In his blog, John Hawks, Professor of Anthropology at the University of Wisconsin, discusses the level of introgression (i.e. the introduction of genes from the gene pool of one species into that of another during hybridization) of Neanderthal genes into modern human populations, using data from the 1000 Genomes Project.

The 1000 Genomes Project is the first project to sequence the genomes of a large number of people, to provide a comprehensive resource on human genetic variation. It aims to investigate relationship between genotype (genetic makeup) and phenotype (observable characteristics or traits). The African genomes in the 1000 Genomes sample include the Yoruba from Nigeria and the Luhya from Kenya. The Asian populations sampled are Japanese and Chinese, including people of Han Chinese ethnicity in Beijing and southern China. The European ancestry samples include British, Tuscan, Spanish and Finnish.

In a series of histograms (graphs showing the distribution of genome and population data), Hawks shows that Asian and European genomes have significantly more Neanderthal DNA than African genomes. The averages for Asian and European samples are around 3% higher than the average for African samples. Whatever gave Africans some degree of similarity to Neanderthals, non-Africans seem to have received around 3% more of it.

Europeans average a bit more Neanderthal DNA than Asians, showing that Europeans probably mixed with Neanderthals as they moved into Europe, adding a secondary mix of Neanderthal DNA into their genome beyond the primary mix shared by their respective ancestors.

The differences in Neanderthal admixture between populations within regions is more interesting. For example, Tuscans have the highest level of Neanderthal similarity of any of the 1000 Genomes Project samples. They have around a half-percent more Neanderthal similarity than the British or the Finnish. This could be show a north-south geographical difference in Neanderthal ancestry, but later population movements in Europe probably masked a significant part of the Upper Paleolithic gene pool. However, the persistence through time of extra Neanderthal ancestry in southern Europe needs further study.

Populations within East Asia also show differences in Neanderthal similarity. North China has a bit more Neanderthal, on average, than South China according to the samples, though all are identified as ethnic Han Chinese.

In Africa, the Yoruba of Nigeria have substantially more Neanderthal similarity than the Luhya of Kenya. This is puzzling, because the geographic location of the Luhya in East Africa seems better placed for Neanderthal similarity to appear, whether through ancient population structure or through the backmigration into Africa of Neanderthal descendants. Instead, the Yoruba in West Africa are the recipients of Neanderthal genes. Much more is still to be learnt about ancient African population structures by using Neanderthal-similar regions of the genome, including ancient populations that do not appear in archaeology.