Modern human origins::X marks the spot?

Reference: Garrigan, Daniel, et al. 2005. "Evidence for archaic Asian ancestry on the human X chromosome. Molecular Biology and Evolution 22(2):189-192.

This is a short study of a single genetic locus, RRM2P4, an X chromosome pseudogene. The interesting thing about this locus is the relatively high diversity of the gene in Asia. This diversity is not only higher than within Africans, but it includes a basal lineage that is not present in Africa.

Most human genes have greater genetic diversity within living Africans, and where there is a difference among continents in the presence of basal lineages, such lineages are found in Africans moreso than elsewhere. The number of genes examined in this way is not presently large. For example, Takahata et al. (2001) included only a dozen or so genes when they considered the geographic origins of genetic variation. Thus, it remains a relative unknown what proportion of genes might still exist that reveal a greater degree of variation outside of Africa.

This genetic locus evidently was one with a long ancestry within Asia. The basal variant exists within some Asian populations at frequencies of over 50 percent, so it is far from evidence of a minimal survival of archaic Asians. At least in the current sample of 570 individuals it provides strong evidence that Africa was not the only source of genetic material that become common in living humans.

Some observations:

  1. Why was important piece of evidence not in a more prestigious journal, with news reports and so on? Well, the news reports may still come, since it is the February issue, but the fact is the locus doesn't tell us all that much we didn't already know. The current genetic evidence makes it quite clear that the replacement of all archaic people by African invaders could not have happened (Templeton 2002, Hawks et al. 2000). This locus doesn't revolutionize what we knew, it just adds.
  2. What does it add, then? Most importantly, it shows that some of the genetic material from ancient Asians not only survived into later populations, it became a central part of the diversity of living Asians. Genetic survival is one thing--for example, morphological evidence suggests that Neandertals in Europe contributed to later European populations, but that their genes became progressively less common over time. In Asia, this gene documents a contribution that may have retained its original frequency, or even increased it. In other words, it is genetic evidence for the adaptability of ancient human gene pools in the face of their contacts with other populations.
  3. What are the prospects for finding more genes like this? The answer to this really depends on the pattern of evolution from archaic morphology to modern human morphology (and possibly behavior). Considering that Africa probably always had more people than other regions, it is not all that surprising that most human genes appear to have a primarily African influence on their early diversification. But the populations in at least some other parts of the world clearly gave rise to local adaptations, so there is no logical reason why they should not also have gbiven rise to global adaptations. This locus is not one of them--it is a pseudogene--but it may be linked to an ancient globally selected gene that originated in Asia. I expect that many more will be found.

Eswaran's CA paper has been influential toward making people think about the introgression of African genes into the other continents. Ultimately, I think this influence has confused the issue rather than clarified it. Mostly, I think this because of its focus on a single event, modeled as a population dispersal from Africa into other continents.

There is no evidence for such a dispersal, genetic or otherwise. There is substantial evidence for gene flow from Africa to other parts of the world, but as shown by Templeton (2002), this gene flow happened on at least several different occasions at different times during the Pleistocene. There is no evidence that there were distinct "occasions" at all, in the sense of dispersals of people. Indeed, gene flow could have been completely uniform and still create the same pattern of variation.