn't we see similar overlap?

Sigh. People on this forum know nothing about genetics.

Ben of course Homo N. and Homo Sapiens have a common progenitor. It may shock you but we and Chimpanzees have common ancestors, and probably all life on this planet has common progenitors.

People instead of speculating idly on their method, just read the godamn link I posted. Its a long paper but its worth it.