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.     

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 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.     

Mitochondrial DNA variability in Russians and Ukrainians: Implication to the origin of the Eastern Slavs

In order to investigate the origin of the Eastern Slavs, mitochondrial DNA (mtDNA) sequence variation was examined in Russians and Ukrainians by hypervariable segment I (HVS I) sequencing and restriction analysis of the haplogroup-specific sites. No significant differences were found for Russians and Ukrainians when compared to other Europeans – in fact, they fall within the range of gene diversity seen throughout Europe and exhibit the unimodal pattern of pairwise sequence differences. Moreover, HVS I sequences in the Russians and Ukrainians are similar or identical to those found in eastern and western European populations. Despite the small genetic distances between Europeans, phylogenetic analysis reveals a considerable heterogeneity of Eastern Slavonic populations – they do not cluster together onto a phylogenetic tree. Analysis of distribution of rare HVS I types shared between populations of Eastern Slavs and other West Eurasians has shown that Russians share rare haplotypes mainly with Germans and Finno–Ugric populations. Of these, subhaplogroup H1 sequence types, which are defined by different combinations of nucleotides 16192T, 16294T, 16304C, 16311C and 16320T, are found predominantly in common between Russians and German-speaking populations. The data obtained allow us to conclude that the Slavonic migrations in early Middle Ages from their putative homeland in central Europe to the east of Europe were accompanied mostly by the same mtDNA types characteristic for the pre-Slavonic populations of eastern Europe.     

Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans

The mitochondrial genomes of haplotypes of the Irish potato famine pathogen, Phytophthora infestans, were sequenced. The genome sizes were 37,922, 39,870 and 39,840 bp for the type Ia, IIa and IIb mitochondrial DNA (mtDNA) haplotypes, respectively. The mitochondrial genome size for the type Ib haplotype, previously sequenced by others, was 37,957 bp. More than 90% of the genome contained coding regions. The GC content was 22.3%. A total of 18 genes involved in electron transport, 2 RNA-encoding genes, 16 ribosomal protein genes and 25 transfer RNA genes were coded on both strands with a conserved arrangement among the haplotypes. The type I haplotypes contained six unique open reading frames (ORFs) of unknown function while the type II haplotypes contained 13 ORFs of unknown function. Polymorphisms were observed in both coding and non-coding regions although the highest variation was in non-coding regions. The type I haplotypes (Ia and Ib) differed by only 14 polymorphic sites, whereas the type II haplotypes (IIa and IIb) differed by 50 polymorphic sites. The largest number (152) of polymorphic sites was found between the type IIb and Ia haplotypes. A large spacer flanked by the genes coding for tRNA-Tyr (trnY) and the small subunit RNA (rns) contained the largest number of polymorphic sites and corresponds to the region where a large indel that differentiates type II from type I haplotypes is located. The size of this region was 785, 2,666 and 2,670 bp in type Ia, IIa and IIb haplotypes, respectively. Among the four haplotypes, 81 mutations were identified. Phylogenetic and coalescent analysis revealed that although the type I and II haplotypes shared a common ancestor, they clearly formed two independent lineages that evolved independently. The type II haplotypes diverged earlier than the type I haplotypes. Thus our data do not support the previous hypothesis that the type II lineages evolved from the type I lineages. The type I haplotypes diverged more recently and the mutations associated with the evolution of the Ia and Ib types were identified. Electronic Supplementary Material Supplementary material is available for this article at     

Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs

To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.European Journal of Human Genetics (2008) 16, 1091-1096; doi:10.1038/ejhg.2008.70; published online 9 April 2008.     

Mutagenesis by Transient Misalignment in the Human Mitochondrial DNA Control Region

To study spontaneous base substitutions in human mitochondrial DNA (mtDNA), we reconstructed the mutation spectra of the hypervariable segments I and II (HVS I and II) using published data on polymorphisms from various human populations. Classification analysis revealed numerous mutation hotspots in HVS I and II mutation spectra. Statistical analysis suggested that strand dislocation mutagenesis, operating in monotonous runs of nucleotides, plays an important role in generating base substitutions in the mtDNA control region. The frequency of mutations compatible with the primer strand dislocation in the HVS I region was almost twice as high as that for template strand dislocation. Frequencies of mutations compatible with the primer and template strand dislocation models are almost equal in the HVS II region. Further analysis of strand dislocation models suggested that an excess of pyrimidine transitions in mutation spectra, reconstructed on the basis of the L‐strand sequence, is caused by an excess of both L‐strand pyrimidine transitions and H‐strand purine transitions. In general, no significant bias toward parent H‐strand‐specific dislocation mutagenesis was found in the HVS I and II regions.     

河北汉族群体mtDNA HV1、HV2重叠片段及编码区8430-8673nt序列多态性

目的了解河北汉族群体线粒体DNA(mitochondrial DNA，mtDNA)HV1、HV2区重叠片段及编码区8430-8673nt的序列多态性。方法采用聚合酶链反应-单链构象多态性结合测序方法对100名河北汉族个体进行单倍型分布调查。结果在河北汉族100名健康无关个体中，共分出91种单倍型。遗传变异度为0．9985．耦合概率为0．0115。测序结果与Anderson序列比较，共检测出65个变异位点，44个与MITOMAP收录的基因突变相同，9个与所收录的不同，12个未见收录。结论线粒体DNA在河北汉族群体中有较好的多态性分布，是法医学个人识别和母系亲属认定良好的遗传标记，为mtDNA在河北法医学鉴定提供了基础数据。     

A Reassessment of Genetic Diversity in Icelanders: Strong Evidence from Multiple Loci for Relative Homogeneity Caused by Genetic Drift

There has been some controversy in the literature concerning whether Icelanders are genetically homogenous or heterogeneous relative to other European populations. We reassess this question in the light of large data sets spanning 83 autosomal SNP loci, 14 serogenetic loci, 6622 Y‐chromosomes and 3214 sequences from mtDNA hypervariable segments 1 and 2 (HVS1 and HVS2). Our results strongly support the hypothesis that genetic drift, with a consequent loss of variation, has had a greater impact on Icelanders than most other Europeans. We also analyse 7245 HVS1 sequences from 25 European populations. In line with other studies, we observe a deficit of rare HVS1 haplotypes and an excess of intermediate frequency haplotypes in Icelanders compared to most European populations, with some measures of genetic diversity indicating relative heterogeneity and others indicating relative homogeneity of Icelanders. Simulations indicate that genetic drift, and not admixture (as proposed by Árnason, 2003 ) is the most likely cause of the atypical Icelandic HVS1 frequency spectrum. These simulations reveal that gene diversity (heterozygosity) and mean pairwise differences are largely insensitive to events in recent population history, while statistics based on the number of haplotypes or segregating sites are much more sensitive. Overall, our analyses strongly indicate that the Icelandic gene pool is less heterogeneous than those of most other European populations.     

广西仫佬族线粒体DNA高变Ⅰ区多态性分析

目的 探讨广西仫佬族人群线粒体DNA高变Ⅰ区的多态性特征,了解仫佬族群体的母系遗传结构。方法 收集91例仫佬族无关男性个体的外周血样本,目标序列用引物L15947和R16488进行PCR扩增,用ABI 3730测序仪正反向测序;计算多态性位点、核苷酸多态性、平均配对差异
数目等多态性指标,以及仫佬族与各民族之间的遗传距离,ME法构建遗传进化树。结果 与修正后的剑桥标准序列（rCRS）比对,91例样本的线粒体高变Ⅰ区序列共界定了74种单倍型,核苷酸多态性为0.0188±0.010,平均核苷酸差异为6.618±3.154;遗传距离显示仫佬族与南方各少数
民族及南方汉族的亲缘关系较近,与北方汉族的亲缘关系较远,进化树中仫佬族与南方少数民族聚为一类。结论 仫佬族在母系遗传上属于典型的南方侗傣族群,可能经历过群体扩张或选择效应;高变Ⅰ区序列具有较高的多态性,可用于法医个体识别、民族起源等方面的研究。     

Mitochondrial DNA mutations in Leigh syndrome and their phylogenetic implications

Of 100 patients with the clinical diagnosis of Leigh syndrome, 21 were found to have specific enzyme defects: 15 involving cytochrome c oxidase (COX); 4, pyruvate dehydrogenase complex (PDHC); one, complex I (reduced nicotinamide adenine dinucleotide [NADH]-coenzyme Q reductase) and one, complex II (succinate-ubiquinone reductase) deficiencies. In addition to the most common form of COX deficiency, mtDNA mutations in the adenosine triphosphatase (ATPase) 6 coding region were also commonly seen. Eighteen patients (18%) had mtDNA mutations at nucleotide position (np) 8993 or 9176. The mutated DNAs were present in a heteroplasmic state, comprising more than 90% of the DNA in muscle and/or blood samples from all patients. Patients with the T-to-G mutation at np 8993 usually had early onset of the disease with rapid progression, showing the typical clinical features of Leigh syndrome. On the other hand, those with the T-to-C 8993 mutation showed a milder and more chronic course. Patients with the mutation at np 9176 showed variable courses. Phylogenetic analysis of mtDNA D-loop sequences for the patients with the ATPase 6 mutations and normal Japanese subjects revealed that a T-to-G/C mutation at np 8993 and a T-to-C mutation at np 9176 occurred many times independently in the Japanese population. Received: September 21, 1999 / Accepted: November 24, 1999     

Ancient DNA and Family Relationships in a Pompeian House

Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related.     

Sequence analysis of the HLA-DRß and HLA-DQß loci from three Pemphigus vulgaris patients

Pemphigus vulgaris (PV) is an autoimmune dermatologic disease that has been associated with the HLA serotypes DR4 and DRw6. In studying this association at the level of coding sequence polymorphism, we have determined the nucleotide sequences of the second variable exons from the HLA-DRß and DQß loci from three PV patients with the HLA serotypes DR414, DR415, and DR415. These exons were enzymatically amplified by polymerase chain reaction (PCR) and cloned directly into an M13 vector for DNA sequencing. Analyses of amino acid sequences translated from the nucleotide sequence data show that all three patients contained a DR4 DRßI sequence associated with the Dw10 DR4 subtype specificity, a relatively rare subtype among U.S. Caucasian DR4 haplotypes. The DQß sequence from three of the four DR4 haplotypes was identical to the sequence (DQß3.2) found on 60–80% of control DR4 haplotypes. These observations suggest that the amino acid residues at position 68, 69, and 72 of the DRßI chain that distinguish Dw10 from the other DR4 subtypes may be involved in disease susceptibility.     

Mitochondrial DNA Portrait of Latvians: Towards the Understanding of the Genetic Structure of Baltic-Speaking Populations

Mitochondrial DNA (mtDNA) variation was investigated in a sample of 299 Latvians, a Baltic-speaking population from Eastern Europe. Sequencing of the first hypervariable segment (HVS-I) in combination with analysis of informative coding region markers revealed that the vast majority of observed mtDNAs belong to haplogroups (hgs) common to most European populations. Analysis of the spatial distribution of mtDNA haplotypes found in Latvians, as well as in Baltic-speaking populations in general, revealed that they share haplotypes with all neighbouring populations irrespective of their linguistic affiliation. Hence, the results of our mtDNA analysis show that the previously described sharp difference between the Y-chromosomal hg N3 distribution in the paternally inherited gene pool of Baltic-speaking populations and of other European Indo-European speakers does not have a corresponding maternal counterpart.     

中国成都汉族群体线粒体DNA控制区序列多态性研究

目的　检测并分析中国成都汉族群体线粒体 DNA控制区多态性 ,为法医学应用提供基础数据。方法　应用 PCR扩增和直接测序方法检测 10 0个不相关中国成都汉族群体线粒体 DNA控制区中高变区 、 的序列多态性。结果　检测高变区 中 4 0 4个核苷酸和高变区 中 379个核苷酸的序列 ,在 区和 区分别检测到 92和 5 0个变异点 ,与 Anderson标准序列比较 ,共检测到 97种单倍型。偶合概率分别为1.84 %与 1.94 % ,两者合并后为 1.18%。结论　提示线粒体 DNA控制区 DNA序列多态性在法医学领域中具有较高的应用价值。     

Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

We have analysed the matrilineal genetic composition of three self‐reported ethnic groups from São Tomé e Príncipe (Gulf of Guinea), an African archipelago whose settlement begun in the late fifteenth century. Sequence data from the hypervariable segments I (HVS‐I) and II (HVS‐II) were obtained for 30 Angolares, 35 Forros and 38 Tongas. The repertory of mtDNA lineages in São Tomé e Príncipe denoted a fully African maternal pool, primarily arisen from a Central/Southwestern substratum. The absence of any lineages of putative European descent means that the European impact at the mitochondrial pool was virtually nil. Angolares showed a clear reduction of mtDNA diversity and a slight genetic differentiation relative to Tongas or Forros, whereas the latter two groups did not present any signs of genetic boundaries between each other. The data obtained here reinforce the depiction of genetic substructuring in São Tomé e Príncipe previously derived from Y‐chromosome STRs. In addition, the crossing of mtDNA and Y‐STR information led to the inference that the female mediated gene flow within the archipelago was less restricted than the male, a pattern that could be framed in the cultural traditions and socio‐historical interactions among the groups.     

SNP profile within the human major histocompatibility complex reveals an extreme and interrupted level of nucleotide diversity

The human major histocompatibility complex (MHC) is characterized by polymorphic multicopy gene families, such as HLA and MIC (PERB11); duplications; insertions and deletions (indels); and uneven rates of recombination. Polymorphisms at the antigen recognition sites of the HLA class I and II genes and at associated neutral sites have been attributed to balancing selection and a hitchhiking effect, respectively. We, and others, have previously shown that nucleotide diversity between MHC haplotypes at non-HLA sites is unusually high (>10%) and up to several times greater than elsewhere in the genome (0.08%-0.2%). We report here the most extensive analysis of nucleotide diversity within a continuous sequence in the genome. We constructed a single nucleotide polymorphism (SNP) profile that reveals a pattern of extreme but interrupted levels of nucleotide diversity by comparing a continuous sequence within haplotypes in three genomic subregions of the MHC. A comparison of several haplotypes within one of the genomic subregions containing the HLA-B and -C loci suggests that positive selection is operating over the whole subgenomic region, including HLA and non-HLA genes. [The sequence data for the multiple haplotype comparisons within the class I region have been submitted to DDBJ/EMBL/GenBank under accession nos. AF029061, AF029062, and AB031005-AB031010. Additional sequence data have been submitted to the DDBJ data library under accession nos. AB031005-AB03101 and AF029061-AF029062.]     

Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome

The principal limitation in forensic mitochondrial DNA (mtDNA) testing is the low power of discrimination that is obtained when common "mtDNA types" are involved in a case. Currently, an "mtDNA type" refers to the sequence within hypervariable regions I and II (HV1/HV2) of the control region, approximately 610 bp. In Caucasians, the most common HV1/HV2 type is found in approximately 7% of the population and there are 12 additional types found at greater than approximately 0.5% (ignoring HV2 C-stretch polymorphism). We are performing large scale sequencing of the entire mtDNA genome (mtGenome), approximately 16,569 bp, of individuals who have common HV1/HV2 types. Of 31 individuals with the most common HV1/HV2 type, only 3 still match after mtGenome sequencing. Similar high discrimination is seen in other common HV1/HV2 types. The sites that discriminate the various common HV1/HV2 types are generally not those that are known to vary widely in more diverse population samples. This indicates that complete mtGenome sequencing of selected HV1/HV2 types may stand as the best way for identifying maximally useful single nucleotide polymorphism sites outside of the control region. Our strategy for identifying SNP sites is useful in resolving U.S. Caucasian, Hispanic, and African American mtDNAs is discussed. We also discuss the development of homogeneous fluorogenic polymerase chain reaction assays that target phenotypically neutral sites for practical use in casework.     

Mitochondrial DNA variation in an isolated area of Central Italy

Abstract

Background: The genetic variation in Italy is the result of ancient population movement, demographic change, and geography. The increasing possibility of studying the maternal genetic structure of selected Italian population samples at a high level of phylogenetic resolution provides a particularly useful model to assess the presence of genetic traces of the ancient people who lived in Italy in pre-Roman times in present populations

Aim: In this study we reconstructed the genetic maternal history of Jenne and Vallepietra, two mountain communities in the Aniene Valley in the Simbruini Mountains near Rome. Both communities have been spared external invasion due to their geographic location, which very likely preserved the genetic pool of these autochthonous populations.

Subjects and methods: The study population (124 individuals from Jenne and Vallepietra) were investigated for D-loop mtDNA hypervariable segments I (HVS-I) and II (HVS-II) and for informative single nucleotide polymorphisms (SNPs) within the coding region. The detected haplotypes were then compared with those of other Italian, European and Mediterranean populations.

Results: The distribution of mtDNA diversity in Jenne and Vallepietra, although similar to that found in other European populations, shows a basic variability and the typical signs of a certain degree of isolation between them and other populations analysed; in particular, the Vallepietra sample showed an unusually high frequency (71.3%) of mtDNA haplogroups which are typical of Near Eastern and South-Western Asian populations.

Conclusion: The high degree of differentiation between the two villages is intriguing, since it suggests a low level of gene flow between them, despite their close geographic proximity and shared linguistic features. The degree of their genetic isolation, also in comparison to other Italian, European and Mediterranean populations, is consistent with isolation among geographically separated populations.     

Multiplex mutagenically separated polymerase chain reaction assay for rapid detection of human mitochondrial DNA variations in coding area

Recently, it has been recognized that information in the mitochondrial DNA (mtDNA) coding region can provide additional forensic discrimination with respect to the standard typing of the D-loop region, increasing the forensic power of mtDNA testing, which is sometimes rather limited. In the present study, we simultaneously typed ten single nucleotide polymorphisms (SNP) in the coding region by use of mutagenically separated polymerase chain reaction (MS-PCR) in the Chinese Chengdu population. This technique, in which different-size allele-specific primers were used, specifically amplified both alleles of mtDNA in the same reaction. Subsequent gel electrophoresis showed ten of the allelic products of different loci. Using multiplex MS-PCR, 30 primers were added simultaneously into one reaction tube to identify ten SNPs. The mtDNA variations of 160 individuals from the Chinese Chengdu population were examined and classified into 18 haplotypes. The multiplex MS-PCR method is suitable for large-scale screening studies of mtDNA variability because it is both rapid and economical.