Phylogeographic analysis of mitochondrial DNA in northern Asian populations

Abstract

To elucidate the human colonization process of northern Asia and human dispersals to the Americas, a diverse subset of 71 mitochondrial DNA (mtDNA) lineages was chosen for complete genome sequencing from the collection of 1,432 control-region sequences sampled from 18 autochthonous populations of northern, central, eastern, and southwestern Asia. On the basis of complete mtDNA sequencing, we have revised the classification of haplogroups A, D2, G1, M7, and I; identified six new subhaplogroups (I4, N1e, G1c, M7d, M7e, and J1b2a); and fully characterized haplogroups N1a and G1b, which were previously described only by the first hypervariable segment (HVS1) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings indicate that the southern Siberian mtDNA pool harbors several lineages associated with the Late Upper Paleolithic and/or early Neolithic dispersals from both eastern Asia and southwestern Asia/southern Caucasus. Moreover, the phylogeography of the D2 lineages suggests that southern Siberia is likely to be a geographical source for the last postglacial maximum spread of this subhaplogroup to northern Siberia and that the expansion of the D2b branch occurred in Beringia ~7,000 years ago. In general, a detailed analysis of mtDNA gene pools of northern Asians provides the additional evidence to rule out the existence of a northern Asian route for the initial human colonization of Asia.

Figure 1.

Population sample sites, with sample sizes given in parentheses

Figure 2.

PC plot based on haplogroup frequencies for the 18 population samples. Populations are coded as follows: PS = Persians, KU = Kurds, TJ = Tajiks, Ko = Koreans, MN = Mongolians, KM = Kalmyks, BR = Buryats, KN = Khamnigans, TV = Tuvinians, EE = East Evenks, WE = West Evenks, YK = Yakuts, SH = Shors, KH = Khakassians, AL = Altaians-Kizhi, TL = Teleuts, TG = Telenghits, and CH = Chukchi.

Figure 3.

The phylogenetic tree of complete mtDNA sequences of haplogroups N1, X2e, and J1b. The tree is rooted in haplogroup N. Mutations are scored relative to the rCRS. The information of the reported samples is presented in table 1. Seven additional complete sequences were taken from the literature,^,,, and particular sequences from these articles are referred to as CH, MP, MR, and NMM, respectively, followed by a number sign (#) and the original sample code. For subhaplogroups I1, I2, and I3, only diagnostic mutations are shown, according to the classification.^,, For sample CH#230, only coding-region information is available. Mutations are shown on the branches and are transitions unless the base change is explicitly indicated. Deletions are indicated by a “D” after the deleted nucleotide position. Underlined nucleotide positions occur at least twice in the tree.

Figure 4.

Phylogenetic tree of complete mtDNA sequences of haplogroups A and Y. The tree is rooted in haplogroup N. The tree includes 36 mtDNAs, of which 31 are novel and 5 were reported elsewhere.^,, Insertions are indicated by a dot followed by the number and type of inserted nucleotide(s). For additional information, see the figure 3 legend.

Figure 5.

Phylogenetic tree of complete mtDNA sequences of haplogroups C1, G1, and D4. The tree is rooted in haplogroup M. For subhaplogroup D2b, only diagnostic mutations for specific lineages are indicated, according to data reported elsewhere. D2 and D2b coalescence-time estimates were obtained with consideration of the whole diversity within D2b subclusters. For additional information, see the figure 3 legend.

Figure 6.

Phylogenetic tree of complete mtDNA sequences of haplogroup M7. The tree is rooted in haplogroup M. For additional information, see the figure 3 legend.