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PubMed1993

Restriction enzyme fragment patterns of mtDNA from a galactose oxidase-producing mold.

1. Mitochondrial DNAs from Dactylium dendroides, Hypomyces rosellus, Fusarium graminearum, Gibberella fujikuroi, Fusarium tricinctum strains and a galactose oxidase (GAO)-producing mold (original strain) presented distinctive restriction enzyme fragment patterns with the endonucleases Hind III and EcoRI. 2. A small number of comigrating bands was found when the GAO-producing mold was compared with the others. The molecular size of mtDNA from the GAO-producing mold, as judged by summation of fragment sizes produced by digestion with EcoRI, Hind III and Bgl II, is 61.3 +/- 2.16 kb. 3. The results suggest that the mtDNA from the GAO-producing mold strain is distinct from that of D. dendroides and all other ascomycetes analyzed.

Basidiomycota↗
PubMed1993

Genetic structure of natural populations of Dryas iulia (Lepidoptera: Nymphalidae) revealed by enzyme polymorphism and mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP).

Dryas iulia appears to have undergone a mode of evolution different from that of other members of its subfamily (Heliconiinae). While other species constitute highly subdivided and inbred populations, those of D. iulia are thought to be large and uniform. Analyzing six samples from Southern Brazil (state of Rio Grande do Sul) in relation to three enzyme systems (EST, LAP, and PGM) and their mtDNA RFLP patterns, we found that they are very similar at the molecular level. The F statistics for enzyme polymorphism data revealed that inbreeding makes a great contribution to the population homozygosity, since FIS equals 0.1322 and FST equals 0.0023. Since the chi-square test showed that FST is not significant, we conclude that all localities belong to the same population. The mtDNA differentiation was about 12 times greater than for nuclear genes; FST was equivalent to 0.0265. We suggest that this difference is due to a higher dispersal of males, in relation to females.

Animals↗
PubMed1994

[mtDNA polymorphism and differentiation of subspecies of Chinese raccoon dog (Nyctereutes procyonides)].

The mtDNA from 14 Raccoon dogs of 7 geographical populations was analyzed with 8 restriction endonucleases, and the restriction map was constructed. Furthermore, UPG molecular phylogenetic trees of the mtDNA were constructed based on the genetic distances. Our results indicated that the differentiation was obvious within geographical populations of the subspecies N. p. procyonoides, and that the event of divergence in Chinese Raccoon dog first occurred between the southern and northern populations, and then, between the western and the eastern populations. We proposed that both of the Huabei and Shanxi populations which had not been identified could be classified into two independent subspecies respectively.

Animals↗
PubMed1996

Testing models of female reproductive migratory behaviour and population structure in the Caribbean hawksbill turtle, Eretmochelys imbricata, with mtDNA sequences.

Information on the reproductive behaviour and population structure of female hawksbill turtles, Eretmochelys imbricata, is necessary to define conservation priorities for this highly endangered species. Two hypotheses to explain female nest site choice, natal homing and social facilitation, were tested by analyzing mtDNA control region sequences of 103 individuals from seven nesting colonies in the Caribbean and western Atlantic. Under the social facilitation model, newly mature females follow older females to a nesting location, and subsequently use this site for future nesting. This model generates an expectation that female lineages will be homogenized among regional nesting colonies. Contrary to expectations of the social facilitation model, mtDNA lineages were highly structured among western Atlantic nesting colonies. These analyses identified at least 6 female breeding stocks in the Caribbean and western Atlantic and support a natal homing model for recruitment of breeding females. Reproductive populations are effectively isolated over ecological time scales, and recovery plans for this species should include protection at the level of individual nesting colonies.

Animals↗
PubMed1996

Origin and evolution of Native American mtDNA variation: a reappraisal.

The timing and number of prehistoric migrations involved in the settlement of the American continent is subject to intense debate. Here, we reanalyze Native American control region mtDNA data and demonstrate that only an appropriate phylogenetic analysis accompanied by an appreciation of demographic factors allows us to discern different migrations and to estimate their ages. Reappraising 574 mtDNA control region sequences from aboriginal Siberians and Native Americans, we confirm in agreement with linguistic, archaeological and climatic evidence that (i) the major wave of migration brought one population, ancestral to the Amerinds, from northeastern Siberia to America 20,000-25,000 years ago and (ii) a rapid expansion of a Beringian source population took place at the end of the Younger Dryas glacial phase approximately 11,300 years ago, ancestral to present Eskimo and Na-Dene populations.

Biological Evolution↗
PubMed1996

Heteroplasmic point mutations in the human mtDNA control region.

As part of an investigation of the fixation mechanisms of mtDNA mutations in humans, we sequenced the first hypervariable segment of the control region in 180 twin pairs and found evidence of site heteroplasmy in 4 pairs. Significant levels of two mitochondrial haplotypes differing by a single point mutation were found in two MZ pairs, and within each pair, both members had similar levels of heteroplasmy. Two DZ pairs were found in which the predominant mitochondrial haplotype differed within the pair. We measured proportions of mitochondrial haplotypes within two twin pairs and their maternal relatives, using primer extension. In both maternal lineages, most family members were heteroplasmic, and the proportions of each genotype varied widely in different individuals. We used the changes in haplotype proportions within mother-offspring pairs to calculate the size range of potential bottlenecks in mitochondrial numbers occurring during development of the offspring. In most individuals, the most likely effective bottleneck sizes ranged from 3 to 20 segregating units, though in two individuals a small bottleneck was very unlikely and there was no upper limit on its possible size. We also used the data from this study, together with unpublished data from other populations, to estimate the frequency of site heteroplasmy in normal human populations. From this, we calculated that the rate of mutation and fixation in the first hypervariable segment of the human mtDNA control region is between 1.2 x 10(-6) and 2.7 x 10(-5) per site per generation. This range is in good agreement with published estimates calculated by other methods.

DNA, Mitochondrial↗
PubMedDate not supplied

mtDNA haplotype analysis in Finnish families with leber hereditary optic neuroretinopathy.

The mitochondrial DNA (mtDNA) sequence variation of 24 Finnish Leber hereditary optic neuroretinopathy (LHON) probands was characterized by sequencing and restriction endonuclease analyses. All LHON-associated substitutions and Caucasoid haplogroup-specific mutations were screened in the families. Analysis of the mtDNAs revealed that the Finnish LHON families have two unique features: an absence of the ND6/14484 mutation and a high number of families (10/24) without the primary mutations ND1/3460 and ND4/11778. Furthermore, the LHON families showed considerable mtDNA heterogeneity: among 24 families 22 haplotypes were detected. Overall, the haplogrouping of LHON families was similar to other European populations. However, the frequency of ND4/11778-positive families in haplogroup J was high, which may indicate that background mutations in this haplogroup together with the ND4/11778 primary mutation promote the penetrance of LHON.

Adolescent↗
PubMed1998

Restriction digest of PCR-amplified mtDNA from fin clips is an assay for sequence genetic "tags" among hundreds of fish in wild populations.

We tested the feasibility of recovering from wild populations mitochondrial DNA genetic "tags" that might result from release of hatchery-reared fingerlings for marine stock enhancement. A practical, nondestructive method of genetic "tag" recovery would allow quantitative assessment of the efficacy of such programs. A rare mtDNA variant with two sites each instead of one for TaqI and RsaI in the control region was used as a mock genetic "tag" in snook (Centropomus undecimalis). We assayed for the variant among nearly 900 fish by restriction digests of DNA amplified by polymerase chain reaction (PCR) obtained from fin-clip extracts, finding only a single second example of the variant. Thus, mtDNA "tags" can be nondestructively assayed for with specificity among hundreds of individuals.

Animals↗
PubMed1998

mtDNA and language support a common origin of Micronesians and Polynesians in Island Southeast Asia.

The origins and relationships among Micronesians, Polynesians, and Melanesians were investigated. Five different mtDNA region V length polymorphisms from 873 individuals representing 24 Oceanic and Asian populations were analyzed. The frequency cline of a common deletion and the distributions of a rare expanded length polymorphism support the origin of both Micronesians and Polynesians in Island Southeast Asia. Genetic, linguistic, and geographic distances were compared to assess the relative importance of isolation and gene flow during the prehistory of 19 Austronesian-speaking populations subdivided into five potential spheres of interaction. We observed significant correlations (P < 0.05) between genetic and linguistic distances in four of five comparisons. These data indicate extensive gene flow throughout much of Micronesia, but substantial isolation in other Pacific regions. Although recent advancements in our understanding of intentional voyaging within Remote Oceania have challenged the existence of the "myth of the primitive isolate," we caution against the adoption of panmictic alternatives.

Asia, Southeastern↗
PubMed1999

Differential contribution of indigenous men and women to the formation of an urban population in the Amazon region as revealed by mtDNA and Y-DNA.

The human populations of the Brazilian Amazon were formed by interethnic crosses between Europeans, Africans, and Amerindians. The relative contribution of men and women of different ethnic groups was not homogeneous, since the social policies of the first three centuries of Brazilian colonization encouraged mating between European men and indigenous women and, later on, African women. In order to test this model based on historical data, we compared the relative contribution of the Y-DNA and mtDNA of Amerindian and non-Amerindian populations to the formation of the urban population of the town of Belém, in the Amazon region, on the basis of a C-->T mutation at locus DYS199 present in 90% of the Amerindian Y-DNA and of five markers that define 99% of the mitochondrial sequences of Amerindians. The contribution of indigenous men to the formation of this population was less than 5%, whereas the contribution of indigenous women was estimated at more than 50% of the mitochondrial sequences of the same population. Thus, the present results demonstrate that the contribution of indigenous women to the formation of the Belém population was 10 times higher than the contribution of indigenous men, a genetic consequence of social behavior and attitudes of the past; our results also help clarify the process of integration of indigenous communities into the urban societies in Brazil and possibly in other countries.

Brazil↗
PubMed2005

Mitochondrial DNA (mtDNA) haplotypes reveal maternal population genetic affinities of Sea Island Gullah-speaking African Americans.

To better understand the population substructure of African Americans living in coastal South Carolina, we used restriction site polymorphisms and an insertion/deletion in mitochondrial DNA (mtDNA) to construct seven-position haplotypes across 1,395 individuals from Sierra Leone, Africa, from U.S. European Americans, and from the New World African-derived populations of Jamaica, Gullah-speaking African Americans of the South Carolina Sea Islands (Gullahs), African Americans living in Charleston, South Carolina, and West Coast African Americans. Analyses showed a high degree of similarity within the New World African-derived populations, where haplotype frequencies and diversities were similar. Phi-statistics indicated that very little genetic differentiation has occurred within New World African-derived populations, but that there has been significant differentiation of these populations from Sierra Leoneans. Genetic distance estimates indicated a close relationship of Gullahs and Jamaicans with Sierra Leoneans, while African Americans living in Charleston and the West Coast were progressively more distantly related to the Sierra Leoneans. We observed low maternal European American admixture in the Jamaican and Gullah samples (m = 0.020 and 0.064, respectively) that increased sharply in a clinal pattern from Charleston African Americans to West Coast African Americans (m = 0.099 and 0.205, respectively). The appreciably reduced maternal European American admixture noted in the Gullah indicates that the Gullah may be uniquely situated to allow genetic epidemiology studies of complex diseases in African Americans with low European American admixture.

Black or African American↗
PubMed1995

MtDNA mutations associated with Leber's hereditary optic neuropathy: studies on cytoplasmic hybrid (cybrid) cells.

Leber's hereditary optic neuropathy (LHON) has been associated with "primary" and "secondary" mtDNA missense point mutations, and a synergistic role has been proposed for secondary mutations. No previous study has investigated the effects of LHON primary or primary plus secondary mutations on the respiratory competence of cell lines. We constructed and compared cybrid cell lines obtained from two unrelated LHON patients both carrying the common 11778/ND4 primary mutation. One of the patients also carried the 13708/ND5 and 4216/ND1 secondary mutations. The cybrid clones were evaluated for growth efficiency, oxygen consumption, complexes I, III and IV enzymatic activity and mitochondrial protein synthesis. Complex activity and mitochondrial protein synthesis were not significantly changed in cybrid clones from the patients. Oxygen consumption was significantly decreased in all clones carrying the 11778/ND4 primary mutation demonstrating its pathogenic role in impairing cell respiration. Clones also carrying the secondary mutations showed an even lower oxygen consumption and a significantly higher doubling time, suggesting that the co-presence of the secondary mutations could be relevant in further reducing the cell fitness.

Adult↗
PubMed1997

Identification of a novel mutation in the mtDNA ND5 gene associated with MELAS.

We report a novel G13513A mutation in the mitochondrial ND5 gene in a patient who had morphologically and biochemically abnormal muscle mitochondria and died at age 45 with a diagnosis of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). The mutation affects an evolutionarily conserved nucleotide and was heteroplasmic in muscle, leukocytes, and several autopsy tissues, including brain. The mutation was less abundant (<5%) in leukocytes from an asymptomatic sister and was not found in over 100 controls, thus satisfying accepted criteria for pathogenicity. Our report reinforces the concept of genetic heterogeneity in MELAS and confirms that MELAS can be due to mutations in polypeptide-coding mtDNA genes.

Amino Acid Sequence↗
PubMed1997

mtDNA mutations confer cellular sensitivity to oxidant stress that is partially rescued by calcium depletion and cyclosporin A.

The complete mechanism by which pathogenic mtDNA mutations cause cellular pathophysiology and in some cases cell death is unclear. Oxidant stress is especially toxic to excitable nerve and muscle cells, cells that are often affected in mitochondrial disease. The sensitivity of cells bearing the LHON, MELAS, and MERRF mutations to oxidant stress was determined. All were significantly more sensitive to H2O2 exposure than their nonmutant cybrid controls, the order of sensitivity was MELAS > LHON > MERRF > controls. Depletion of Ca2+ from the medium protected all cell lines from oxidant stress, consistent with the hypothesis that death induced by oxidant stress is Ca(2+)-dependent. A potential downstream target of Ca2+ is the mitochondrial permeability transition, MPT, which is inhibited by cyclosporin A. Treatment of MELAS, LHON, and MERRF cells with cyclosporin A caused significant rescue from oxidant exposure, and in each case significantly greater rescue of mutant than control cells. The pronounced oxidant-sensitivity of mutant cells, and their protection by Ca2+ depletion and CsA, has potential implications for both the pathophysiological mechanism and therapy of these mitochondrial genetic diseases.

Calcium↗
PubMed1999

Long-term analysis of differentiation in human myoblasts repopulated with mitochondria harboring mtDNA mutations.

Short-term analysis of myogenesis in respiration-deficient myoblasts demonstrated that respiratory chain dysfunction impairs muscle differentiation. To investigate long-term consequences of a deficiency in oxidative phosphorylation on myogenesis, we quantitated myoblast fusion and expression of sarcomeric myosin in respiration-deficient myogenic cybrids. We produced viable myoblasts harboring exclusively mtDNA with large-scale deletions by treating wild-type myoblasts with rhodamine 6G and fusing them with cytoplasts homoplasmic for two different mutated mtDNAs. Recovery of growth in transmitochondrial myoblasts demonstrated that respiratory chain function is not required for recovery of rhodamine 6G-treated cells. Both transmitochondrial respiration-deficient cultures exhibited impaired myoblast fusion. Expression of sarcomeric myosin was also delayed in deficient myoblasts. However, 4 weeks after induction of differentiation, one cell line was able to quantitatively recover its capacity to form postmitotic muscle cells. This indicates that while oxidative phosphorylation is an important source of ATP for muscle development, myoblast differentiation can be supported entirely by glycolysis.

Biomarkers↗
PubMed2001

Correlation of functional and ultrastructural abnormalities of mitochondria in mouse heart carrying a pathogenic mutant mtDNA with a 4696-bp deletion.

We examined the correlation of functional and structural abnormalities of cardiac mitochondria created by pathogenic mutant mtDNAs using mito-mice with hearts carrying 88% mutant DeltamtDNA4696 with a 4696 deletion. COX histochemistry, quantitative PCR analysis, and electronmicrographs showed that accumulation of 91.6% DeltamtDNA4696 in single cardiac muscle fibers induced progressive reduction of COX activity to form COX-negative fibers. Moreover, hearts carrying 88% DeltamtDNA4696 consisted of three types of cardiac muscle fibers with different functional properties, COX-positive, -negative, and -intermediate fibers, which corresponded respectively to three types of fibers with different structural properties; type A fibers containing mitochondria with only lamellar cristae, type B containing mitochondria with only tubular cristae, and type C possessing mitochondria with both lamellar and tubular cristae. These observations suggest that lamellar cristae with COX activity transform into tubular cristae without COX activity along with the accumulation of DeltamtDNA4696, which would be responsible for insufficient supply of mtDNA products required to keep the normal structure and function of mitochondrial cristae. The correlation of these structural and functional abnormalities of cristae should provide important insight into diagnosis of cardiomyopathies caused by accumulation of pathogenic mutant mtDNAs.

Animals↗
PubMed1994

Evolution of mtDNA D-loop sequences and their use in phylogenetic studies of shrews in the subgenus Otisorex (Sorex: Soricidae: Insectivora).

mtDNA D-loop sequences were examined in shrews of the genus Sorex. All specimens possessed an array of tandem repeats in which each repeat was 78 to 80 base pairs (bp) in length. Each specimen also possessed a 76-bp imperfect copy of the tandem repeats. Three observations are consistent with the tandem repeats being the product of concerted evolution: (1) the repeats are capable of forming secondary structures; (2) there was minimal sequence divergence between tandem repeats within individuals; and (3) although the tandem repeats and the imperfect repeat presumably arose due to a duplication event in an ancestor of the shrews, the imperfect repeat per se was not copied in any of the specimens observed. Interspecific homology can therefore be assumed for the imperfect repeat. Furthermore, given the apparent high rate of concerted evolution within a genome, tandem repeats in different individuals may be compared as though only a single copy were present. By including data from the imperfect repeat, the last tandem repeat, and the surrounding unique sequence cladistic and genetic distance approaches to phylogeny reconstruction indicated two sister groups within the subgenus Otisorex. One group was composed of Sorex fumeus and the S. cinereus species complex and the other group was composed of S. hoyi, S. monticolus, S. vagrans, and S. palustris. Resolution of relationships among recently evolved taxa demonstrated the usefulness of selected regions of the D-loop for molecular systematic studies.

Animals↗
PubMed1995

MtDNA phylogeography of the California newt, Taricha torosa (Caudata, Salamandridae).

Thirty-six individuals of the California newt, Taricha torosa, representing 22 populations from throughout the range of the two currently recognized subspecies, torosa and sierrae, were examined for sequence variation in a segment (375 bp) of the mitochondrial (mt) cytochrome b gene. The maximum sequence divergence within T. torosa is about 9%. Phylogenetic analyses used the sister taxa T. rivularis and T. granulosa as outgroups. Eighteen haploid sequence types found in T. torosa were grouped by parsimony, maximum likelihood, and neighbor-joining analyses into five mitochondrial clusters: two in torosa (the northern and southern clusters) and three in sierrae (the northern, central, and southern clusters). The southern sierrae cluster apparently shared a most recent common ancestor with the northern torosa cluster. The approximate time of sequence divergence within the current species was calibrated using the known fossil record (0.8% divergence per million years or 0.01 maximum likelihood distance per million years). Phylogenetic implications of mtDNA sequence variation for evolution and biogeography of the T. torosa species complex are discussed.

Amino Acid Sequence↗