Mitochondrial DNA Evolution Research Articles

Mammalian mitochondrial DNA evolution: A comparison of the cytochrome b and cytochrome c oxidase II genes

The evolution of two mitochondrial genes, cytochrome b and cytochrome c oxidase subunit II, was examined in several eutherian mammal orders, with special emphasis on the orders Artiodactyla and Rodentia. When analyzed using both maximum parsimony, with either equal or unequal character weighting, and neighbor joining, neither gene performed with a high degree of consistency in terms of the phylogenetic hypotheses supported. The phylogenetic inconsistencies observed for both these genes may be the result of several factors including differences in the rate of nucleotide substitution among particular lineages (especially between orders), base composition bias, transition/transversion bias, differences in codon usage, and different constraints and levels of homoplasy associated with first, second, and third codon positions. We discuss the implications of these findings for the molecular systematics of mammals, especially as they relate to recent hypotheses concerning the polyphyly of the order Rodentia, relationships among the Artiodactyla, and various interordinal relationships.

Heteroplasmy in the European rabbit: Mitochondria and mitochondrial DNA evolution through the germ line

Heteroplasmy in the European rabbit: Mitochondria and mitochondrial DNA evolution through the germ line

Neutral and non-neutral evolution of Drosophila mitochondrial DNA.

To test hypotheses of neutral evolution of mitochondrial DNA (mtDNA), nucleotide sequences were determined for 1515 base pairs of the NADH dehydrogenase subunit 5 (ND5) gene in the mitochondrial DNA of 29 lines of Drosophila melanogaster and 9 lines of its sibling species Drosophila simulans. In contrast to the patterns for nuclear genes, where D. melanogaster generally exhibits much less nucleotide polymorphism, the number of segregating sites was slightly higher in a global sample of nine ND5 sequences in D. melanogaster (s = 8) than in the nine lines of D. simulans (s = 6). When compared to variation at nuclear loci, the mtDNA variation in D. melanogaster does not depart from neutral expectations. The ND5 sequences in D. simulans, however, show fewer than half the number of variable sites expected under neutrality when compared to sequences from the period locus. While this reduction in variation is not significant at the 5% level, HKA tests with published restriction data for mtDNA in D. simulans do show a significant reduction of variation suggesting a selective sweep of variation in the mtDNA in this species. Tests of neutral evolution based on the ratios of synonymous and replacement polymorphism and divergence are generally consistent with neutral expectations, although a significant excess of amino acid polymorphism within both species is localized in one region of the protein. The rate of mtDNA evolution has been faster in D. melanogaster than in D. simulans and the population structure of mtDNA is distinct in these species. The data reveal how different rates of mtDNA evolution between species and different histories of neutral and adaptive evolution within species can compromise historical inferences in population and evolutionary biology.

Parallels between island lizards suggests selection on mitochondrial DNA and morphology

Parallels between species on historically independent islands have been shown to be a powerful means of testing for the action of natural selection on morphology. Mitochondrial DNA evolution is often assumed to be selectively neutral, but this is difficult to test empirically. Here we show that parallels are present between two species of lizards on the geologically distinct but ecologically similar Lesser Antillean islands of Dominica and Basse Terre (Guadeloupe). These parallels are found not only in morphological variation but also in mitochondrial DNA variation and these are correlated with similar ecological gradients. A morphological cline in Anolis oculatus along the Caribbean coast of Dominica is compared to sequence variation in the cytochrome b gene, which shows exceptionally high variability. Patterns of sequence variation and morphology (especially scalation) are congruent, and are significantly correlated with moisture gradients. Anolis marmoratus on the adjacent island of Basse Terre (Guadeloupe) shows parallel patterns of morphological and cytochrome b variation along the Caribbean coast, and these are also significantly correlated with moisture gradients.

Resolving the Archaic‐to‐Modern Transition

1993 The Eve Hypothesis: A Genetic Critique and Reanalysis. American Anthropologist 95:51-72. Templeton, A. Rt, K. A. Crandall, and C. F. Sing 1992 A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. Genetics 132:619-633. Templeton, A. R., and C. F. Sing 1993 A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping. IV. Nested Analyses with Cladogram Uncertainty and Recombination. Genetics 134:659-669. Torroni, A., O. Semino, R. Scozzari, G. Sirugo, G. Spedini, N. Abbas, M. Fellous, and A. S. Santachiara Benerecetti 1990 Y Chromosome DNA Polymorphisms in Human Populations: Differences between Caucasoids and Africans Detected by 49a and 49f Probes. Annals of Human Genetics 54:287-296. Vigilant, L., M. Stoneking, H. Harpending, K. Hawkes, and A. C. Wilson 1991 African Populations and the Evolution of Human Mitochondrial DNA. Science 253:1503-1507. Wills, C. 1992 Human Origins. Nature 356:389390.

Molecular biology of human male infertility: links with aging, mitochondrial genetics, and oxidative stress?

Molecular biology of human male infertility: links with aging, mitochondrial genetics, and oxidative stress?

The human colonisation of Australia: optical dates of 53,000 and 60,000 years bracket human arrival at Deaf Adder Gorge, Northern Territory

The date at which people entered Australia has important implications for the debate on modern human origins. Thermoluminescence dates of 50–60 ka, reported for initial occupation of the Malakunanja II site in northern Australia, have been used as a means of calibrating the rate of mitochondrial and nuclear DNA evolution in modern humans. Optical dating of unburnt quartzose sediments from a rock shelter site (Nauwalabila I, Lindner Site) in Deaf Adder Gorge, 70 km south of Malakunanja II, provides new evidence for the timing of the colonisation of the continent. Optical dates were determined for several stratigraphic levels within a 3 m deep excavation, in which flaked stone artefacts and ground pigments were found in primary depositional setting. The lowest human occupation levels are bracketed by dates of 53.4 ± 5.4 ka and 60.3 ± 6.7 ka, while the upper levels show good agreement between optical and calibrated 14C age estimates. High-quality haematite with ground facets and striations is associated directly with the 53 ka level and indicates the use of pigments by these early Australians. The optical dates independently confirm evidence for the colonisation of northern Australia shortly after 60 ka and should be seen in the context of this region as having been a likely entry route for the first human movements into Sahul.

Endotherms, ectotherms, and mitochondrial genome-size variation

The patterns of mitochondrial genome-size variation were investigated in endothermic and ectothermic species to examine the role that thermal habit might play in the evolution of animal mitochondrial DNA (mtDNA). Data on mtDNA size (the modal, largest, and smallest mtDNA reported within a species), the percent variation in mtDNA size (the difference in size between the largest and smallest mtDNAs divided by the model genome size for a given species), and the frequency of heteroplasmic individuals (those carrying more than one mtDNA length variant) were tabulated from the literature. Endotherms showed significantly less variation in mtDNA size and tended to have smaller mtDNAs than ectotherms. Further comparisons between endothermic and ectothermic vertebrates revealed that the largest genome and the percent variation in genome size were significantly smaller in the former than the latter. There was no difference between endotherms and ectotherms in the frequency of heteroplasmy. These data are discussed in light of two hypotheses: (1) more intense directional and purifying selection for small genome size in the cytoplasms of species with higher metabolic rates and (2) reduced mutation pressures generating mtDNA size variants in endotherms relative to those in ectotherms. The general trends are consistent with the selection hypothesis but in certain species mtDNA size variation appears to be governed by mutational pressures. To test these competing hypotheses further, comparative studies are proposed where mitochondrial genome size is quantified in sister taxa and tissue types with very different metabolic rates.

Molecular characterization and evolution of a duck mitochondrial genome

We sequenced 6,478 bp of mitochondrial DNA from Peking duck (Anas platyrhyncos). Eight protein genes, 11 tRNAs, part of the small and large ribosomal subunits, and the control region sequences were compared to homologous chicken sequences. The gene organization in duck and chicken is identical but differs from other vertebrates in the juxtaposition of the tRNA(Glu)-ND6 genes next to the control region and in the lack of a hairpinlike structure between the genes for tRNA(Asn) and tRNA(Cys) used for light-strand replication. Protein, tRNA, and rRNA genes evolved mainly through base substitutions and small insertions and deletions. Transitions greatly outnumber transversions in the tRNA and rRNA genes, but this bias is not evident in protein genes; the control region has a higher proportion of transversions. The duck and chicken control regions show a high frequency of length mutations. Large A-T-rich nucleotide stretches dispersed across the region between the bidirectional transcription promoter and the heavy-strand replication origin in the chicken are absent in the duck. Sequence elements for heavy-strand replication in mammals are conserved in the duck and chicken control regions. Estimates of divergence for ribosomal RNAs and proteins based on total substitutions, transversions, and amino acid replacements show that all the duck/chicken values are lower than the corresponding mammal/mammal (cow, human, mouse) values. If paleontological data suggesting that avian and eutherian ordinal radiation occurred at approximately the same time are correct, this suggests that at great evolutionary distance, rate of mitochondrial DNA evolution in birds is somewhat decelerated compared to mammals.

Population evolution of western Canary Island lizards (Gallotia galloti): 4-base endonuclease restriction fragment length polymorphisms of mitochondrial DNA

Abstract The mitochondrial DNA evolution of the western Canary Island lacertid, Galloti galloti , was studied using six restriction enzymes ( Hae III, Mva I, Hin fI, Taq I, Msp I and Dsa V). The population phylogeny ( G. stehlini , from the adjacent island of Gran Canaria, was used as an outgroup) based on 56 restriction fragments from the first two enzymes indicates two distinct lineages; a 'northern' lineage of La Palma, north Tenerife and south Tenerife populations and a 'southern' lineage of populations from Gomera and Hierro. The relationships within the northern lineage are also supported by an additional analysis of 132 restriction fragments from the remaining four enzymes. This molecular phylogeny argues for the recognition of two subspecies corresponding to the two main lineages and against the recognition of the six current subspecies which are based on inadequate 'conventional' criteria.

Population evolution of western Canary Island lizards (Gallotia galloti): 4-base endonuclease restriction fragment length polymorphisms of mitochondrial DNA

The mitochondrial DNA evolution of the western Canary Island lacertid, Galloti galloti , was studied using six restriction enzymes (Hae III, Mva I, Hin fI, Taq I, Msp I and Dsa V). The population phylogeny (G. stehlini, from the adjacent island of Gran Canaria, was used as an outgroup) based on 56 restriction fragments from the first two enzymes indicates two distinct lineages; a 'northern' lineage of La Palma, north Tenerife and south Tenerife populations and a 'southern' lineage of populations from Gomera and Hierro. The relationships within the northern lineage are also supported by an additional analysis of 132 restriction fragments from the remaining four enzymes. This molecular phylogeny argues for the recognition of two subspecies corresponding to the two main lineages and against the recognition of the six current subspecies which are based on inadequate 'conventional' criteria.

Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: Rapid evolution in warm-blooded vertebrates

By using complete sequence data of mitochondrial DNAs, three Markov models (Dayhoff, Proportional, and Poisson models) for amino acid substitutions during evolution were applied in maximum likelihood analyses of mitochondrially encoded proteins to estimate a phylogenetic tree depicting human, cow, whale, and murids (mouse and rat), with chicken, frog, and carp as outgroups. A cow/whale clade was confirmed with a more than 99.8% confidence level by any of the three models, but the branching order among human, murids, and the cow/whale clade remained uncertain. It turned out that the Dayhoff model is by far the most appropriate model among the alternatives in approximating the amino acid substitutions of mitochondrially encoded proteins, which is consistent with a previous analysis of a more limited data set. It was shown that the substitution rate of mitochondrially encoded proteins has increased in the order of fishes, amphibians, birds, and mammals and that the rate in mammals is at least six times, probably an order of magnitude, higher than that in fishes. The higher evolutionary rate in birds and mammals than in amphibians and fishes was attributed to relaxation of selective constraints operating on proteins in warm-blooded vertebrates and to high mutation rate of bird and mammalian mitochondrial DNAs.

Phylogeny of the slow lorises (genusNycticebus): An approach using mitochondrial DNA restriction enzyme analysis

Mitochondrial DNA polymorphisms in 15 specimens of three species of slow lorises-Nycticebus coucang, N. intermedius, andN. pygmaeus-were analyzed in order to study the evolutionary relationships among the species. Eight restriction types were observed in the samples. Phylogenetic trees constructed on the basis of genetic distances showed that the slow lorises sort into two clusters: four types ofN. coucang and three types ofN. intermedius plus one type ofN. pygmaeus. Our results suggest that there are two valid species in the genusNycticebus-N. coucang, andN. pygmaeus-and thatN. intermedius should be included withinN. pygmaeus. Divergence between the two species may have begun 2.7 Ma (million years ago). Evolution of gross morphology, chromosomes, and mitochondrial DNA in the slow lorises appears to be concordant.

Mitochondrial DNA evolution at a turtle's pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines.

Evidence is compiled suggesting a slowdown in mean microevolutionary rate for turtle mitochondrial DNA (mtDNA). Within each of six species or species complexes of Testudines, representing six genera and three taxonomic families, sequence divergence estimates derived from restriction assays are consistently lower than expectations based on either (a) the dates of particular geographic barriers with which significant mtDNA genetic clades appear associated or (b) the magnitudes of sequence divergence between mtDNA clades in nonturtle species that otherwise exhibit striking phylogeographic concordance with the genetic partitions in turtles. Magnitudes of the inferred rate slowdowns average eightfold relative to the "conventional" mtDNA clock calibration of 2%/Myr sequence divergence between higher animal lineages. Reasons for the postulated deceleration remain unknown, but two intriguing correlates are (a) the exceptionally long generation length most turtles and (b) turtles' low metabolic rate. Both factors have been suspected of influencing evolutionary rates in the DNA sequences of some other vertebrate groups. Uncertainities about the dates of cladogenetic events in these Testudines leave room for alternatives to the slowdown interpretation, but consistency in the direction of the inferred pattern, across several turtle species and evolutionary settings, suggests the need for caution in acceptance of a universal mtDNA-clock calibration for higher animals.

Animal Mitochondrial DNA: Structure and Evolution

Publisher Summary This chapter describes structural features and evolution of metazoan mitochondrial DNA (mtDNA) molecules. Throughout the evolution of metazoa, gene content of mitochondria-genomes is highly conserved, as has the close packing of genes. Most of the occasional sequence expansions that have occurred, by way of either repeated or noncoding unique sequences, are found in the control or putative control region, rather than being dispersed between genes. Of the 13 open reading frames recognized in the human mtDNA molecules, four (COI, COII, COIII, and Cyt b) are originally identified in regard to the proteins they encode, from similarities of their predicted amino acid sequences to known amino acid sequences of bovine proteins, and predicted amino acid sequences of yeast mt-protein genes. Among mtDNAs of vertebrates and higher invertebrates, there are genes that overlap. Some overlaps are among the 3′ ends of two genes that are encoded in opposite strands of the molecule. The extent of size reduction within metazoan mitochondrial-transfer RNA (mt-tRNA) gene sets strongly correlates with the degree to which the more variable secondary structure element-forming regions of mt-rRNA genes are lost.

African Populations and the Evolution of Human Mitochondrial DNA

The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.

Mitochondrial DNA evolution in lagomorphs: Origin of systematic heteroplasmy and organization of diversity in European rabbits

A characterization was conducted on mitochondrial DNA (mtDNA) molecules extracted separately from 107 European rabbits (Oryctolagus cuniculus) both wild and domestic, 13 European hares (Lepus capensis), and 1 eastern cottontail (Sylvilagus floridanus). Experimentally this study took into account restriction site polymorphism, overall length variation of the noncoding region, and numbers of repeated sequences. Nucleotide divergences indicate that the mtDNAs from the three species derived from a common ancestor some 6–8 million years (Myr) ago. Every animal appeared heteroplasmic for a set of molecules with various lengths of the noncoding region and variable numbers of repeated sequences that contribute to them. This systematic heteroplasmy, most probably generated by a rate of localized mtDNA rearrangements high enough to counterbalance the cellular segregation of rearranged molecules, is a shared derived character of leporids. The geographic distribution of mtDNA polymorphism among wild rabbit populations over the western European basin shows that two molecular lineages are represented, one in southern Spain, the second over northern Spain, France, and Tunisia. These two lineages derived from a common ancestor some 2 Myr ago. Their present geographical distribution may be correlated to the separation of rabbits into two stocks at the time of Mindel glaciation. Finally the distribution of mtDNA diversity exhibits a mosaic pattern both at inter- and intrapopulation levels.

Mitochondrial DNA Variation and the Phylogeny of Zonotrichia

Mitochondrial DNA Variation and the Phylogeny of Zonotrichia

Mitochondrial DNA Variation, Population Structure, and Evolution of the Common Grackle (Quiscalus quiscula)

Mitochondrial DNA Variation, Population Structure, and Evolution of the Common Grackle (Quiscalus quiscula)

The evolution of mitochondrial DNA in Partula

The mitochondrial DNA of species of land snails of the genus Partula from the Society Islands has been analysed by means of restriction enzymes to determine relationships within the genus. Seventeen variable restriction sites were mapped onto the 14.5 kb mtDNA. These sites are highly variable within species. In P. suturalis, those genotypes occurring within a population are usually separated by single-step changes, and the differences between populations are geographically coherent. There is no detectable association between the distribution of mitochondrial genotypes and the occurrence of dextral or sinistral populations, confirming that chirality does not constitute a genetic barrier in this species. P. taeniata also shows a coherent geographic pattern of genotype distribution within and between populations. The mitochondrial differences between morphologically similar populations in the northeast and northwest suggest that the similarity may be the result of convergence. Despite the regular patterns of distribution within species, some genotypes are widely shared among species. One pattern was found in four species on Moorea and two species on the neighbouring island of Tahiti. Shared genotypes may represent ancestral forms or they may have resulted from hybridization. However we believe that the most attractive hypothesis is that they are subject to selection. Studies of Partula demonstrate that the evolution of the morphological, electro-phoretic, and mitochondrial phenotypes occur at variable rates, independently of one another.