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.     

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= 0.742) corresponded to the highest h values observed in Europe. The reasons for genetic differentiation of the Russian population (historical, ecological, and adaptive) are discussed.     

Russian ethnic history inferred from mitochondrial DNA diversity

With the aim of gaining insight into the genetic history of the Russians, we have studied mitochondrial DNA diversity among a number of modern Russian populations. Polymorphisms in mtDNA markers (HVS-I and restriction sites of the coding region) of populations from 14 regions within present-day European Russia were investigated. Based on analysis of the mitochondrial gene pool geographic structure, we have identified three different elements in it and a vast "intermediate" zone between them. The analysis of the genetic distances from these elements to the European ethnic groups revealed the main causes of the Russian mitochondrial gene pool differentiation. The investigation of this pattern in historic perspective showed that the structure of the mitochondrial gene pool of the present-day Russians largely conforms to the tribal structure of the medieval Slavs who laid the foundation of modern Russians. Our results indicate that the formation of the genetic diversity currently observed among Russians can be traced to the second half of the first millennium A.D., the time of the colonization of the East European Plain by the Slavic tribes. Patterns of diversity are explained by both the impact of the native population of the East European Plain and by genetic differences among the early Slavs.     

Mitochondrial DNA Variation in Russian Populations of Krasnodar Krai,Belgorod, and Nizhni Novgorod Oblast

Mitochondrial DNA (mtDNA) polymorphism was examined in three Russian populations from the European part of Russia (Krasnodar Krai, Belgorod, and Nizhnii Novgorod oblast). This analysis revealed that mitochondrial gene pool of Russians was represented by the mtDNA types belonging to groups H, V, pre-V, HV*, J, T, U, K, I, W, and X. The major groups (average frequency over 5%) were H, V, J, T, and U. Mongoloid admixture in Russians, constituting only 1%, was revealed in the form of mtDNA types of groups C and D. Analysis of the frequency distribution of the mtDNA type groups indicated the absence of genetic differences between the Russian populations studied.     

Variability in mitochondrial DNA in Russian inhabitants from Krasnodar Krai, Belgorod and the lower Novgorod region]

Mitochondrial DNA (mtDNA) polymorphism was examined in three Russian populations from the European part of Russia (Krasnodar Krai, Belgorod, and Nizhnii Novgorod oblast). This analysis revealed that mitochondrial gene pool of Russians was represented by the mtDNA types belonging to groups H, V, pre-V, HV*, J, T, U, K, I, W, and X. The major groups (average frequency over 5%) were H, V, J, T, and U. Mongoloid admixture in Russians, constituting only 1%, was revealed in the form of mtDNA types of groups C and D. Analysis of the frequency distribution of the mtDNA type groups indicated the absence of genetic differences between the Russian populations studied.     

A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.     

Mitochondrial DNA polymorphism in Russian population form five oblasts of the European part of Russia

New data on mitochondrial DNA polymorphism among Russian population from five oblasts, located within the main ethnic area of Russians, specifically, Ryazan' oblast, Ivanovo oblast, Vologda oblast, Orel oblast, and Tambov oblast (N = 177) are presented. RFLP analysis of the mtDNA coding region showed that most of the mtDNA diversity in the populations examined could be described by main European haplogroups H, U, T, J, K, I, V, W, and X. Haplogroup frequency distribution patterns in the populations of interest were analyzed in comparison with the European and Uralic populations. Based on the haplogroup frequencies, the indices of intraethnic population diversity, Wright's F(st) statistics, and the values of squared deviation from the mean, as well as genetic distances between Russians and European and Uralic populations were estimated. Analysis of these indices along with the anthropological data provided identification of a number of regional groups within the populations examined, which could either result from the interaction of ancient Slavs with different non-Slavic tribes, or could be caused by the ethnic heterogeneity of the ancient Slavs themselves.     

Differentiation of mitochondrial DNA and Y chromosomes in Russian populations

The genetic composition of the Russian population was investigated by analyzing both mitochondrial DNA (mtDNA) and Y-chromosome loci polymorphisms that allow for the different components of a population gene pool to be studied, depending on the mode of DNA marker inheritance. mtDNA sequence variation was examined by using hypervariable segment I (HVSI) sequencing and restriction analysis of the haplogroup-specific sites in 325 individuals representing 5 Russian populations from the European part of Russia. The Y-chromosome variation was investigated in 338 individuals from 8 Russian populations (including 5 populations analyzed for mtDNA variation) using 12 binary markers. For both uniparental systems most of the observed haplogroups fell into major West Eurasian haplogroups (97.9% and 99.7% for mtDNA and Y-chromosome haplogroups, respectively). Multidimensional scaling analysis based on pairwise F(ST) values between mtDNA HVSI sequences in Russians compared to other European populations revealed a considerable heterogeneity of Russian populations; populations from the southern and western parts of Russia are separated from eastern and northern populations. Meanwhile, the multidimensional scaling analysis based on Y-chromosome haplogroup F(ST) values demonstrates that the Russian gene pool is close to central-eastern European populations, with a much higher similarity to the Baltic and Finno-Ugric male pools from northern European Russia. This discrepancy in the depth of penetration of mtDNA and Y-chromosome lineages characteristic for the most southwestern Russian populations into the east and north of eastern Europe appears to indicate that Russian colonization of the northeastern territories might have been accomplished mainly by males rather than by females.     

Genetic variation of mitochondrial DNA in Chinese populations of Pectinophora gossypiella (Lepidoptera: Gelechiidae)

The pink bollworm Pectinophora gossypiella is an invasive pest insect that has successfully established populations in many cotton growing regions around the world. In this study, the genetic diversity and population structure of Chinese populations of P. gossypiella were evaluated using mitochondrial DNA sequence data (COII and Nad4). For comparison, individuals of Pakistan and America were also sequenced at the same two mtDNA regions. Extremely low genetic variation was observed in the two mitochondrial regions among all populations examined. Most of the populations harbored only one to two haplotypes. Although the Nad4 region showed relatively high haplotype diversity and nucleotide variation, ranging from 0.363 to 0.591 and from 0.00078 to 0.00140, respectively, there were only three haplotypes observed in this region. COII and Nad4 haplotype networks shaved one or two common haplotype(s) forming the center of a star-shaped phylogeny. Pairwise tests showed that most of the populations were not significantly differentiated from each other. The Chinese populations were differentiated from the Pakistani and American populations in the Nad4 region. The low level of population genetic variation of P. gossypiella is attributed to invasion bottlenecks, which may have been subsequently strengthened by its nonmigratory biology and the mosaic pattern of agricultural activities.     

Mitochondrial DNA Polymorphism in Russian Population form Five Oblasts of the European Part of Russia

New data on mitochondrial DNA polymorphism among Russian population from five oblasts, located within the main ethnic area of Russians, specifically, Ryazan' oblast, Ivanovo oblast, Vologda oblast, Orel oblast, and Tambov oblast (N = 177) are presented. RFLP analysis of the mtDNA coding region showed that most of the mtDNA diversity in the populations examined could be described by main European haplogroups H, U, T, J, K, I, V, W, and X. Haplogroup frequency distribution patterns in the populations of interest were analyzed in comparison with the European and Uralic populations. Based on the haplogroup frequencies, the indices of intraethnic population diversity, Wright's F_st statistics, and the values of squared deviation from the mean, as well as genetic distances between Russians and European and Uralic populations were estimated. Analysis of these indices along with the anthropological data provided identification of a number of regional groups within the populations examined, which could either result from the interaction of ancient Slavs with different non-Slavic tribes, or could be caused by the ethnic heterogeneity of the ancient Slavs themselves.     

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 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.     

Polymorphism of hypervariable segment I of mitochondrial DNA in three ethnic groups of the Volga-Ural region

A population genetic study of the polymorphism in the first hypervariable segment (HVSI) of mitochondrial DNA control region was carried out for three ethnic populations of the Volga-Ural region, Bashkirs, Russians, and Komi-Permyaks. This analysis showed that most of the mtDNA HVSI haplotypes detected in the populations of Bashkirs, Russians and Komi-Permyaks contained the combinations of nucleotide substitutions detected earlier in Asian, European, and Finno-Ugric populations. These findings are consistent with historical, anthropological, and ethnographical data suggesting the presence of European and Mongoloid components of different geographical descent in the gene pool of the contemporary population of the Volga-Ural region. The data on the genetic structure and the phylogenetic relationships between populations of the Volga-Ural region based on modern molecular genetic methods of mitochondrial genome investigation would be a substantial addition to the already existing information for some other regions of Europe and Asia. These data would provide more complete examination of the development of interethnic diversity of mitochondrial gene pools of contemporary ethnic populations with the purpose of reconstructing the genetic demographic processes that accompanied peopling of the Middle Ural and Volga region.     

Polymorphism of Hypervariable Segment I of Mitochondrial DNA in Three Ethnic Populations from the Volga–Ural Region

A population genetic study of the polymorphism in the first hypervariable segment (HVSI) of mitochondrial DNA control region was carried out for three ethnic populations of the Volga–Ural region, Bashkirs, Russians, and Komi-Permyaks. This analysis showed that most of the mtDNA HVSI haplotypes detected in the populations of Bashkirs, Russians and Komi-Permyaks contained the combinations of nucleotide substitutions detected earlier in European, and, to a lesser extent, Asian. These findings are consistent with historical, anthropological, and ethnographical data suggesting the presence of European and Mongoloid components of different geographical descent in the gene pool of the contemporary population of the Volga–Ural region. The data on the genetic structure and the phylogenetic relationships between populations of the Volga– Ural region based on modern molecular genetic methods of mitochondrial genome investigation would be a substantial addition to the already existing information for some other regions of Europe and Asia. These data would provide more complete examination of the development of interethnic diversity of mitochondrial gene pools of contemporary ethnic populations with the purpose of reconstructing the genetic demographic processes that accompanied peopling of the Middle Ural and Volga region.     

光裸方格星虫野生与养殖群体线粒体控制区序列的遗传差异分析

基于线粒体控制区序列对光裸方格星虫（Sipunculus nudus Linnaeus,1766）的2个养殖群体（营盘YP、竹林ZL）和4个野生群体（防城港FC、钦州QZ、大冠沙DG和越南海防YN）的91个个体进行遗传差异分析,研究光裸方格星虫养殖和野生群体的遗传变异情况。结果显示:获得的514 bp DNA序列中,野生与养殖群体的多态性位点数分别为82和60,均显示出对AT的偏倚性。共定义85个单倍型,共享单倍型4个,其中共享单倍型Hap5为原始单倍型,营盘群体均为独享单倍型。各群体的单倍型多样性（H_d）相同,野生群体的平均核苷酸多样性（P_i）（0.01531）略高于养殖群体（0.01514）,6个群体的遗传多样性水平依次为YN > YP > QZ > FC > ZL > DG。各群体间的遗传分化并不显著（P>0.05）,光裸方格星虫的遗传变异主要来自群体内个体间（99.08%）,同时未发现明显的地理谱系结构。研究表明,光裸方格星虫野生群体的遗传多样性水平总体略高于养殖群体;滩涂底播养殖方式较池塘养殖更利于维持光裸方格星虫遗传多样性;各群体间不存在显著的遗传分化,养殖群体正逐渐积累遗传变异,但尚未足够以形成其独立的遗传结构。     

Mitochondrial DNA variation and population genetic structure of the northern redbelly dace (Phoxinus eos)

Two sections of the control region and the genes coding for NADH dehydrogenase sub-units 5 and 6 (ND-5/6) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-5/6 fragment was sequenced in from each end only. Additionally, the entire ND-5/6 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-5/6 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-5/6 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-5/6 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes.     

Molecular evolution and population genetics of Greater Caribbean green turtles (Chelonia mydas) as inferred from mitochondrial DNA control region sequences

The molecular evolution and population genetics of migratory green turtles (Chelonia mydas) in the Greater Caribbean were examined with mitochondrial DNA (mtDNA) control region I sequences. A total of 488 base positions (bp) per individual were aligned for 44 individuals from four nesting populations in Florida, Costa Rica, Aves Island (Venezuela), and Surinam. Twelve sequence polymorphisms were detected, representing ten transitions, one transversion, and one 10-bp repeat. Sequence analyses of within- and between-population diversity revealed a deep divergence between western and eastern Caribbean nesting colonies and an inverse relationship between reproductive female population size and mtDNA diversity. In small populations, genetic admixture was important to maintaining high diversity, whereas larger populations appear to have experienced historical bottlenecks or resulted from founder effects. Mitochondrial DNA sequences of the control region offer an order of magnitude greater resolution than restriction site data for addressing questions about mtDNA variation, both within and between populations of green turtles.     

Analysis of mitochondrial DNA in Bolivian llama,alpaca and vicuna populations: a contribution to the phylogeny of the South American camelids

The objectives of this work were to assess the mtDNA diversity of Bolivian South American camelid (SAC) populations and to shed light on the evolutionary relationships between the Bolivian camelids and other populations of SACs. We have analysed two different mtDNA regions: the complete coding region of the MT‐CYB gene and 513 bp of the D‐loop region. The populations sampled included Bolivian llamas, alpacas and vicunas, and Chilean guanacos. High levels of genetic diversity were observed in the studied populations. In general, MT‐CYB was more variable than D‐loop. On a species level, the vicunas showed the lowest genetic variability, followed by the guanacos, alpacas and llamas. Phylogenetic analyses performed by including additional available mtDNA sequences from the studied species confirmed the existence of the two monophyletic clades previously described by other authors for guanacos (G) and vicunas (V). Significant levels of mtDNA hybridization were found in the domestic species. Our sequence analyses revealed significant sequence divergence within clade G, and some of the Bolivian llamas grouped with the majority of the southern guanacos. This finding supports the existence of more than the one llama domestication centre in South America previously suggested on the basis of archaeozoological evidence. Additionally, analysis of D‐loop sequences revealed two new matrilineal lineages that are distinct from the previously reported G and V clades. The results presented here represent the first report on the population structure and genetic variability of Bolivian camelids and may help to elucidate the complex and dynamic domestication process of SAC populations.     

Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolation

Mitochondrial haplotype diversity in sympatric populations of Ohrid trout, Salmo letnica was investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mtDNA control region and ND1, ND3/4, ND5/6 segments. A 310 bp fragment at the 5' end, and a 340-572 bp fragment at the 3' end of the control region were sequenced from representatives of the populations studied. Based on pairwise comparison of the sequences, five new haplotypes were identified plus one identical with the brown trout Andalusian haplotype from the southern Iberian Peninsula. The combination of both RFLP and sequence data sets yielded a total of 10 composite haplotypes. A high degree of genetic subdivision between S. letnica typicus and S. letnica aestivalis populations was observed. The notion of a sympatric origin for the two morphs is discussed. Length variation of the mtDNA control region due to the presence of an 82 bp unit, tandemly repeated one to four times, in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA is reported. Further, we demonstrate that a single duplication of the approximately 82 bp repeat unit is a common element of the salmonid mitochondrial control region. The unique genetic structure of Ohrid trout represents a highly valuable genetic resource that deserves appropriate management and conservation.     

白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对白鱼(Anabarilius grahami)DNA进行PCR扩增,获得了白鱼线粒体DNA控制区基因全序列(930bp)。控制区T、C、A和G碱基组成为29.8%、22.5%、33.0%和14.7%。对照其他已报道的鱼类控制区结构,对白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列(CSB-F、CSB-D、CSB-1、CSB-2、CSB-3)。同时运用DNA分析软件对白鱼一个驯养种群(中国科学院昆明动物研究所珍稀鱼类繁育中心)及两个自然地理种群(江川县明星鱼洞、江川县牛摩村)进行了遗传多样性分析。结果显示:两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好。