Analysis of Neanderthal DNA.

Analysis of one million base pairs of Neanderthal DNA.
Nature 444, 330-336 (16 November 2006)
Green, R. E., et al.

a segment of the hypervariable control region of the maternally inherited mitochondrial DNA (mtDNA)

it has been estimated that a maximal overall genetic contribution of Neanderthals to the contemporary human gene pool is between 25% and 0.1%. Because the latter conclusions are based on mtDNA, a single maternally inherited locus, they are limited in their ability to detect a Neanderthal contribution to the current human gene pool both by the vagaries of genetic drift and by the possibility of a sex bias in reproduction.

Roughly 35 million nucleotide differences exist between the genomes of humans and chimpanzees, our closest living relatives.

genetic changes that occurred during the last few hundred thousand years, when fully anatomically and behaviourally modern humans appeared.

Using these PCR-confirmed substitutions and a divergence time between humans and chimpanzees of 4.7–8.4 million years40–42, we estimate the divergence time for the mtDNA fragments determined here to be 461,000–825,000 years. This is in general agreement with previous estimates of Neanderthal–human mtDNA divergence of 317,000–741,000 years6 based on mtDNA hypervariable region sequences and is compatible with our presumption that the mtDNA sequences determined fromthe Vi-80 extract are ofNeanderthal origin.

If the human–chimpanzee divergence time is set to 6,500,000 years (refs 40, 41, 44), this implies an average human–Neanderthal DNA sequence divergence time of, 516,000 years. A 95% confidence interval generated by bootstrap re-sampling of the alignment data gives a range of 465,000 to 569,000 years. Obviously, these divergence estimates are dependent on the human–chimpanzee divergence time, which is a much larger source of uncertainty.

The average divergence time between alleles within humans is thus, 459,000 years with a 95% confidence interval between 419,000 and 498,000 years. As expected, this estimate of the average human diversity is less than the divergence seen between the human and the Neanderthal sequences, but constitutes a large fraction of it because much of the human sequence diversity is expected to predate the human–Neanderthal split.

related:
http://www.npr.org/blogs/health/2014/01/28/267923336/neanderthal-genes-live-on-in-our-hair-and-skin
Africans didn’t pick up those traits, since Neanderthals originated in Europe.

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