The Y chromosome and the replacement hypothesis.

Ke et al. (1) raised old questions about the origins and evolution of modern humans in East Asia. Unfortunately, they have shed no new light on the subject, their study amounting only to a large-scale genotyping of three previously observed Asian Y chromosome alleles (2). The authors provided no explicit statistical tests of any of their conclusions, which in any event are not new (3). Nor did they address the relationship of the information from the Y chromosome, a single genetic locus in the classical sense, to other genetic loci that might provide independent evidence for their preferred phylogenetic scheme— other than to assert that other loci are inadequate for such inferences by virtue of their mutational dynamics. The inadequacy of scientific and historical perspectives in the paper may leave many readers wondering how any competent researcher could possibly hold a view contrary to that of these authors. Many do disagree, however. In particular, no information provided by Ke et al. contradicts the studies of Hammer et al. (4) and Templeton (5), which viewed Y chromosome variation from a multilocus perspective. These earlier studies concluded that a global replacement of ancient Y chromosome variation did occur, probably from an African source. This ancient event apparently did not result in the replacement of the entire nuclear or mitochondrial genomes, but instead reflected a more limited genetic phenomenon upon a background of worldwide gene flow and isolation by distance. Furthermore, the Y chromosome variation appeared to indicate a later population movement out of Asia into Africa. It is not clear whether the ultimate explanation for Y chromosome variation is selection or male reproductive dynamics, but whatever is the case, there need be no a priori expectation that Y chromosome variation must be the only element of genetic variation requiring explanation, as assumed by Ke et al. (1). Perhaps Ke et al. disagree with the conclusions of these earlier papers, but they presented no reasons to disbelieve them, and any argument based only upon data from a single locus can never fully address the evolutionary history of the people who carried that gene. Also, notwithstanding the implication of Ke et al., fossils and archaeology are not silent on this issue. Although diagnostic skeletal remains between 120,000 and 50,000 years old within China are rare, the supposed absence of “missing links” (1) is not particularly relevant. The important morphological and archaeological observations relevant to the possibility of population replacement are (i) the occurrence of distinctive morphologies in both archaic and recent Asian populations, and (ii) the complete absence of any archaeological evidence for an influx of a new, presumably African population (6–8). Absent extraordinary circumstances—such as the replacement of archaic East Asians only by the Africans who look most similar to them, and only by those willing to abandon their own material culture and pick up the indigenous material culture—the most reasonable explanation for these facts is a partial contribution of archaic East Asians to the present human population. Remarkably, the only citations provided by Ke et al. (1) to contest the continuity of morphology and archaeology in East Asia were the previous assertions by some of their own coauthors, all laboratory geneticists. At the moment, at least, the only strong evidence for replacement of East Asian populations comes from the Y chromosome. It is important not to overinterpret this single source of evidence, but instead to view it in light of data from other genetic sources and archaeological and fossil sources into a comprehensive view. Such a balanced view argues against a simple hypothesis of replacement for East Asians or, indeed, for any ancient human population.