Genetic diversity of X-chromosome in populations of aboriginal Siberian ethnic groups: linkage disequilibrium structure and haplotype philogeography of ZFX locus

The structure of gene pool of the Siberian aboriginal population has been described based on the data on polymorphism of ZFX gene located on X-chromosome. In ten populations under study 49 haplotypes have been determined, three of which are presented with high frequency. Comparing the obtained results with the available data from HapMap project unique "African" haplotypes were revealed, which occurred in Yoruba population with the frequency of 3-7% and were not found in other populations. A coefficient of genetic differentiation of the Siberian ethnic groups under study amounted to 0.0486. Correlation analysis involving Mantel test did not reveal any significant correlations between a matrix of genetic distances and the matrices of geographic, linguistic and anthropological differences, where a maximum coefficient was obtained at the comparison with the anthropological matrix. Phylogenetic analysis proved strong isolation of African population from the other investigated ethnic groups. The Siberian populations were subdivided into two separate clusters: the first one included Yakuts, Buryats and Kets, while the second cluster included Altaians, Tuvinians and Khanty. A principal component analysis enabled to combine the investigated populations in three groups, which clearly differed by a degree of manifestation of Caucasoid and Mongoloid components. The first group included Europe inhabitants and one of Khanty populations, the second one--populations of South Siberia and China inhabitants. Mongoloid populations of East Siberia, the Japanese and Kets were combined in the third group. The results of barrier analysis revealed similar structure of genetic differentiation in the Siberian population. Linkage disequilibrium structure was obtained for six ethnic groups of Siberia. A unified linkage block by ten SNP of ZFX gene was found in five of the presented ethnic groups (excluding Ket population).     

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.     

Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians

The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.     

Digital dermatoglyphic patterns of Eskimo and Amerindian populations: relationships between geographic, dermatoglyphic, genetic, and linguistic distances.

Dermatoglyphic traits have been used to assess population affinities and structure. Here, we describe the digital patterns of four Eskimo populations from Alaska: two Yupik-speaking villages from St. Lawrence Island and two Inupik groups presently residing on mainland Alaska. For a broader evolutionary perspective, these four Eskimo populations are compared to other Inuit groups, to North American Indian populations, and to Siberian aggregates. The genetic structures of 18 New and Old World populations were explored using R-matrix plots and Wright's FST values. The relationships between dermatoglyphic, blood genetic, geographic, and linguistic distances were assessed by comparing matrices through Mantel correlations and through partial and multiple correlations. Statistically significant relationships between dermatoglyphics and genetics, genetics and geography, and geography and language were revealed. In addition, significant correlations between dermatoglyphics and geography, with linguistic variation constant, were noted for females but not for males. These results attest to the usefulness of dermatoglyphics in resolving various evolutionary questions concerning normal human variation.     

Languages, geography and HLA haplotypes in native American and Asian populations

A number of studies based on linguistic, dental and genetic data have proposed that the colonization of the New World took place in three separate waves of migration from North-East Asia. Recently, other studies have suggested that only one major migration occurred. It is the aim of this study to assess these opposing migration hypotheses using molecular-typed HLA class II alleles to compare the relationships between linguistic and genetic data in contemporary Native American populations. Our results suggest that gene flow and genetic drift have been important factors in shaping the genetic landscape of Native American populations. We report significant correlations between genetic and geographical distances in Native American and East Asian populations. In contrast, a less clear-cut relationship seems to exist between genetic distances and linguistic affiliation. In particular, the close genetic relationship of the neighbouring Na-Dene Athabaskans and Amerindian Salishans suggests that geography is the more important factor. Overall, our results are most congruent with the single migration model.     

Immunoglobulin allotypes (GM and KM) indicate multiple founding populations of Native Americans: evidence of at least four migrations to the New World.

On the basis of GM and KM typing and language, approximately 28,000 Amerindians were divided into 4 groups of populations: non-Nadene South American (8 groups), non-Nadene North American (7 groups), Nadene (4 groups), and Eskaleuts (6 groups). These groups were compared to four groups of Asian populations. The distribution of GM haplotypes differed significantly among and within these groups as measured by chi-square analysis. Furthermore, as reflected in a maximum linkage cluster analysis, Amerindian populations in general cluster along geographic divisions, with Eskaleuts and Nadenes clustering with the Asian populations and non-Nadene North American and non-Nadene South American populations forming two additional clusters. Based on GM haplotype data and other genetic polymorphisms, the divisions appear to reflect populations that entered the New World at different times. It appears that the South American non-Nadene populations are the oldest, characterized by the haplotypes GM*A G and GM*X G, whereas later North American non-Nadene populations are characterized by high frequencies of GM*A G and low frequencies of GM*X G and GM*A T. In contrast, Eskaleuts appear to have only GM*A G and GM*A T. The Nadene speakers have GM*X G and GM*A T in higher and approximately equal frequencies. Maximum linkage cluster analysis places the Alaskan Athapaskans closest to northwestern Siberian populations and the Eskaleuts closest to the Chukchi, their closest Asian neighbor. These analyses, when combined with other data, suggest that, in the peopling of the New World, at least four separate migrant groups crossed Beringia at various times. It appears likely that the South American non-Nadene entered the New World before 17,000 years B.P. and that the North American non-Nadene entered in the immediate postglacial period, with the Eskaleut and Nadene arriving at a later date.     

Phylogenetic information in polymorphic L1 and Alu insertions from East Asians and Native American populations

This study attempts to ascertain genetic affinities between Native American and East Asian populations by analyzing four polymorphic Alu insertions (PAIs) and three L1 polymorphic loci. These two genetic systems demonstrated strong congruence when levels of diversity and genetic distances were considered. Overall, genetic relatedness within Native American groups does not correlate with geographical and linguistic structure, although strong grouping for Native Americans with East Asians was demonstrated, with clear discrimination from African and European groups. Most of the variation was assigned to differences occurring within groups, but the interpopulation variation found for South Amerindians was recognizably higher in comparison to the other sampled groups of populations. Our data suggest that bottleneck events followed by strong influence of genetic drift in the process of the peopling of the Americas may have been determinant factors in delineating the genetic background of present-day South Amerindians. Since no clear subgroups were detected within Native Americans and East Asians, there is no indication of multiple waves in the early colonization of the New World.     

Craniometric variation and the settlement of the Americas: testing hypotheses by means of R-matrix and matrix correlation analyses

New archaeological findings and the incorporation of new South American skull samples have raised fundamental questions for the classical theories of the Americas' settlement. The aim of this study was to estimate craniometric variability among several Asian and Native American populations in order to test goodness of fit of the data to different models of ancient population entries and dispersions into the New World. Our data set includes Howells' variables recorded on East Asian, North American, and South American natives (except for Na-Dene speakers). Five Fuego-Patagonian samples and one Paleoamerican sample were also included. A multivariate extension of the R-matrix method for quantitative traits was used to obtain Fst values, which were considered estimations of intergroup variation. Three main models for the peopling of the New World were represented in hypothetical design matrices. Matrix permutation tests were performed to quantify the fit of the observed data with 1) geographical separation of the samples and 2) three ways of settlement, which were the Three Migration Model (TMM), the Single Wave Migration model (SWM), and the Two Components Settlement Model (TCS). R-matrix results showed high levels of heterogeneity among Native Americans. Matrix permutation analyses suggested that the model involving high Amerindian heterogeneity and two different morphological patterns or components (derived "Mongoloid" vs. generalized "non-Mongoloid") explains better the variation observed, even when the effects of geographical separation are removed. Whether these patterns arose as a result of two separate migration events or by local evolution from Paleoamericans to Amerindians remains unresolved.     

Geographical, linguistic, and cultural influences on genetic diversity: Y-chromosomal distribution in Northern European populations

We analyzed 10 Y-chromosomal binary markers in 363 males from 8 populations in Northern Europe and 5 Y microsatellites in 346 of these individuals. These populations can be grouped according to cultural, linguistic, or geographical criteria, and the groupings are different in each case. We can therefore ask which criterion best corresponds to the distribution of genetic variation. In an AMOVA analysis using the binary markers, 13% of the Y variation was found between populations, indicating a high level of differentiation within this small area. No significant difference was seen between the traditionally nomadic Saami and the neighboring, historically farming, populations. When the populations were divided into Uralic speakers and Indo-European speakers, 8% of the variation was found between groups, but when they were divided according to geographical location, 14% of the variation was between groups. Geographical factors have thus been the most important in limiting gene flow between these populations, but linguistic differences have also been important in the east.     

High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life

We examined genetic variation on the nonrecombining portion of the Y chromosome (NRY) to investigate the paternal population structure of indigenous Siberian groups and to reconstruct the historical events leading to the peopling of Siberia. A set of 62 biallelic markers on the NRY were genotyped in 1432 males representing 18 Siberian populations, as well as nine populations from Central and East Asia and one from European Russia. A subset of these markers defines the 18 major NRY haplogroups (A-R) recently described by the Y Chromosome Consortium (YCC 2002). While only four of these 18 major NRY haplogroups accounted for -95% of Siberian Y-chromosome variation, native Siberian populations differed greatly in their haplogroup composition and exhibited the highest phiST value for any region of the world. When we divided our Siberian sample into four geographic regions versus five major linguistic groupings, analyses of molecular variance (AMOVA) indicated higher phiST and phiCT values for linguistic groups than for geographic groups. Mantel tests also supported the existence of NRY genetic patterns that were correlated with language, indicating that language affiliation might be a better predictor of the genetic affinity among Siberians than their present geographic position. The combined results, including those from a nested cladistic analysis, underscored the important role of directed dispersals, range expansions, and long-distance colonizations bound by common ethnic and linguistic affiliation in shaping the genetic landscape of Siberia. The Siberian pattern of reduced haplogroup diversity within populations combined with high levels of differentiation among populations may be a general feature characteristic of indigenous groups that have small effective population sizes and that have been isolated for long periods of time.     

Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska

The linguistically distinctive Haida and Tlingit tribes of Southeast Alaska are known for their rich material culture, complex social organization, and elaborate ritual practices. However, much less is known about these tribes from a population genetic perspective. For this reason, we analyzed mtDNA and Y-chromosome variation in Haida and Tlingit populations to elucidate several key issues pertaining to the history of this region. These included the genetic relationships of Haida and Tlingit to other indigenous groups in Alaska and Canada; the relationship between linguistic and genetic data for populations assigned to the Na-Dene linguistic family, specifically, the inclusion of Haida with Athapaskan, Eyak, and Tlingit in the language family; the possible influence of matrilineal clan structure on patterns of genetic variation in Haida and Tlingit populations; and the impact of European entry into the region on the genetic diversity of these indigenous communities. Our analysis indicates that, while sharing a "northern" genetic profile, the Haida and the Tlingit are genetically distinctive from each other. In addition, Tlingit groups themselves differ across their geographic range, in part due to interactions of Tlingit tribes with Athapaskan and Eyak groups to the north. The data also reveal a strong influence of maternal clan identity on mtDNA variation in these groups, as well as the significant influence of non-native males on Y-chromosome diversity. These results yield new details about the histories of the Haida and Tlingit tribes in this region.     

Demographic Histories,Isolation and Social Factors as Determinants of the Genetic Structure of Alpine Linguistic Groups

Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.     

Gm haplotype distribution in Amerindians: Relationship with geography and language

A review is made of the Gm haplotype distribution in 60 groups of Eskimos, North, Central and South American Indians, totaling 22,808 individuals. Differences were observed in the shapes of the distribution of Gm*ag and the other markers. Nearly identical values for F_ST and average heterozygosities were obtained in the North+Central/South comparisons. North-South and Southwest/Northeast clinal differences were observed in the Americas using correspondence factorial analysis. The two haplotypes mainly responsible for these differences are Gm*axg and Gm*abOst. When the populations are classified by language groups, besides the recognized differences between Eskimos and Athabaskan (Na-Dene) speakers compared with Amerinds, others are found. For instance, Uto-Aztecan speakers of the United States and Mexico differ in Gm frequencies from the Nuclear Chibchan, Macro-Arawak, and Carib speakers of Central and South America. The notion of a homogeneous Amerind genetic pool does not conform with these and other results. © 1993 Wiley-Liss, Inc.     

Mitochondrial DNA Variation in the Kets and Nganasans and Its Implications for the Initial Peopling of Northern Eurasia

Mitochondrial DNA (mtDNA) variation was studied in 38 Kets and 24 Nganasans, the indigenous inhabitants of the north of the Yenisey River Basin and the Taimyr Peninsula. The results were compared with the analogous data obtained for 59 Kondinski and 39 Sos'vinski Mansi. As a whole, mitochondrial gene pool of Mansi, Nganasans, and Kets was characterized by unique combination of European-specific (H, H2, H3, H8, U2, U4, U5, U7, J2, and W) and Asian-specific (A, C, D, and Z) mtDNA haplogroups. Specific features of the haplogroup geographical distribution along with the results of phylogenetic reconstruction favor the hypothesis of the genetic trace left in Trans-Urals and the adjacent Siberian territories by early migrations from the Near East.     

mtDNA variability in two Bantu‐speaking populations (Shona and Hutu) from Eastern Africa: Implications for peopling and migration patterns in sub‐Saharan Africa

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu‐speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu‐speaking populations. Moreover, by comparing our data with those from other Niger‐Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub‐Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu‐speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu‐speaking populations, but also between Bantu and non‐Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu‐speakers, with strong interactions between the different lines of Bantu‐speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Asian affinities and continental radiation of the four founding Native American mtDNAs.

The mtDNA variation of 321 individuals from 17 Native American populations was examined by high-resolution restriction endonuclease analysis. All mtDNAs were amplified from a variety of sources by using PCR. The mtDNA of a subset of 38 of these individuals was also analyzed by D-loop sequencing. The resulting data were combined with previous mtDNA data from five other Native American tribes, as well as with data from a variety of Asian populations, and were used to deduce the phylogenetic relationships between mtDNAs and to estimate sequence divergences. This analysis revealed the presence of four haplotype groups (haplogroups A, B, C, and D) in the Amerind, but only one haplogroup (A) in the Na-Dene, and confirmed the independent origins of the Amerinds and the Na-Dene. Further, each haplogroup appeared to have been founded by a single mtDNA haplotype, a result which is consistent with a hypothesized founder effect. Most of the variation within haplogroups was tribal specific, that is, it occurred as tribal private polymorphisms. These observations suggest that the process of tribalization began early in the history of the Amerinds, with relatively little intertribal genetic exchange occurring subsequently. The sequencing of 341 nucleotides in the mtDNA D-loop revealed that the D-loop sequence variation correlated strongly with the four haplogroups defined by restriction analysis, and it indicated that the D-loop variation, like the haplotype variation, arose predominantly after the migration of the ancestral Amerinds across the Bering land bridge.     

History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation

Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.     

Mitochondrial DNA variation in Kets and Nganasans and the early peoples of Northern Eurasia

Mitochondrial DNA (mtDNA) variation was studied in 38 Kets and 24 Nganasans, the indigenous inhabitants of the north of the Yenisey River Basin and the Taimyr Peninsula. The results were compared with the analogous data obtained for 59 Kondinski and 39 Sos'vinski Mansi. As a whole, mitochondrial gene pool of Mansi, Nganasans, and Kets was characterized by unique combination of European-specific (H, H2, H3, H8, U2, U4, U5, U7, J2, and W) and Asian-specific (A, C, D, and Z) mtDNA haplogroups. Specific features of the haplogroup geographical distribution along with the results of phylogenetic reconstruction favor the hypothesis of the genetic trace left in Eastern Cis-Urals and the adjacent Siberian territories by early migrations from the Near East.     

Mitochondrial DNA diversity in Siberian Tatars of the Tobol-Irtysh basin

Data on the variation of the nucleotide sequence of hypervariable segment I (HVSI) and restriction fragment length polymorphism (RFLP) of the coding region of mitochondrial DNA (mtDNA) have been used to characterize the mitochondrial gene pool of Siberian Tatars of the Tobol-Irtysh basin (N = 218), one of three geographic/linguistic groups of Siberian Tatars. The gene pool of Siberian Tatars has been shown to contain both Asian and European mtDNA lineages at a ratio of 1.0 : 1.5. The mtDNA diversity of Siberian Tatars is substantially higher than that of other Turkic-speaking populations of North and Central Asia. The position of the mitochondrial gene pool of Tatars of the Tobol-Irtysh basin in the genetic space of northern Eurasia populations has been determined.     

High mitochondrial sequence diversity in linguistic isolates of the Alps.

Segment I of the control region of mtDNA (360 bases) was sequenced in seven samples, each of 10 individuals inhabiting villages in the eastern Italian Alps (South Tyrol and Trentino). Three linguistic groups, German, Italian, and Ladin, were represented by two samples each; the seventh sample comes from an isolated group of German origin, the Mocheni, who are linguistically distinct and geographically separated from the bulk of the German speakers. Seventy-four polymorphic sites were identified, defining 63 different haplotypes. Mocheni and Ladin speakers tend to form two clusters in the evolutionary trees inferred from sequences. Analysis of molecular variance shows significant differentiation within samples, among them, and among linguistic groups. Genetic differences between the Ladins and the other groups are not much smaller than between Europeans and some Africans; variation is large within groups, as well, with the exception of only the Mocheni. In the evolutionary trees where the four alpine groups are compared with other European populations, Mocheni and especially Ladins appear as clear outliers. Romansch-speaking Swiss, who are linguistically related to Ladins, are not genetically similar to them, for this segment of DNA. Because the time elapsed since colonization of the Alps (< or = 12,000 years) is short in mutational terms, the only model accounting for the observed relationships between mtDNA variation and linguistic identity seems one in which a population ancestral to Ladin speakers was already differentiated long before the Alps were settled and the current linguistic affiliations were established. For the Mocheni, the results are consistent with a simpler episode of allele loss, from an original genetic pool common to the ancestors of the current German speakers.