Complete Mitochondrial DNA Analysis of Eastern Eurasian Haplogroups Rarely Found in Populations of Northern Asia and Eastern Europe

<div><p>With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.</p> </div

MDS plot based on FST statistics calculated from mtDNA HVS1 sequences for population samples from northern, eastern, central and western Asia.

<p>Linguistic affiliation of populations is indicated by different colors: Turkic group of Altaic family – in red, Mongolic group of Altaic family – in yellow, Tungusic group of Altaic family – in green, Northern group of Chukotko-Kamchatkan family – in blue, Indo-Iranian group of Indo-European family – in purple, Chinese group of Sino-Tibetan family – in grey, language isolate – in black.</p

Diversity indices and neutrality tests for the studied populations based on HVS1 variability data.

a<p>Sample size.</p>b<p>Sequence diversity (H) and standard error (SE).</p>c<p>Number of different haplotypes and percentage of sample size in parentheses.</p>d<p>Number of segregating sites.</p>e<p>Average number of pairwise differences (Pi) with standard error (SE).</p>f<p>All P values are <0.05 (for Tajima's D) and <0.02 for Fu's F_S), except where noted.</p

Complete mtDNA phylogenetic tree of haplogroup B4'B5.

<p>This schematic tree is based on phylogenetic tree presented in Figure S1. Time estimates (in kya) shown for mtDNA subclusters are based on the coding region substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032179#pone.0032179-Perego1" target="_blank">[11]</a>, coding region synonymous substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032179#pone.0032179-Soares1" target="_blank">[19]</a> and complete genome substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032179#pone.0032179-Soares1" target="_blank">[19]</a>. The size of each circle is proportional to the number of individuals sharing the corresponding haplotype, with the smallest size corresponding to one individual. Geographical origin is indicated by different colors: northern Asian – in blue, central Asian – in pink, eastern Asian – in red, Indian – in grey, European – in white, Mainland southeastern Asian - in orange, Island southeastern Asian – in yellow, Oceania – in green, and Native American – in purple.</p

Mitochondrial super-haplogroup U diversity in Serbians

<p><b>Background:</b> Available mitochondrial (mtDNA) data demonstrate genetic differentiation among South Slavs inhabiting the Balkan Peninsula. However, their resolution is insufficient to elucidate the female-specific aspects of the genetic history of South Slavs, including the genetic impact of various migrations which were rather common within the Balkans, a region having a turbulent demographic history.</p> <p><b>Aim:</b> The aim was to thoroughly study complete mitogenomes of Serbians, a population linking westward and eastward South Slavs.</p> <p><b>Subjects and methods:</b> Forty-six predominantly Serbian super-haplogroup U complete mitogenomes were analysed phylogenetically against ∼4000 available complete mtDNAs of modern and ancient Western Eurasians.</p> <p><b>Results:</b> Serbians share a number of U mtDNA lineages with Southern, Eastern-Central and North-Western Europeans. Putative Balkan-specific lineages (e.g. U1a1c2, U4c1b1, U5b3j, K1a4l and K1a13a1) and lineages shared among Serbians (South Slavs) and West and East Slavs were detected (e.g. U2e1b1, U2e2a1d, U4a2a, U4a2c, U4a2g1, U4d2b and U5b1a1).</p> <p><b>Conclusion:</b> The exceptional diversity of maternal lineages found in Serbians may be associated with the genetic impact of both autochthonous pre-Slavic Balkan populations whose mtDNA gene pool was affected by migrations of various populations over time (e.g. Bronze Age pastoralists) and Slavic and Germanic newcomers in the early Middle Ages.</p