mtDNA Variation in the Altai-Kizhi Population of Southern Siberia: A Synthesis of Genetic Variation

Human Biology, Aug 2006 by Phillips-Krawczak, Christine, Devor, Eric, Zlojutro, Mark, Moffat-Wilson, Kristin, Crawford, Michael H

Coalescent dates were computed using the Tau (τ) parameter from Rogers and Harpending's mismatch model using the HVS-I mutation rate (μ) of 16.5% per nucleotide site per million years (Ward et al. 1991). Because τ was estimated from the mismatch distribution for the total sample, the corresponding coalescent date is not population specific (i.e., relating to ethnogenesis) but is more a reflection of the demographic processes that molded the Asian mtDNA landscape due to the disproportionate influence of intermediate- and high-frequency variants of the ancestral branches between the major haplogroups on the modal value of a mismatch distribution.

The F^sub s^ statistic is based on the probability of observing a random neutral sample with a number of alleles (k) similar to or smaller than the observed value, given the observed number of pairwise differences, taken as an estimator of θ. If there is an excess of rare alleles, a product of a starlike genealogy, then F^sub s^ will have large negative values. Both measures were calculated using Arlequin, version 2.0. The statistical significance was tested by generating random samples under selective neutrality and population equilibrium using a coalescent simulation algorithm, with p values representing the proportion of random statistics less than or equal to the observation (Hudson 1990).

Multidimensional Scaling. Multidimensional scaling (MDS) was performed using the software package NTSYS (Applied Biostatistics, Port Jefferson, New York) on Nei's intermatch-mismatch distance (D^sub A^) matrices (Nei and Li 1979) to provide a two-dimensional representation of the genetic relationships between the various populations considered in this study.

Results

mtDNA Haplogroups. European populations are mainly composed of 10 mtDNA haplogroups: HV, H, V, J, T, U, K, I, W, and X. The common Asian haplogroups are A, B, C, D, E, F, G, Y, Z, and M (Derenko et al. 2001a). As the Altaians' diverse ethnic history would suggest, the Altaian mtDNA gene pool displays both European and Asian mtDNA components. The mtDNA haplogroups present in Mendur-Sokkon are summarized in Table 2 and were identified through RFLP analyses.

Twelve identified haplogroups are present in the Mendur-Sokkon population, with 5.1% of the sample set unclassified. The most common haplogroup is C (35.7%), followed by D (13.3%) and "other" M haplogroups (10.2%), that is, samples possessing the 10394 DdeI and 10397 AluI sites that define macrohaplogroup M but not belonging to haplogroups C, D, E, or G. One individual in the sample of the community exhibited haplogroup X.

mtDNA Sequences. The mtDNA HVS-I sequences found in the MendurSokkon sample are listed in Table 3, based on the nucleotide range 16151-16383, and are referenced against the Cambridge Reference Sequence (Anderson et al. 1981).

Haplogroups are listed in the far left-hand column, with the frequency (number of sequences shared by individual samples) of each haplotype indicated in the adjacent column. Thirty different haplotypes were identified, representing 32 transitions and 2 transversions. Figure 3 displays the median-joining network of the Mendur-Sokkon mtDNA sequence data.