Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data

In order to clarify the history of gene pool formation of the indigenous populations of the Northern Priokhotye (the northern coast of the Sea of Okhotsk), Y-chromosome polymorphisms were studied in the Koryaks and Evens living in the Magadan region. The results of the study showed that the male gene pool of the Koryaks is represented by haplogroups C-B90-B91, N-B202, and Q-B143, which are also widespread in other peoples of Northeastern Siberia, mainly of Paleo-Asiatic origin. High frequency of haplogroup C-B80, typical of other Tungus-Manchurian peoples, is characteristic of the Evens of the Magadan region. The shared components of the gene pools of the Koryaks and Evens are haplogroups R-M17 and I-P37.2 inherited as a result of admixture with Eastern Europeans (mainly Russians). The high frequency of such Y chromosome haplogroups in the Koryaks (16.7 %) and Evens (37.8 %) is indicative of close interethnic contacts during the last centuries, and most probably especially during the Soviet period. The genetic contribution of the European males' Y chromosome significantly prevails over that of maternally inherited mitochondrial DNA. The study of the Y chromosome haplogroup diversity has shown that only relatively young phylogenetic branches have been preserved in the Koryak gene pool. The age of the oldest component of the Koryak gene pool (haplogroup C-B90-B91) is estimated to be about 3.8 thousand years, the age of the younger haplogroups Q-B143 and N-B202 is about 2.8 and 2.4 thousand years, respectively. Haplogroups C-B90-B91 and N-B202 are Siberian in origin, and haplogroup Q-B143 was apparently inherited by the ancestors of the Koryaks and other Paleo-Asiatic peoples from the Paleo-Eskimos as a result of their migrations to Northeast Asia from the Americas. The analysis of microsatellite loci for haplogroup Q-B143 in the Eskimos of Greenland, Canada and Alaska as well as in the indigenous peoples of Northeastern Siberia showed a decrease in genetic diversity from east to west, pointing to the direction of distribution of the Paleo-Eskimo genetic component in the circumpolar region of America and Asia. At the same time, the Evens appeared in the Northern Priokhotye much later (in the XVII century) as a result of the expansion of the Tungusic tribes, which is confirmed by the results of the analysis of haplogroup C-B80 polymorphisms.

A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe

Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used-Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846-1.000 for all classes.

Evaluating the role of selection in the evolution of mitochondrial genomes of aboriginal peoples of Siberia

Studies of the nature of mitochondrial DNA (mtDNA) variability in human populations have shown that protein-coding genes are under negative (purifying) selection, since their mutation spectra are characterized by a pronounced predominance of synonymous substitutions over non-synonymous ones (Ka/Ks < 1). Meanwhile, a number of studies have shown that the adaptation of populations to various environmental conditions may be accompanied by a relaxation of negative selection in some mtDNA genes. For example, it was previously found that in Arctic populations, negative selection is relaxed in the mitochondrial ATP6 gene, which encodes one of the subunits of ATP synthase. In this work, we performed a Ka/Ks analysis of mitochondrial genes in large samples of three regional population groups in Eurasia: Siberia (N = 803), Western Asia/Transcaucasia (N = 753), and Eastern Europe (N = 707). The main goal of this work is to search for traces of adaptive evolution in the mtDNA genes of aboriginal peoples of Siberia represented by populations of the north (Koryaks, Evens) and the south of Siberia and the adjacent territory of Northeast China (Buryats, Barghuts, Khamnigans). Using standard Ka/Ks analysis, it was found that all mtDNA genes in all studied regional population groups are subject to negative selection. The highest Ka/Ks values in different regional samples were found in almost the same set of genes encoding subunits of ATP synthase (ATP6, ATP8), NADH dehydrogenase complex (ND1, ND2, ND3), and cytochrome bc1 complex (CYB). The highest Ka/Ks value, indicating a relaxation of negative selection, was found in the ATP6 gene in the Siberian group. The results of the analysis performed using the FUBAR method (HyPhy software package) and aimed at searching for mtDNA codons under the influence of selection also showed the predominance of negative selection over positive selection in all population groups. In Siberian populations, nucleotide sites that are under positive selection and associated with mtDNA haplogroups were registered not in the north (which is expected under the assumption of adaptive evolution of mtDNA), but in the south of Siberia.

Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry

Genetic markers for the prediction of biogeographical ancestry have proved to be effective tools for law enforcement agencies for many years now. In this study, we attempted to assess the potential of insertion-deletion markers (InDel) and microsatellites (STRs) as subsidiary polymorphisms for inference of Slavic population ancestry. For that purpose, we genotyped Slavic-speaking populations samples from Belarus, the Czech Republic, Poland, Serbia, Ukraine and Russia in 46 InDels and 15 STRs by PCR and capillary electrophoresis and analyzed for between-population differentiation with the use of distance-based methods (FST, principal component analysis and multidimensional scaling). Additionally, we studied a sample from a Polish individual of well-documented genealogy whose biogeographic ancestry had previously been inferred by commercial genomic services using autosomal single nucleotide polymorphisms (SNPs), mitochondrial DNA and Y-SNP markers. For comparative purposes, we used genotype data collected in the “forInDel” browser and allele frequencies from previously published papers. The results obtained for InDels and STRs show that the Slavic populations constitute a genetically homogeneous group, with the exception of the Czechs differing clearly from the other tested populations. The analysis of the known Polish sample in the Snipper application proves the usefulness of the InDel markers on the continental level only. Conversely, microsatellites not only improve prediction, but are also informative if considered as an independent set of ancestry markers. Weryfikacja markerów insercyjno-delecyjnych (InDels) i mikrosatelitarnych (STR) jako narzędzi pomocniczych do wnioskowania o pochodzeniu populacji słowiańskiej Markery genetyczne do przewidywania pochodzenia biogeograficznego od wielu lat okazują się skutecznymi narzędziami dla organów ścigania. W tym badaniu podjęliśmy próbę oceny potencjału markerów insercyjno-delecyjnych (InDel) i mikrosatelitarnych (STR) jako pomocniczych polimorfizmów do wnioskowania o pochodzeniu populacji słowiańskiej. W tym celu genotypowaliśmy próbki populacji słowiańskojęzycznych z Białorusi, Czech, Polski, Serbii, Ukrainy i Rosji w w zakresie 46 markerów InDel oraz 15 loci STR za pomocą PCR i elektroforezy kapilarnej oraz analizowaliśmy pod kątem różnicowania między populacjami za pomocą metod bazujących na dystansach genetycznych (FST, analiza głównych składowych i skalowanie wielowymiarowe). Dodatkowo zbadaliśmy próbkę mężczyzny z populacji polskiej o dobrze udokumentowanej genealogii, którego pochodzenie biogeograficzne zostało wcześniej ustalone przez komercyjne usługi genomiczne przy użyciu autosomalnych polimorfizmów pojedynczych nukleotydów (SNP), mitochondrialnego DNA i markerów Y-SNP. Do celów porównawczych wykorzystaliśmy dane genotypowe zebrane w przeglądarce „forInDel” i częstości alleli z wcześniej opublikowanych artykułów. Uzyskane wyniki dla InDels i STR wskazują, że populacje słowiańskie stanowią grupę genetycznie jednorodną, z wyjątkiem Czechów wyraźnie różniących się od pozostałych badanych populacji. Analiza znanej polskiej próbki w aplikacji Snipper dowodzi przydatności markerów InDel jedynie na poziomie kontynentalnym. Z kolei, mikrosatelity nie tylko poprawiają wyniki predykcji, ale są informatywne jako niezależny zestaw markerów pochodzenia biogeograficznego.

An association between copy number variation of enhancer involved in craniofacial development and biogeographic ancestry

Human facial morphology is a combination of many complex traits and is determined by a large number of genes and enhancers. Here, we report a Copy Number Variation (CNV) study of enhancer hs1431 in populations of Central European and South Siberian ancestry. Central European samples included 97 Poles, while South Siberian samples included 78 Buryats and 27 Tuvinians. CNVs were detected by real-time PCR, using ViiA™ 7 Real-Time PCR System (Applied Biosystems). We revealed significant differences in CNV of hs1431 enhancer between Polish and Buryat population (p=0.0378), but not between Central European and South Siberian population (p=0.1225). Our results suggest that an increase in copy number variation of hs1431 enhancer is associated with biogeographic ancestry. However, this result needs extending and replicating in larger cohorts. This is the first study revealing the presence of copy number variation of enhancer hs1431 in humans.

[Mitochondrial Genome Variability in the Wolverine (Gulo gulo)]

The nucleotide sequence of an extended mitochondrial genome segment (11473 base pairs in size) was determined in the wolverine (Gulo gulo) from Magadan oblast. Phylogenetic and statistical analyses of mitochondrial DNA (mtDNA) sequences of mustelids showed that the separation of the Gulo phylogenetic branch occurred at the Miocene--early Pliocene (about 5.6 million years ago (MYA)), while the formation of the species G. gulo took place in the Middle Pleistocene (181 and 234 thousand years ago (KYA), according to the results of molecular dating based on the variability of the extended mtDNA segment and the mitochondrial cytochrome b gene, respectively). The molecular data were in agreement with the fossil records for wolverines.

[Topological Conflicts in Phylogenetic Analysis of Different Regions of the Sable (Martes zibellina L.) Mitochondrial Genome]

Phylogenetic analysis of different regions of the mitochondrial genome of the sable showed the presence of several topologies of phylogenetic trees, but the most statistically significant topology is A-BC, which was obtained as a result of the analysis of the mitochondrial genome as a whole, as well as of the individual CO1, ND4, and ND5 genes. Analysis of the intergroup divergence of the mtDNA haplotypes (Dxy) indicated that the maximum Dxy values between A and BC groups were accompanied by minimum differences between B and C groups only for six genes showing the A-BC topology (12S rRNA; CO1, CO2, ND4, ND5, and CYTB). It is assumed that the topological conflicts observed in the analysis of individual sable mtDNA genes are associated with the uneven distribution of mutations along the mitochondrial genome and the mitochondrial tree. This may be due to random causes, as well as the nonuniform effect of selection.

[Phylogenetic relationships among Asiatic salamanders of the genus Salamandrella based on variability of nuclear genes]

Based on sequence variation of three nuclear genome genes (BDNF, POMC, and RAG1), the phylogenetic relationships among Asiatic salamanders of the genus Salamandrella, Siberian salamander (S. keyserlingii) and Schrenk salamander (S. schrenkii), were examined. Both species demonstrated high levels of heterozygosity determined by intraspecific polymorphism. Fixed interspecific differences were revealed at one nucleotide position of the RAG1 gene, and thus the level of interspecific divergence over the three genes constituted only 0.04%. Analysis of the RAG1 polymorphism across the whole range of S. keyserlingii showed that only one gene variant, encoding for modified RAG1 recombinase, had the highest distribution to the north of the Amur region (west and northeast of Siberia). It is possible that the changes in the RAG1 gene in Siberian salamander are of an adaptive nature. However, cases of interspecific hybridization were identified in Jewish autonomous oblast (JAO), which contains one of the range borders between the two Salamandrella species.

Genome-wide analysis of cold adaptation in indigenous Siberian populations

Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

[Episodes of adaptive evolution of mitochondrial genome in Asiatic salamanders (Amphibia, Caudata, Hynobiidae)]

To elucidate the effect of natural selection on the evolution of mitochondrial DNA (mtDNA) in Asiatic salamanders of the family Hynobiidae, nucleotide sequences of 12 protein-coding genes were analyzed. Using a mixed effects model of evolution, it was found that, in spite of the pronounced effect of negative selection on the mtDNA evolution in Hynobiidae (which is typical for the animals in general), two phylogenetic clusters, the West Asian one, represented by the genera Ranodon and Paradactylodon, and North Eurasian one, represented by the genus Salamandrella, were formed under the influence of episodic positive selection. Analysis of protein sequences encoded by the mitochondrial genome also supported the influence of positive selection on the evolution of Hynobiidae at some stages of their cladogenesis. It is suggested that the signatures of adaptive evolution detected in the mtDNA of Hynobiidae were determined by the complex and long-lasting history of their formation, accompanied by adaptation to the changing environment.

[Peculiarities of phosphoglycerate kinase-1 pseudogene evolution in Schrenck salamander (Salamandrella schrenckii Strauch, 1870)]

Processed copies of genes generally evolve in neutral mode as pseudogenes, however, some of them might be important sources of new functional genes. The psiPGK1 pseudogene has been discovered in Schrenck salamander (Salamandrella schrenckii, Amphibia, Caudata, Hynobiidae) via polymerase chain reaction used to amplify the phosphoglycerate kinase 1 gene (PGK1). This pseudogene is an intronless copy of PGK1 gene absent of exon 6. Analysis of psiPGK1 pseudogene polymorphism has demonstrated that it lacks mutations, which results in shifts in the stop codons and reading frames, as well as that the interspecies variation of this pseudogene was inconsistent with the neutral model of evolution. In addition, the pattern of phylogeographic differentiation of the psiPGK1 variants mainly coincides with that observed in mitochondrial DNA. These observations allow it to be suggested that the psiPGK1 pseudogene is a new functional gene in the Schrenck salamander.

[Population structure of Volga Tatars inferred from the mitochondrial DNA diversity data]

The data on mitochondrial DNA (mtDNA) variation in two populations of Volga Tatars, representing the population of Buinsk and Aznakaevo districts of the Republic of Tatarstan are presented. Comparative analysis of the data on mtDNA variation in the populations of Eastern Europe showed that Volga Tatars were characterized by low interpopulation differentiation (F(ST) = 0.33%), while the level of interethnic differentiation in Eastern Europe is 1.8%. Genetic similarity of Tatars from the eastern regions of Tatarstan to Bashkirs, as well as of Tatars from western regions to Chuvashes, with whom they share territorial borders, was revealed. Positive correlation between population genetic structure in Eastern Europe and linguistic affiliation of the ethnic groups studied was observed.

[Intraspecific structure of sable Martes zibellina inferred from nucleotide variation of the mitochondrial DNA cytochrome b gene]

A fragment of the mitochondrial DNA (mtDNA) cytochrome b gene was sequences in sable from Magadan oblast, Khabarovsk krai, and Kamchatka. Using phylogenetic analysis, the presence of two clusters (A and BC), with the divergence value of 1.4%, was demonstrated. Analysis of the cytochrome b gene median networks indicated that split of the ancestral population took place in early Pleistocene (about one Myr ago), while expansion of its more young phylogenetic group A occurred in late Pleistocene, about 120,000 years ago.

[Different instability of microsatellite CAG repeat in two groups of haplotypes of the human mitochondrial gamma-DNA-polymerase gene]

Polymorphism of two single nucleotide loci rs758130 (T/C) and rs2238296 (T/C) of mitochondrial DNA-polymerase gamma (POLG1) gene has been studied in individuals of different ethnoracial ancestry in Russians and Buryats) with already known genotypes of microsatellite CAG-repeat of this gene. It was found that alleles with the number of repeats unequal to 10 are more often detected on the background of haplotype TT than CC. Results of phylogenetic analysis of the POLG1 gene intron 2 nucleotide sequences in humans and chimpanzee have shown that haplotype TT heterogeneous in relation to CAG-repeat polymorphism appears to be evolutionary younger than haplotype CC. The data obtained can be used for further studies of relationships between CAG-repeat polymorphisms and male infertility.

[Polymorphism of pigmentation genes (OCA2 and ASIP) in some populations of Russia]

In Russian populations, polymorphism of two pigmentation system genes, OCA2 (loci 305, 355, and 419, tested in Russians, Buryats, Chukchi, Koryaks, and Evens) and ASIP (locus 8818, tested in Russians and Buryats) was examined. Pairwise comparisons of the F(ST) distances between the populations showed that only the populations from Northeast Asia (Chukchi, Koryaks, and Evens) were statistically significantly different from all other populations, at least relative to one of the OCA2 locus. In Russians from Pskov oblast and Novgorod oblast, increased frequency (up to 6%) of the OCA2 allele 419A was revealed. In earlier studies, as association of this allele with green eye color was demonstrated. The data obtained in terms of their application for ethnic population genetics.

[Genetic structure of populations of Schrenck newt (Salamandrella schrenckii) based on mitochondrial DNA cytochrome b variability data]

Data on variability of nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome b gene of Schrenck newt, Salamandrella schrenckii (Strauch, 1870), from populations of Primorie and Khabarovsk regions have been received. By means of phylogenetic analysis, two clusters of haplotypes--'southern' cluster 1 and 'northern' cluster 2, with divegence level between them estimated as 3%-- were revealed. Results of analysis of mtDNA and cytochrome b amino acid variation allow us to assume that development of a modern area of Schrenck newt occurred from the south on the north of Primorie region. It was found that 'northern'cluster in contrast to the 'southern' one demonstrates all signs of demographic expansion (i.e., unimodal type of pairwise nucleotide differences, results of tests of selective neutrality of mtDNA variation and good correspondence of genetic parameters to expectations following from the models of demographic expansions).

[Origin of the Mongoloid component in the mitochondrial gene pool of Slavs]

The data on mitochondrial DNA (mtDNA) restriction polymorphism in Czech population (n = 279) are presented. It was demonstrated that in terms of their structure, mitochondrial gene pools of Czechs and other Slavic populations (Russians, Poles, Slovenians, and Bosnians) were practically indistinguishable. In Czechs, the frequency of eastern-Eurasian (Mongoloid) mtDNA lineages constituted 1.8%. The spread of eastern-Eurasian mtDNA lineages belonging to different ethnolinguistic groups in the populations of Europe was examined. Frequency variations of these DNA lineages in different Slavic groups was observed, with the range from 1.2 and 1.6% in Southern and Western Slavs, respectively, to 1.3 to 5.2% in Eastern Slavs, the Russian population of Eastern Europe. The highest frequency of Mongoloid component was detected in the mitochondrial gene pools of Russian populations from the Russian North and the Northwestern region of Russia. This finding can be explained in terms of assimilation of northern-European Finno--Ugric populations during the formation of the Russian population of these regions. The origin of Mongoloid component in the gene pools of different groups of Slavs is discussed.

[Gene pool structure of Russian populations from the European part of Russia inferred from the data on Y chromosome haplogroups distribution]

Population structure of Russian population from the European part of Russia was investigated by analyzing the distribution of 23 SNP makers of Y chromosome in Russian populations from Kaluga oblast, Yaroslavl' oblast, Vladimir oblast, Nizhny Novgorod oblast, Pskov oblast, Tula oblast, Belgorod oblast, and Novgorod oblast. In the populations studied a total of 14 Y-chromosome haplogroups (E, F*, I, J, K*, N3a, N2, P*, R1*, R1a1, C3, H, and A) were discovered, of which haplogroups R1a1, I, and N3a were the prevailing. Analysis of Phi statistics in the populations grouped in accordance to the dialect subdivision of the Russian language, showed the absence of statistically significant differences between Russian population groups. Analysis of the Y-chromosome markers distribution patterns among Russian population (10 population groups) in comparison with the population of Germany (11 population groups) revealed statistically significant differences between the gene pools of Slavs (Russians and Poles) and Teutons (Germans).

Mitochondrial DNA variability in Slovaks, with application to the Roma origin

To gain insight into the mitochondrial gene pool diversity of European populations, we studied mitochondrial DNA (mtDNA) variability in 207 subjects from western and eastern areas of Slovakia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding region haplogroup-specific RFLP-markers, revealed that the majority of Slovak mtDNAs belong to the common West Eurasian mitochondrial haplogroups (HV, J, T, U, N1, W, and X). However, a few sub-Saharan African (L2a) mtDNAs were detected in a population from eastern part of Slovakia. In addition, about 3% of mtDNAs from eastern Slovakia encompass Roma-specific lineages. By means of complete mtDNA sequencing we demonstrate here that the Roma-specific M-lineages observed in gene pools of different Slavonic populations (Slovaks, Poles and Russians), belong to Indian-specific haplogroups M5a1 and M35. Moreover, we show that haplogroup J lineages found in gene pools of the Roma and some Slavonic populations (Czechs and Slovaks) belong to new subhaplogroup J1a, which is defined by coding region mutation at position 8460.

Mitochondrial DNA variability in the Czech population, with application to the ethnic history of Slavs

Mitochondrial DNA (mtDNA) variability was studied in a sample of 179 individuals representing the Czech population of Western Bohemia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding-region haplogroup-specific RFLP markers revealed that most Czech mtDNAs belong to the common West Eurasian mitochondrial haplogroups (H, pre-V HV*, J, T, U, N1, W, and X). However, about 3% of Czech mtDNAs encompass East Eurasian lineages (A, N9a, D4, M*). A comparative analysis with published data showed that different Slavonic populations in Central and Eastern Europe contain small but marked amounts of East Eurasian mtDNAs. We suggest that the presence of East Eurasian mtDNA haplotypes is not an original feature of the gene pool of the proto-Slavs but rather may be mostly a consequence of admixture with Central Asian nomadic tribes, who migrated into Central and Eastern Europe in the early Middle Ages.

[Variability of fifteen autosomal microsatellite DNA loci in five populations of aboriginal South Siberians]

The allele distributions for 15 STR loci included in the AmpFISTR SGM Plus and AmpFISTR Profiler Plus kits ("Applied Biosystems", USA) were determined in 261 healthy unrelated individuals belonging to five indigenous populations of South Siberia: in Buryats, Altaians, Tofalars, Sojots and Khakassians. No significant differences in allele frequencies were found between populations studied. Combined power of discrimination (PD) for the STR loci investigated were estimated for the populations under study.

Complex interactions of the Eastern and Western Slavic populations with other European groups as revealed by mitochondrial DNA analysis

Mitochondrial DNA sequence variation was examined by the control region sequencing (HVS I and HVS II) and RFLP analysis of haplogroup-diagnostic coding region sites in 570 individuals from four regional populations of Poles and two Russian groups from northwestern part of the country. Additionally, sequences of complete mitochondrial genomes representing K1a1b1a subclade in Polish and Polish Roma populations have been determined. Haplogroup frequency patterns revealed in Poles and Russians are similar to those characteristic of other Europeans. However, there are several features of Slavic mtDNA pools seen on the level of regional populations which are helpful in the understanding of complex interactions of the Eastern and Western Slavic populations with other European groups. One of the most important is the presence of subhaplogroups U5b1b1, D5, Z1 and U8a with simultaneous scarcity of haplogroup K in populations of northwestern Russia suggesting the participation of Finno-Ugrian tribes in the formation of mtDNA pools of Russians from this region. The results of genetic structure analyses suggest that Russians from Velikii Novgorod area (northwestern Russia) and Poles from Suwalszczyzna (northeastern Poland) differ from all remaining Polish and Russian samples. Simultaneously, northwestern Russians and northeastern Poles bear some similarities to Baltic (Latvians) and Finno-Ugrian groups (Estonians) of northeastern Europe, especially on the level of U5 haplogroup frequencies. The occurrence of K1a1b1a subcluster in Poles and Polish Roma is one of the first direct proofs of the presence of Ashkenazi-specific mtDNA lineages in non-Jewish European populations.

[Distribution of the male lineages of Genghis Khan's descendants in northern Eurasian populations]

Data on the variation of 12 microsatellite loci of Y-chromosome haplogroup C3 were used to screen lineages included in the cluster of Genghis Khan's descendants in 18 northern Eurasian populations (Altaian Kazakhs, Altaians-Kizhi, Teleuts, Khakassians, Shorians, Tyvans, Todjins, Tofalars, Sojots, Buryats, Khamnigans, Evenks, Mongols, Kalmyks, Tajiks, Kurds, Persians, and Russians; the total sample size was 1437 people). The highest frequency of haplotypes from the cluster of the Genghis Khan's descendants was found in Mongols (34.8%). In Russia, this cluster was found in Altaian Kazakhs (8.3%), Altaians (3.4%), Buryats (2.3%), Tyvans (1.9%), and Kalmyks (1.7%).

[Variability at 15 autosomal microsatellite DNA loci in Russian population]

The paper presents allele frequencies at 15 STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSFIPO, D5S818, D13S317, D7S820, D16S539, D2Sl338, D8S1179, D21S1l, D18S51, D19S433), used in forensic medicine, in Russian sample (n = 176) representing population of the European part of the Russian Federation. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 STR loci were 0.999 999 999 999 999 986 and 0.999 999 331 310 171 000, respectively. The data obtained for allele and genotype frequencies conformed to Hardy-Weinberg expectations. According to the presented data, loci D2S1338, D18S51, D21Sll and FGA are the most informative markers for Russians. The data obtained may be used as reference database for forensic medicine laboratories in Russian Federation.

Optimization of the Y831C mutation detection in human DNA polymerase gamma by allelic discrimination assay

Many well-defined mutations in the gene for the catalytic subunit of polymerase gamma (POLG1) have been found to be associated with disease, whereas the status of several mutations remains unresolved due to the conflicting reports on their frequencies in populations of healthy individuals. Here, we have developed a highly sensitive, real-time allelic discrimination assay enabling detection of the Y831C mutation in the POLG1 gene. The Y831C mutation is present in the Polish population at a frequency of 2.25%. The new assay is well suited to both extensive population studies and molecular diagnostics of POLG1.

Mitochondrial DNA diversity in the Polish Roma

Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment-length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*-lineage belongs to the Indian-specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261-16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224-16234-16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations.

Low variability of the POLG (CAG)n repeat in north Eurasian populations

We investigated the frequency of different repeat-length alleles of the trinucleotide CAG microsatellite repeat in the coding sequence of the nuclear gene for the catalytic subunit of mitochondrial DNA polymerase gamma (POLG) in 12 ethnic groups from northern Eurasia. The population sample consisted of 1,330 individuals from 3 large geographic areas: Europe, Southwest Asia, and Siberia/East Asia. We found that the 10-repeat allele of the POLG gene is the most frequent in all analyzed populations, with a frequency of 88-96%. The heterozygosity level ranges from 22% in Europe to 13.6% in Southwest Asia with the lowest value of 7.4% in Siberia/East Asia. The present study provides evidence of clinal distribution of POLG gene heterozygosity in North Eurasian populations. In general, we found an extremely low variability of the trinucleotide CAG microsatellite repeat, suggesting that purifying selection acts against deleterious alleles, although low mutability of the repeated region cannot be ruled out.

Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius

Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.

Optimization of the Y831C mutation detection in human DNA polymerase gamma by allelic discrimination assay

Many well-defined mutations in the gene for the catalytic subunit of polymerase gamma (POLG1) have been found to be associated with disease, whereas the status of several mutations remains unresolved due to the conflicting reports on their frequencies in populations of healthy individuals. Here, we have developed a highly sensitive, real-time allelic discrimination assay enabling detection of the Y831C mutation in the POLG1 gene. The Y831C mutation is present in the Polish population at a frequency of 2.25%. The new assay is well suited to both extensive population studies and molecular diagnostics of POLG1.

Genetic variation of 15 STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820, D16S539, D2S1338, D8S1179, D21S11, D18S51, and D19S433) in populations of north and central Poland

Allele frequencies for 15 short tandem repeats (STRs) included in AmpFlSTR Profiler and AmpFlSTR SGM Plus kits were obtained from populations of Pomorze Gdanskie, Wielkopolska, Kujawy, Pomorze Zachodnie, Mazury and Mazowsze regions of Poland.

[Restriction polymorphism of mitochondrial DNA in Koreans and Mongolians]

Using the data on mitochondrial DNA (mtDNA) restriction polymorphism, the gene pools of Koreans (N = 164) and Mongolians (N = 48) were characterized. It was demonstrated that the gene pools were represented by the common set of mtDNA haplogroups of East Asian origin (M*, M7, M8a, M10, C, D4, G*, G2, A, B*, B5, F1, and N*). In addition to this set, mtDNA haplogroups D5 and Y were identified in Koreans while Mongolians possessed haplogroup Z. Only in Mongolians, a European component with the frequency of 10.4% and represented by the mtDNA types belonging to haplogroups K, U4, and N1, was identified. Phylogenetic and statistical analyses of the data on mtDNA variation in the populations of South Siberia, Central, and East Asia suggested the existence of interpopulation differentiation within these regions, the main role in which was played by the geographical and linguistic factors. Analysis of the pairwise F(ST) distances demonstrated close genetic similarity of Koreans to Northern Chinese, which in turn, were clearly different from Southern Chinese populations. Mongolians occupied an intermediate position between the ethnic groups of South Siberia and Central/East Asia.

Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia

It has been often stated that the overall pattern of human maternal lineages in Europe is largely uniform. Yet this uniformity may also result from an insufficient depth and width of the phylogenetic analysis, in particular of the predominant western Eurasian haplogroup (Hg) H that comprises nearly a half of the European mitochondrial DNA (mtDNA) pool. Making use of the coding sequence information from 267 mtDNA Hg H sequences, we have analyzed 830 mtDNA genomes, from 11 European, Near and Middle Eastern, Central Asian, and Altaian populations. In addition to the seven previously specified subhaplogroups, we define fifteen novel subclades of Hg H present in the extant human populations of western Eurasia. The refinement of the phylogenetic resolution has allowed us to resolve a large number of homoplasies in phylogenetic trees of Hg H based on the first hypervariable segment (HVS-I) of mtDNA. As many as 50 out of 125 polymorphic positions in HVS-I were found to be mutated in more than one subcluster of Hg H. The phylogeographic analysis revealed that sub-Hgs H1*, H1b, H1f, H2a, H3, H6a, H6b, and H8 demonstrate distinct phylogeographic patterns. The monophyletic subhaplogroups of Hg H provide means for further progress in the understanding of the (pre)historic movements of women in Eurasia and for the understanding of the present-day genetic diversity of western Eurasians in general.

Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia

It has been often stated that the overall pattern of human maternal lineages in Europe is largely uniform. Yet this uniformity may also result from an insufficient depth and width of the phylogenetic analysis, in particular of the predominant western Eurasian haplogroup (Hg) H that comprises nearly a half of the European mitochondrial DNA (mtDNA) pool. Making use of the coding sequence information from 267 mtDNA Hg H sequences, we have analyzed 830 mtDNA genomes, from 11 European, Near and Middle Eastern, Central Asian, and Altaian populations. In addition to the seven previously specified subhaplogroups, we define fifteen novel subclades of Hg H present in the extant human populations of western Eurasia. The refinement of the phylogenetic resolution has allowed us to resolve a large number of homoplasies in phylogenetic trees of Hg H based on the first hypervariable segment (HVS-I) of mtDNA. As many as 50 out of 125 polymorphic positions in HVS-I were found to be mutated in more than one subcluster of Hg H. The phylogeographic analysis revealed that sub-Hgs H1*, H1b, H1f, H2a, H3, H6a, H6b, and H8 demonstrate distinct phylogeographic patterns. The monophyletic subhaplogroups of Hg H provide means for further progress in the understanding of the (pre)historic movements of women in Eurasia and for the understanding of the present-day genetic diversity of western Eurasians in general.

[Mitochondrial DNA variation in two Russian populations from Novgorod oblast]

Mitochondrial DNA (mtDNA) polymorphism was examined in two Russian populations of Novgorod oblast, from the city of Velikii Novgorod (n = 81), and the settlement of Volot (n = 79). This analysis showed that the mitochondrial gene pool of Russians examined was represented by the mtDNA types belonging to 20 haplogroups and subhaplogroups distributed predominantly among the European populations. Haplogroups typical of the indigenous populations of Asia were found in the population sample from Velikii Novgorod with the average frequency of 3.7% (haplogroups A, Z, and D5), and with the frequency of 6.3% (haplogroups Z, D, and M*) in the Volot population. It was demonstrated that the frequency of the mitochondrial lineages combination, D5, Z, U5b-16144, and U8, typical of the Finnish-speaking populations of Northeastern Europe, was somewhat higher in the urban population (7.4%) compared to rural one (3.8%). The problem of genetic differentiation of Russians from Eastern Europe inferred from mtDNA data, is discussed.

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

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

Mitochondrial DNA variability in Bosnians and Slovenians

Mitochondrial DNA variability in two Slavonic-speaking populations of the northwestern Balkan peninsula, Bosnians (N = 144) and Slovenians (N = 104), was studied by hypervariable segments I and II (HVS I and II) sequencing and restriction fragment-length polymorphism (RFLP) analysis of the mtDNA coding region. The majority of the mtDNA detected in Southern Slavonic populations falls into the common West Eurasian mitochondrial haplogroups (e.g., H, pre-V, J, T, U, K, I, W, and X). About 2% of the Bosnian mtDNAs encompass East Eurasian and African lineages (e.g., M and L1b, respectively). The distribution of mtDNA subclusters in Bosnians, Slovenians and the neighbouring European populations reveals that the common genetic substratum characteristic for Central and Eastern European populations (such as Germans, Poles, Russians and Finns) penetrates also South European territories as far as the Western Balkans. However, the observed differentiation between Bosnian and Slovenian mtDNAs suggests that at least two different migration waves of the Slavs may have reached the Balkans in the early Middle Ages.

Diversity of mitochondrial DNA lineages in South Siberia

To investigate the origin and evolution of aboriginal populations of South Siberia, a comprehensive mitochondrial DNA (mtDNA) analysis (HVR1 sequencing combined with RFLP typing) of 480 individuals, representing seven Altaic-speaking populations (Altaians, Khakassians, Buryats, Sojots, Tuvinians, Todjins and Tofalars), was performed. Additionally, HVR2 sequence information was obtained for 110 Altaians, providing, in particular, some novel details of the East Asian mtDNA phylogeny. The total sample revealed 81% East Asian (M*, M7, M8, M9, M10, C, D, G, Z, A, B, F, N9a, Y) and 17% West Eurasian (H, U, J, T, I, N1a, X) matrilineal genetic contribution, but with regional differences within South Siberia. The highest influx of West Eurasian mtDNAs was observed in populations from the East Sayan and Altai regions (from 12.5% to 34.5%), whereas in populations from the Baikal region this contribution was markedly lower (less than 10%). The considerable substructure within South Siberian haplogroups B, F, and G, together with the high degree of haplogroup C and D diversity revealed there, allows us to conclude that South Siberians carry the genetic imprint of early-colonization phase of Eurasia. Statistical analyses revealed that South Siberian populations contain high levels of mtDNA diversity and high heterogeneity of mtDNA sequences among populations (Fst = 5.05%) that might be due to geography but not due to language and anthropological features.

[Mitochondrial DNA variation in Russian populations of Stavropol krai, Orel and Saratov oblasts]

Mitochondrial DNA (mtDNA) polymorphism was examined in three Russian populations from the European part of Russia (Stavropol krai, Orel oblast, and Saratov oblast). This analysis showed that mitochondrial gene pool of Russians was represented by the mtDNA types belonging to haplogroups H, V, HV*, J, T, U, K, I, W, and X. A mongoloid admixture (1.5%) was revealed in the form of mtDNA types of macrohaplogroup M. Comparative analysis of the mtDNA haplogroup frequency distribution patterns in six Russian populations from the European part of Russia indicated the absence of substantial genetic differences between them. However, in Russian populations from the southern and central regions the frequency of haplogroup V (average frequency 8%) was higher than in the populations from more northern regions. Based on the data on mtDNA HVS1 sequence variation, it was shown that the diversity of haplogroup V in Russians (h = 0.72) corresponded to the highest h values observed in Europe. The reasons for genetic differentiation of the Russian population (historical, ecological, and adaptive) are discussed.

[Molecular genetic differentiation of ethnic populations in Southern and Eastern Siberia based on mitochondrial DNA polymorphism]

Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the ethnic groups inhabiting South and East Siberia, including Altaians, Buryats, Tuvinians, Todjins, Tofalars, Yakuts, and Evenks were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E/G, G, A, B, and F) and Caucasoid (H, HV, I, J, K, T, U, and X) mtDNA lineages. All the populations studied carried a marked Mongoloid component, maximum frequency of which was observed in Evenks (92.4%) and Buryats (90.1%). Maximum frequencies of Caucasoid mtDNA lineages were detected in Tofalars (20.7%) and Yakuts (14.5%). Statistically significant interpopulation differences regarding the frequencies of mtDNA haplogroups were observed between all populations examined, excluding the pairs of Evenks-Yakuts, Evenks-Tuvinians, and Tuvinians-Todjins. Differentiation of the ethnic groups inhabiting South and East Siberia, as well as Central and Middle Asia, is discussed based on genetic, linguistic, and anthropological data.

[Origin of caucasoid-specific mitochondrial DNA lineages in the ethnic populations of the Altai-Sayan region]

The data on sequence variation in the first hypervariable segment (HVSI) of human mitochondrial DNA (mtDNA) representing Caucasoid mtDNA lineages in the gene pools of Altaians and Khakassians are presented. Identification of the subgroups of Caucasoid mtDNA lineages found in the gene pools of the ethnic populations of the Altai-Sayan region and the adjacent territories, Altaians, Khakassians, Tuvinians, Buryats, and Yakuts was carried out. All Caucasoid mtDNA lineages belonged to groups H, HV1, J*, J1, J1b1, T1, T4, U1a, U2, U3, U4, U5a1, I, X and N1a. Taking into consideration possible contribution of southern Caucasoid and eastern European components to the formation of the anthropological type of Altai-Sayan ethnic populations, distribution of the revealed Caucasoid mtDNA lineages among the ethnic populations of the Central Asia, Western Asia, Caucasus, and Eastern Europe was examined. The applied approach permitted identification of 60% of mtDNA types the majority of which had southern Caucasoid origin. Less than 10% of mtDNA types were of eastern European origin. The gene pools of Altaians and Khakassians displayed the presence of autochthonous components represented by mtDNA types from subgroups U2 and U4.

Mitochondrial DNA variability in Poles and Russians

Mitochondrial DNA (mtDNA) sequence variation was examined in Poles (from the Pomerania-Kujawy region; n = 436) and Russians (from three different regions of the European part of Russia; n = 201), for which the two hypervariable segments (HVS I and HVS II) and haplogroup-specific coding region sites were analyzed. The use of mtDNA coding region RFLP analysis made it possible to distinguish parallel mutations that occurred at particular sites in the HVS I and II regions during mtDNA evolution. In total, parallel mutations were identified at 73 nucleotide sites in HVS I (17.8%) and 31 sites in HVS II (7.73%). The classification of mitochondrial haplotypes revealed the presence of all major European haplogroups, which were characterized by similar patterns of distribution in Poles and Russians. An analysis of the distribution of the control region haplotypes did not reveal any specific combinations of unique mtDNA haplotypes and their subclusters that clearly distinguish both Poles and Russians from the neighbouring European populations. The only exception is a novel subcluster U4a within subhaplogroup U4, defined by a diagnostic mutation at nucleotide position 310 in HVS II. This subcluster was found in common predominantly between Poles and Russians (at a frequency of 2.3% and 2.0%, respectively) and may therefore have a central-eastern European origin.

Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region

Analysis of mutations in mitochondrial DNA is an important issue in population and evolutionary genetics. To study spontaneous base substitutions in human mitochondrial DNA we reconstructed the mutational spectra of the hypervariable segments I and II (HVS I and II) using published data on polymorphisms from various human populations. An excess of pyrimidine transitions was found both in HVS I and II regions. By means of classification analysis numerous mutational hotspots were revealed in these spectra. Context analysis of hotspots revealed a complex influence of neighboring bases on mutagenesis in the HVS I region. Further statistical analysis suggested that a transient misalignment dislocation mutagenesis operating in monotonous runs of nucleotides play an important role for generating base substitutions in mitochondrial DNA and define context properties of mtDNA. Our results suggest that dislocation mutagenesis in HVS I and II is a fingerprint of errors produced by DNA polymerase gamma in the course of human mitochondrial DNA replication

[Mitochondrial DNA polymorphism in populations of the Caspian region and southeastern Europe]

Mitochondrial DNA (mtDNA) restriction polymorphism was examined in Turkmens, Eastern Iranians, and Ukrainians. The gene pools of all populations studied were characterized by the presence of European mtDNA lineages. Mongoloid component observed in Turkmen and Iranian populations with the frequencies of about 20% was represented by groups C, D, and E/G in Turkmens, and by M*, D, A, and B in Iranians. The relative positions of the populations studied, of populations from the Caucasus, Western Iran, and Russian populations from the Krasnodar krai and Belgorod oblast in the space of principal components revealed a geographically specific pattern of the population clustering. The data on mtDNA polymorphism indicated pronounced differentiation of Eastern and Western Iranians. The latter were characterized by a mtDNA group composition similar to that in Eastern Slavs. The historical role of the Caspian populations in the formation of the population of Southeastern Europe is discussed.