The rate of adaptive evolution in animal mitochondria

Molecular Ecology

Volumn 25, Issue 1, 2016, Pages 67-78

  James, Jennifer E ^a   Piganeau, Gwenael ^b,c   Eyre Walker, Adam ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b SORBONNE UNIVERSITÉ   (France)

^c LABORATOIRE ARAGO   (France)

Author keywords

adaptive evolution; distribution of fitness effects; genetic diversity; mitochondria; mutation rate; site frequency spectrum

Indexed keywords

MITOCHONDRIAL DNA;

ADAPTATION; ANIMAL; BIOLOGICAL MODEL; GENETIC POLYMORPHISM; GENETICS; MITOCHONDRION; MOLECULAR EVOLUTION; MUTATION RATE;

ADAPTATION, BIOLOGICAL; ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; MITOCHONDRIA; MODELS, GENETIC; MUTATION RATE; POLYMORPHISM, GENETIC;

EID: 84954078814     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.13475     Document Type: Review

References (57)

1. Ballard JWO, Kreitman M, (1994) Unraveling selection in the mitochondrial genome of Drosophila. Genetics, 138, 757-772
2. Ballard JWO, Rand DM, (2005) The population biology of mitochondrial DNA and its phylogenetic implications. Annual Review of Ecology, Evolution, and Systematics, 36, 621-642
3. Ballard JWO, Whitlock MC, (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729-744
4. Bazin E, Duret L, Penel S, Galtier N, (2005) Polymorphix: a sequence polymorphism database. Nucleic Acids Research, 33 (Database Issue), 481-484
5. Bazin E, Glémin S, Galtier N, (2006) Population size does not influence mitochondrial genetic diversity in animals. Science, 312, 570-572
6. Berlin S, Tomaras D, Charlesworth B, (2007) Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome. Heredity, 99, 389-396
7. Betancourt AJ, Welch JJ, Charlesworth B, (2009) Reduced effectiveness of selection caused by a lack of recombination. Current Biology, 19, 655-660
8. Birky CW, (1995) Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proceedings of the National Academy of Sciences of the United States of America, 92, 11331-11338
9. Boore JL, (1999) Animal mitochondrial genomes. Nucleic Acids Research, 27, 209-210
10. Boyko AR, Williamson S, Indap A, et al. (2008) Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genetics, 4, e1000083
11. Brown WM, George M, Wilson AC, (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America, 76, 1967-1971
12. Campos JL, Halligan DL, Haddrill PR, Charlesworth B, (2014) The relation between recombination rate and patterns of molecular evolution and variation in drosophila melanogaster. Molecular Biology and Evolution, 31, 1010-1028
13. Castellano D, Coronado-Zamora M, Campos JL, Eyre-Walker A, (2015) Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila. Molecular Biology and Evolution, in press
14. Castellana S, Vicario S, Saccone C, (2011) Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein-coding genes. Genome Biology and Evolution, 3, 1067-1079
15. Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD, (2008) Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS ONE, 3, e2201
16. Charlesworth J, Eyre-Walker A, (2006) The rate of adaptive evolution in enteric bacteria. Molecular Biology and Evolution, 23, 1348-1356
17. Charlesworth J, Eyre-Walker A, (2008) The McDonald-Kreitman test and slightly deleterious mutations. Molecular Biology and Evolution, 25, 1007-1015
18. Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK, (2000) High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science, 289, 2342-2344
19. Doan JW, Schmidt TR, Wildman DE, et al. (2004) Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitution in anthropoid primates. Molecular Phylogenetics and Evolution, 33, 944-950
20. Dos Reis M, Yang Z, (2013) Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics, 195, 195-204
21. Dowling DK, Abiega KC, Arnqvist G, (2007) Temperature-specific outcomes of cytoplasmic-nuclear interactions on egg-to-adult development time in seed beetles. Evolution, 61, 194-201
22. Eyre-Walker A, Keightley PD, (2009) Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Molecular Biology and Evolution, 26, 2097-2108
23. Eyre-Walker A, Woolfit M, Phelps T, (2006) The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics, 173, 891-900
24. Fan W, Waymire KG, Narula N, et al. (2008) A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations. Science, 319, 958-962
25. Fay JC, Wyckoff GJ, Wu C, (2001) Positive and negative selection on the human genome. Genetics, 158, 1227-1234
26. da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A, (2008) The adaptive evolution of the mammalian mitochondrial genome. BMC Genomics, 9, 119
27. Galtier N, Nabholz B, Glémin S, Hurst GDD, (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology, 18, 4541-4550
28. Goldman N, Yang Z, (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11, 725-736
29. Gossmann TI, Keightley PD, Eyre-Walker A, (2012) The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes. Genome Biology and Evolution, 4, 658-667
30. Grossman LI, Wildman DE, Schmidt TR, Goodman M, (2004) Accelerated evolution of the electron transport chain in anthropoid primates. Trends in Genetics, 20, 578-585
31. Haldane JBS, (1937) The effect of variation on fitness. The American Naturalist, 71, 337-349
32. Hickey AJR, (2008) Avian mtDNA diversity?: an alternate explanation for low mtDNA diversity in birds: an age-old solution? Heredity, 100, 443
33. Hurst GDD, Jiggins FM, (2005) Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proceedings Biological Sciences/The Royal Society, 272, 1525-1534
34. Keightley PD, Eyre-Walker A, (2012) Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small. Journal of Molecular Evolution, 74, 61-68
35. Lynch M, (2010) Evolution of the mutation rate. Trends in Genetics, 26, 345-352
36. Meiklejohn CD, Montooth KL, Rand DM, (2007) Positive and negative selection on the mitochondrial genome. Trends in Genetics, 23, 259-263
37. Messer PW, Petrov DA, (2013) Frequent adaptation and the McDonald-Kreitman test. Proceedings of the National Academy of Sciences of the United States of America, 110, 8615-8620
38. Nabholz B, Mauffrey J-F, Bazin E, Galtier N, Glémin S, (2008) Determination of mitochondrial genetic diversity in mammals. Genetics, 178, 351-361
39. Nachman MW, (1998) Deleterious mutations in animal mitochondrial DNA. Genetica, 102-103, 61-69
40. Naylor GJ, Collins TM, Brown WM, (1995) Hydrophobicity and phylogeny. Nature, 373, 565-566
41. Otto SP, Whitlock MC, (1997) The probability of fixation in populations of changing size. Genetics, 146, 723-733
42. Pesole G, Gissi C, De Chirico A, Saccone C, (1999) Nucleotide substitution rate of mammalian mitochondrial genomes. Journal of Molecular Evolution, 48, 427-434
43. Piganeau G, Eyre-Walker A, (2009) Evidence for variation in the effective population size of animal mitochondrial DNA. PLoS ONE, 4, 2-9
44. Popadin K, Polishchuk LV, Mamirova L, Knorre D, Gunbin K, (2007) Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proceedings of the National Academy of Sciences of the United States of America, 104, 13390-13395
45. Rand DM, Kann LM, (1996) Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Molecular Biology and Evolution, 13, 735-748
46. Rand DM, Kann LM, (1998) Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica, 102-103, 393-407
47. Shen Y-Y, Shi P, Sun Y-B, Zhang Y-P, (2009) Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Research, 19, 1760-1765
48. Shen Y-Y, Liang L, Zhu Z-H, Zhou W-P, Irwin DM, Zhang Y-P, (2010) Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proceedings of the National Academy of Sciences of the United States of America, 107, 8666-8671
49. Smith NGC, Eyre-Walker A, (2003) Partitioning the variation in mammalian substitution rates. Molecular Biology and Evolution, 20, 10-17
50. Stewart JB, Larsson N-G, (2014) Keeping mtDNA in Shape between Generations. PLoS Genetics, 10, e1004670
51. Stewart JB, Freyer C, Elson JL, Larsson N-G, (2008a) Purifying selection of mtDNA and its implications for understanding evolution and mitochondrial disease. Nature Reviews Genetics, 9, 657-662
52. Stewart JB, Freyer C, Elson JL, et al. (2008b) Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biology, 6, 0063-0071
53. Stoletzki N, Eyre-Walker A, (2011) Estimation of the neutrality index. Molecular Biology and Evolution, 28, 63-70
54. Sun Z, Wan D-G, Murphy RW, Ma L, Zhang X-S, Huang D-W, (2009) Comparison of base composition and codon usage in insect mitochondrial genomes. Genes & Genomics, 31, 65-71
55. Torroni A, Achilli A, Macaulay V, Richards M, Bandelt H-J, (2006) Harvesting the fruit of the human mtDNA tree. Trends in Genetics, 22, 339-345
56. Yang Z, (2006) Computational Molecular Evolution. Oxford University Press, New York
57. Yang Z, (2007) PAML 4: a program package for phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24, 1586-1591