East Asian and Melanesian ancestry in Polynesians.

To the Editor: Kayser et al.1xGenome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. Kayser, M., Lao, O., Saar, K., Brauer, S., Wang, X., Nurnberg, P., Trent, R.J., and Stoneking, M. Am. J. Hum. Genet. 2008; 82: 194–198Abstract | Full Text | Full Text PDF | PubMed | Scopus (67)See all References1 estimated the ancestry of Polynesians by using 377 autosomal microsatellite loci and concluded that 0.79 of the ancestry was from East Asians (95% CI, 0.76–0.84) and 0.21 from Melanesians. In contrast, maternally inherited mtDNA ancestry was previously estimated to be 0.94 East Asian and 0.06 Melanesian and paternally inherited Y chromosome ancestry was estimated to be 0.28 East Asian and 0.66 Melanesian.2xMelanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific. Kayser, M., Brauer, S., Cordaux, R., Casto, A., Lao, O., Zhivotovsky, L.A., Moyse-Faurie, C., Rutledge, R.B., Schiefenhoevel, W., Gil, D. et al. Mol. Biol. Evol. 2006; 23: 2234–2244Crossref | PubMed | Scopus (132)See all References2 One might guess that the East Asian autosomal ancestry would be approximately the arithmetic average of the mtDNA and Y ancestry, 0.61, but the estimated autosomal ancestry of 0.79 is substantially higher. To account for this difference and the different estimates in ancestry from different chromosomes, strong sex differences in gene flow, occurring in a particular chronological order, are necessary. Here I present a simple two-phase scenario to explain the different observed ancestries for autosomal, mtDNA, and Y markers and then discuss how this scenario could be modified and still result in the observed patterns.First, assume that a population of East Asian ancestry, which eventually became the Polynesians, settled in Melanesia and that subsequently there was male gene flow from Melanesians into this population. This pattern is consistent with both matrilocality and matrilinearity in this population.1xGenome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. Kayser, M., Lao, O., Saar, K., Brauer, S., Wang, X., Nurnberg, P., Trent, R.J., and Stoneking, M. Am. J. Hum. Genet. 2008; 82: 194–198Abstract | Full Text | Full Text PDF | PubMed | Scopus (67)See all References1 The effect of this male gene flow at a rate of mm per generation over t generations on Y ancestry can be given3xAdmixture dynamics in Hispanics: a shift in the nuclear genetic ancestry of a South American population isolate. Bedoya, G., Montoya, P., Garcia, J., Soto, I., Bourgeois, S., Carvajal, L., Labuda, D., Alvarez, V., Ospina, J., Hedrick, P.W., and Ruiz-Linares, A. Proc. Natl. Acad. Sci. USA. 2006; 103: 7234–7239Crossref | PubMed | Scopus (111)See all References3 aswhere q0 and qt are the initial and t generation East Asian ancestry in the population and qMel is the East Asian ancestry in the Melanesian migrants. Assuming that qMel = 0, q0 = 1, and qt = 0.28, thenFor example, if t = 50, then mm = 0.0251.For autosomal loci in this population, the East Asian ancestry iswhere mf is the per-generation rate of female gene flow. Again, assume that qMel = 0, q0 = 1, mf = 0, and with the estimated mm of 0.0251 used,. For example, if t = 50, then qt = 0.532.Second, assume that subsequently there was female gene flow from the East Asians into this population for x generations so that the autosomal East Asian ancestry can be expressed aswhere qEA is the East Asian ancestry in the East Asian female migrants. Assuming that qEA = 1, qt = 0.532, qt+x = 0.79, and mm = 0,For example, if x = 50, then mf = 0.0318.This two-phase scenario is presented in Figure 1Figure 1, which shows a decline in Y and autosomal East Asian ancestry over the first 50 generations and then an increase in autosomal East Asian ancestry and no change in Y ancestry over the second 50 generations. Note that the mtDNA East Asian ancestry is 1.0 throughout the whole scenario (essentially the same as the estimated 0.94).Figure 1Change in East Asian AncestryThe change in East Asian ancestry in Polynesians for autosomal and Y chromosome loci for 50 generations of male gene flow from Melanesians followed by 50 generations of female gene flow from East Asians.View Large Image | View Hi-Res Image | Download PowerPoint SlideSeveral models of gene flow can be excluded as possible explanations for the observed pattern of ancestry. First, if gene flow is not sex-specific, then it cannot result in the observed pattern. Second, male gene flow must start before female gene flow (female gene flow from East Asians can influence the East Asian autosomal population ancestry only after it has some Melanesian ancestry). If the female gene flow and the male gene flow start at the same time, then the total amount of female gene flow must be even larger than that given in the above example.In a more realistic model, the patterns of gene flow may differ somewhat from the above scenario and could vary over generations and still provide similar results. For example, gene flow from the two sexes from the different source populations could overlap; that is, the female gene flow from East Asians could start while male gene flow continues from Melanesians. Also, female gene flow from East Asians may not actually be from outside females with high East Asian ancestry but could occur because females of high East Asian ancestry had higher reproductive success in the population for some social or cultural reasons. Finally, it is possible that the Y ancestry in the Polynesians has been reduced by genetic drift, making arithmetic average of mtDNA and Y ancestry before genetic drift higher and, therefore, the difference between this average and the estimated autosomal ancestry of 0.79 smaller. Overall, though, it appears that an estimated male Melanesian gene flow of 0.0251 per generation for 50 generations and a subsequent estimated female East Asian gene flow of 0.0318 per generation for 50 generations, or the equivalent, are necessary to result in the observed pattern of ancestry over the autosomal, mtDNA, and Y chromosome markers.