Gene pool of Siberian Tatars: Five ways of origin for five subethnic groups

Siberian Tatars form the largest Turkic-speaking ethnic group in Western Siberia. The group has a complex hierarchical system of ethnographically diverse populations. Five subethnic groups of Tobol–Irtysh Siberian Tatars (N = 388 samples) have been analyzed for 50 informative Y-chromosomal SNPs. The subethnic groups have been found to be extremely genetically diverse (F _ST = 21%), so the Siberian Tatars form one of the strongly differentiated ethnic gene pools in Siberia and Central Asia. Every method employed in our studies indicates that different subethnic groups formed in different ways. The gene pool of Isker–Tobol Tatars descended from the local Siberian indigenous population and an intense, albeit relatively recent gene influx from Northeastern Europe. The gene pool of Yalutorovsky Tatars is determined by the Western Asian genetic component. The subethnic group of Siberian Bukhar Tatars is the closest to the gene pool of the Western Caucasus population. Ishtyak–Tokuz Tatars have preserved the genetic legacy of Paleo-Siberians, which connects them with populations from Southern, Western, and Central Siberia. The gene pool of the most isolated Zabolotny (Yaskolbinsky) Tatars is closest to Ugric peoples of Western Siberia and Samoyeds of the Northern Urals. Only two out of five Siberian Tatar groups studied show partial genetic similarity to other populations calling themselves Tatars: Isker–Tobol Siberian Tatars are slightly similar to Kazan Tatars, and Yalutorovsky Siberian Tatars, to Crimean Tatars. The approach based on the full sequencing of the Y chromosome reveals only a weak (2%) Central Asian genetic trace in the Siberian Tatar gene pool, dated to 900 years ago. Hence, the Mongolian hypothesis of the origin of Siberian Tatars is not supported in genetic perspective.     

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.     

New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.     

Population genetics of taiga hunters-deer breeders. Characteristics of the prevalence of HLA system markers among the native population of Central Siberia

The postulated peculiarities of distribution of the HLA antigens in the Evenk population of the Central Siberia indicate this population to be, on the whole, Mongoloid. Prolonged isolated existence of small inbred populations of the Evenks resulted in the number of specific HLA-complex features, such as poor antigen diversity, low level of heterozygosity. Non-homogeneity of gene frequencies was noted, the prevailing genes being A9, B40 with frequencies reaching 50%. Of the remaining alleles found in the Evenks A2, Aw19 in A locus, B5, B15, B17, B27, Bw35 in B locus and Cw2, Cw3, Cw4-in C locus are only widely spread. Similar heterozygosis levels and the HLA-system profiles draw the Evenks and the populations of American Indians and Eskimos closer to one another. On the basis of the fact that significant positive correlation exists between genetic and geographic distances determined for the Evenks and the native populations of America, genetic resemblance of these populations may be considered as evidence for their original relationship. Postulated closeness of native Central-Siberian populations to Americanoids, as regards HLA-system, makes it possible to consider formation of specific complex of HLA-system peculiarities in native American population in the light of their Siberian origin, for the first time.     

Genetic structure and inferences on potential source areas for Bactrocera dorsalis (Hendel) based on mitochondrial and microsatellite markers

Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan.     

Geographic limits of a clonal population of wheat yellow rust in the Mediterranean region

Most plant pathogens present complex life cycles, in which the clonal reproduction may impede the delimitation of population entities. By studying the genetic structure of the wheat yellow rust caused by Puccinia striiformis f.sp. tritici (PST), we highlighted difficulties impeding population delimitation in highly clonal species. Despite the high dispersal potential of PST, southern France isolates were shown to be divergent from a northwestern European population. A 2-year survey was performed in the Mediterranean region to assess the geographic distribution of southern isolates: 453 isolates collected in 11 countries were genotyped using 15 simple sequence repeat markers. A subsample was analysed for virulence against 23 resistance genes. The dominant strain in the western Mediterranean region was further studied with amplified fragment length polymorphism markers to test for a geographic substructure. Both 'individual'- and 'population'-centred analyses of polymorphism markers revealed two south-specific groups: a predominant group, with a broad variability and a wide distribution in both western and eastern Mediterranean countries, and a minor group in the western Mediterranean. The east–west gradient of genetic diversity suggested gene flow from the Middle East with subsequent founder effects and genetic divergence, and demonstrated the local survival of a western Mediterranean population. The high frequency of the resistance gene Yr8 observed in cultivars from Tunisia and Algeria may contribute to maintain the north/south structure observed in France. In addition to migration and local adaptation, the dynamics of clonal lineage diversification and replacement should be considered to define population entities in strongly clonal species.     

Genetic structure of native circumpolar populations based on autosomal,mitochondrial, and Y chromosome DNA markers

This study investigates the genetic structure of the present‐day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a “ubiquitous” allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non‐native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the “ubiquitous” allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935‐GQ922973. Am J Phys Anthropol 143:62–74, 2010. © 2010 Wiley‐Liss, Inc.     

Phylogeography of the Temminck’s Stint (Calidris temminckii): historical vicariance but little present genetic structure in a regionally endangered Palearctic wader

Aim We study the population differentiation and phylogeography of the Temminck’s Stint (Calidris temminckii). Specifically, we seek signs of past and present population size changes and dispersal events and evaluate management and conservation unit status of the populations. We also study the possibility of introgression as the origin of two mitochondrial DNA (mtDNA) lineages found and estimate the divergence time of the lineages. Location Northern Eurasia. Methods We analysed 583 bp of mtDNA control region domains I and II and 11 microsatellite loci from 13 localities throughout the breeding range. In addition, we used mitochondrial cytochrome c oxidase subunit I (COI), a barcoding gene, to search for signs of introgression. Results More population differentiation was found from microsatellites than from mtDNA, although differentiation was weak in both markers. Signs of past population growth were observed, in addition to more recent decline in some areas. Both control region and COI sequences revealed two maternal lineages coexisting in Fennoscandia and in north‐west Siberia. No signs of introgression were detected. Lineage divergence time was estimated to have occurred during the glacial periods of Pleistocene. Main conclusions Slight differences in mtDNA and microsatellite differentiation and diversity may reflect different features – such as the mutation rate and effective population size – of the markers used, or female‐biased dispersal pattern and high male site‐fidelity of the species. The coexistence of the two mitochondrial lineages is most likely a consequence of post‐glacial mixing of two refugial Pleistocene populations. Based on genetic information alone, global conservation concerns are not imminent. However, fast decline of a marginal Bothnian Bay population and the smallness and remoteness of a Central Yakutian population warrant conservation actions.     

Nuclear and chloroplast microsatellites show multiple introductions in the worldwide invasion history of common ragweed, Ambrosia artemisiifolia

Background

Ambrosia artemisiifolia is a North American native that has become one of the most problematic invasive plants in Europe and Asia. We studied its worldwide population genetic structure, using both nuclear and chloroplast microsatellite markers and an unprecedented large population sampling. Our goals were (i) to identify the sources of the invasive populations; (ii) to assess whether all invasive populations were founded by multiple introductions, as previously found in France; (iii) to examine how the introductions have affected the amount and structure of genetic variation in Europe; (iv) to document how the colonization of Europe proceeded; (v) to check whether populations exhibit significant heterozygote deficiencies, as previously observed.

Principal Findings

We found evidence for multiple introductions of A. artemisiifolia, within regions but also within populations in most parts of its invasive range, leading to high levels of diversity. In Europe, introductions probably stem from two different regions of the native area: populations established in Central Europe appear to have originated from eastern North America, and Eastern European populations from more western North America. This may result from differential commercial exchanges between these geographic regions. Our results indicate that the expansion in Europe mostly occurred through long-distance dispersal, explaining the absence of isolation by distance and the weak influence of geography on the genetic structure in this area in contrast to the native range. Last, we detected significant heterozygote deficiencies in most populations. This may be explained by partial selfing, biparental inbreeding and/or a Wahlund effect and further investigation is warranted.

Conclusions

This insight into the sources and pathways of common ragweed expansion may help to better understand its invasion success and provides baseline data for future studies on the evolutionary processes involved during range expansion in novel environments.     

Gene flow between chromosomal forms of the malaria vector Anopheles funestus in Cameroon, Central Africa, and its relevance in malaria fighting

Knowledge of population structure in a major vector species is fundamental to an understanding of malaria epidemiology and becomes crucial in the context of genetic control strategies that are being developed. Despite its epidemiological importance, the major African malaria vector Anopheles funestus has received far less attention than members of the Anopheles gambiae complex. Previous chromosomal data have shown a high degree of structuring within populations from West Africa and have led to the characterization of two chromosomal forms, "Kiribina" and "Folonzo." In Central Africa, few data were available. We thus undertook assessment of genetic structure of An. funestus populations from Cameroon using chromosomal inversions and microsatellite markers. Microsatellite markers revealed no particular departure from panmixia within each local population and a genetic structure consistent with isolation by distance. However, cytogenetic studies demonstrated high levels of chromosomal heterogeneity, both within and between populations. Distribution of chromosomal inversions was not random and a cline of frequency was observed, according to ecotypic conditions. Strong deficiency of heterokaryotypes was found in certain localities in the transition area, indicating a subdivision of An. funestus in chromosomal forms. An. funestus microsatellite genetic markers located within the breakpoints of inversions are not differentiated in populations, whereas in An. gambiae inversions can affect gene flow at marker loci. These results are relevant to strategies for control of malaria by introduction of transgenes into populations of vectors.     

Molecular Evidence of Demographic Expansion of the Chagas Disease Vector Triatoma dimidiata (Hemiptera,Reduviidae, Triatominae) in Colombia

Background

Triatoma dimidiata is one of the most significant vectors of Chagas disease in Central America and Colombia, and, as in most species, its pattern of genetic variation within and among populations is strongly affected by its phylogeographic history. A putative origin from Central America has been proposed for Colombian populations, and high genetic differentiation among three biographically different population groups has recently been evidenced. Analyses based on putatively neutral markers provide data from which past events, such as population expansions and colonization, can be inferred. We analyzed the genealogies of the nicotinamide adenine dinucleotide dehydrogenase 4 (ND4) and the cytochrome oxidase subunit 1-mitochondrial genes, as well as partial nuclear ITS-2 DNA sequences obtained across most of the eco-geographical range in Colombia, to assess the population structure and demographic factors that may explain the geographical distribution of T. dimidiata in this country.

Results

The population structure results support a significant association between genetic divergence and the eco-geographical location of population groups, suggesting that clear signals of demographic expansion can explain the geographical distribution of haplotypes of population groups. Additionally, empirical date estimation of the event suggests that the population''s expansion can be placed after the emergence of the Panama Isthmus, and that it was possibly followed by a population fragmentation process, perhaps resulting from local adaptation accomplished by orographic factors such as geographical isolation.

Conclusion

Inferences about the historical population processes in Colombian T. dimidiata populations are generally in accordance with population expansions that may have been accomplished by two important biotic and orographic events such as the Great American Interchange and the uplift of the eastern range of the Andes mountains in central Colombia.     

Mitochondrial genome variation in domesticated sable (Martes zibellina)

The first comparison of mitochondrial variations in sables from captive and natural populations of the Urals, Central Siberia, Yakutia, Kamchatka, and Japan has been performed. The object of comparative analysis was a 427-bp 5' fragment of the mitochondrial control region, including the D-loop. Two main haplogroups of the sable mitochondrial genome have been found, which provides new data for reconstruction of the spread of the sable over its current range. Asymmetry of the haplotype abundances in the captive populations of sables has been detected. The mitochondrial haplotypes characteristic of sable breeds have been identified. The possible role of the frequent mitochondrial haplotypes of the captive population in the sable adaptation to the conditions of captivity is discussed.     

Mitochondrial genome variation in domesticated sable (<Emphasis Type="Italic">Martes zibellina</Emphasis>)

The first comparison of mitochondrial variations in sables from captive and natural populations of the Urals, Central Siberia, Yakutia, Kamchatka, and Japan has been performed. The object of comparative analysis was a 427-bp 5′ fragment of the mitochondrial control region, including the D-loop. Two main haplogroups of the sable mitochondrial genome have been found, which provides new data for reconstruction of the spread of the sable over its current range. Asymmetry of the haplotype abundances in the captive populations of sables has been detected. The mitochondrial haplotypes characteristic of sable breeds have been identified. The possible role of the frequent mitochondrial haplotypes of the captive population in the sable adaptation to the conditions of captivity is discussed.     

Local adaptation, patterns of selection, and gene flow in the Californian serpentine sunflower (Helianthus exilis)

The traditional view of the species as the fundamental unit of evolution has been challenged by observations that in heterogeneous environments, gene flow may be too restricted to overcome the effects of local selection. Whether a species evolves as a cohesive unit depends critically on the dynamic balance between homogenizing gene flow among populations and potentially disruptive local adaptation. To examine this evolutionary balance between "global" gene flow and local selection, we studied northern Californian populations of Helianthus exilis, the serpentine sunflower, within a mosaic of contrasting serpentine and nonserpentine areas that differ considerably in soil chemistry and water availability. Local adaptation to riparian and serpentine habitats was studied in Helianthus exilis along with an analysis of gene flow patterns among populations within these habitats. Local adaptation was assessed in H. exilis during 2002 and 2003 using reciprocal transplant experiments at multiple locations within serpentine and riparian habitats. Effects of competition and germination date on the expression of local adaptation were also examined within the reciprocal transplant experiments. Local adaptation was detected in both years at the local site level and at the level of habitat. The analysis of the transplanted populations indicated that the patterns of selection differed considerably between riparian and serpentine sites. Differential survivorship occurred in serpentine habitats, whereas selection on reproductive output predominated in riparian habitats. Local adaptation was expressed only in the absence of competition. Local adaptation in terms of survivorship was most strongly expressed in treatments with delayed seed germination. Microsatellite markers were used to quantify population genetic parameters and examine the patterns of gene flow among sampled populations. Analysis of molecular markers revealed a system of population patches that freely exchange genes with each other. Strong selection seems to maintain ecotypic variation within this endemic sunflower species, while extensive gene flow among populations prevents local speciation between serpentine and riparian ecotypes.     

The Dual Origin and Siberian Affinities of Native American Y Chromosomes

The Y chromosomes of 549 individuals from Siberia and the Americas were analyzed for 12 biallelic markers, which defined 15 haplogroups. The addition of four microsatellite markers increased the number of haplotypes to 111. The major Native American founding lineage, haplogroup M3, accounted for 66% of male Y chromosomes and was defined by the biallelic markers M89, M9, M45, and M3. The founder haplotype also harbored the microsatellite alleles DYS19 (10 repeats), DYS388 (11 repeats), DYS390 (11 repeats), and DYS391 (10 repeats). In Siberia, the M3 haplogroup was confined to the Chukotka peninsula, adjacent to Alaska. The second major group of Native American Y chromosomes, haplogroup M45, accounted for about one-quarter of male lineages. M45 was subdivided by the biallelic marker M173 and by the four microsatellite loci alleles into two major subdivisions: M45a, which is found throughout the Americas, and M45b, which incorporates the M173 variant and is concentrated in North and Central America. In Siberia, M45a haplotypes, including the direct ancestor of haplogroup M3, are concentrated in Middle Siberia, whereas M45b haplotypes are found in the Lower Amur River and Sea of Okhotsk regions of eastern Siberia. Among the remaining 5% of Native American Y chromosomes is haplogroup RPS4Y-T, found in North America. In Siberia, this haplogroup, along with haplogroup M45b, is concentrated in the Lower Amur River/Sea of Okhotsk region. These data suggest that Native American male lineages were derived from two major Siberian migrations. The first migration originated in southern Middle Siberia with the founding haplotype M45a (10-11-11-10). In Beringia, this gave rise to the predominant Native American lineage, M3 (10-11-11-10), which crossed into the New World. A later migration came from the Lower Amur/Sea of Okhkotsk region, bringing haplogroup RPS4Y-T and subhaplogroup M45b, with its associated M173 variant. This migration event contributed to the modern genetic pool of the Na-Dene and Amerinds of North and Central America.     

Generating and maintaining diversity at the elite level in crop breeding

Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may "pollute" the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.     

Widespread hybridization in the introduced hog deer population of Victoria,Australia, and its implications for conservation

In Australia, many species have been introduced that have since undergone drastic declines in their native range. One species of note is the hog deer (Axis porcinus) which was introduced in the 1860s to Victoria, Australia, and has since become endangered in its native range throughout South‐East Asia. There is increased interest in using non‐native populations as a source for genetic rescue; however, considerations need to be made of the genetic suitability of the non‐native population. Three mitochondrial markers and two nuclear markers were sequenced to assess the genetic variation of the Victorian population of hog deer, which identified that the Victorian population has hybrid origins with the closely related chital (Axis axis), a species that is no longer present in the wild in Victoria. In addition, the mitochondrial D‐loop region within the Victorian hog deer is monomorphic, demonstrating that mitochondrial genetic diversity is very low within this population. This study is the first to report of long‐term persistence of hog deer and chital hybrids in a wild setting, and the continual survival of this population suggests that hybrids of these two species are fertile. Despite the newly discovered hybrid status in Victorian hog deer, this population may still be beneficial for future translocations within the native range. However, more in‐depth analysis of genetic diversity within the Victorian hog deer population and investigation of hybridization rates within the native range are necessary before translocations are attempted.     

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.     

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, RPS4Y₇₁₁, 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.