Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes

@article{Pesole1999NucleotideSR,
  title={Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes},
  author={Graziano Pesole and Carmela Gissi and Anna De Chirico and Cecilia Saccone},
  journal={Journal of Molecular Evolution},
  year={1999},
  volume={48},
  pages={427-434}
}
Abstract. We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some important ``genomic laws.'' The main conclusions can be summarized as follows. (1) High intragenomic… 
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TLDR
The variability of the mitochondrial metazoan genome is discussed, with particular reference to mitochondrial DNA in mammals, and in light of the recent assumption that a small segment of mitochondrial DNA may be used, particularly in Metazoa, as a species marker, some data on mitochondrial gene variability at the inter-species/intra-species boundary are reported.
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References

SHOWING 1-10 OF 50 REFERENCES
Rate variation in nucleotide substitutions among sites of the D-loop region of humans
The pattern of rate variation in nucleotide substitutions among sites has been investigated on the main non coding region (D-loop) of human mitochondrial (mt) DNA. The D-loop, which contains
Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes.
  • M. Lynch
  • Biology, Medicine
    Molecular biology and evolution
  • 1996
TLDR
A comparative study of the transfer RNA genes in animal mitochondrial and nuclear genomes demonstrates that the former accumulate nucleotide substitutions much more rapidly than do the latter, and several lines of evidence are consistent with the idea that the excess substitutions are mildly deleterious.
Rapid evolution of animal mitochondrial DNA.
  • W. Brown, M. George, A. Wilson
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1979
TLDR
The rate of evolution of the mitochondrial genome appears to exceed that of the single-copy fraction of the nuclear genome by a factor of about 10 and is likely to be an extremely useful molecule to employ for high-resolution analysis of the evolutionary process.
Rates of mitochondrial DNA evolution in sharks are slow compared with mammals
TLDR
Examination of mtDNA sequence variation for 13 species of sharks from two orders that are well represented in the fossil record to test the constancy hypothesis finds differences in mtDNA substitution rates among taxa indicate that it is inappropriate to use a calibration for one group to estimate divergence times or demographic parameters for another group.
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.
  • K. H. Wolfe, W. Li, P. Sharp
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1987
TLDR
The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.
Mitochondrial DNA and two perspectives on evolutionary genetics
This essay reviews comparative studies of animal mitochondrial DNA (mtDNA), with emphasis on findings made and ideas developed at Berkeley. It argues that such studies are bringing together two
The marsupial mitochondrial genome and the evolution of placental mammals.
TLDR
The entire nucleotide sequence of the mitochondrial genome of the American opossum, Didelphis virginiana, was determined and it can be shown that rodents represent an earlier branch among placental mammals than primates and artiodactyls and that artiodACTyls share a common ancestor with carnivores.
Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome.
TLDR
Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog and a mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of vertebrate mitochondrial genes, implicate gene order as a reliable phylogenetic character.
Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes
TLDR
The old CUN gene now codes for an extra 24 amino acids at the amino end of subunit 5 in NADH dehydrogenase, which leads us to propose a pathway relating the arrangements of other genes in mitochondrial DNAs from four animal phyla.
The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA
TLDR
It has been shown that, with the exception of the D loop and another small segment near the origin of replication, the mtDNA sequences are completely saturated by the rRNAs, poly(A)-containing RNAs and tRNA coded for by the two strands.
...
1
2
3
4
5
...