Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster

@article{HaagLiautard2008DirectEO,
  title={Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster},
  author={C. Haag-Liautard and Nicole R Coffey and D. Houle and M. Lynch and B. Charlesworth and P. Keightley},
  journal={PLoS Biology},
  year={2008},
  volume={6}
}
Mitochondrial DNA (mtDNA) variants are widely used in evolutionary genetics as markers for population history and to estimate divergence times among taxa. Inferences of species history are generally based on phylogenetic comparisons, which assume that molecular evolution is clock-like. Between-species comparisons have also been used to estimate the mutation rate, using sites that are thought to evolve neutrally. We directly estimated the mtDNA mutation rate by scanning the mitochondrial genome… Expand
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References

SHOWING 1-10 OF 54 REFERENCES
Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA
Two patterns are presented that illustrate the interaction of mutation and selection in the evolution of animal mtDNA: 1) variation among taxa in the ratio of polymorphism to divergence (rpd) atExpand
Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes.
TLDR
A large data set of complete vertebrate mitochondrial genomes is analyzed and it is indicated that different types of mutation respond differently to the D(ssH) gradient, which should form the basis of more realistic models of DNA and protein evolution in mitochondria. Expand
Comparative Genomics of Mitochondrial DNA in Drosophila simulans
  • J. Ballard
  • Biology, Medicine
  • Journal of Molecular Evolution
  • 2000
TLDR
A single evolutionary force may be causally linked to the observed patterns of mtDNA variation—a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci. Expand
Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary considerations.
TLDR
The sequence of a 8351-nucleotide mitochondrial DNA fragment has been obtained extending the knowledge of the Drosophila melanogaster mitochondrial genome to 90% of its coding region, and reflects a strong bias against G + C on both strands. Expand
The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA.
  • K. Tamura
  • Biology, Medicine
  • Molecular biology and evolution
  • 1992
TLDR
Both parametric and nonparametric analyses revealed a strong transition-transversion bias in nucleotide substitution, as was observed in mammalian mtDNA, which seems to be responsible for the extremely A+T-rich base composition of Drosophila mtDNA. Expand
Mitochondrial genotype affects fitness in Drosophila simulans.
TLDR
It is found that flies with the siI haplotype are fastest developing and have the lowest probability of surviving to three experimental periods, and Wild-type males with siIII mtDNA were more active while disruption of specific coadapted nucleo-mitochondrial complexes caused a significant decrease in activity. Expand
Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA
TLDR
This study presents the first direct experimental observations of the fate of random mtDNA mutations in the mammalian germ line and demonstrates the importance of purifying selection in shaping mitochondrial sequence diversity. Expand
Comparative Genomics of Mitochondrial DNA in Members of the Drosophila melanogaster Subgroup
  • J. Ballard
  • Biology, Medicine
  • Journal of Molecular Evolution
  • 2000
TLDR
Data presented here indicate that at least three broad mechanisms shape the evolutionary dynamics of mtDNA in these taxa, and the potential for comparative genomics to tease apart subtle forces that shape the evolution of DNA is shown. Expand
Incomplete maternal transmission of mitochondrial DNA in Drosophila.
TLDR
The possibility of incomplete maternal transmission of mitochondrial DNA (mtDNA) in Drosophila, previously suggested by the presence of heteroplasmy, was examined by intra- and interspecific backcrosses of Dosophila simulans and its closest relative, Drosophile mauritiana, and showed clear evidence for paternal leakage of mtDNA. Expand
High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome
TLDR
A direct and unbiased estimate of the nuclear mutation rate and its molecular spectrum is provided with a set of C. elegans mutation-accumulation lines that reveal a mutation rate about tenfold higher than previous indirect estimates and an excess of insertions over deletions. Expand
...
1
2
3
4
5
...