Mitogenomics of the Koryaks and Evens of the northern coast of the Sea of Okhotsk.

Due to the geographical proximity of the northern coast of the Sea of Okhotsk and Kamchatka Peninsula to the Beringia, the indigenous populations of these territories are of great interest for elucidating the human settlement history of northern Asia and America. Meanwhile, there is a clear shortage of genetic studies of the indigenous populations of the northern coast of the Sea of Okhotsk. Here, in order to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 203 complete mitogenomes (174 of which are new) from population samples of the Koryaks and Evens of the northern coast of the Sea of Okhotsk and the Chukchi of the extreme northeast Asia. The patterns observed underscore the reduced level of genetic diversity found in the Koryak, Even, and Chukchi populations, which, along with the high degree of interpopulation differentiation, may be the result of genetic drift. Our phylogeographic analysis reveals common Paleo-Asiatic ancestry for 51.1% of the Koryaks and 17.8% of the Evens. About third of the mitogenomes found in the Koryaks and Evens might be considered as ethno-specific, as these are virtually absent elsewhere in North, Central and East Asia. Coalescence ages of most of these lineages coincide well with the emergence and development of the Tokarev and Old Koryak archaeological cultures associated with the formation of the Koryaks, as well as with the period of separation and split of the North Tungusic groups migrated northwards from the Lake Baikal or the Amur River area.

Atmospheric Air Pollution by Stationary Sources in Ulan-Ude (Buryatia, Russia) and Its Impact on Public Health.

For the first time in the territory of the Russian Far East, a study related to the establishment of correlations between air quality and public health in Ulan-Ude (Buryatia, Russia) was carried out. This study is based on the analysis of official medical statistics on morbidity over several years, the data on the composition and volume of emissions of harmful substances into the air from various stationary sources, and laboratory measurements of air pollutants in different locations in Ulan-Ude. This study confirmed that the morbidity of the population in Ulan-Ude has been increasing every year and it is largely influenced by air pollutants, the main of which are benzo(a)pyrene, suspended solids, PM2.5, PM10, and nitrogen dioxide. It was found that the greatest contribution to the unfavorable environmental situation is made by three types of stationary sources: large heating networks, autonomous sources (enterprises and small businesses), and individual households. The main air pollutants whose concentrations exceed the limits are benzo(a)pyrene, formaldehyde, suspended particles PM2.5, PM10, and nitrogen dioxide. A comprehensive assessment of the content of various pollutants in the atmospheric air showed that levels of carcinogenic and non-carcinogenic risks to public health exceeded allowable levels. Priority pollutants in the atmosphere of Ulan-Ude whose concentrations create unacceptable levels of risk to public health are benzo(a)pyrene, suspended solids, nitrogen dioxide, PM2.5, PM10, formaldehyde, and black carbon. The levels of morbidity in Ulan-Ude were higher than the average for Buryatia by the main disease classes: respiratory organs-by 1.19 times, endocrine system-by 1.25 times, circulatory system-by 1.11 times, eye diseases-by 1.06 times, neoplasms-by 1.47 times, congenital anomalies, and deformations and chromosomal aberrations-by 1.63 times. There is an increase in the incidence of risk-related diseases of respiratory organs and the circulatory system. A strong correlation was found between this growth of morbidity and atmospheric air pollution in Ulan-Ude.

Mitogenomics of modern Mongolic-speaking populations.

Here, we present a comprehensive data set of 489 complete mitogenomes (211 of which are new) from four Mongolic-speaking populations (Mongols, Barghuts, Khamnigans, and Buryats) to investigate their matrilineal genetic structure, ancestry and relationship with other ethnic groups. We show that along with very high levels of genetic diversity and lack of genetic differentiation, Mongolic-speaking populations exhibit strong genetic resemblance to East Asian populations of Chinese, Japanese, and Uyghurs. Phylogeographic analysis of complete mitogenomes reveals the presence of different components in the gene pools of modern Mongolic-speaking populations-the main East Eurasian component is represented by mtDNA lineages of East Asian, Siberian and autochthonous (the Baikal region/Mongolian) ancestry, whereas the less pronounced West Eurasian component can be ascribed to Europe and West Asia/Caucasus. We also observed that up to one third of the mtDNA subhaplogroups identified in Mongolic-speaking populations can be considered as Mongolic-specific with the coalescence age of most of them not exceeding 1.7 kya. This coincides well with the population size growth which started around 1.1 kya and is detectable only in the Bayesian Skyline Plot constructed based on Mongolic-specific mitogenomes. Our data suggest that the genetic structure established during the Mongol empire is still retained in present-day Mongolic-speaking populations.

Mitogenomic diversity and differentiation of the Buryats.

In this paper we present a results of first comprehensive study of the complete mitogenomes in the Buryats with regard to their belonging to the main regional (eastern and western Buryats); tribal (Khori, Ekhirid, Bulagad, and Khongodor), and ethno-territorial (Aginsk, Alar, Balagansk, Barguzin, Ida, Khorinsk, Kuda, Selenga, Verkholensk, Olkhon, Tunka, and Shenehen Buryats) groups. The analysis of molecular variation performed using regional, tribal, and ethno-territorial divisions of the Buryats showed lack of genetic differentiation at all levels. Nonetheless, the complete mitogenome analysis revealed a very high level of genetic diversity in the Buryats which is the highest among Siberian populations and comparable to that in populations of eastern and western Asia. The AMOVA and MDS analyses results imply to a strong genetic similarity between the Buryats and eastern Asian populations of Chinese and Japanese, suggesting their origin on the basis of common maternal ancestry components. Several new Buryat-specific branches of haplogroup G (G2a2a, G2a1i, G2a5a) display signals of dispersals dating to 2.6-6.6 kya with a possible origin in eastern Asia, thus testifying Bronze Age and Neolithic arrival of ancestral eastern Asian component to the South Siberia region.

Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407.

Y chromosome microsatellite (Y-STR) diversity has been studied in different Mongolic-speaking populations from South Siberia, Mongolia, North-East China and East Europe. The results obtained indicate that the Mongolic-speaking populations clustered into two groups, with one group including populations from eastern part of South Siberia and Central Asia (the Buryats, Barghuts and Khamnigans) and the other group including populations from western part of Central Asia and East Europe (the Mongols and Kalmyks). High frequency of haplogroup C3-M407 (>50%) is present in the Buryats, Barghuts and Khamnigans, whereas in the Mongols and Kalmyks its frequency is much lower. In addition, two allelic combinations in DYS385a,b loci of C3-M407 haplotypes have been observed: the combination 11,18 (as well as 11,17 and 11,19) is frequent in different Mongolic-speaking populations, but the 11,11 branch is present mainly in the Kalmyks and Mongols. Results of locus-specific sequencing suggest that the action of gene conversion is a more likely explanation for origin of homoallelic 11,11 combination. Moreover, analysis of median networks of Y-STR haplotypes demonstrates that at least two gene conversion events can be revealed-one of them has probably occurred among the Mongols, and the other event occurred in the Barghuts. These two events give an average gene conversion rate range of 0.24-7.1 × 10(-3) per generation.

A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate.

As microsatellites located on Y chromosome mutate with different rates, they may be exploited in evolutionary studies, genealogical testing of a variety of populations and even, as proven recently, aid individual identification. Currently available commercial Y-STR kits encompass mostly low to moderately mutating loci, making them a perfect choice for the first two applications. Some attempts have been made so far to utilize Y-STRs to provide a discriminatory tool for forensic purposes. Although all 13 rapidly mutating Y-STRs were already multiplexed, no single assay based on single-copy markers allowing at least a portion of close male relatives to be differentiated from one another is available. To fill in the blanks, we constructed and validated an assay comprised of single-copy Y-STR markers only with a mutation rate ranging from 8×10(-3) to 1×10(-2). Performance of the resulting combination of nine RM Y-STRs and four moderately mutating ones was tested on 361 father-son pairs and 1326 males from 9 populations revealing an overall mutation rate of 1.607×10(-1) for the assay as a whole. Application of the proposed 13 Y-STR set to differentiation of haplotypes present among homogenous population of Buryats resulted in a threefold increase of discrimination as compared with 10 Y-STRs from the PowerPlex(®) Y.

Western Eurasian ancestry in modern Siberians based on mitogenomic data.

BACKGROUND: Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. RESULTS: We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1-6 kya (coding region rate). CONCLUSIONS: The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions.

Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe.

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.

Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a.

To investigate the structure of Y chromosome haplogroups R-M207 and Q-M242 in human populations of North Asia, we have performed high-resolution genotyping using both single nucleotide polymorphisms and short tandem repeat (STR)-based approaches of 121 M207- and M242-derived samples from 885 males of 16 ethnic groups of Siberia and East Asia. As a result, the following Y chromosome haplogroups were revealed: R1b1b1-M73 (2.0%), R1b1b2-M269 (0.7%), R2-M124 (1.1%), Q1a*-MEH2 (0.5%), Q1a2-M25 (0.1%), Q1a3*-M346 (9.2%) and Q1a3a-M3 (0.2%). Despite the low coalescence age of haplogroup Q1a3*-M346, which is estimated in South Siberia as about 4.5±1.5 thousand years ago (Ka), divergence time between these Q1a3*-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 13.8±3.9 Ka, pointing to a relatively recent entry date to America. In addition, unique cluster of haplotypes belonging to Q1a*-MEH2 was found in Koryaks inhabiting the Sea of Okhotsk coast (at a frequency of 10.3%). Although the level of STR diversity associated with Q1a*-MEH2 is very low, this lineage appears to be closest to the extinct Palaeo-Eskimo individuals belonging to the Saqqaq culture arisen in the New World Arctic about 5.5 Ka. This finding suggests that Q1a*-MEH2 likely traces a population migration originating in Northeast Siberia across the Bering Strait.

Phylogeography of the Y-chromosome haplogroup C in northern Eurasia.

To reconstruct the phylogenetic structure of Y-chromosome haplogroup (hg) C in populations of northern Eurasia, we have analyzed the diversity of microsatellite (STR) loci in a total sample of 413 males from 18 ethnic groups of Siberia, Eastern Asia and Eastern Europe. Analysis of SNP markers revealed that all Y-chromosomes studied belong to hg C3 and its subhaplogroups C3c and C3d, although some populations (such as Mongols and Koryaks) demonstrate a relatively high input (more than 30%) of yet unidentified C3* haplotypes. Median joining network analysis of STR haplotypes demonstrates that Y-chromosome gene pools of populations studied are characterized by the presence of DNA clusters originating from a limited number of frequent founder haplotypes. These are subhaplogroup C3d characteristic for Mongolic-speaking populations, "star cluster" in C3* paragroup, and a set of DYS19 duplicated C3c Y-chromosomes. All these DNA clusters show relatively recent coalescent times (less than 3000 years), so it is probable that founder effects, including social selection resulting in high male fertility associated with a limited number of paternal lineages, may explain the observed distribution of hg C3 lineages.

Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia.

More than a half of the northern Asian pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. While there has been considerable recent progress in studying mitochondrial variation in eastern Asia and America at the complete genome resolution, little comparable data is available for regions such as southern Siberia--the area where most of northern Asian haplogroups, including C and D, likely diversified. This gap in our knowledge causes a serious barrier for progress in understanding the demographic pre-history of northern Eurasia in general. Here we describe the phylogeography of haplogroups C and D in the populations of northern and eastern Asia. We have analyzed 770 samples from haplogroups C and D (174 and 596, respectively) at high resolution, including 182 novel complete mtDNA sequences representing haplogroups C and D (83 and 99, respectively). The present-day variation of haplogroups C and D suggests that these mtDNA clades expanded before the Last Glacial Maximum (LGM), with their oldest lineages being present in the eastern Asia. Unlike in eastern Asia, most of the northern Asian variants of haplogroups C and D began the expansion after the LGM, thus pointing to post-glacial re-colonization of northern Asia. Our results show that both haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene.

Phylogeographic analysis of mitochondrial DNA in northern Asian populations.

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.

Y-chromosome haplogroup N dispersals from south Siberia to Europe.

In order to reconstruct the history of Y-chromosome haplogroup (hg) N dispersals in north Eurasia, we have analyzed the diversity of microsatellite (STR) loci within two major hg N clades, N2 and N3, in a total sample of 1,438 males from 17 ethnic groups, mainly of Siberian and Eastern European origin. Based on STR variance analysis we observed that hg N3a is more diverse in Eastern Europe than in south Siberia. However, analysis of median networks showed that there are two STR subclusters of hg N3a, N3a1 and N3a2, that are characterized by different genetic histories. Age calculation of STR variation within subcluster N3a1 indicated that its first expansion occurred in south Siberia [approximately 10,000 years (ky)] and then this subcluster spread into Eastern Europe where its age is around 8 ky ago. Meanwhile, younger subcluster N3a2 originated in south Siberia (probably in the Baikal region) approximately 4 ky ago. Median network and variance analyses of STR haplotypes suggest that south Siberian N3a2 haplotypes spread further into Volga-Ural region undergoing serial bottlenecks. In addition, median network analysis of STR data demonstrates that haplogroup N2-A is represented by two subclusters, showing recent expansion times. The data obtained allow us to suggest Siberian origin of haplogroups N3 and N2 that are currently widespread in some populations of Eastern Europe.

Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia.

We have obtained Y-STR haplotypes in 12 loci (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439) from 215 Buryat males. We have found that one haplotype (15-11,18-13-28-23-10-11-14-14-10-12) comprises more than 30% of Y chromosomes in this population while another haplotype (14-11,13-14-30-23-10-14-14-14-10-10) comprises additional 14% of chromosomes. The population under study seems to be very homogenous as far as Y chromosome is regarded and the most frequent haplotype seems to be the modal haplotype for Buryats.

Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions.

In order to investigate the genetic history of autochthonous South Siberian populations and to estimate the contribution of distinct patrilineages to their gene pools, we have analyzed 17 Y-chromosomal binary markers (YAP, RPS4Y(711), SRY-8299, M89, M201, M52, M170, 12f2, M9, M20, 92R7, SRY-1532, DYS199, M173, M17, Tat, and LLY22 g) in a total sample of 1,358 males from 14 ethnic groups of Siberia (Altaians-Kizhi, Teleuts, Shors, Tuvinians, Todjins, Tofalars, Sojots, Khakassians, Buryats, Evenks), Central/Eastern Asia (Mongolians and Koreans) and Eastern Europe (Kalmyks and Russians). Based on both, the distribution pattern of Y-chromosomal haplogroups and results on AMOVA analysis we observed the statistically significant genetic differentiation between the populations of Baikal and Altai-Sayan regions. We suggest that these regional differences can be best explained by different contribution of Central/Eastern Asian and Eastern European paternal lineages into gene pools of modern South Siberians. The population of the Baikal region demonstrates the prevalence of Central/Eastern Asian lineages, whereas in the populations of Altai and Sayan regions the highest paternal contribution resulted from Eastern European descent is revealed. Yet, our data on Y-chromosome STRs variation demonstrate the clear differences between the South Siberian and Eastern European R1a1-lineages with the evolutionary ages compatible with divergence time between these two regional groups.

Mitochondrial DNA variation in the aboriginal populations of the Altai-Baikal region: implications for the genetic history of North Asia and America.

The discovery of mtDNA types common to Asians and Amerinds (types A, B, C, and D) forced investigators to search for those nations of Asia which, though not considered the ancestors of the Amerinds, have retained a close genetic resemblance with them. We collected samples and studied the gene pools of the Turkic-speaking nations of South Siberia: Altaians, Khakassians, Shorians, Tuvinians, Todjins, Tofalars, Sojots, as well as Mongolian-speaking Buryats. The data indicate that nearly all Turkic-speaking nations of Siberia and Central Asia, as well as the Buryats, have types A, B, C, and D in their gene pool. The highest total frequency of these types is observed in the Tuvinians and Sojots. They, as well as the Buryats, also have the lowest frequency of the europeoid types. The most mixed Asian-Europeoid gene pool examined turned out to be that of the Shorians. An important finding was the presence of type X in the Altaians, which had not yet been detected in Asia. As shown by computer analysis, this DNA sequence is not a late European admixture. Rather, the Altai variant X is ancient and can be close to the ancestral form of the variants of contemporary Europeans and Amerinds. The presented results prove that of all nations in Asia, the Turkic-speaking nations living between Altai and Baikal along the Sayan mountains are genetically closest to the Amerinds.