mtDNA Types Research Articles

Continental and subcontinental distributions of mtDNA control region types.

When the mtDNA profile of a crime scene matches that of a suspect, it is necessary to determine the probability of a chance match by consulting the frequencies of the identified allele in a "reference population". The ceiling principle suggests that that population should be chosen in which the allele of the suspect is found at the highest frequency, in order to give the suspect the maximum benefit of doubt. Recently, we advocated the use of a worldwide mitochondrial database combined with a geographical information system to identify the regions of the world with the highest frequencies of matching mtDNA types. Here, we demonstrate that the alternative approach of defining a ceiling reference population on the basis of continent or phenotype (race) is too coarse for a non-negligible percentage of mtDNA control region types.

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.

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.

Diversity of Mitochondrial DNA Haplogroups in Ethnic Populations of the Volga-Ural Region

The mtDNA polymorphism was analyzed in eight ethnic groups (N = 979) of the Volga–Ural region. Most mtDNA variants belonged to haplogroups H, U, T, J, W, I, R, and N1 characteristic of West Eurasian populations. The most frequent were haplogroups H (12–42%) and U (18–44%). East Eurasian mtDNA types (A, B, Y, F, M, N9) were also observed. Genetic diversity was higher in Turkic than in Finno-Ugric populations. The frequency of mtDNA types characteristic of Siberian and Central Asian populations substantially increased in the ethnic groups living closer to the Urals, a boundary between Europe and Asia. Geographic distances, rather than linguistic barriers, were assumed to play the major role in distribution of mtDNA types in the Volga–Ural region. Thus, as concerns the maternal lineage, the Finno-Ugric populations of the region proved to be more similar to their Turkic neighbors rather than to linguistically related Balto-Finnish ethnic groups.

Age-related atrophy of rat soleus muscle is accompanied by changes in fibre type composition, bioenergy decline and mtDNA rearrangements.

A variety of techniques have been applied to investigate the interrelationship between age-related atrophy of rat soleus muscle and other signs of muscle aging, such as changes in muscle fibre type composition, decrease in bioenergy capacity and accumulation of mitochondrial DNA (mtDNA) arrangements. Age-related atrophy of rat soleus muscle was shown to start at the age of about 28 months. It was accompanied by a decrease in the number of slow twitch muscle fibres (type I) and an increase in the proportion of muscle fibres co-expressing slow and fast myosins (type Ic and IIc fibres). Bioenergy capacity of the soleus muscle, assessed by the level of measurable cytochrome c oxidase (COX) activity, was found to be decreased both in the middle age and old rats compared to the young animals. Muscle atrophy was also accompanied by a decrease in the amount of full-length mitochondrial DNA (FL-mtDNA) amplifiable by the extra-long PCR (XL-PCR) and the increase in the number of mtDNA deletions. The results of the study show that the decline in the bioenergy capacity of the rat soleus occurs by the middle age. It is followed by the onset of the age-related muscle atrophy that is accompanied by both fibre type changes and functional mtDNA degradation.

A Large-scale Analysis of Human Mitochondrial DNA Sequences with Special Reference to the Population History of East Eurasian.

Ancient DNA technique is a very powerful tool for the studies on past human populations. However, in most cases ancient DNA is extremely degraded into short fragments, and the information is limited because of the damaged state. A large-scale data analysis for human mitochondrial DNA (mtDNA) was carried out to assess validity of the short nucleotide sequence for closely related human populations. We retrieved mtDNA data from the DDBJ/EMBL/GenBank nucleotide sequence database and constructed a data set containing 414 distinct mtDNA types derived from 19 populations of East Eurasia and the surrounding area. A series of new procedures were applied and an mtDNA phylogenetic tree was constructed. Six major star-like clusters were observed in this tree, and the corresponding six radiation groups (I-VI) were characterized. Frequency distributions of each radiation group showed remarkable difference in each geographical area, suggesting that the short mtDNA nucleotide sequences were valuable in analyzing ancient human populations. The efficient procedure for data analysis will enhance the usefulness of ancient DNA data. Additionally, we discuss a possibility of two human migration routes from Africa to East Eurasia based on the mtDNA tree topology and the coalescence times in each radiation group.

A spatial aspect on mitochondrial DNA genealogy in Apodemus peninsulae from East Asia.

Apodemus peninsulae is a field mouse that inhabits the broad-leafed forests of temperate Eurasia. We examined the mitochondrial cytochrome b gene in 57 in dividuals of A. peninsulae from northeastern Asia, including Siberia, Primorye, Magadan region, Sakhalin, Hokkaido, and the Korean Peninsula. The genealogy of the mitochondrial DNA (mtDNA) in A. peninsulae was shown to have substantial geographic affinity, suggesting geographic architecture of northeastern Asia, including the islands of Sakhalin and Hokkaido, played important roles on the cladogenesis. Taking into account the presence of region-specific anciently divergent mtDNA types, three parts of the regions of Primorye, Siberia, and the Korean Peninsula can be denoted as refugia for A. peninsulae during the substantial period of the Quaternary glacial ages. Among the geographic regions examined, Primorye is likely to be the most influential one, from which the mtDNA is thought to have migrated to the neighboring regions of Sakhalin, Hokkaido, the Magadan region, and Siberia during the evolution of this species.

Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution.

In the past decade, mitochondrial DNA (mtDNA) of 826 representative East Asians and Papuans has been typed by high-resolution (14-enzyme) restriction fragment length polymorphism (RFLP) analysis. Compared with mtDNA control region sequencing, RFLP typing of the complete human mitochondrial DNA generally yields a cleaner phylogeny, the nodes of which can be dated assuming a molecular clock. We present here a novel star contraction algorithm which rigorously identifies starlike nodes (clusters) diagnostic of prehistoric demographic expansions. Applied to the Asian and Papuan data, we date the out-of-Africa migration of the ancestral mtDNA types that founded all Eurasian (including Papuan) lineages at 54,000 years. While the proto-Papuan mtDNA continued expanding at this time along a southern route to Papua New Guinea, the proto-Eurasian mtDNA appears to have drifted genetically and does not show any comparable demographic expansion until 30,000 years ago. By this time, the East Asian, Indian, and European mtDNA pools seem to have separated from each other, as postulated by the weak Garden of Eden model. The east Asian expansion entered America about 25,000 years ago, but was then restricted on both sides of the Pacific to more southerly latitudes during the Last Glacial Maximum around 20,000 years ago, coinciding with a chronological gap in our expansion dates. Repopulation of northern Asian latitudes occurred after the Last Glacial Maximum, obscuring the ancestral Asian gene pool of Amerinds.

Unique mutations in mitochondrial DNA of senescence-accelerated mouse (SAM) strains.

Mitochondrial DNA (mtDNA) is exclusively inherited maternally and hence could offer a good method for tracing the lineage of mouse strains. We examined the mtDNA sequence of senescence-accelerated mouse (SAM) strains as well as other laboratory strains of inbred mice to deduce the ancestral strain of SAM. Four unique mutations were identified at bases 2256, 10,847, 11,181, and 13,053 in SAM strains. The mutations were not found in other mouse strains including AKR/J, one of the parental strains of SAM. Comparison of the mtDNA sequences also led to the consensus mtDNA sequence of laboratory strains of inbred mice. The seven laboratory strains of common inbred mice showed polymorphisms at base 9348, thymine repeat from base 9818, and adenine repeat from base 9821, and could be classified into five types by combination of the differences. Although we could not identify mouse strains with the same type of mtDNA as SAM in this study, the polymorphisms would provide a promising clue to ascertain the ancestral strain(s) of SAM. The polymorphism in mtDNA could be used to ascertain the genealogy of other mouse strains as well.

Genetic and morphological evidence for reproductive isolation between sympatric populations of Galaxias (Teleostei: Galaxiidae) in South Island, New Zealand

New Zealand's South Island houses a flock of closely related stream-resident fish taxa (Galaxias vulgaris sensu lato), including a number of species recently described on the basis of subtle morphological differences. The taxonomic status of some members of the species complex remains uncertain. This study examines the degree of reproductive isolation between recently recognized morphotypes from Southland (G. «southern», flatheads G. gollumoides, roundheads) which co-occur in Bushy Creek, a tributary of the Mataura R. Although these morphotypes are broadly sympatric in Southland and Stewart Island, Bushy Creek is their only documented zone of contact. Molecular (microsatellite, isozyme and mtDNA markers) and morphological analyses of 139 fish samples across a 500-m transect (seven stations) reveal a cline from predominantly G. «southern» (N=85) to predominantly G. gollumoides (N=54), corresponding with a gradual increase in stream gradient. Multivariate analyses of genotypic and morphological data independently reveal distinct clusters that are completely congruent with mtDNA type, suggesting an absence of mtDNA introgression. Our data support the separate species status of G. «southern» and G. gollumoides under both biological and phylogenetic species concepts. We suggest that the speciation of these taxa occurred in allopatry through independent losses of diadromy, with sympatry resulting from secondary contact.

Genetic and morphological evidence for reproductive isolation between sympatric populations of Galaxias (Teleostei: Galaxiidae) in South Island, New Zealand

Abstract New Zealand's South Island houses a flock of closely related stream-resident fish taxa ( Galaxias vulgaris sensu lato ), including a number of species recently described on the basis of subtle morphological differences. The taxonomic status of some members of the species complex remains uncertain. This study examines the degree of reproductive isolation between recently recognized morphotypes from Southland ( G. «southern» , flatheads G. gollumoides , roundheads) which co-occur in Bushy Creek, a tributary of the Mataura R. Although these morphotypes are broadly sympatric in Southland and Stewart Island, Bushy Creek is their only documented zone of contact. Molecular (microsatellite, isozyme and mtDNA markers) and morphological analyses of 139 fish samples across a 500-m transect (seven stations) reveal a cline from predominantly G. «southern» ( N =85) to predominantly G. gollumoides ( N =54), corresponding with a gradual increase in stream gradient. Multivariate analyses of genotypic and morphological data independently reveal distinct clusters that are completely congruent with mtDNA type, suggesting an absence of mtDNA introgression. Our data support the separate species status of G. «southern» and G. gollumoides under both biological and phylogenetic species concepts. We suggest that the speciation of these taxa occurred in allopatry through independent losses of diadromy, with sympatry resulting from secondary contact.

Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification

Restriction analysis detected two types of bigeye tuna (α and β); the α type was in the majority in the Atlantic but nearly absent in the Indo‐Pacific. The β type shared a larger number of restriction sites with other species than the conspecific β type, but bigeye‐specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub‐species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas.

An antigenomic strategy for treating heteroplasmic mtDNA disorders

In mammals, mitochondrial DNA (mtDNA) is the only autonomously replicating source of DNA outside the nucleus. Housed in the mitochondrial matrix, this molecule encodes thirteen polypeptides, all of which are believed to be essential components of the mitochondrial respiratory chain. Defects of the mitochondrial genome can cause severe neurological and multi-systemic disorders. As the genetic defect causes a dysfunction in the terminal stage of oxidative metabolism, there is little potential for pharmacological intervention. Thus, there is currently no effective therapy for these chronic progressive disorders. In the disease state, pathogenic mtDNA molecules often cohabit the same cell and tissue with wild type mtDNA, a situation termed heteroplasmy. Manifestation of biochemical and clinical defects occur only when a threshold level of heteroplasmy has been passed. The mitochondrial genome must be continually turned over. Consequently, if a pathogenic mtDNA molecule were to be targeted to prevent it from replicating, the wild type copy would be given a propagative advantage. Over time, therefore, the biochemical and, potentially, the clinical deficiency could be reversed. This manuscript summarises our attempts to identify such an antigenomic molecule, to localise this molecule to mitochondria and to assess its function in whole cells. Finally, we discuss the importance of identifying and designing new antigenomic molecules which may prove effective in treating patients with disorders of the mitochondrial genome.

Leber hereditary optic neuropathy: clinical and molecular genetic findings.

Leber hereditary optic neuropathy (LHON) is a maternally inherited disease characterized by acute or subacute painless central visual loss usually in young adults, predominantly in males. Except for optic atrophy, LHON patients are usually otherwise healthy. Occasionally, LHON is associated with neurological, cardiac, and skeletal changes. The clinical course of LHON has several stages. Peripapillary microangiopathy is present from the beginning. Microangiopathy disappears as the disease progresses towards the end stages. Simultaneously, the retinal nerve fiber layer fades from view, first papillomacular nerve fiber bundles, and months later, the whole nerve fiber layer becomes atrophic. At the end stage the centrocecal scotoma is large and absolute. Loss of vision is usually permanent, but spontaneous recovery can occur. Despite a few attempts, no effective treatment to prevent or halt LHON has been found. Several mitochondrial DNA (mtDNA) mutations are associated with LHON, but the pathogenic processes leading to optic nerve atrophy are largely unknown. About 15% of the families are heteroplasmic, i.e., both mutant and wild type mtDNA coexist within an individual. The level of heteroplasmy between different tissues can vary markedly. mtDNA mutations are not sufficient to cause visual loss in LHON, since not all individuals harboring a pathogenic LHON mutation express the disease. There are additional genetic and/or environmental precipitating factors, but thus far they are unknown.

Interaction between mitochondria derived from incompatible black Aspergillus isolates.

As black Aspergillus isolates are highly heterokaryon-incompatible mitochondrial transmissions were performed by protoplast fusion. Donor strains with oligomycin-resistant mitochondria and sensitive recipient partners of various A. japonicus isolates were applied and the progeny were selected for oligomycin resistance and for recipient nuclear phenotype. These strains basically inherited the mitochondrial DNA of the donor strain, which might remain unchanged (substituted progeny) or might be modified by specific sequences of the recipient mtDNAs (recombinant progeny). Different mobile elements characteristic of the recipient parents were exclusively responsible for the development of the feature of recombinant mtDNAs. Substituted progeny were either stable wild-type-like strains as a result of compatible co-operation between donor mitochondria and recipient nuclei, or aconidial strains with a reduced fitness, exhibiting a certain instability. The latter type was probably due to the less compatible communication between nuclear and extrachromosomal genetic systems originating from different parents. These progeny were able to undergo some developmental (segregation) processes during subsequent cultivation, resulting in a stable, wild-type phenotype which possessed a new type of mtDNA resembling that of the acceptor parents.

Wolbachia in the Asian rice gall midge, Orseolia oryzae (Wood-Mason): correlation between host mitotypes and infection status.

Using a PCR-based method, we detected Wolbachia in the Asian rice gall midge. Furthermore, results showed that all females across all biotypes are infected with Wolbachia. However, all male flies are not infected and show different infection frequency in different biotypes. We have also identified three mitotypes, in the rice gall midge, based on DraI restriction pattern of a portion of the 12S rRNA gene that was PCR amplified using primers specific to this gene. All the females and infected male flies had type 1 mtDNA while uninfected males showed only type 2 or 3 mtDNA. Inheritance patterns of mtDNA revealed the existence of a correlation between mtDNA type and Wolbachia infection in the Asian rice gall midge. Evidence for paternal inheritance of mtDNA in Wolbachia-free gall midge is also presented.

Increases of mitochondrial mass and mitochondrial genome in association with enhanced oxidative stress in human cells harboring 4,977 BP-deleted mitochondrial DNA.

In order to investigate the effect of aging- and disease-associated deletion of mtDNA on cellular functions, we used cytoplasm fusion to construct a series of the cybrids harboring varying proportions of mtDNA with 4,977 bp deletion from skin fibroblasts of a patient with chronic progressive external ophthalmoplegia. The cybrids were grown in the Dulbecco's modified Eagle medium supplemented with 5% fetal bovine serum, 100 microg/ml pyruvate and 50 microg/ml uridine. The population doubling time was longer for the cybrids containing higher proportions of 4,977 bp-deleted mtDNA. In addition, we found that the respiratory function was decreased with the increase of mtDNA with 4,977 bp deletion in the cybrids. Since impairment of the respiratory system of mitochondria increases the electron leak of the respiratory chain, we further determined the oxidative stress in these cybrids. The results showed that the specific contents of 8-hydroxy 2'-deoxyguanosine and lipid peroxides of the cybrids harboring > 65% of the 4,977 bp-deleted mtDNA were significantly increased as compared with those of the cybrids containing undetectable mutant mtDNA. On the other hand, we found that the mitochondrial mass and the relative content of the mitochondrial genome in the cybrids harboring 4,977 bp-deleted mtDNA were higher than those of the cybrids containing only wild type mtDNA. The relative content of mtDNA was increased 17% and 30%, respectively, in the cybrids harboring 17% and 56% of mtDNA with 4,977 bp deletion. Moreover, both mitochondrial mass and mtDNA content were concurrently increased by treatment of the cybrids with 180 microM of hydrogen peroxide. Taken these findings together, we conclude that increase of mitochondrial mass and mtDNA are the molecular events associated with enhanced oxidative stress in human cells with impaired respiratory function caused by mtDNA deletion.

Variation of human mitochondrial DNA: distribution of hot spots in hypervariable segment I of the major noncoding region

Mitochondrial DNA (mtDNA) samples belonging to fifteen phylogenetically related mtDNA types specific to the populations of Europe (H, V, J, T, U, K, I, W, and X) and Northern Asia (A, C, D, G, Y, and Z) were typed for sequence variation in hypervariable segment I (HVSI). The approach used allowed to distinguish several hypervariable sites at nucleotide positions 16093, 16129, 16189, 16311, and 16362. Identical mutations at these sites were found in 10-11 out of 15 mtDNA groups examined. Positions 16126, 16172, 16192, 16256, 16261, 16291, 16293, and 16298 appeared to be less variable, since parallel mutations at these sites were found in 6-8 European and Asian mtDNA groups. The examples of the effects of mutations in hypervariable positions at the major noncoding mtDNA region on the frequency of reverse mutations in other mtDNA regions are presented. It was shown that such effects of nucleotide context on the mutation rate could be observed in phylogenetic mtDNA networks such as cyclic structures like rhombs and cubes. Analogous structures in the networks could be seen also in the case of the appearance of recombinant mtDNA types resulted from homologous recombination between mtDNA molecules in heteroplasmic mixture. The problem of the effect of polynucleotide context on the intensity of mtDNA mutagenesis is discussed. Recombination processes along with site-directed mutagenesis caused by action of genetic factors (of nuclear genome) and/or of the environment are considered as possible mechanisms of mitochondrial genome evolution.

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.

The T4336C Variant Is a Marker of Mitochondrial Subhaplogroup H1, a Common Component of the Russian and German Gene Pools

Analysis of mitochondrial DNA (mtDNA) restriction polymorphism carried out in a sample of Russians from Magadan (n= 150) showed that the frequency of the +4332AvaII variant (a T–C transition at nucleotide position 4336) in this population was 4.7%. All +4332AvaII types of mtDNA belonged to the mitochondrial group H. They were characterized by a back of the AluI restriction endonuclease site at position 7025. According to hypervariable segment 1 sequencing data, they contained the 16304C variant, and thus belong to the subgroup H1. Thus, the +4332AvaII (T4336C) variant is a marker of the mitochondrial subgroup H1, chiefly occurring in German-speaking populations. Utilization of the H1-mtDNA markers for the investigation of the genetic history and the origin of Slavs is discussed.