scholarly journals Nonneutral Mitochondrial DNA Variation in Humans and Chimpanzees

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 953-963 ◽  
Author(s):  
Michael W Nachman ◽  
Wesley M Brown ◽  
Mark Stoneking ◽  
Charles F Aquadro
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Mitochondrial Diseases ◽  
Neutral Model ◽  
Nucleotide Substitutions ◽  
Dna Variation ◽  
Mtdna Sequence ◽  
Restriction Sites ◽  
Complete Mtdna

Abstract We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases.

Mitochondrial DNA variation and genetic relationships of Populus species

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 87-93 ◽  
Author(s):  
John W. Barrett ◽  
Om P. Rajora ◽  
F. C. H Yeh ◽  
Bruce P. Dancik ◽  
Curtis Strobeck
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Genetic Relationships ◽  
Mitochondrial Genomes ◽  
Nucleotide Substitutions ◽  
Dna Variation ◽  
Eastern Cottonwood ◽  
Length Polymorphisms ◽  
Populus Species ◽  
Atpase 6

We examined variation in and around the region coding for the cytochrome c oxidase I (coxI) and ATPase 6 (atp6) genes in the mitochondrial genomes of four Populus species (P. nigra, P. deltoides, P. maximowiczii, and P. tremuloides) and the natural hybrid P. × canadensis (P. deltoides × P. nigra). Total cellular DNAs of these poplars were digested with 16 restriction endonucleases and probed with maize mtDNA-specific probes (CoxI and Atp6). The only variant observed for Atp6 was interspecific, with P. maximowiczii separated from the other species as revealed by EcoRI digestions. No intraspecific mtDNA variation was observed among individuals of P. nigra, P. maximowiczii, P. × canadensis, or P. tremuloides for the CoxI probe. However, two varieties of P. deltoides were distinct because of a single site change in the KpnI digestions, demonstrating that P. deltoides var. deltoides (eastern cottonwood) and var. occidentalis (plains cottonwood) have distinct mitochondrial genomes in the region of the coxI gene. Populus × canadensis shared the same restriction fragment patterns as its suspected maternal parent P. deltoides. Nucleotide substitutions per base in and around the coxI and atp6 genes among the Populus species and the hybrid ranged from 0.0017 to 0.0077. The interspecific estimates of nucleotide substitution per base suggested that P. tremuloides was furthest removed from P. deltoides and P. × canadensis and least diverged from P. nigra. Populus maximowiczii was placed between these two clusters.Key words: mitochondrial DNA, poplars, phylogenetics, variation, restriction fragment length polymorphisms.

Mitochondrial DNA variation in Drosophila pseudoobscura and related species in Pacific Northwest populations

1985 ◽  
Vol 27 (3) ◽  
pp. 357-364 ◽  
Author(s):  
Lawrence R. Hale ◽  
Andrew T. Beckenbach
Keyword(s):  
Mitochondrial Dna ◽  
Pacific Northwest ◽  
Restriction Enzymes ◽  
The Other ◽  
Drosophila Pseudoobscura ◽  
Rich Region ◽  
Dna Variation ◽  
Restriction Sites ◽  
Dna Restriction ◽  
Tandem Duplications

We have analysed mitochondrial DNA (mtDNA) from Pacific Northwest populations of Drosophila pseudoobscura, D. persimilis, and D. miranda using six restriction enzymes. We find that HpaII restriction sites are hypervariable compared to the other enzymes used. This hypervariability allows construction of a maximum parsimony map linking each mtDNA genotype. Small insertions, possibly tandem duplications, appear to have arisen concomitantly with, or subsequent to, speciation events, perhaps within the A + T rich region. Convergence of mtDNA genotypes is also evident. Unlike findings for other populations of these species, we find little evidence of mitochondrial introgression between D. pseudoobscura and D. persimilis, despite their ability to produce fertile hybrid females.Key words: mitochondrial DNA, restriction endonucleases, Drosophila, evolution.

scholarly journals Phylogeny of water birds inferred from mitochondrial DNA sequences of nine protein coding genes

2014 ◽  
Author(s):  
Tsendsesmee Lkhagvajav Treutlein ◽  
Javier Gonzalez ◽  
Michael Wink
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Mitochondrial Protein ◽  
Sister Relationship ◽  
Protein Coding ◽  
Water Bird ◽  
Protein Coding Genes ◽  
Reconstruction Methods ◽  
Mtdna Sequence ◽  
Water Birds

Background: The phylogeny of birds which are adapted to aquatic environments is controversial because of convergent evolution. Methods: To understand water bird evolution in more detail, we sequenced the majority of mitochondrial protein coding genes (6699 nucleotides in length) of 14 water birds, and reconstructed their phylogeny in the context of other taxa across the whole class of birds for which complete mitochondrial DNA (mtDNA) sequences were available. Results: The water bird clade, as defined by Hackett et al. (2008) based on nuclear DNA (ncDNA) sequences, was also found in our study by Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. In both reconstruction methods, genera belonging to the same family generally clustered together with moderate to high statistical support. Above the family level, we identified three monophyletic groups: one clade consisting of Procellariidae, Hydrobatidae and Diomedeidae, and a second clade consisting of Sulidae, Anhingidae and Phalacrocoracidae, and a third clade consisting of Ardeidae and Threskiornithidae. Discussion: Based on our mtDNA sequence data, we recovered a robust direct sister relationship between Ardeidae and Threskiornithidae for the first time for mtDNA. Our comprehensive phylogenetic reconstructions contribute to the knowledge of higher level relationships within the water birds and provide evolutionary hypotheses for further studies.

scholarly journals Classification of European mtDNAs From an Analysis of Three European Populations

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1835-1850 ◽  
Author(s):  
Antonio Torroni ◽  
Kirsi Huoponen ◽  
Paolo Francalacci ◽  
Maurizio Petrozzi ◽  
Laura Morelli ◽  
...  
Keyword(s):  
Control Region ◽  
Restriction Site ◽  
Sequence Data ◽  
Restriction Analysis ◽  
Nucleotide Substitutions ◽  
Mtdna Haplogroups ◽  
Mtdna Mutations ◽  
Mtdna Sequence ◽  
And Control

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations

A new molecular nomenclature for Taenia hydatigena: mitochondrial DNA sequences reveal sufficient diversity suggesting the assignment of major haplotype divisions

Parasitology ◽  
2020 ◽  
pp. 1-16
Author(s):  
John Asekhaen Ohiolei ◽  
Hong-Bin Yan ◽  
Li Li ◽  
Wen-Hui Li ◽  
Yao-Dong Wu ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Mitochondrial Protein ◽  
Nucleotide Substitutions ◽  
Taenia Hydatigena ◽  
Protein Coding ◽  
Major Haplotype ◽  
Cysticercus Tenuicollis ◽  
Larval Stages ◽  
Veterinary Importance

Abstract Cysticercosis caused by the metacestode larval stage of Taenia hydatigena formerly referred to as Cysticercus tenuicollis is a disease of veterinary importance that constitutes a significant threat to livestock production worldwide, especially in endemic regions due to condemnation of visceral organs and mortality rate of infected young animals. While the genetic diversity among parasites is found to be potentially useful in many areas of research including molecular diagnostics, epidemiology and control, that of T. hydatigena across the globe remains poorly understood. In this study, analysis of the mitochondrial DNA (mtDNA) of adult worms and larval stages of T. hydatigena isolated from dogs, sheep and a wild boar in China showed that the population structure consists of two major haplogroups with very high nucleotide substitutions involving synonymous and non-synonymous changes. Compared with other cestodes such as Echinococcus spp., the genetic variation observed between the haplogroups is sufficient for the assignment of major haplotype or genotype division as both groups showed a total of 166 point-mutation differences between the 12 mitochondrial protein-coding gene sequences. Preliminary analysis of a nuclear protein-coding gene (pepck) did not reveal any peculiar changes between both groups which suggests that these variants may only differ in their mitochondrial makeup.

Phylogenetic Relationships among Members of the Coregoninae Inferred from Direct Sequencing of PCR-Amplified Mitochondrial DNA

1993 ◽  
Vol 50 (10) ◽  
pp. 2112-2118 ◽  
Author(s):  
S. Fournier Lockwood ◽  
Robert E. Dillinger Jr. ◽  
Tim P. Birt ◽  
John M. Green ◽  
Thomas P. Snyder
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Cladistic Analysis ◽  
Sequence Divergence ◽  
Amino Acid Replacement ◽  
Mitochondrial Cytochrome B ◽  
Mtdna Sequence ◽  
Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for eight members of the Coregoninae (Salmonidae) from North America in an effort to elucidate phylogenetic relationships in the subfamily. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Direct estimates of mitochondrial DNA (mtDNA) sequence divergence among taxa ranged from 0.0% between Arctic cisco (Coregonus autumnalis) from the Mackenzie River, Canada, and cisco (C. artedi) from the Laurentian Great Lakes to 5.8% between the inconnu (Stenodus leucichthys) and the round whitefish (Prosopium cylindraceum). As has been noted in other fish species and vertebrates in general, third position silent substitutions predominated over any other type of nucleotide change. No amino acid replacement substitutions were found among any of the eight taxa examined. Comparison of mtDNA sequence divergence estimates from this and other studies suggests that the radiation of the genera within the Coregoninae occurred relatively recently (2–6 million yr B.P.). Cladistic analysis of the mtDNA sequence data yields a hypothesis of relationships that supports previous genetic and morphological classifications of coregonines.

scholarly journals HUMAN MITOCHONDRIAL DNA VARIATION AND EVOLUTION: ANALYSIS OF NUCLEOTIDE SEQUENCES FROM SEVEN INDIVIDUALS

Genetics ◽  
1983 ◽  
Vol 103 (2) ◽  
pp. 287-312
Author(s):  
Charles F Aquadro ◽  
Barry D Greenberg
Keyword(s):  
Mitochondrial Dna ◽  
Nucleotide Sequences ◽  
Sequence Length ◽  
Length Variation ◽  
Nucleotide Substitutions ◽  
Sequence Comparisons ◽  
Restriction Endonuclease Site ◽  
Human Mitochondrial Dna ◽  
Mtdna Sequence ◽  
Nucleotide Sequence Variation

ABSTRACT We have analyzed nucleotide sequence variation in an approximately 900-base pair region of the human mitochondrial DNA molecule encompassing the heavy strand origin of replication and the D-loop. Our analysis has focused on nucleotide sequences available from seven humans. Average nucleotide diversity among the sequences is 1.7%, several-fold higher than estimates from restriction endonuclease site variation in mtDNA from these individuals and previously reported for other humans. This disparity is consistent with the rapidly evolving nature of this noncoding region. However, several instances of convergent or parallel gain and loss of restriction sites due to multiple substitutions were observed. In addition, other results suggest that restriction site (as well as pairwise sequence) comparisons may underestimate the total number of substitutions that have occurred since the divergence of two mtDNA sequences from a common ancestral sequence, even at low levels of divergence. This emphasizes the importance of recognizing the large standard errors associated with estimates of sequence variability, particularly when constructing phylogenies among closely related sequences. Analysis of the observed number and direction of substitutions revealed several significant biases, most notably a strand dependence of substitution type and a 32-fold bias favoring transitions over transversions. The results also revealed a significantly nonrandom distribution of nucleotide substitutions and sequence length variation. Significantly more multiple substitutions were observed than expected for these closely related sequences under the assumption of uniform rates of substitution. The bias for transitions has resulted in predominantly convergent or parallel changes among the observed multiple substitutions. There is no convincing evidence that recombination has contributed to the mtDNA sequence diversity we have observed.

THE ROLE OF HETEROPLASMY IN THE DIAGNOSIS AND MANAGEMENT OF MATERNALLY INHERITED DIABETES AND DEAFNESS

2020 ◽  
Vol 26 (2) ◽  
pp. 241-246 ◽  
Author(s):  
Katie Nahay Robinson ◽  
Sari Terrazas ◽  
Samantha Giordano-Mooga ◽  
Neena A. Xavier
Keyword(s):  
Diabetes Mellitus ◽  
Mitochondrial Dna ◽  
Gastrointestinal Disease ◽  
Clinical Manifestations ◽  
Mitochondrial Diseases ◽  
Signs And Symptoms ◽  
Mtdna Sequence ◽  
Scientific Papers ◽  
Organ Specific ◽  
Inherited Diabetes

Objective: Maternally inherited diabetes and deafness (MIDD) is a rare diabetic syndrome mainly caused by a point mutation in the mitochondrial DNA (mtDNA), mt3243 adenine to guanine (A>G). The objective of this paper is to review the genetic inheritance, clinical manifestations, and treatment of patients with MIDD. Methods: The current review used a literature search of scientific papers on this rare syndrome. Results: mtDNA is primarily inherited through the maternal oocyte; therefore, the genetic abnormalities in MIDD are associated with maternal inheritance. Mitochondria contain circular mtDNA, which codes for various mitochondrial genes. The mtDNA can be heteroplasmic, containing more than one type of mtDNA sequence; if one of the mtDNAs contains the mt3243 A>G mutation, a patient may develop MIDD. Patients can inherit different amounts of mutated mtDNA and normal mtDNA that affect the severity of the clinical manifestations of MIDD. The most common clinical manifestations include diabetes mellitus, deafness, ophthalmic disease, cardiac disease, renal disease, gastrointestinal disease, short stature, and myopathies. In order to effectively treat patients with MIDD, it is important to recognize the underlying pathophysiology of this specific form of diabetes and the pathophysiology associated with the organ-specific complications present in this disease. Conclusion: The heteroplasmic inheritance of mutated mtDNA plays an important role in the clinical manifestations of various mitochondrial diseases, specifically MIDD. This review will alert endocrinologists of the signs and symptoms of MIDD and important clinical considerations when managing this disease. Abbreviations: ATP = adenosine triphosphate; CoQ10 = coenzyme Q10; MELAS = mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke; MIDD = maternally inherited diabetes and deafness; mtDNA = mitochondrial DNA; tRNA = transfer ribonucleic acid; ROS = reactive oxygen species; T2DM = type 2 diabetes mellitus

scholarly journals Mitochondrial DNA variation of Apis mellifera iberiensis: further insights from a large-scale study using sequence data of the tRNAleu-cox2 intergenic region

Apidologie ◽  
2017 ◽  
Vol 48 (4) ◽  
pp. 533-544 ◽  
Author(s):  
Julio Chávez-Galarza ◽  
Lionel Garnery ◽  
Dora Henriques ◽  
Cátia J. Neves ◽  
Wahida Loucif-Ayad ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Apis Mellifera ◽  
Intergenic Region ◽  
Large Scale ◽  
Sequence Data ◽  
Dna Variation ◽  
Large Scale Study
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