Leber's hereditary optic neuropathy in Indonesia: two families with the mtDNA 11778G>A and 14484T>C mutations.
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Amino Acid Substitution↗
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A new human mtDNA polymorphism: MTND6: 14562 (C-->T).
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DNA↗
Mutation analysis in 16 patients with mtDNA depletion.
Sixteen unrelated Southern European patients with the mitochondrial depletion syndrome (MDS) were analyzed for mutations in the TK2 and DGUOK genes. Three novel mutations were identified in TK2 (R183G, R254X, and 142insG). When we analyzed additional genes involved in the dNTPs pool, such as SLC25A19 (DNC) and NT5M (d-NT2), we did not detect mutations. The current study suggest that scanning the TK2, DGUOK, SLC25A19, and NT5M genes is likely to help about 10% of MDS families in terms of genetic counseling. Also, our findings indicate that genotype-phenotype correlations are not straightforward in MDS.
Age of Onset↗
Phylogeographic inferences from the mtDNA variation of the three-toed skink, Chalcides chalcides (Reptilia: Scincidae).
Genetic diversity was analyzed in Chalcides chalcides populations from peninsular Italy, Sardinia, Sicily and Tunisia by sequencing 400 bp at the 5' end of the mitochondrial gene encoding cytochrome b (cyt b) and by restriction fragment length polymorphism (RFLP) analysis of two mitochondrial DNA segments (ND-1/2 and ND-3/4). The results of the phylogenetic analysis highlighted the presence of three main clades corresponding with three of the four main geographical areas (Tunisia, Sicily and the Italian peninsula), while Sardinia proved to be closely related to Tunisian haplotypes suggesting a colonization of this island from North Africa by human agency in historical times. On the contrary, the splitting times estimated on the basis of cyt b sequence data seem to indicate a more ancient colonization of Sicily and the Italian Peninsula, as a consequence of tectonic and climatic events that affected the Mediterranean Basin during the Pleistocene. Finally, the analysis of the genetic variability of C. chalcides populations showed a remarkable genetic homogeneity in Italian populations when compared to the Tunisian ones. This condition could be explained by a rapid post-glacial expansion from refugial populations that implied serial bottlenecking with progressive loss of haplotypes, resulting in a low genetic diversity in the populations inhabiting the more recently colonized areas.
Analysis of Variance↗
Mutations of mtDNA in renal cell tumours arising in end-stage renal disease.
Toxic effects in the uraemic state or during maintenance dialysis have been suggested to be responsible for DNA damage and tumour development in end-stage renal disease (ESRD). This study therefore analysed the mitochondrial DNA alterations in six kidneys with ESRD and in nine renal cell tumours arising in these kidneys. Sequencing the entire 16 569 bp mitochondrial genome disclosed 94 sequence variations in normal and corresponding tumour tissues. Thirty-eight polymorphisms occurred in the D-loop region, 40 in the polypeptide coding regions, 12 in the rRNAs, and four in the tRNAs. Nine somatic nucleotide changes were found in seven of the nine tumours analysed; four of them were G to A transitions. Two of the G to A changes occurred in the D-loop region, one in the MTTA gene, and one in the MTND2 gene. An A to G substitution was seen in the control region at the mtTF1 binding site. A T to C transition also occurred also in the D-loop region. A T insertion was seen in MTRNR2 (16S rRNA). One C insertion in MTND4 and one A deletion in the polyA tract of the MTND5 gene resulted in frameshift mutations in two tumours. This study reveals a high mutational rate of the mitochondrial DNA in tumours, which may correspond to the increased level of reactive oxidative species in renal parenchymal cells in ESRD.
Adult↗
Pattern descriptors and the unidentified reading frame 6 human mtDNA dinucleotide-binding site.
In an effort to identify the structural elements essential to a given protein function a new pattern-directed inference system has been developed. It has been employed to identify a potential dinucleotide-binding domain within the human mitochondrial unidentified reading frame 6 product, thereby supporting an earlier study that this gene may encode a NADH dehydrogenase subunit.
Binding Sites↗
Multiple deletions of mtDNA remove the light strand origin of replication.
Idiopathic inflammatory myopathies are progressive, debilitating muscle diseases. The pathogenesis of these disorders is multifactorial and appears to include mutations of the mitochondrial genome, which are usually indicated by morphological changes of mitochondria. The vast majority of all mitochondrial DNA deletions found are located between the origins of replication in the "major region" between nt5760-nt190. Using long distance PCR and sequencing techniques, we detected deletions which were unusually large (ca. 10500-12800 bp) and show uncommon 5'-breakpoints between nt800 and nt3326. Unlike most other deletions, their breakpoints are far upstream of the "major region." The atypical location of these deletions suggests a different pathomechanism. The impact of the mitochondrial DNA deletions in the pathogenetic cascade remains uncertain.
Aged↗
Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha).
Patterns of evolutionary relationships among haplotype clades of sequences of the mitochondrial cytochrome b DNA gene are examined for five genera of arboreal rodents of the Caviomorph family Echimyidae from the Amazon Basin. Data are available for 798 bp of sequence from a total of 24 separate localities in Peru, Venezuela, Bolivia, and Brazil for Mesomys, Isothrix, Makalata, Dactylomys, and Echimys. Sequence divergence, corrected for multiple hits, is extensive, ranging from less than 1% for comparisons within populations of over 20% among geographic units within genera. Both the degree of differentiation and the geographic patterning of the variation suggest that more than one species composes the Amazonian distribution of the currently recognized Mesomys hispidus, Isothrix bistriata, Makalata didelphoides, and Dactylomys dactylinus. There is general concordance in the geographic range of haplotype clades for each of these taxa, and the overall level of differentiation within them is largely equivalent. These observations suggest that a common vicariant history underlies the respective diversification of each genus. However, estimated times of divergence based on the rate of third position transversion substitutions for the major clades within each genus typically range above 1 million years. Thus, allopatric isolation precipitating divergence must have been considerably earlier than the late Pleistocene forest fragmentation events commonly invoked for Amazonian biota.
Animals↗
The complete mitochondrial DNA sequence of the white rhinoceros, Ceratotherium simum, and comparison with the mtDNA sequence of the Indian rhinoceros, Rhinoceros unicornis.
The complete nucleotide sequence of the mitochondrial genome of the white rhinoceros, Ceratotherium simum, was determined. The length of the reported sequence is 16,832 nucleotides. This length can vary, however, due to pronounced heteroplasmy caused by differing numbers of a repetitive motif (5'-CG-CATATACA-3') in the control region. The 16,832 nucleotide sequence presented here is the longest version of the molecule and contains 35 copies of this motif. Comparison between the complete mitochondrial sequences of the white and the Indian (Rhinoceros unicornis) rhinoceroses allowed an estimate of the date of the basal evolutionary divergence among extant rhinoceroses. The calculation suggested that this divergence took place approximately 27 million years before present.
Animals↗
Phylogeny of the side-blotched lizards (Phrynosomatidae:Uta) based on mtDNA sequences: support for midpeninsular seaway in Baja California.
We investigated the phylogenetic relationships of western North American Side-blotched lizards, genus Uta, using mitochondrial DNA partial gene sequences from cytochorme b and ATPase 6. Uta stejnegeri appeared basal in our tree followed by U. palmeri. Uta stansburiana from the islands of Angel de la Guarda, Mejia, and Raza formed the next clade, followed by U. antiqua and other populations of U. stansburiana. These relationships suggest that the populations on the Angel de la Guarda island block should be recognized as a distinct species. Remaining populations of U. stansburiana formed two clades, corresponding to the northern and southern Baja California peninsula. Uta stellata and U. squamata occurred within the northern and southern clades, respectively. The discontinuity requires a long-lasting isolation, the only reasonable explanation being a former midpeninsular seaway. Correlations between our cladogram and magnetic anomalies in the Gulf of California date formation of the seaway at 1 million years ago.
Animals↗
Phylogeny of fungus-growing ants (Tribe Attini) based on mtDNA sequence and morphology.
We examined the phylogenetic relationships among taxa of attine or "fungus-growing" ants (Tribe Attini) using parsimony analyses of molecular and morphological data. We sequenced a region of mitochondrial DNA from 13 taxa of attines and from one closely related outgroup species, Wasmannia auropunctata. Our study sequence included the 3' end of the cytochrome c oxidase subunit I (CO I) locus (183 to 198 total sites; 91 informative sites), an intergenic spacer region of variable size (0 to 152 sites), the tRNA leucine locus (65 to 74 sites), and the 5' end of the cytochrome c oxidase subunit II (co II) locus (292 total sites; 140 informative sites). The inferred relationships among the attine taxa based on an unweighted analysis of the nucleotide sequence data closely matched the relationships inferred from an analysis of larval morphological characters from 11 of the taxa. In fact, the inferred relationships were completely congruent among the protein parsimony analysis of amino acid data, the morphology analysis, and "total evidence" analysis combining the amino acid and morphology data. The congruent conclusions we obtained from two independent data sets increases our confidence in the reliability of our analyses.
Animals↗
A molecular phylogeny of four endangered Madagascar tortoises based on MtDNA sequences.
Four of the five tortoise species in Madagascar, Pyxis arachnoides, P. planicauda, Geochelone radiata, and G. yniphora, are endemic and on the verge of extinction. Their phylogenetic relationships remain controversial and unresolved. Here we address the phylogeny of this group using DNA sequences for the 12S and 16S rDNA and cyt b genes in mitochondrial DNA. As outgroups we used two species of Geochelone, pardalis (mainland Africa) and nigra (Galápagos), as well as a more distant North American tortoise, Gopherus polyphemus. We conclude that the two Pyxis species are sister taxa and are imbedded in the genus Geochelone, rendering this latter genus paraphyletic. There is moderate support for the sister status of the two Madagascar Geochelone and for the monophyletic origin of all four endemics, suggesting a single colonization of the island. The separation of Madagascar from other land masses (90-165 mya) predates the origin of the endemic tortoises (estimated to be 14-22 mya). This suggests founding by rafting, a process known to have occurred with other tortoises. The derived morphological divergence of the Pyxis species in a relatively short period of time (13-20 my) stands in contrast to the notoriously slow rate of morphological evolution in most lineages of Chelonia.
Animals↗
Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA.
The bear family (Ursidae) presents a number of phylogenetic ambiguities as the evolutionary relationships of the six youngest members (ursine bears) are largely unresolved. Recent mitochondrial DNA analyses have produced conflicting results with respect to the phylogeny of ursine bears. In an attempt to resolve these issues, we obtained 1916 nucleotides of mitochondrial DNA sequence data from six gene segments for all eight bear species and conducted maximum likelihood and maximum parsimony analyses on all fragments separately and combined. All six single-region gene trees gave different phylogenetic estimates; however, only for control region data was this significantly incongruent with the results from the combined data. The optimal phylogeny for the combined data set suggests that the giant panda is most basal followed by the spectacled bear. The sloth bear is the basal ursine bear, and there is weak support for a sister taxon relationship of the American and Asiatic black bears. The sun bear is sister taxon to the youngest clade containing brown bears and polar bears. Statistical analyses of alternate hypotheses revealed a lack of strong support for many of the relationships. We suggest that the difficulties surrounding the resolution of the evolutionary relationships of the Ursidae are linked to the existence of sequential rapid radiation events in bear evolution. Thus, unresolved branching orders during these time periods may represent an accurate representation of the evolutionary history of bear species.
Animals↗
MtDNA phylogeography and recent intra-island diversification among Canary Island Calathus beetles.
The genus Calathus Bonelli comprises 24 species on the Canary Islands. Sequences of 927 and 687 bp of the mitochondrial cytochrome oxidase I and II genes, respectively, as well as the intervening tRNA leu gene in 21 of the 24 species, have identified three genetically divergent and unequivocally monophyletic groupings. A phylogeographic analysis is presented for the major monophyletic group comprising all the species of Gran Canaria, La Gomera, and El Hierro, and two Tenerifean species. A distance-based phylogenetic analysis and maximum parsimony analysis have clearly shown that this clade is composed of four distinct lineages. DNA sequence data suggest a recent origin for this clade and that lineages have not evolved at the same rate. Compared with diversification patterns observed in other Coleoptera on the Canary Islands, diversification has been recent relative to the time of colonization within the islands of Gran Canaria and La Gomera. Calathus diversification on La Gomera has been greater than on Gran Canaria. The influences of geological and ecological history are discussed in relation to Calathus diversification.
Animals↗
Phylogeny of "Oxycanus" lineages of hepialid moths from New Zealand inferred from sequence variation in the mtDNA COI and II gene regions.
The phylogeny of the New Zealand hepialid moths was estimated from a 527-bp nucleotide sequence from the mitochondrial DNA cytochrome oxidase subunit I and II gene regions. New haplotypes were identified for Wiseana cervinata, W. copularis, and W. signata. Phylogenetic reconstructions using maximum parsimony and maximum likelihood methods indicated that the four hepialid lineages Aenetus, Aoraia, "Oxycanus" Cladoxycanus, and "Oxycanus" s. str. hypothesized by Dugdale (1994) based on a morphological taxonomic revision were monophyletic within New Zealand. Addition of exemplars from the Australian genera Fraus, Jeana, Oxycanus, and Trictena to the data set tentatively support the monophyly of the New Zealand "Oxycanus" lineages. Estimated times of divergence for the genus Wiseana taxa fitted well with known geological events and suggest that the genus may have diverged 1-1.5 mya.
Animals↗
Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences.
Published molecular phylogenetic studies of elapid snakes agree that the marine and Australo-Melanesian forms are collectively monophyletic. Recent studies, however, disagree on the relationships of the African, American, and Asian forms. To resolve the relationships of the African, American, and Asian species to each other and to the marine/Australo-Melanesian clade, we sequenced the entire cytochrome b gene for 28 elapids; 2 additional elapid sequences from GenBank were also included. This sample includes all African, American, and Asian genera (except for the rare African Pseudohaje), as well as a representative sample of marine/Australo-Melanesian genera. The data were analyzed by the methods of maximum-parsimony and maximum-likelihood. Both types of analyses yielded similar trees, from which the following conclusions can be drawn: (1) Homoroselaps falls outside a clade formed by the remaining elapids; (2) the remaining elapids are divisible into two broad sister clades, the marine/Australo-Melanesian species vs the African, American, and Asian species; (3) American coral snakes cluster with Asian coral snakes; and (4) the "true" cobra genus Naja is probably not monophyletic as the result of excluding such genera as Boulengerina and Paranaja.
Animals↗
Phylogeny of the syrphoidea (Diptera) inferred from mtDNA sequences and morphology with particular reference to classification of the pipunculidae (Diptera).
Sequence data from 420 bp of mitochondrial 12s ribosomal DNA and 490 bp of 16s rDNA were analyzed for 27 species of Syrphoidea (Diptera) and two outgroup taxa. Morphological data for the Pipunculidae were combined with the pipunculid molecular data set. A partition homogeneity test on these data sets revealed no significant incongruence. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology, with differences only with respect to the Nephrocerinae. There is very strong support for the monophyly of the Pipunculinae and the Chalarinae. The Nephrocerinae are hypothesized to be paraphyletic. Within the Syrphidae, there is support for a monophyletic Syrphinae and Microdontinae, but the Eristalinae are paraphyletic. More data are needed to resolve the eristaline phylogeny.
Animals↗
Phylogeography and speciation of the morphologically variable, widespread species Bufo valliceps, based on molecular evidence from mtDNA.
The widespread, lowland toad Bufo valliceps has an unusual distribution in North and Middle America that straddles two major biogeographic areas; previous morphological studies of this species suggested the existence of two species. We used mitochondrial DNA sequences to examine the phylogeography of this species and discovered the existence of two distinct clades. We recognize these as two species: B. valliceps and B. nebulifer. These molecular data support morphological data from previous studies. Our results show low levels of molecular variation in a morphologically uniform temperate species (B. nebulifer) and high levels of molecular variation in a morphologically variable tropical species (B. valliceps), providing an example of molecules matching morphology. Two biogeographic hypotheses are tested to explain the current distribution of these species, based on a calibrated rate of evolution and the percent sequence divergence between the two species. A more recent Pleistocene dispersal event, followed by vicariance associated with rising sea level, is rejected in favor of an earlier Miocene-Pliocene vicariant hypothesis associated with the formation of the Trans-Mexican Neovolcanic Belt.
Animals↗