Neanderthal admixture in modern Eurasians Dec 16, 2011 14:05:39 GMT -5
Post by Bozur on Dec 16, 2011 14:05:39 GMT -5
May 07, 2010
Tales of Neanderthal admixture in modern Eurasians
I was wary of this paper's conclusion as soon as I realized that the authors contended that Europeans and East Asians did not differ significantly in their levels of Neanderthal admixture. You see, Neandertals were absent from East Asia, so there is no reason for East Asians to have such admixture at all, or to have much less of it than West Eurasians do.
Even if we assumed that undifferentiated Eurasians picked up Neandertal admixture in West Asia, the fact would remain that Europeans co-existed with Neandertals after the ancestors of East Asians had moved on towards the Pacific. So, they ought to have more Neandertal admixture -if such admixture ever took place. Indeed, one of the main arguments for introgression of Neandertal genes in modern humans is the long co-existence of modern humans with Neandertals in Europe.
It could be argued that Neandertal admixture was indeed higher in West Eurasians initially, but the difference was evened out by gene flow across Eurasia. This, however, makes no sense, as the history of Eurasians post-Out of Africa was one of genetic differentiation, which suggests barriers to gene flow, and it would be difficult to imagine a scenario in which the Neandertal component would even out in Eurasia across populations from the Atlantic to the Pacific.
We should also note that the present paper's line of genetic evidence is not really complementary to the palaeoanthropological argument for admixture, as that argument is based on observing phenotypic continuities between Neandertals and modern Caucasoids that could not (according to the argument's proponents) be explained by the simple Out of Africa model and/or observing phenotypic traits of Upper Paleolithic Europeans that seem to be shared with Neandertals but not with UP sapiens outside Europe.
In short: those who use skulls to argue Neandertal introgression predict that Europeans should be somehow closer to Neandertals than East Asians are, but this paper fails to find evidence of this.
So what really happened: an alternative hypothesis
The authors do make an important observation: Neandertal genomes were closer to those of modern Eurasians than to modern Africans. This is an important finding that is incompatible with pure Out-of-Africa. But, Neandertal admixture is not the only way to explain the data.
There is an alternative explanation. It involves the emergence of Homo sapiens and Homo neanderthalensis from a common ancestor and the subsequent admixture of Homo sapiens with populations that have branched out before this divergence. This would account for increased similarity between Eurasians and Neandertals, but without the problem of explaining how "Neandertal" ancestry is so similar in Europeans and East Asians.
What about Africans? Why do they stand further away from Neandertals? The answer is simple: low-level of admixture with archaic humans in Africa itself. It is fairly clear to me that the sapiens line whose earliest examples are in East/South Africa must have been an offshoot of an older African set of populations. We are lucky that Neandertals lived in a climate conducive to bone (or even DNA) preservation, while the African populations inhabiting the tropics left no traces of their existence.
In conclusion: I am not at all convinced that the authors have uncovered evidence of Neanderthal admixture in Eurasians; the alternative explanation is that modern humans and Neandertals were related, modern humans spread from East Africa/West Asia and as they entered deeper into Africa, they interacted with archaic human populations there.
PS: The only potential argument in favor of the authors' hypothesis is the following:
Non-Africans haplotypes match Neandertals unexpectedly often. An alternative approach to detect gene flow from Neandertals into modern humans is to focus on patterns of variation in present-day humans—blinded to information from the Neandertal genome—in order to identify regions that are the strongest candidates for being derived from Neandertals. If these candidate regions match the Neandertals at a higher rate than is expected by chance, this provides additional evidence for gene flow from Neandertals into modern humans.
We thus identified regions in which there is considerably more diversity outside Africa than inside Africa, as might be expected in regions that have experienced gene flow from Neandertals to non-Africans. We used 1,263,750 Perlegen Class A SNPs, identified in individuals of diverse ancestry (78), and found 13 candidate regions of Neandertal ancestry (SOM Text 17). A prediction of Neandertal-to-modern human gene flow is that DNA sequences that entered the human gene pool from Neandertals will tend to match Neandertal more often than their frequency in the present-day human population. To test this prediction, we identified 166 "tag SNPs" that separate 12 of the haplotype clades in non-Africans (OOA) from the cosmopolitan haplotype clades shared between Africans and non-Africans (COS) and for which we had data from the Neandertals. Overall, the Neandertals match the deep clade unique to non- Africans at 133 of the 166 tag SNPs, and 10 of the 12 regions where tag SNPs occur show an excess of OOA over COS sites. Given that the OOA alleles occur at a frequency of much less than 50% in non-Africans (average of 13%, and all less than 30%) (Table 5), the fact that the candidate regions match the Neandertals in 10 of 12 cases (P = 0.019) suggests that they largely derive from Neandertals. The proportion of matches is also larger than can be explained by contamination, even if all Neandertal data were composed of present-day non-African DNA (P = 0.0025) (SOM Text 17).
The problem with the above analysis is in the underlined portion. The deep clade is rather unique to non-Americans of African ancestry, as per reference (78), i.e., a very limited sample of Africans. In short, there is no reason to believe that the identified deep clades matching the Neandertals are really unique to non-Africans, and the pattern can be easily explained by geographical structure within Africa itself.
Related: for a contrary view see John Hawks.
UPDATE: To their credit, the authors consider the scenario I am advocating it here, labeling it Scenario 4. They write:
Although gene flow from Neandertals into modern humans when they first left sub-Saharan Africa seems to be the most parsimonious model compatible with the current data, other scenarios are also possible. For example, we cannot currently rule out a scenario in which the ancestral population of present-day non-Africans was more closely related to Neandertals than the ancestral population of present-day Africans due to ancient substructure within Africa (Fig. 6). If after the divergence of Neandertals there was incomplete genetic homogenization between what were to become the ancestors of non-Africans and Africans, present-day non-Africans would be more closely related to Neandertals than are Africans. In fact, old population substructure in Africa has been suggested based on genetic (81) as well as paleontological data (86).
Whether their model is more parsimonious than Scenario 4 is up to the reader. We know that there is population structure in Africa today, and as the authors note there are reasons why this ought to have been true in the past. So, while Scenario 4 makes up a reasonable xtra assumption (the one I describe in my post), the authors' favored scenario does not explain easily how a species that inhabited Western Eurasia (Neandertals) ended up contributing not-too different amounts of DNA to Europeans and Chinese. So, for the time being, I'm sticking to my guns and saying that the paper has uncovered something important, but probably not Neandertal admixture.
UPDATE II (May 11): Direction of gene flow (to or from Neanderthals, or ...?)
Science 7 May 2010:
Vol. 328. no. 5979, pp. 710 - 722
A Draft Sequence of the Neandertal Genome
Richard E. Green et al.
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.