Jomon: Paleolithic Contingent in Modern Japanese Jul 5, 2018 18:47:34 GMT
Post by Admin on Jul 5, 2018 18:47:34 GMT
Phylogenetic tree of the complete mitochondrial genomes for the four ethnic groups. It is divided into MtA and MtB. MtA contains East Asian and European individuals together while MtB includes East Asian individuals only.
For the male lineages, we used the Y-STR markers for 453 individuals covering Japanese, Korean, Mongolian (Khalkh), American, and European people. We determined the evolutionary distances (RST) among them, and constructed a phylogenetic tree using the NJ method (Saitou and Nei 1987), as shown in figure 1. The Y-STR tree revealed that the male ancestral lineage contained two clades (Yap-A and Yap-B). While Yap-A clade includes the East Asian individuals only, Yap-B clade contains the East Asian and European individuals together. Surprisingly, the European males never formed an independent clade. Instead, they formed separate clades within Yap-B.
We then constructed a phylogenetic tree (Mt tree) for the 72 complete mtDNAs including the four ethnic groups, as shown in figure 2. We used Kimura’s two parameter method (Kimura 1980) for computing evolutionary distances among them and the NJ method for the tree construction. The Mt tree revealed two female descendant clades (Mt A and Mt B). Mt B consisted of the East Asian females only, while Mt A contained the East Asian and European females together. As in the case of males, the European females did not form an independent clade, but comprised several groups within the Mt A tree. As the Mt A cluster includes roughly as many European individuals as East Asian individuals, it is not clear which of them is ancestral to the other. The node marked with the blue circle in figure 2 suggests that the East Asians are ancestral to the Europeans. The bootstrap value of the node is 99%. Therefore, both male and female lineages suggest that Europeans diverged from within East Asian ancestors or that they interbred with East Asian individuals up to a certain divergence time.
Our next question was thus to estimate the divergence time of the European clade within the East Asian lineage, for males and females separately. To address that question, we computed the evolutionary distance (RST) between every pair of the male individuals to construct the Y-STR tree in figure 1. The RST value between the bottom and root of A and B clades in the tree was 16.91, while that between the bottom and root of the European male clade in the B clade was 12.31. Based on a divergence of East Asians from Africans of 55,000 years ago (Nei and Roychoudhury 1974, 1993), and assuming that RST is proportional to time, we can estimate the evolutionary rate of Y-STR by using the Y-STR tree. In the tree the RST value between the deepest root and the bottom is 16.91, and that between the common ancestor of Europeans males and the bottom is 12.31. The rate is thus estimated as 16.91/55,000 = 3.07 × 10−4 per repeat per year, which leads us to the conclusion that the divergence time of the European males is ∼40,100 years ago.
In the case of the Mt tree, we first transformed it into tree in which the lengths of a pair of branch lengths from the common node were equal to one another, as in the UPGMA tree (Sokal 1958), because we now dealt with the evolutionary time rather than distance (Kumada 1993). In the transformed tree, the topology was kept unchanged. We call the transformed tree the evolutionary time (ET) tree (fig. 3), because the tree reflects the evolutionary time rather than the distance, we call the tree showing evolutionary distance the evolutionary distance (ED) tree.