Raising a peace banner in the Neandertal Wars

The two camps in the Second Neandertal Wars (*)  have assumed maximalist positions on opposing sides of the argument: African structure explains it! vs. Neandertal admixture explains it!. Armed with the Vindija genome, that marvel of technological ingenuity, and a suite of impressive statistical models, the two sides have reached completely opposing conclusions.

In order to formulate my own position, I decided to do what I love best, i.e., to look at the data for myself. My main idea is that the signals of Neandertal and Denisova admixture as measured by these quantities (D-statistics) ...

D(Pop1, Yoruba, Neandertal, Chimp)

D(Pop1, Yoruba, Denisova, Chimp)

... will vary on different SNP ascertainment panels. SNPs ascertained in Africans may have a great number of Palaeoafrican alleles; SNPs in Neandertal-admixed populations will have a great number of Neandertal alleles; SNPs in Denisova-admixed populations will have a great number of Denisova alleles. If a population has admixture from hominin X, this admixture, as measured by the D-statistic, will tend to be inflated in panels possessing alleles that introgressed from X, and suppressed in panels that lack them.

The issue of ascertainment and archaic admixture was addressed by Skoglund and Jakobsson (2011); my aim is different: I am not so much interested in how ascertainment affects admixture estimates, but rather in exploiting the observation of the preceding paragraph (that Palaeoafrican, Neandertal, or Denisovan SNPs will lurk at different rates when ascertained in different individuals) to see what it tells us about human differences.

The signal of "archaic admixture" may be generated by genuine archaic admixture in one population (e.g., Eurasians), making it more similar to the archaic group (e.g., Neandertals), or by archaic admixture -of a different sort- in another population (e.g., Africans), making it less similar to that group. Both these processes may be at work, operating at different intensity in different populations and across different timelines.

I used the Harvard HGDP set, which contains 12 SNP panels, each of which has been ascertained in two chromosomes of a single individual. These panels are:

San, Yoruba, Mbuti, French, Sardinian, Han, Cambodian, Mongolian, Karitiana, Papuan1, Papuan2, Melanesian

A D-statistic was calculated relative to either Neandertal or Denisova for all HGDP populations, as well as the two archaic hominins. Subsequently, I used MCLUST to infer the number of different clusters on the basis of these statistics. In the optimal solution, MCLUST inferred 7 clusters, with each archaic hominin getting its own cluster, while the modern human populations were assigned to 5 clusters corresponding to five major human races recognized by traditional physical anthropology (Mongoloid, Negroid, Australoid, Capoid, and Caucasoid).

Note that these are not admixture proportions, but assignment probabilities! All populations fell into their expected clusters. The populations from Pakistan who are believed to be predominantly Caucasoid with varying degrees of minor admixture of an Ancestral South Indian element were assigned to the Caucasoid cluster. So did the Mozabite Berbers, a Caucasoid population with minority Negroid admixture. Finally, of the Central Asian populations, the Hazara of Pakistan showed mixed affiliations in the Caucasoid and Mongoloid clusters, while the Uygur were assigned to the Mongoloid cluster.

It is noteworthy that by exploiting patterns of relationship of modern to regional archaic humans, we have managed to recreate the major human groups. This is, perhaps, supportive of those who have argued that a degree of regional continuity across the Old World, and not only recent post-Out of Africa genetic divergence is responsible for present-day inter-population differences.

MCLUST also gave us the D-statistic means for the 7 inferred clusters. Remember that these are differences between a population Pop1 and Yoruba, relative to an archaic hominin (Neandertal or Denisova), and for 12 different ascertainment panels:

There are wonderful patterns to be discovered here; you can look at the data for yourselves; that's the open science thing to do.

All our ideas about human origins are conditioned on the availability of genomes from two archaic Eurasian hominins, and the lack of genomes of similar age from Africa.

But, remember:

• You can fit Europe, China, India, and the US into Africa, with room to spare. 
• If Vindija and Denisova, two caves less than 5,000km apart were home to people more divergent from each other than any two humans are today, it's strange to think that only "modern humans" inhabited Africa at the same time. 
• The maximum genetic distance between living Africans is much higher than the maximum distance between living Eurasians: Africa is much more diverse than Eurasia. It's simpler to assume that the same relative pattern was true during the Middle Stone Age. The palaeoanthropology seems to support this, showing archaic forms present even during the terminal Pleistocene in Africa.
• If modern humans did interbreed with 2/2 archaic humans whose sequences we possess, it's strange to think that they somehow shunned the African Others.

In view of the above, I humbly raise my peace banner in the Neandertal Wars, and declare that it isn't either-or: it's both!

(*) The First Neandertal Wars were fought decades ago by anthropologists working with calipers and magnifying lenses. Their outcome was to relegate Neandertals from the enviable position of our likely ancestors to that of an irrelevant sidekick, although a not-negligible minority continued an insurgency against the Out-of-Africa-only victors.