Genetic peculiarity of the yakut population from the autosomal loci data

The autosomal gene pool of Yakuts was analyzed with a panel of polymorphic Alu insertions. The observed allele frequencies were typical for other Asian ethnic groups. Genetic differentiation of three Yakut populations was relatively high, 2%. East Siberian ethnic groups were shown to have a common gene pool and to experience no intense gene flow from other populations. Development of the Yakut gene pool was assumed to involve no substantial genetic effect of neighboring populations. The results fit both autochthonous and southern origin hypotheses.     

The origin of Yakuts: analysis of Y-chromosome haplotypes

Gene pool structure of Sakha Republic (Yakutia) native population has been studied: we defined composition and frequencies of Y-chromosome haplogroups for Yakuts. Six haplogroups: C3 x M77, C3c, N*, N2, N3a and R1a1 have been revealed in Yakut gene pool. A greater part of Y-chromosome in Yakut population belongs to N3a haplogroup (89%). All investigated Yakut population samples have low values of gene diversity, calculated based on haplogroup frequencies. Gene differentiation of the investigated samples estimated using the analysis of molecular variance (AMOVA) by two marker systems (haplogroup frequencies and microsatellite haplotypes of Y-chromosome) revealed a portion of interpopulation differences amounting to 0.24 and 2.85%, respectively. Frequencies and molecular phylogeny of YSTR-haplotypes were revealed for N3a haplogroup of Y-chromosome. Altogether forty haplotypes were found in Yakuts. Evenks and Yakuts are characterized by overlapping and very specific spectrum of N3a haplotypes, which is not typical for other Siberian ethnic groups. Cluster analysis of populations by N3a YSTR-haplotypes shows Yakut isolation from Turkic-speaking populations in the South Siberia. Genetic diversity generation time for a specific spectrum of Yakut haplotypes was estimated as 4.45 +/- 1.96 thousand years. As opposed to the data on mtDNA, the obtained results give an evidence for significant contribution of a local palaeolithic component into Y-chromosomal Yakut gene pool. Ethnogenetic reconstruction of the present picture of genetic diversity in N3a haplogroup in the territory of Siberia is under consideration.     

Analysis of Mitochondrial DNA Lineages in Yakuts

To study the mitochondrial gene pool structure in Yakuts, polymorphism of mtDNA hypervariable segment I (16,024–16,390) was analyzed in 191 people sampled from the indigenous population of the Sakha Republic. In total, 67 haplotypes of 14 haplogroups were detected. Most (91.6%) haplotypes belonged to haplogroups A, B, C, D, F, G, M*, and Y, which are specific for East Eurasian ethnic groups; 8.4% haplotypes represented Caucasian haplogroups H, HV1, J, T, U, and W. A high frequency of mtDNA types belonging to Asian supercluster M was peculiar for Yakuts: mtDNA types belonging to haplogroup C, D, or G and undifferentiated mtDNA types of haplogroup M (M*) accounted for 81% of all haplotypes. The highest diversity was observed for haplogroups C and D, which comprised respectively 22 (44%) and 18 (30%) haplotypes. Yakuts showed the lowest genetic diversity (H = 0.964) among all Turkic ethnic groups. Phylogenetic analysis testified to common genetic substrate of Yakuts, Mongols, and Central Asian (Kazakh, Kyrgyz, Uighur) populations. Yakuts proved to share 21 (55.5%) mtDNA haplotypes with the Central Asian ethnic groups and Mongols. Comparisons with modern Paleoasian populations (Chukcha, Itelmen, Koryaks) revealed three (8.9%) haplotypes common for Yakuts and Koryaks. The results of mtDNA analysis disagree with the hypothesis of an appreciable Paleoasian contribution to the modern Yakut gene pool.     

Population Study of Frequency of Methylenetetrahydrofolate Reductase C677T Gene Polymorphism in Yakutia

The enzyme methylenetetrahydrofolate reductase (MTHFR) catalyzes synthesis of 5-methylenehydrofolate, which is the methyl donor for the conversion of homocysteine to methionine. According to the numerous literature data, polymorphic variant of the MTHFR-encoding gene, C677T, is associated with hyperhomocysteinemia, vascular pathologies, neural tube defects, dementia, perinatal mortality, mental disorders, long-term neurodegenerative disorders, lens displacement, arachnodactyly, and venous thromboses. The present study was focused on the analysis of the C677T polymorphism (missence mutation leading to the replacement of cytosine by thymine at position 677) of the MTHFR gene in three indigenous populations of the Republic of Sakha (Yakutia), living in the settlements of Cheriktei, Byadi, and Dyupsya. Comparison of the genotype and allele frequencies revealed no substantial differences between the three Yakut populations, as well as between Yakuts and other Mongoloid ethnic groups.     

The origin of Yakuts: Analysis of the Y-chromosome haplotypes

The gene pool structure was studied for the indigenous population of the Sakha Republic (Yakutia). The composition and frequencies of Y-chromosome haplotypes in Yakuts were characterized. Six haplogroups were observed: C3×M77, C3c, N*, N2, N3a, and R1a1, N3a being the most common (89%). The gene diversity computed from the haplogroup frequencies was low in all samples examined. Gene differentiation was analyzed by AMOVA with two marker systems (haplogroup frequencies and Y-chromosomal microsatellite haplotypes) and was estimated at 0.24 and 2.85%, respectively. The frequencies and molecular phylogeny of the YSTR haplotypes were studied for the N3a haplogroup. In total, 40 haplotypes were found in Yakuts. Evenks and Yakuts displayed highly specific overlapping N3a haplotype spectra, atypical for other Siberian ethnic groups. Cluster analysis with N3a YSTR haplotypes showed that Yakuts are isolated from other Turkic-speaking populations of Southern Siberia. The genetic diversity generation time was estimated at 4450 ± 1960 years for the Yakut haplotype spectrum. In contrast to mtDNA data, the results suggest a significant contribution of the local Paleolithic component to the Y-chromosome gene pool of Yakuts. Ethnogenetic reconstructions were inferred from the diversity and phylogeography of the N3a haplogroup in Siberia.     

Analysis of mitochondrial DNA haplotypes in yakut population

To study the mitochondrial gene pool structure in Yakuts, polymorphism of mtDNA hypervariable segment I (16,024-16,390) was analyzed in 191 people sampled from the indigenous population of the Sakha Republic. In total, 67 haplotypes of 14 haplogroups were detected. Most (91.6%) haplotypes belonged to haplogroups A, B, C, D, F, G, M*, and Y, which are specific for East Eurasian ethnic groups; 8.4% haplotypes represented Caucasian haplogroups H, HV1, J, T, U, and W. A high frequency of mtDNA types belonging to Asian supercluster M was peculiar for Yakuts: mtDNA types belonging to haplogroup C, D, or G and undifferentiated mtDNA types of haplogroup M (M*) accounted for 81% of all haplotypes. The highest diversity was observed for haplogroups C and D, which comprised respectively 22 (44%) and 18 (30%) haplotypes. Yakuts showed the lowest genetic diversity (H = 0.964) among all Turkic ethnic groups. Phylogenetic analysis testified to a common genetic substrate of Yakuts, Mongols, and Central Asian (Kazakh, Kyrgyz, Uigur) populations. Yakuts proved to share 21 (55.5%) mtDNA haplogroups with the Central Asian ethnic groups and Mongols. Comparisons with modern paleo-Asian populations (Chukcha, Itelmen, Koryaks) revealed three (8.9%) haplotypes common for Yakuts and Koryaks. The results of mtDNA analysis disagree with the hypothesis of an appreciable paleo-Asian contribution to the modern Yakut gene pool.     

Genetic diversity of the chromosome X in aboriginal Siberian populations: The structure of linkage disequilibrium and haplotype phylogeography of the <Emphasis Type="Italic">ZFX</Emphasis> locus

The gene pool structure of aboriginal Siberian populations has been described based on the polymorphism of the ZFX gene located on the chromosome X. In the ten populations studied, 49 haplotypes were present, three of them with high frequencies. Comparison of the obtained results with the available data from the HapMap project revealed unique African haplotypes that occurred in the Yoruba with the frequency of 3–7% and were not found in other populations. The genetic differentiation coefficient of the Siberian ethnic groups studied was 0.0486. Correlation analysis using Mantel’s test did not detect significant correlations between the genetic distance matrix and the matrices of geographic, linguistic, and anthropological differences, although the correlation with the anthropological matrix was the highest. Phylogenetic analysis proved strong isolation of the African population from the other ethnic groups investigated. The Siberian populations were divided into two separate clusters: the first one included Yakuts, Buryats, and Kets, while the second cluster included Altaians, Tuvinians, and Khanty. Using the principal component analysis, the populations were combined into three groups clearly differing by manifestation of Caucasoid and Mongoloid components. The first group included residents of Europe and one of Khanty populations, the second group included populations of South Siberia and residents of China. Mongoloid populations of East Siberia, the Japanese, and Kets were combined into the third group. Barrier analysis revealed a similar structure of genetic differentiation of Siberian populations. Linkage disequilibrium structure was obtained for six ethnic groups of Siberia. In five of them (except for the Ket population), ten ZFX SNPs formed a single linkage block.     

Population study of frequency of methylenetetrahydrofolate reductase C677T gene polymorphism in Yakutia

The enzyme methylenetetrahydrofolate reductase (MTHFR) catalyzes synthesis of 5'-methylenehydrofolate, which is the methyl donor for the conversion of homocysteine to methionine. According to the numerous literature data, polymorphic variant of the MTHFR-encoding gene, C677T, is associated with hyperhomocysteinemia, vascular pathologies, neural tube defects, dementia, perinatal mortality, mental disorders, long-term neurodegenerative disorders, lens displacement, arachnodactyly, and venous thromboses. The present study was focused on the analysis of the C677T polymorphism (missence mutation leading to the replacement of cytosine by thymine at position 677) of the MTHFR gene in three indigenous populations of the Republic of Sakha (Yakutia), living in the settlements of Cheriktei, Byadi, and Dyupsya. Comparison of the genotype and allele frequencies revealed no substantial differences between the three Yakut populations, as well as between Yakuts and other Mongoloid ethnic groups.     

DNA diversity of human populations from Eastern Europe and Siberia studied by multilocus DNA fingerprinting

We used DNA fingerprinting with M13 phage DNA as a probe to estimate the degree of genomic variability and genetic relationships in a heterogeneous group of 13 populations from Eastern Europe and Siberia. The popultaions belong to three language families: Indo-European (Slavonic: Russians, Byelorussians), Uralic (Finno-Ugric: Maris, Mordvinians, Udmurts), and Altaic (Turkic: Bashkirs, Tatars, Chuvashes, Yakuts). Multivariate statistical analyses were used (multidimensional scaling, cluster, and multiple correspondence analyses), and coefficients of gene differentiation (Gst) were evaluated. The level of interpopulation subdivision in the various ethnic groups appeared to be different: the Byelorussian populations revealed no regional differences, in contrast to the Bashkir populations, which formed a heterogeneous group. The populations subdivided into three general clusters: Slavonic populations formed a separate tight cluster characterized by a minimal level of interpopulation diversity, Bashkir and Yakut populations formed the second cluster, and the Finno-Ugric and several populations of the Turkic linguistic groups formed the third cluster. The robustness of these results obtained by different statistical data treatments reveals that multilocus DNA fingerprinting can be reliably used for population studies.Communicated by G. P. Georgiev     

Phylogenetic analysis of ancient mitochondrial DNA lineages of human remains found in Yakutia

Molecular genetic analysis of ancient human remains is mostly based on mtDNA owing to its better preservation in human bones in comparison with nuclear DNA. A study was made of mtDNA extracted from human skeletons found in graves in Yakutia, in order to determine the haplotypes and to compare them with lineages of modern populations. Ancient DNA was extracted from fragments of three skeletons of Yakut graves at At-Dabaan, Ojuluun, and Jaraama sites (dating back to the 18th century) and two skeletons of the Late Neolithic Kerdugen grave (2000–1000 B.C.). All graves were found in central Yakutia (Churapchinskii, Khangalasskii, and Megino-Khangalasskii districts of Yakutia). Five different haplotypes belonging to specific Asian haplogroups were identified. The mtDNA lineages of Yakut graves belong to haplogroups C4a, D5a2, and B5b. The results indicate the continuity of mitochondrial lineages in the Yakut gene pool in the past 300 years. The haplotypes of two humans from the Kerdugen site graves belong to haplogroups A4 and G2a/D. These haplotypes were compared with those of 40000 Eurasian individuals, including 900 from Yakutia. No exact matches were found in Paleo-Asian populations of Chukchi, Eskimos, Koryaks, and Itelmen. Phylogenetically close haplotypes (±1 mutation) were found in Yakut and Evenk populations, as well as in some populations of China and South and West Siberia.     

The Dagestan gene pool: Polymorphism of immunogenetic and biochemical markers in Kumyks

This study is a part of long-term investigations devoted to the analysis of the gene pool of Dagestan ethnic groups. The phenotype (in %), gene, and haplotype frequencies in Kumyk ethnic group are reported. A total of 39 alleles and six haplotypes of 14 loci (AB0, Rhesus, P, Levis, Kell, HP, GC, C’3, TF, 6PGD, GLO1, ESD, ACP, and PGM1) of immunobiochemical genetic marker systems were examined. Rare haplotypes of the Rhesus system were identified, including CDE in the Karabudakhkent population with the frequency of 0.030, and Cde and cdE in the Dorgeli population with the frequencies of 0.034 and 0.38, respectively. Similarly to the other ethnic populations of Dagestan examined, Kukyk populations carried rare, albeit typically “Caucasoid” gene ACP1 ^c of the AcP1 locus. The frequency of this allele in the two populations was similar, constituting 0.031 for Karabudakhkent and 0.032 for Dorgeli. In Kumyks, allele frequencies of the AB0, Rhesus, P, Lewis, Kell, HP, GC, C′3, TF, 6PGD, GLO1, ESD, ACP, but not PGM1, systems were similar to the mean allele frequencies at these loci observed in the other ethnic groups from the Dagestan, Caucasus, and the whole European historical ethnographic province. At the same time, the allele frequency values obtained were different from those for the populations of Kazakhstan, Central Asia, Siberia, and the Ruswsian Far East. Thus, the results obtained for classical genetic markers indicate that Kumyks are genetically closer to the indigenous populations of Dagestan than to Turkic-speaking populations. Analysis of the fit of the observed phenotype frequencies to the Hardy-Weinberg expectations showed that compared to other indigenous populations of Dagestan examined, in Kumyks the genetic state of the population upon random allele association was close to equilibrium. Probably, this state was determined by practical absence of the consanguineous marriages upon preservation of intra-aul endogamy.     

Molecular genetic analysis of 400-year-old human remains found in two Yakut burial sites

The excavation of five frozen graves at the Sytygane Syhe and Istekh-Myrane burial sites (dated at 400 years old) in central Yakutia revealed five human skeletons belonging to the Yakut population. To investigate the origin and evolution of the Yakut population as well as the kinship system between individuals buried in these two sites, DNA was extracted from bone samples and analyzed by autosomal short tandem repeats (STRs) and by sequencing hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed a diversity of sepulchral organizations linked probably to the social or genetic background of the subjects. Comparison of STR profiles, mitochondrial haplotypes, and haplogroups with data from Eurasian populations indicated affinities with Asian populations and suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last five centuries. Moreover, our results did not support a Central Asian (with the exception of maternal lineage of West Eurasian origin) or Siberian origin of the maternal lineages of these ancient Yakut subjects, implying an ethnogenesis of the Yakut population probably more complex than previously proposed.     

Genetic diversity and relationships of populations of northern Eurasia by polymorphic Alu insertions

Autosomal gene pools of 27 populations representing 12 ethnic groups of Siberia, Central Asia, and the Far East have been characterized for the first time using a set of eight polymorphic Alu insertions. The results of our analysis indicate a significant level of genetic diversity in populations of northern Eurasian and the considerable differentiation of their gene pool. It was shown that the frequency of the Alu (?) allele at the CD4 locus was inversely related to the magnitude of the Mongoloid component of the gene pool: the lowest and highest frequencies of the CD4 Alu deletion were recorded in Eskimos (0.012) and in Russians and Ukrainians (0.35), respectively. A gene flow analysis showed that Caucasoid populations (Russians, Tajiks, and Uzbeks), as well as Turkic ethnic groups of southern Siberia (Altaians and Tuvans), Khanty, and Mansi populations, in contrast to ethnic groups of eastern Siberia and the Far East, have been recipients of a considerable gene flow. A correlation analysis showed that genetic distances determined using polymorphic Alu insertions were correlated with the anthropological characteristics of the populations studied.     

Genetic diversity of the Khakass gene pool: Subethnic differentiation and the structure of Y-chromosome haplogroups

The structure of Khakass gene pool has been investigated: Y-chromosome haplogroup compositions and frequencies were described in seven population samples of two basic subethnic groups, Sagai and Kachins, from three geographically separated regions of the Khakass Republic. Eight haplogroups were detected in the Khakass gene pool: C3, E, N*, N1b, N1c, R1a1a, and R1b1b1. The haplogroup spectra and the genetic diversity by haplogroups and YSTR haplotypes differed significantly between Sagai and Kachins. Kachins had a low level of gene diversity, whereas the diversity of Sagai was similar to that of other South-Siberian ethnic groups. Sagai samples from the Askizskii district were very similar to each other, and so were two Kachin samples from the Shirinskii district, while Sagai samples from the Tashtypskii district differed considerably from each other. The contribution of intergroup differences among ethnic groups was high, indicating significant genetic differentiation among native populations in Khakassia. The Khakass gene pool was strongly differentiated both by haplogroup frequencies and by YSTR haplotypes within the N1b haplogroup. The frequencies of YSTR haplotypes within the chromosome Y haplogroups N1b, N1c, and R1a1 were determined and their molecular phylogeny was investigated. Factor and cluster analysis, as well as AMOVA, suggest that the Khakass gene pool is structured by territory and subethnic groups.     

Genetic Differentiation of the Population of Central Asia Inferred from Autosomal Markers

The gene pool of five ethnic groups of the Central Asian population was characterized using nine human-specific polymorphic insertion/deletion loci (ACE, PLAT, APOA1, PV92, F13B, A25, B65, CD4, Mt-Nuc). It has been shown for the first time that at the CD4 locus, the frequency of Alu(–) is inversely related to the Mongoloid component of the population. For the Central Asian populations, the lowest and highest frequencies of the Alu deletion at locus CD4 were recorded respectively in Dungans (0.04), immigrants from China, and Tajiks (0.15). The coefficient of gene differentiation in the Central Asian populations for all the genes was 2.8%, which indicates a relatively low level of population genetic subdivision in this region. The unity of the gene pool of the Central Asian Caucasoids was shown.     

The Population Gene Pool of Yakutia: Cartographic Analysis Based on the Polymorphism of Biochemical Markers and the AB0 System

The gene pool of the indigenous population of Sakha Republic (Yakutia) has been studied within the borders of this republic coinciding with the main area of Yakuts, which was formed by the end of the 19th century and have remained stable until the present time. Maps of the geographic variation of the integral characteristics of the Yakut gene pool, including the principal components, parameters of genetic diversity, and genetic distances from the “average” Yakut population are presented. It has been demonstrated that ethnographers' reports on intense internal assimilation in modern Yakutia agree with genetic data. The stratification of the Yakut gene pool reflected in the maps of two principal components corresponds to the observed total (H_T) and interpopulation (F_ST) gene diversities.     

Characterization of <Emphasis Type="Italic">Streptococcus mutans</Emphasis> diversity by determining restriction fragment-length polymorphisms of the <Emphasis Type="Italic">gtfB</Emphasis> gene of isolates from 5-year-old children and their mothers

The diversity between Streptococcus mutans clinical isolates from 5-year-old children and their mothers in two South African ethnic groups was investigated. The gtfB gene encoding for glucosyltransferase (EC 2.4.1.5), an enzyme responsible for the synthesis of extracellular polysaccharides was characterized by PCR-RFLP with HaeIII restriction enzyme digestion. Forty-seven children were examined for dental caries and 128 S. mutans clinical isolates cultured from samples of their saliva and plaque and from the saliva of their mothers. Thirty-three children had active caries (70%) and the remainder (n = 14) were caries-free. Caries prevalence was significantly different (p = 0.02) between black African and coloured children, but no differences were found between gtfB amplitypes by caries or ethnic grouping. Thirty-four (27%) of the S. mutans clinical isolates investigated did not ferment melibiose. Melibiose-negative phenotypes (n = 10) isolated from four families showed gtfB RFLP patterns identical to each other. Mothers and children harboured between one and three amplitypes. GtfB amplitypes were identical in 17 families (17/47), of which nine only were identical to S. mutans reference strains. The percentage match between S. mutans amplitype from mothers and their children was low (13%) in the caries-free group compared to children with caries (44%). RFLP analysis of the gtfB gene showed the diversity of S. mutans genotypes within two South African populations that were acquired from mothers and other sources.     

Polymorphism of immunogenetic and biochemical markers in Siberian (Tobol-Irtysh) Tatars

The polymorphism of immunogenetic and biochemical markers has been studied in nine populations of five ethnic-geographic groups of Siberian (Tobol-Irtysh) Tatars. Data on the frequency distributions of 33 alleles and 6 haplotypes of 14 loci (ABO, RHD, RHC, RHE, P, KEL, HP, C′3, TF, GLO1, ESD, ACP, PGD, and PGM1) in sample of 354 subjects have been obtained. Comparison with other ethnic groups has shown that the gene pool of Tobol-Irtysh Tatars contains an ancient autochthonic genetic stratum similar to that found in the neighboring Ob’ Ugrian population. Genetic relationships of various strengths with Central Asian Turks and the ethnic groups of the Volga region have been found, which apparently reflect different stages of the ethnogenesis of the Tobol-Irtysh Tatars.     

The population gene pool of Yakutia: cartographic analysis based on the polymorphism of immune and biochemical markers

The gene pool of the indigenous population of Sakha Republic (Yakutia) has been studied within the borders of this republic coinciding with the main area of Yakuts, which was formed by the end of the 19th century and have remained stable until the present time. Maps of the geographic variation of the integrated characteristics of the Yakut gene pool, including the principal components, parameters of genetic diversity, and genetic distances from the "average" Yakut population are presented. It has been demonstrated that ethnographers' reports on intense internal assimilation in modem Yakutia agree with genetic data. The stratification of the Yakut gene pool reflected in the maps of two principal components corresponds to the observed general (H(T)) and interpopulation (FST) gene diversities.     

Glutathione-S-transferase gene polymorphism in Russian populations of European part of Russia

Distribution of several widespread, extensively studied polymorphic variants of genes of the cytosol glutathione-S-transferase subfamily (GSTA1, GSTM1, GSTM3, GSTP1, and GSTT1) has been studied in samples from Russian populations of European Russia, as well as Komi and Yakut populations used for comparison. Analysis of the GSTP1 and GSTM3 polymorphisms has not revealed significant differences in the distribution of alleles of the loci, including two-site GSTP1 haplotypes, in most Russian populations and between Komi populations. Only in the Yakut sample have a significant difference been found with respect to these loci in each pairwise comparison. Regarding the GSTT1 and GSTA1 genes, in addition to differences between the Yakut population and all other populations with respect to the GSTA1 gene, it has been found that the frequencies of the GSTT1 0/0 deletion genotype and GSTA1 ?69T allele in the Russian sample from Mezen’ (Arkhangel’sk oblast) are substantially lower than in other Russian populations and Komi populations. The significance of these differences has been confirmed by tests for heterogeneity of the entire pool of Russian populations.