Gene-pool structure of Tuvinians inferred from Y-chromosome marker data

The gene-pool structure of Tuvinians was examined in terms of the composition and frequency of Y-chromosome haplogroups in five geographically distanct populations. In the Tuvinian gene pool, a total of 22 haplogroups were identified with six of these, which were the most frequent (C3c, C3*, N1b, N1c1, Q1a3, and R1a1a). It was demonstrated that eastern regions of Tuva were most different from the other regions in haplotype frequencies. The evaluation of genetic diversity based on the frequencies of biallelic haplogroups and YSTR haplotypes revealed very high diversity values for all samples. In general, the genetic diversity values identified in Tuvinians were the highest for the indigenous ethnic groups of Siberia. The evaluation of the genetic differentiation of the samples examined using the analysis of molecular variance (AMOVA) showed that the gene pool of Tuvinians was relatively poorly differentiated with respect to haplogroup frequencies. Phylogenetic analysis within haplogroup N1b revealed strong founder effect, i.e., reduced diversity and star-like phylogeny of the median network of haplotypes, which formed a separate subcluster exclusive to Tuvinians. It was demonstrated that, in Tuvinians, haplogroup N1c1 was the most heterogeneous in haplotype profile and consisted of three different haplotype clusters, demonstrating considerable differences of western population from the rest of the Tuva populations. Phylogenetic analysis of haplogroups revealed common components for Tuvinians, Khakasses, Altaians, and Mongols.     

新疆阿勒泰地区图瓦人与邻近人群遗传关系初探

在中国新疆阿勒泰地区哈纳斯景区内, 生活着一个特殊的人群—— 新疆图瓦人。他们在50年代初期第一次民族识别过程中被认定为蒙古族, 但他们自认为与蒙古人具有不同的历史渊源。为了探讨新疆图瓦人的族源问题和阐明其与邻近人群的遗传学关系, 文章采集了新疆阿勒泰地区150份男性图瓦人样本, 对其Y染色体非重组区的14个标记位点进行了分型, 构建了11种单倍型群。结果显示, 新疆图瓦人具有高频率的K^*-M9 和Q^*-M242单倍型群, 这两个单倍型群在俄罗斯图瓦人中也具有较高的频率, 而在蒙古人群和哈萨克人群中的频率则较低。主成分分析和多维尺度分析均显示新疆图瓦人与蒙古人和哈萨克人遗传上相隔较远。系统分子进化分析也表明新疆图瓦人位于与周围人群相隔较远的分化枝上。依据这些结果, 文章认为新疆图瓦人是与邻近人群如蒙古人和哈萨克人有较大遗传差异的人群。     

Restriction polymorphism of the major noncoding region of mtDNA in the indigenous population of the TUVA republic]

Mitochondrial DNA sequence variation was examined in three rural populations of the indigenous inhabitants from the Tuva Republic. The frequencies of restriction sites within the D-loop region of mtDNA were determined. The three populations studied demonstrated similar patterns of mtDNA polymorphism. Like other Siberian populations, Tuvinians were characterized by high frequencies of the HaeIII 16517 and AspS9I (Cfr13I) 16516 restriction sites (about 75%). Moreover, in Tuvinians, a relatively low (71 to 81%) frequency of the KpnI 16129 restriction site was observed. The frequency of the mitotype differing from the Cambridge sequence by the HaeIII 16517 and KpnI 16129 sites in Tuvinians was higher than in Mongols and Russians. The features of mtDNA polymorphism point to the similarity between Tuvinians and other Siberian ethnic groups (Sel'kups in particular). This can be explained by the contribution of the Samoyed component, along with the Turkic and Mongoloid ones, to the formation of the Tuvinian ethnic group.     

Genetic demographic characteristics of the rural population of the Tuva Republic: ethnic and tribal composition and sex and age structure]

The ethnic, tribal, sex, and age composition was studied in populations of three districts of the Tuva Republic that were remote from one another. These were the Kyzylskii (the Shinaan population), Todzhinskii, and Bai-Taiginskii raions. The Todzhinskii population was characterized by a mixed ethnic composition dominated by Tuvinians and Russians (62.35 and 35.52%, respectively); the other two districts were only inhabited by Tuvinians. The studied populations differed from one another in the set and proportions of tribal groups--in the Todzhinskii raion, Turkic tribal groups were prevalent, whereas in the Shinaan and Bai-Taiginskii populations, many tribal groups of Mongolian origin were found. The estimations of relationship by isonymy indicated a considerable contribution of geographic isolation to the genetic differentiation of the populations: the estimated relationship between the highland Shinaan and Todzhinskii populations, which are difficult of access, was the minimum (Ri = 0.00262); the coefficients of the relationship by isonymy between the Shinaan and Bai-Taiginskii populations and between the Todzhinskii and Bai-Taiginskii populations were 0.00336 and 0.00483, respectively. All the studied populations were characterized by a "growing" age pyramid; however, the Bai-Taiginskii and Todzhinskii populations showed a tendency to narrowing its base. In addition, these two populations exhibited an unfavorable sex ratio at the reproductive age. The obtained results suggest that the Tuva population is genetically heterogeneous, which is accounted for by the tribal characteristics, the history of populations, and the geographic characteristics of the region.     

Analysis of allele frequency of seven microsatellite loci of Y chromosome in three Tuva populations

The allele frequency distribution of seven microsatellite loci of the nonrecombining region of the Y chromosome (Y-STRs) was analyzed in three geographically distant indigenous populations of the Tuva Republic. The populations did not differ in allele frequency distribution of the seven Y-STRs. The Y-chromosome microsatellite loci in Tuvinians showed a high diversity (H = 0.575) that was nearly identical in all three populations. The genetic distance Ddm between the three populations was low, suggesting no subdivision of the modern male population of Tuva. Estimates of the period of linear changes in Ddm showed that Y-chromosome microsatellites can be used to reconstruct evolutionary events dating back no more than 40,000-50,000 years. The problems of human population phylogeny are discussed on the basis of data on Y-chromosome STRs.     

Genetic differentiation of the Tuva population with respect to the Alu insertions]

Polymorphism of three rural populations of the Tuva Republic was examined using a set of five autosomal Alu insertions at the ACE, PLAT, PV92, APOA1, and F13B loci. The allele frequency distribution patterns revealed in Tuvinians were typical to Mongoloid populations of Asia and were characterized by relatively high frequency of the Alu-repeat insertion at the PV92 and F13B loci along with relatively low insertion frequency at the APOA1 locus. With respect to the test systems used, Tuvinian populations examined displayed high levels of genetic diversity. The mean expected heterozygosity values in the populations of Kugurtug, Toora-Khem, and Teeli were 0.433, 0.407, and 0.437, respectively. The level of genetic diversity in the pooled Tuvinian sample was 0.432. The coefficient of genetic differentiation in the three populations studied was 1.45 pointing to relatively low level of genetic subdivision of the indigenous Tuvinian populations. However, estimates of genetic differentiation of the Tuvinian gene pool made by use of the Alu-repeat system were higher compared to those performed using classical protein systems, mtDNA, or Y-chromosomal haplotypes. Even though Tuvinian populations were characterized by common gene pool, some features specific to Western Tuvinian population could be distinguished. These features could be associated with higher contribution of the Caucasian component to the gene pool of this population. Phylogenetic analysis demonstrated close genetic relationships between the Tuvinian and Altaic ethnic populations.     

Analysis of distribution of "mongoloid" haplogroups of mitochondrial DNA among indigenous population of the Tuva Republic

Variation of Mongoloid-specific restriction sites of mitochondrial genome was analyzed in three territorial groups of Tuvinians. Distribution of mitochondrial DNA haplogroups A, B, C, and D on the territory of the Tuva Republic was estimated. The populations studied did not display distinct differentiation in respect to the mtDNA polymorphism. The specific feature of Tuvinian mitochondrial gene pool was the prevalence of only one haplogroup C (over 40%), mainly represented by two mitotypes. The high frequency of this haplogroup makes Tuvinians similar to more northern Siberian populations. On the other hand, the presence of haplogroup B indicates that Tuvinians have affinity to ethnic groups of Central Asia.     

Genetic demographic characteristics of the rural population of the Tuva Republic: marriage structure and inbreeding]

Marriage structure was studied in three rural populations of the Tuva Republic: the Shinaan population and the populations of Todzhinskii and Bai-Taiginskii raions (districts). The Shinaan and Bai-Taiginskii populations had high levels of endogamy (0.6704 and 0.6050, respectively). In the Todzhinskii population, which was characterized by a mixed ethnic composition, endogamy was 0.3779 for the total population and 0.4626 for Tuvinians; interethnic marriages in this population were rare. The values of marriage assortativeness with respect to birthplace were 19.38, 40.75, 75.87, and 41.87% in the Shinaan, Bai-Taiginskii, all the Todzhinskii populations, and Tuvinian monoethnic marriages in the Todzhinskii raion, respectively. High marriage assortativeness with respect to ethnicity was found. Its values (A') were 91.85 and 93.49% in Tuvinians and Russians, respectively. Tuvinian populations were characterized by high inbreeding. The total (F(it)), random (Fst), and nonrandom inbreeding (Fis) estimated by isonymy were 0.004237, 0.002298, and 0.001944 in the Shinaan population, 0.007292, 0.009448, and -0.002177 in the Bai-Taiginskii population, and 0.003846, 0.004152, and -0.000307 in the Todzhinskii population, respectively (in the latter populations, the F(it), Fst, and Fis values for Tuvinian marriages alone were 0.005000, 0.007222, and -0.002238, respectively). The results obtained indicate that individual territorial groups of Tuvinians retain a high degree of genetic isolation from one another.     

Distribution of “Mongoloid” Haplogroups of Mitochondrial DNA Among Indigenous Population of the Tuva Republic

Variation of Mongoloid-specific restriction sites of mitochondrial genome was analyzed in three territorial groups of Tuvinians. Distribution of mitochondrial DNA haplogroups A, B, C, and D on the territory of the Tuva Republic was estimated. The populations studied did not display distinct differentiation in respect to the mtDNA polymorphism. The specific feature of Tuvinian mitochondrial gene pool was the prevalence of only one haplogroup C (over 40%), mainly represented by two mitotypes. The high frequency of this haplogroup makes Tuvinians similar to more northern Siberian populations. On the other hand, the presence of haplogroup B indicates that Tuvinians have affinity to ethnic groups of Central Asia.     

Genetic Differentiation of the Tuva Population with Respect to the AluInsertions

Polymorphism of three rural populations of the Tuva Republic was examined using a set of five autosomal Aluinsertions at the ACE, PLAT, PV92, APOA1,and F13Bloci. The allele frequency distribution patterns revealed in Tuvinians were typical to Mongoloid populations of Asia and were characterized by relatively high frequency of the Alu-repeat insertion at the PV92and F13Bloci along with relatively low insertion frequency at the APOA1locus. With respect to the test systems used, Tuvinian populations examined displayed high levels of genetic diversity. The mean expected heterozygosity values in the populations of Kungurtug, Toora-Khem, and Teeli were 0.433, 0.407, and 0.437, respectively. The level of genetic diversity in the pooled Tuvinian sample was 0.432. The coefficient of genetic differentiation in the three populations studied was 1.4% pointing to relatively low level of genetic subdivision of the indigenous Tuvinian populations. However, estimates of genetic differentiation of the Tuvinian gene pool made by use of the Alu-repeat system were higher compared to those performed using classical protein systems, mtDNA, or Y-chromosomal haplotypes. Even though Tuvinian populations were characterized by common gene pool, some features specific to Western Tuvinian population could be distinguished. These features could be associated with higher contribution of the Caucasian component to the gene pool of this population. Phylogenetic analysis demonstrated close genetic relationships between the Tuvinian and Altaic ethnic populations.     

Microsatellite haplotypes of the Y-chromosome demonstrate the absence of subdivisions and presence of several components in the Tuvinian male gene pool

The haplotype analysis of seven Y-chromosome microsatellites in three regional populations of Tuvinians revealed high intrapopulation variation in the male gene pool of the modern population of the Tuva Republic. In total, 49 haplotypes were found in 111 individuals; only four haplotypes occurred at a frequency higher than 5%. High genetic diversity (H = 0.935) suggested a high power of discrimination for the Y-chromosome haplotypes. The analysis of molecular variance (AMOVA) and other data did not reveal subdivision of the Tuvinian population with respect to Y-chromosome haplotypes. Most haplotypes found in Tuvinians formed two lines. Line A included approximately 64% of the haplotypes found, line B, approximately 24%. A putative ancestral haplotype of line B was similar to a haplotype most common in modern Caucasoids (Md = 3), whereas a putative ancestral haplotype of line A proved to be distant from the ancestral haplotype of line A and haplotypes common for Caucasoids and Mongoloids. Estimates of the age of the Y-chromosome lines showed that the male gene pool of modern Tuvinians originated in the late Paleolithic or Neolithic period. With two methods, the age of line A was estimated at 3500 or 18,000 years and the age of line B was approximately at 5500 or 15,000 years. Considering the less conservative estimates to be more reliable, line B was assumed to originate from the ancient Caucasoid population of the Tuva region. The more widespread and evolutionarily younger line A was associated with the peopling region by ancient Mongoloid tribes of the Turkic language group in the Hun-Sarmatian period.     

A comparative analysis of tuberculosis susceptibility genetic make-up in Tuvinians and Russians

The results of the first Russian study of polymorphisms of tuberculosis (TB) susceptibility genes SLC11A1, VDR, IL12B, IL1B, IL1RN in Tuvinians from Tuva Republic and Russians from Tomsk city are presented. In Tuvinians, as compared with Russians, the significantly higher prevalence of potentially disease-associated alleles of the genes studied was shown: SLC11A1*543N (0.139 and 0.043, respectively, p = 4.6E-5), IL12B*1188C (0.378 and 0.174, respectively, p = 1.1E-8), VDR*b (0.825 and 0.532, respectively, p = 3.2E-16), IL1B*(+3953A1) (0.865 and 0.806, respectively, p = 0.035). However, no one of these alleles was associated with TB in Tuvinians, whereas, in Russians TB patients, in comparison with the controls, there was a higher prevalence of the following markers: IL1RN*A2 (0.258 and 0.186, respectively, p = 0.024), SLC11A1*274T (0.251 and 0.164, respectively, p = 0.009), IL12B*1188C (0.240 and 0.174, respectively, p = 0.044), ILIB*(+3953A2) (0.259 and 0.194, respectively, p = 0.044). Distinct patterns of linkage disequilibrium between pairs of the polymorphisms studied in Tuvinians and Russians were shown. At whole, the data obtained demonstrate the ethnic specificity of the distribution and pathogenetic significance of the alleles of the TB susceptibility genes.     

Brief communication: Y-chromosome haplogroup analysis indicates that Chinese Tuvans share distinctive affinity with Siberian Tuvans

Tuvans are mainly distributed in Siberia (the Republic of Tuva), Mongolia, and China. The genetic origin of Chinese Tuvans remains controversial. The Tuvans in China were classified as Mongolians in the early 1950s by the National Ethnic Affairs Commission of China, but they defined themselves as a separate group. To resolve this dispute and determine their genetic relationships with the peoples in Central Asia, we randomly selected 150 male subjects from the Tuvans in the Altai region of Xinjiang Uygur Autonomous Region in China. Fourteen Y chromosomal markers were genotyped using the RFLP method or direct sequencing. These haplogroup data were combined with public data for 15 populations in South Siberia and Central Asia. Tuvans in both China and the Republic of Tuva had the highest frequencies of haplogroups K-M9 and Q-M242. Principal component analysis demonstrated that the Tuvans in China were of a distinct cluster, separated from their neighbors, the Mongolians and Kazakhs, which finding was consistent with the Analysis of Molecular Variances. Further population tree analysis revealed that Tuvans were on a far-separated cluster from their neighbors. Based on these results, we propose that the Tuvans (in both China and the Republic of Tuva) constitute a group distinct from Mongolians and from other Central Asia populations. However, the genetic results might be the consequence of some evolutionary forces like genetic drift and founder effect, and do not necessarily reflect their ultimate origin.     

Distribution of a deletion-insertion polymorphism in intergenic region V of mitochondrial DNA among the aboriginal population of Tuva

Mitochondrial DNA region V deletion-insertion polymorphism was examined in three Tuvinian populations inhabiting western, northeastern, and southeastern parts of the republic. The 9-bp deletion was characterized by nonrandom distribution across the Tuva territory: its frequency in the western population (13.37%) was statistically significantly higher than that in the northeastern (4.62%), and southeastern populations, as well as in Mongols, who are territorially and ethnically close to Tuvinians. The insertion mutation in the region V was detected with a frequency of about 3% in two out of the three populations tested.     

Genetic Diversity and Population Differentiation of Liaoning Weedy Rice Detected by RAPD and SSR Markers

Weedy rice refers to populations of usually annual Oryza species that diminish farmer income through reduction of grain yield and lowered commodity value at harvest. The genetic diversity and population genetic structure of weedy rice in Liaoning Province were studied by RAPD and SSR markers. The results indicate that the level of genetic diversity of Liaoning weedy rice is very low, with polymorphic loci being only 3.70% (RAPDs) and 47.62% (SSRs). On the other hand, high genetic differentiation was found among populations, in particular between two regions (Shenyang and Dandong), with Fst values of 0.746 (RAPDs) and 0.656 (SSRs), suggesting that more than two thirds of the genetic variation resides among regions. Combined with our investigations of cultural traditions, the low level of genetic diversity in Liaoning Province is attributed to its narrow genetic background enhanced by exchanges of cultivar seeds, whereas the high genetic differentiation between the two regions is most likely the result of different founding parents and gene flow from local rice varieties to weedy rice. The rice cultivars in the two regions are all local varieties and are different genetically. A comparison of the two marker systems demonstrates that SSR is more informative and powerful in terms of the assessment of genetic variability, although both RAPD and SSR provide useful genetic information on weedy rice.     

Comparative analysis of ISSR marker polymorphism in populations of yak (Bos mutus) and in F1 hybrids between yak and cattle in the Sayan-Altai region

The genetic variability in seven yak populations from the Sayan-Altai region and in F₁ hybrids between yak and cattle (khainags) was investigated with the help of a technique that involves the use of inter simple sequence repeat (ISSR) markers generated with PCR primers (AG)⁹C and (GA)⁹C. Samples for the analysis were collected in Mongolia, Tuva, and Altai from 2008 through 2012. The examined yak populations differed in in the presence/absence of ISSR fragments, as well as in their frequency. In total, 46 ISSR fragments were identified using two marker systems; the proportion of polymorphic loci constituted 76% and 90% for the AG-ISSR and GA-ISSR markers, respectively. For the total sample of yaks, total genetic diversity (H _t), within-population diversity (H _s), and interpopulation diversity (G _st) constituted 0.081, 0.044, and 0.459 for the AG-ISSR and 0.137, 0.057, and 0.582 for the GA-ISSR markers, respectively. Based on ISSR finger-printing, species- and breed-specific DNA patterns were described for the three groups of animals (yaks, cattle, khainags). For the domestic yak, the species-specific profile was represented by eight ISSR fragments. Genetic relationships between the yak populations, cattle breeds, and khainags were examined with the help of four different approaches used in the analysis of population structure: estimation of phylogenetic similarity, multidimensional scaling, principal component analysis, and cluster analysis. Clear evidence on the differentiation of the populations examined at the interspecific, as well as at intraspecific, level were obtained. Similar (relative), as well as remote (isolated), yak populations were identified. Khainags occupy an intermediate position between yak and cattle. However, the data on the ISSR-PCR marker polymorphism (genome polymorphism, population structure) indicate that part of the analyzed khainag genome was more similar to the yak genome than to the cattle genome.     

Mitochondrial DNA polymorphism in Tuvinian population of reindeer Rangifer tarandus L

Mitochondrial DNA variation was examined in one of the southern most populations of domestic reindeer, inhabiting Tyva Republic (Tuva). In Tuvinian population sequence polymorphism of the mitochondrial DNA D loop region was demonstrated. In a sample of 29 individuals 7 mitotypes were distinguished, pointing to the preservation of rather high level of genetic diversity in this population.     

Mitochondrial DNA polymorphism in Tuvinian population of reindeer Rangifer tarandus L.

Mitochondrial DNA variation was examined in one of the southem most populations of domestic reindeer, inhabiting Tyva Republic (Tuva). In Tuvinian population sequence polymorphism of the mitochondrial DNA D-loop region was demonstrated. In a sample of 29 individuals 7 mitotypes were distinguished, pointing to the preservation of rather high level of genetic diversity in this population.     

Weedy adaptation in Setaria spp. II. Genetic diversity and population genetic structure in S. glauca,S. geniculata,and S. faberii (Poaceae)

Setaria glauca (yellow foxtail), S. geniculata (knotroot foxtail), and S. faberii (giant foxtail) are important cosmopolitan weeds of temperate and tropical regions. Isozyme markers were used to investigate genetic diversity and population genetic structure in 94 accessions of yellow foxtail, 24 accessions of knotroot foxtail, and 51 accessions of giant foxtail, collected mainly from North America and Eurasia. Giant foxtail populations were nearly identical genetically, with only one population exhibiting isozyme polymorphism. Yellow and knotroot foxtail populations had low genetic diversity but marked population differentiation. Although the latter species are similar morphologically, they are readily distinguished electrophoretically, with Nei's genetic identity being 0.83. In both species, genetic divergence between accessions from Eurasia and North America was minimal. Populations from the native ranges had slightly greater genetic diversity than those from the respective introduced ranges. Yellow foxtail populations genetically clustered into Asian, European, and North American groups. Within North America, yellow foxtail populations from Iowa were genetically diverse whereas populations collected from other North American locations were nearly monomorphic for the same multilocus genotype. Knotroot foxtail populations in North America were genetically differentiated into northern and southern groups on either side of a line at ≈37° N latitude. No genetic patterning was evident in knotroot foxtail populations from Eurasia. In both yellow and knotroot foxtail, patterns of population genetic structure have been influenced by several factors, including genetic bottlenecks associated with founder events, genetic drift, and natural selection.     

Geographical variation of genetic and phenotypic traits in the Mexican sailfin mollies, Poecilia velifera and P. petenensis

Comparing the patterns of population divergence using both neutral genetic and phenotypic traits provides an opportunity to examine the relative importance of evolutionary mechanisms in shaping population differences. We used microsatellite markers to examine population genetic structure in the Mexican sailfin mollies Poecilia velifera and P. petenensis. We compared patterns of genetic structure and divergence to that in two types of phenotypic traits: morphological characters and mating behaviours. Populations within each species were genetically distinct, and conformed to a model of isolation by distance, with populations within different geographical regions being more genetically similar to one another than were populations from different regions. Bayesian clustering and barrier analyses provided additional support for population separation, especially between geographical regions. In contrast, none of the phenotypic traits showed any type of geographical pattern, and population divergence in these traits was uncorrelated with that found in neutral markers. There was also a weaker pattern of regional differences among geographical regions compared to neutral genetic divergence. These results suggest that while divergence in neutral traits is likely a product of population history and genetic drift, phenotypic divergence is governed by different mechanisms, such as natural and sexual selection, and arises at spatial scales independent from those of neutral markers.