Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups

Abstract

In search of the ancestors of Native American mitochondrial DNA (mtDNA) haplogroups, we analyzed the mtDNA of 531 individuals from nine indigenous populations in Siberia. All mtDNAs were subjected to high-resolution RFLP analysis, sequencing of the control-region hypervariable segment I (HVS-I), and surveyed for additional polymorphic markers in the coding region. Furthermore, the mtDNAs selected according to haplogroup/subhaplogroup status were completely sequenced. Phylogenetic analyses of the resulting data, combined with those from previously published Siberian arctic and sub-arctic populations, revealed that remnants of the ancient Siberian gene pool are still evident in Siberian populations, suggesting that the founding haplotypes of the Native American A-D branches originated in different parts of Siberia. Thus, lineage A complete sequences revealed in the Mansi of the Lower Ob and the Ket of the Lower Yenisei belong to A1, suggesting that A1 mtDNAs occasionally found in the remnants of hunting-gathering populations of northwestern and northern Siberia belonged to a common gene pool of the Siberian progenitors of Paleoindians. Moreover, lineage B1, which is the most closely related to the American B2, occurred in the Tubalar and Tuvan inhabiting the territory between the upper reaches of the Ob River in the west, to the Upper Yenisei region in the east. Finally, the sequence variants of haplogroups C and D, which are most similar to Native American C1 and D1, were detected in the Ulchi of the Lower Amur. Overall, our data suggest that the immediate ancestors of the Siberian/Beringian migrants who gave rise to ancient (pre-Clovis) Paleoindians have a common origin with aboriginal people of the area now designated the Altai-Sayan Upland, as well as the Lower Amur/Sea of Okhotsk region.

Figure 1

Approximate location of Siberian populations analysed for mtDNA variation.

Figure 2

Schematic phylogeny of haplogroup B mtDNAs found in Native Siberians and Native Americans. The phylogeny is rooted from macrohaplogroup N as inferred from the complete sequences of Siberian/Asian haplogroup A, B, and Y (Ingman et al. 2000; Herrnstadt et al. 2002; Mishmar et al. 2003; this study). Mutation positions, relative to the revised Cambridge Reference Sequence (Andrews et al. 1999), are transitions unless the base change is specified. Underlining indicates recurrent mutations. Founding motifs are shown in bold type.

Figure 3

Schematic phylogeny of haplogroup C, D, S and Z mtDNAs found in Native Siberians in comparison with their Native American counterparts. The phylogeny is rooted from macrohaplogroup M. Note that a transition at np 13879 in the Amerindian D1b mtDNA was erroneously shown in the legend of Figure 4 by Derbeneva et al. (2002a).

Figure 4

Phylogenetic relationships between 16 Siberian and two Native American populations of the North Pacific Rim (Aleut and Haida), determined by neighbor-joining using the frequencies of the 31 observed subhaplogroups. Haplogroup composition and frequencies in Haida and Aleut mtDNAs were adopted from Ward et al. (1993), and Derbeneva et al. (2002) and Rubicz et al. (2003) respectively.