Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela

New data were obtained on mitochondrial DNA (mtDNA) from Guahibo from Venezuela, a group so far not studied using molecular data. A population sample (n = 59) was analyzed for mtDNA variation in two control-region hypervariable segments (HV1 and HV2) by sequencing. The presence or absence of a 9-bp polymorphism in the COII/tRNA(Lys) region was studied by direct amplification and electrophoretic identification. Thirty-eight variable sites were detected in regions HV1 and HV2, defining 26 mtDNA lineages; 23.7% of these were present in a single individual. The 9-bp deletion was found in 3.39% of individuals. Nucleotide and haplotype diversities were relatively high compared with other New World populations. The identified sequence haplotypes were classified into four major haplogroups (A-D) according to previous studies, with high frequencies for A (47.46%) and C (49.15%), low frequency for B (3.39%), and an absence of D.     

Analysis of Human Mitochondrial DNA Polymorphisms in the Japanese Population

The highly polymorphic nature and high amplification efficiency of mitochondrial DNA (mtDNA) is valuable for the analysis of biological evidence in forensic casework, such as the identification of individuals and assignment of race/ethnicity. To be useful, a mtDNA polymorphism database for the Japanese population requires an understanding of the range of haplotype variation and phylogenies of mtDNA sequences. To extend current knowledge on the haplotypes in the Japanese population, this study defines new lineages and provides more detail about some of those previously described. We compared the hypervariable regions (HVRs) of 270 healthy, unrelated Japanese individuals and demonstrated 192 haplotypes. Combining HVR1 and HVR2, the genetic diversity was 0.9935, thus providing a high level of identification capability. Haplogroup status was defined for 160 individuals using HVR1, HVR2, and particular coding region polymorphisms; these individuals belonged to 94 haplotypes, four of which were new lineages. The complete mtDNA sequence was also determined from seven individuals.     

Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes.

A method for detecting sequence variation of hypervariable segments of the mtDNA control region was developed. The technique uses hybridization of sequence-specific oligonucleotide (SSO) probes to DNA sequences that have been amplified by PCR. The nucleotide sequences of the two hypervariable segments of the mtDNA control region from 52 individuals were determined; these sequences were then used to define nine regions suitable for SSO typing. A total of 23 SSO probes were used to detect sequence variants at these nine regions in 525 individuals from five ethnic groups (African, Asian, Caucasian, Japanese, and Mexican). The SSO typing revealed an enormous amount of variability, with 274 mtDNA types observed among these 525 individuals and with diversity values, for each population, exceeding .95. For each of the nine mtDNA regions significant differences in the frequencies of sequence variants were observed between these five populations. The mtDNA SSO-typing system was successfully applied to a case involving individual identification of skeletal remains; the probability of a random match was approximately 0.7%. The potential useful applications of this mtDNA SSO-typing system thus include the analysis of individual identity as well as population genetic studies.     

A sensitive denaturing gradient-Gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region

A population study of heteroplasmy in the hypervariable region 1 (HV1) portion of the human mtDNA control region was performed. Blood samples from 253 randomly chosen individuals were examined using a sensitive denaturing gradient-gel electrophoresis (DGGE) system. This method is capable of detecting heteroplasmic proportions as low as 1% and virtually all heteroplasmy where the minor component is > or = 5%. Heteroplasmy was observed in 35 individuals (13.8%; 95% confidence interval [CI] 9.6-18.0). Of these individuals, 33 were heteroplasmic at one nucleotide position, whereas 2 were heteroplasmic at two different positions (a condition known as "triplasmy"). Although heteroplasmy occurred at a total of 16 different positions throughout HV1, it was most frequently observed at positions 16093 (n=13) and 16129 (n=6). In addition, the majority of heteroplasmic variants occurred at low proportions and could not be detected by direct sequencing of PCR products. This study indicates that low-level heteroplasmy in HV1 is relatively common and that it occurs at a broad spectrum of sites. Our results corroborate those of other recent reports indicating that heteroplasmy in the control region is more common than was previously believed-a finding that is of potential importance to evolutionary studies and forensic applications that are based on mtDNA variation.     

DNA diversity in the studies of genetic distance among isolated human populations in bosnia

Different degrees of isolation found in various part of Bosnia and Herzegovina may be induced by various factors. Bjelasnica-Treskavica region, located around 40 kilometers southwest from Sarajevo — capital of Bosnia and Herzegovina, is highly specific in that way. We chose three isolated communities: Dejcici, Bobovica and Lukomir for the study of genetic structure of isolated human populations. Based on general data three relative degrees of isolation/openness among the villages have been presumed as follows: first (lower-Dejcici), second (middle — Bobovica) and third (higher — Lukomir) 15 short tandem repeat (STR) loci and hypervariable region of mtDNA were chosen as a markers for study of population structure. Microsatellite allele frequencies, and mtDNA molecular diversity of Heterozigosity and coefficient of gene differentiation across all observed STR loci were estimated. Also, gene and nucleotide diversity of observed mtDNA regions were obtained. Genetic distance between three populations was calculated using method of Reynolds et al. (1983). For analysis of interpopulation relationship based on polymorphism of HV I and HV II region, estimation of pairwise differences was used. results of this research showed consistence with initial hypothesis on divergence based on socio-cultural factors.     

Determination of polymorphism of the cytochrome b gene fragment of mitochondrial DNA of chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> (Walbaum) from the Ola River (northern Coast of the Sea of Okhotsk)

Sequencing of 395 bp long fragments of cytochrome b gene occupying the 15396–15790 bp positions of mtDNA, the data on the structure and variability of the studied region in chum salmon from the Ola River (northern coast of the Sea of Okhtosk) were obtained for the first time. Nine haplotype variants and four protein modifications were obtained. The medial net was built reflecting the variability and phylogenetic relationships of haplotypes in the gene pool of the studied population of the chum salmon from the Ola River. Comparative analysis of the published and original data showed that the Ola chum salmon differs from the Canadian salmon ninth genotypically (in structure of cytochrome b gene) and in the amino acid sequence of the studied site of the enzyme.     

The 9-bp deletion between the mitochondrial lysine tRNA and COII genes in tribal populations of India

A 9-base-pair (bp) deletion located between the lysine tRNA (MTTK) and COII (MTCOX*2) genes in the human mitochondrial genome is a valuable marker for tracing population relationships. Previous research has shown that the 9-bp deletion is associated with two major clusters of control region sequences; one occurs in sub-Saharan Africa, while the other is associated with Asian populations and populations of Asian origin. We surveyed 898 individuals from 16 tribal populations in India and found 6 individuals with the 9-bp deletion. Sequences of the first hypervariable segment (HV1) of the mtDNA control region from these 9-bp deletion-bearing mtDNAs were compared to those previously reported from Asian and African populations. Phylogenetic analysis indicates three distinct clusters of tribal Indian 9-bp deletion mtDNA types. One cluster, found in northeast India, includes southeast Asian and Indonesian mtDNA types. The remaining two clusters appear to have unique origins in southern India. These data provide further evidence of past migrations from Asia into the northeast corner of the Indian subcontinent.     

New haplotype of the complete mitochondrial genome of <Emphasis Type="Italic">Crocodylus siamensis</Emphasis> and its species-specific DNA markers: distinguishing <Emphasis Type="Italic">C. siamensis</Emphasis> from <Emphasis Type="Italic">C. porosus</Emphasis> in Thailand

Based on molecular phylogeny of available complete mitochondrial DNA (mtDNA) genome sequences reveals that Crocodylus siamensis and C. porosus are closely related species. Yet, the sequence divergence of their mtDNA showed only a few values under conspecific level. In this study, a new haplotype (haplotype2, EF581859) of the complete mtDNA genome of Siamese crocodile (C. siamensis) was determined. The genome organization, which appeared to be highly similar to haplotype1 (DQ353946) mtDNA genome of C. siamensis, was 16,814 bp in length. However, the sequence divergence between the two genomes differed by around 7–10 and 0.7–2.1% for the haplotype1 between C. siamensis and C. porosus (AJ810453). These results were consistent with the phylogenetic relationship among the three genomes, suggesting that C. siamensis haplotype1 mtDNA genome might be the hybrid or the intraspecific variation of C. porosus. On the other hand, our specimen was found to be a true C. siamensis. Simultaneously, the seven species-specific DNA markers designed based on the distinctive site between haplotype2 mtDNA sequences of C. siamensis and haplotype1 mtDNA sequence of C. siamensis–C. porosus were successfully used to distinguish C. siamensis from C. porosus. These effective markers could be used primarily for rapid and accurate species identification in population, ecology and conservation studies.     

Individual human hair mitochondrial DNA control region heteroplasmy proportions in mothers and children

Due to maternal inheritance, lack of recombination and a high polymorphic density, the mtDNA control region hypervariable (HV) regions are well suited for forensic identification using a maternal relative as the known sample. This analysis can be performed in hair, however, heteroplasmy in this tissue is not rare and can result in an apparent sequence mismatch that complicates this application. There is little data comparing mother and child mtDNA-CR heteroplasmic proportions in hair. In this study, we assayed four hairs per individual in 26 mother-child pairs by TTGE for heteroplasmy across HV1. Single nucleotide heteroplasmy was detected in seven families, and in four families at least two hairs were heteroplasmic. In each of the latter families, sequencing and PCR-RFLP confirmed single nucleotide heteroplasmy in proportions of the variant ranging from < or =10 to > or =90% in the mothers, with far less variability in their children. Sequencing alone would have revealed apparent homoplasmic differences at one nucleotide in these families, possibly resulting in an 'inconclusive' verdict for relatedness of child and mother. However, mother-child heteroplasmic variability did not exceed intra-individual variability in the mothers alone.     

安徽汉族群体mtDNA高变区I序列多态性分析

以Anderson标准序列作为对照,用GeneDOC软件确定42个安徽汉族无关个体的mtDNA高变区I序列在线粒体基因组中的位置,通过序列比对软件clustalX分析安徽汉族群体mt DNA高变区I序列多态性,共检测到38种单倍型和57个变异位点.在mtDNA高变区I序列中14个bp的高变结构域中,安徽汉人16183位点变异率高达38%,在16187位点的变异率为4.8%.同时发现,安徽汉人与成都汉人在mtDNA高变区I 16183和16189位点的变异率接近,明显高于广东汉人.     

Molecular genetic analysis of Dongzhou-period ancient human of Helingeer in Inner Mongolia, China

The mtDNA hypervariable region I (HVR-I) of 10 ancient individuals from Dongzhou-period ancient human populations in Helingeer county of Inner Mongolia were amplified and sequenced to investigate the genetic structure. The relationships between the ancient population and related extant populations, as well as its possible origin at the molecular level, were also studied. Moreover, phylogenetic analysis and multidimensional scaling analysis were also performed based on the mtDNA data of the ancient population in Helingeer and the related Eurasian population. The results showed that the ancient population in Helingeer were closer to the northern Asian populations than to the other compared populations in matrilineal lineage. Combining the research results of archaeology and anthropology as well as molecular biology, we inferred that they were nomads who migrated from Mongolia plateau and cis-Baikal region to Helingeer in Inner Mongolia, China. __________ Translated from Journal of Jilin University (Science Edition), 2006, 44 (5): 824–828 [译自: 吉林大学学报(理学版)]     

Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations

Over the last 50 years, Spanish Atlantic salmon (Salmo salar) populations have been in decline. In order to bolster these populations, rivers were stocked with fish of northern European origin during the period 1974–1996, probably also introducing the furunculosis-inducing pathogen, Aeromonas salmonicida. Here we assess the relative importance of processes influencing mitochondrial (mt)DNA variability in these populations from 1948 to 2002. Genetic material collected over this period from four rivers in northern Spain (Cantabria) was used to detect variability at the mtDNA ND1 gene. Before stocking, a single haplotype was found at high frequency (0.980). Following stocking, haplotype diversity (h) increased in all rivers (mean h before stocking was 0.041, and 0.245 afterwards). These increases were due principally to the dramatic increase in frequency of a previously very low frequency haplotype, reported at higher frequencies in northern European populations proximate to those used to stock Cantabrian rivers. Genetic structuring increased after stocking: among-river differentiation was low before stocking (1950s/1960s Φ _ST = –0.00296–0.00284), increasing considerably at the height of stocking (1980s Φ _ST = 0.18932) and decreasing post-stocking (1990s/2002 Φ _ST = 0.04934–0.03852). Gene flow from stocked fish therefore seems to have had a substantial role in increasing mtDNA variability. Additionally, we found significant differentiation between individuals that had probably died from infectious disease and apparently healthy, angled fish, suggesting a possible role for pathogen-driven selection of mtDNA variation. Our results suggest that stocking with non-native fish may increase genetic diversity in the short term, but may not reverse population declines.     

Frequency and Pattern of Heteroplasmy in the Control Region of Human Mitochondrial DNA

In this work, we present the results of the screening of human mitochondrial DNA (mtDNA) heteroplasmy in the control region of mtDNA from 210 unrelated Spanish individuals. Both hypervariable regions of mtDNA were amplified and sequenced in order to identify and quantify point and length heteroplasmy. Of the 210 individuals analyzed, 30% were fully homoplasmic and the remaining presented point and/or length heteroplasmy. The prevalent form of heteroplasmy was length heteroplasmy in the poly(C) tract of the hypervariable region II (HVRII), followed by length heteroplasmy in the poly(C) tract of hypervariable region I (HVRI) and, finally, point heteroplasmy, which was found in 3.81% of the individuals analyzed. Moreover, no significant differences were found in the proportions of the different kinds of heteroplasmy in the population when blood and buccal cell samples were compared. The pattern of heteroplasmy in HVRI and HVRII presents important differences. Moreover, the mutational profile in heteroplasmy seems to be different from the mutational pattern detected in population. The results suggest that a considerable number of mutations and, particularly, transitions that appear in heteroplasmy are probably eliminated by drift and/or by selection acting at different mtDNA levels of organization. Taking as a whole the results reported in this work, it is mandatory to perform a broad-scale screening of heteroplasmy to better establish the heteroplasmy profile which would be important for medical, evolutionary, and forensic proposes.     

STR polymorphism of mtDNA D-loop in rhesus macaques of Bangladesh

Molecular variation of mitochondrial DNA (mtDNA) was investigated for rhesus macaques (Macaca mulatta) of Bangladesh. A partial sequence (583–599 bp) of mtDNA containing the second variable region of the D-loop was compared for 39 individuals from five localities in the country. A total of seven haplotypes were detected with substitutional or insertion/deletion mutations. They contained a unique polymorphism of pentanucleotide STRs (short tandem repeats). There were at least four different length types, from two to five repeats of the unit nucleotide. One site of substitution and one site of single nucleotide insertion/deletion were also involved in the polymorphism. The mutation hot spots of the STR polymorphism were located between the first and second conserved sequence blocks (CSB1 and CSB2), as observed previously in some other mammals. The geographical distribution of the STR polymorphism revealed local differences; the northeastern population was polymorphic with three STR haplotypes, but other local populations were simply monomorphic with a single STR haplotype. Molecular phylogenetic analysis with reported sequences from outside Bangladesh indicated a low substitution diversity of mtDNA in Bangladesh. Clustering results suggested a close relationship to India and divergence from Laos and China.     

Variation in the nuclear ribosomal DNA internal transcribed spacer (ITS) region of Pinus rzedowskii revealed by PCR-RFLP

 In the genus Pinus the internal transcribed spacers (ITS1 and ITS2) and the 5.8s region of the nuclear ribosomal DNA are approximately 3000 bp in length. ITS1 is considerably longer than ITS2 and partial sequences of ITS1 indicate that this region is evolving rapidly and exhibits intraspecific variation. The ITS2 and 5.8s regions are relatively conserved. We surveyed restriction fragment length variability of PCR-amplified fragments (PCR-RFLP) of the ITS region in four populations (86 individuals) of Pinus rzedowskii, a pine endemic to western Michoacán, Mexico. Five of the restriction endonucleases assayed revealed variation, with a total of 13 variants, most of which were length mutations of 300–900 bp. A moderate degree of population differentiation was detected. The average diversity (Shannon’s index) of ITS fragment size patterns was 1.19, with 34% of the variation due to differences among populations and 66% due to differences among individuals within populations. The same individuals were assayed for nine polymorphic isozymes, which gave diversity measures similar to those of each restriction endonuclease. Received: 25 August 1997 / Accepted: 19 September 1997     

Fennoscandian phylogeography of the common shrew <Emphasis Type="Italic">Sorex araneus</Emphasis>. Postglacial recolonisation—combining information from chromosomal variation with mitochondrial DNA data

We examine mtDNA variation of the common shrew in Fennoscandia to explore the incongruence found in previous studies using chromosomal and mitochondrial markers, aiming to reveal post-glacial recolonisation patterns. A total of 241 common shrews from 51 localities in Fennoscandia were analysed. This area includes a secondary contact zone between two groups (the Northern group and the Western group) showing distinct karyotypes. All individuals were sequenced for 447 bp of the mitochondrial control region. No significant differentiation in the mtDNA variation was observed between the two major chromosomal groups in Fennoscandia. The star-like shape of the sequence network for the entire study area shows the most common haplotype A as ancestral in all regions but one, in situ formation of most haplotypes and population expansion. The only significant mtDNA structure observed occurs between south Finland and the rest of Fennoscandia. We propose that the Northern and Western group shared a common refugium during the Last Glacial Maximum but recolonised Fennoscandia via two routes. Karyotypic differences between south and north Finland has led researchers to suggest that both regions originate from the same ancestral population east of Finland. The observed divergence of mtDNA variation between these two regions supports this hypothesis.     

The specific mitochondrial DNA polymorphism found in Klinefelter's syndrome

Hypervariable segments of mitochondrial DNA (mtDNA) (HV1 and HV2) were analyzed in Klinefelter's syndrome and compared to normal population data. One pair of samples consisting of a Japanese mother and affected son with Klinefelter's syndrome (involved in a criminal case), and seven unrelated DNA samples from Caucasian Klinefelter males (two involved in criminal cases and five diagnosed) were collected in Japan and the United States. The diagnosis of Klinefelter's syndrome was established previously by multiplex XY-STR typing detecting two X alleles and one Y allele in the samples. Haplotype analysis of the mtDNA sequence in Klinefelter males was found to be identical, unique, and specific, as it was not found in the normal population. Astonishingly, family data exhibited that the haplotype of the mtDNA in the son was apparently different from the mother's, suggesting that the mtDNA of Klinefelter male would not be inherited from mother to son. Our data indicate that possible interaction of the sex chromosome and the mtDNA exists, and suggests that the specific mtDNA haplotype could cause the abnormal cell to fertilize and reproduce itself.     

Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris)

Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) ofPanthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8–17 million years ago in the tiger and 4.6–16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular ‘fossils’ that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.     

Genetic population structure of a reef goby, <Emphasis Type="Italic">Bathygobius cocosensis</Emphasis>, in the northwestern Pacific

To investigate the genetic population structure of a reef goby, Bathygobius cocosensis, in the northwestern Pacific in relation to major oceanic currents (North Equatorial and Kuroshio Currents), the mitochondrial DNA (mtDNA) phylogeny and demography of the species were inferred from partial nucleotide sequences of the mitochondrial NADH dehydrogenase 5 subunit (ND5) gene (945 bp). The resultant mtDNA tree and population genetic analyses showed that the Bonin Islands’ population apparently differed from the other populations in the Japan–Ryukyu–Guam region, which lie along the routes of the North Equatorial and Kuroshio Currents. A test calculation indicated the divergence date to be approximately 1 million years ago. The population expansion parameters indicated that the Bonin Islands’ population had survived during the fluctuations in sea level in the Pleistocene–Holocene age and that the population had expanded thereafter.     

Non-homogeneous infinite sites model under demographic change: mathematical description and asymptotic behavior of pairwise distributions

We developed a mathematical model, which makes possible to predict joint distributions of numbers of mismatches in two or more linked regions of the genome, based on the Infinite Sites Models, under mutation-drift equilibrium as well as under various patterns of population growth. With mutation rates varying in the region, one of the predictions is different correlation between numbers of mismatches in the two regions, depending on the pattern of the past population growth (constant, slowly growing, or rapidly growing). Also, for slower growth patterns of population sizes, the coalescence tree is not necessarily 'starlike'. Thus, the joint distribution of mismatches, predicted by the model, provides additional insights into the demographic history of the populations. We also developed expectations and variances of sample statistics under different growth scenarios. As an application we used a sample of mitochondrial sequences from hypervariable regions 1 and 2 (HV1 and HV2), representing major world populations (Europeans, Asians and Africans). The patterns of joint distributions of numbers of mismatches differ markedly from one population to another. In addition, there is a considerable variability in the proportion of numbers of mismatches between HV1 and HV2 sequences. The patterns of bivariate distributions from the HV1 and HV2 data in these data are consistent with those generated by the model involving a stepwise change in population size.