Accelerated evolution of cytochrome b in simian primates: Adaptive evolution in concert with other mitochondrial proteins?

Journal of Molecular Evolution

Volumn 47, Issue 3, 1998, Pages 249-257

  Andrews, T Daniel ^a   Jermiin, Lars S ^a   Easteal, Simon ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Adaptive; Coevolution; Cytochrome b; Cytochrome c oxidase; Fourfold degenerate; Mitochondrial DNA; Nonsynonymous; Primate; Relative rate; Transversion

Indexed keywords

CYTOCHROME B; CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

ADAPTATION; AMINO ACID SUBSTITUTION; ANIMAL TISSUE; ARTICLE; EVOLUTION; GENE SEQUENCE; MITOCHONDRION; MONKEY; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIMATE; SEQUENCE ANALYSIS;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SEQUENCE; ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CATS; CYTOCHROME B GROUP; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; HOMINIDAE; HUMANS; MAMMALS; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PRIMATES; RATS;

ANIMALIA; CETACEA; FELIS CATUS; MAMMALIA; PRIMATES; SIMIAE; TARSIUS BANCANUS; TARSIUS SYRICHTA;

EID: 0031714828     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006382     Document Type: Article

References (47)

1. Adkins RM, Honeycutt RL (1994) Evolution of the primate cytochrome c oxidase subunit II gene. J Mol Evol 38:215-231
2. Adkins RM, Honeycutt RL, Disotell TR (1996) Evolution of eutherian cytochrome c oxidase subunit II: heterogeneous rates of protein evolution and altered interaction with cytochrome c. Mol Biol Evol 13:1393-1404
3. Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organisation of the human mitochondrial genome. Nature 290:457-465
4. Arnason U, Gullberg A, Widegren B (1991) The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. J Mol Evol 33:556-568
5. Arnason U, Bodin K, Gullberg A, Ledje C, Mouchaty S (1995) A molecular view of pinniped relationships with particular emphasis on the true seals. J Mol Evol 40:78-85
6. Asenjo AB, Rim J, Oprian DD (1994) Molecular determinants of human red/green colour discrimination. Neuron 12:1131-1138
7. Baba ML, Darga LL, Goodman M, Czelusniak J (1981) Evolution of cytochrome c investigated by the maximum parsimony method. J Mol Evol 17:197-213
8. Brasseur G, Saribas AS, Daldal F (1996) A compilation of mutations located in the cytochrome b subunit of the bacterial and mitochondrial bcl complex. Biochim Biophys Acta 1275:61-69
9. Cann RL, Brown WM, Wilson AC (1984) Polymorphic sites and the mechanism of evolution in human mitochondrial DNA. Genetics 106:479-499
10. Collura RV, Stewart CB (1995) Insertion and duplications of mtDNA in the nuclear genomes of old world monkeys and hominoids. Nature 378:485-489
11. Evans MJ, Scarpulla RC (1988) The human somatic cytochrome c gene: two classes of processed pseudogenes demarcate a period of rapid molecular evolution. Proc Natl Acad Sci USA 85:9625-9629
12. Fitch W (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223-257
13. Gadaleta G, Pepe G, De Candia G, Quagliariello C, Sbisa E, Saccone C (1989) The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J Mol Evol 28:497-516
14. Groves CP (1989) A theory of human and primate evolution. Oxford University Press, Oxford
15. Hatefi Y (1985) The mitochondrial electron transport and oxidative phosphorylation system. Annu Rev Biochem 54:1015-1069
16. Irwin DM, Arnason U (1994) Cytochrome b gene of maritime mammals: phylogeny and evolution. J Mammal Evol 2:37-55
17. Irwin DM, Kocher TD, Wilson AC (1991) Evolution of the cytochrome b gene of mammals. J Mol Evol 32:128-144
18. Janke A, Feldmaier-Fuchs G, Thomas WK, von Haessler A, Pääbo A (1994) The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256
19. Jermiin LS, Graur D, Lowe RM, Crozier RH (1994) Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes. J Mol Evol 39:160-173
20. Jermiin LS, Olsen GJ, Mengersen KL, Easteal S (1997) Majority-rule consensus of phylogenetic trees obtained by maximum-likelihood analysis. Mol Biol Evol 14:1296-1302
21. Komiyama NH, Miyazaki G, Tame J, Nagai K (1995) Transplanting a unique allosteric effect from crocodile into human haemoglobin. Nature 373:244-246
22. Kornegay JR, Schilling JW, Wilson AC (1994) Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin. Mol Biol Evol 11:921-928
23. Kreitman M, Akashi H (1995) Molecular evidence for natural selection. Annu Rev Ecol Syst 26:403-422
24. Li W-H (1993) Unbiased estimation of the rates of synonymous and non-synonymous substitution. J Mol Evol 36:96-99
25. Li W-H (1997) Fundamentals of molecular evolution. Sinauer, Sunderland, MA
26. Linnane AW, Zhang C, Baumer A, Nagley P (1992) Mitochondrial DNA mutation and the ageing process: bioenergy and pharmacological intervention. Mutat Res 275:195-208
27. Lopez JV, Cevario S, O'Brien SJ (1996) Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and transposed mtDNA repeat, Numt, in the nuclear genome. Genomics 33:229-246
28. Ma D-P, Zharkikh A, Graur D, VandeBerg JL, Li W-H (1993) Structure and evolution of opossum, guinea pig and porcupine cytochrome b genes. J Mol Evol 36:327-334
29. Muse SV, Weir BS (1992) Testing for equality of evolutionary rates. Genetics 132:269-276
30. Osheroff N, Speck SH, Margoliash E, Veerman ECI, Wilms J, Konig BW, Muijsers AO (1983) The reaction of primate cytochromes c with cytochrome c oxidase. J Biol Chem 258:5731-5738
31. Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes: rates and interdependence between genes. Mol Biol Evol 10:271-281
32. Perutz MF (1983) Species adaptation in a protein molecule. Mol Biol Evol 1:1-28
33. Ramharack R, Deeley RG (1987) Structure and evolution of primate cytochrome c oxidase subunit II gene. J Biol Chem 262:14014-14021
34. Saitou N, Nei M (1987) The neighbour joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
35. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbour, NY.
36. Smith CAB (1986) Chi-squared tests with small numbers. Ann Hum Genet 50:163-167
37. Stewart CB, Schilling JW, Wilson AC (1987) Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330:401-404
38. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
39. Wolf MJ, Jermiin LS, Easteal S, Kahn S, McKay BD (1998) TrExML - a maximum likelihood program for exhaustive tree-space exploration (submitted)
40. Wu C-I, Li W-H (1985) Evidence for higher rates of nucleotide substitution in rodents that in man. Proc Natl Acad Sci USA 82:1741-1745
41. Wu W, Goodman M, Lomax MI, Grossman LI (1997) Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates. J Mol Evol 44:477-491
42. Xia D, Yu C-A, Kim H, Xia J-Z, Kachurin AM, Zhang L, Yu L, Deisenhofer J (1997) Crystal structure of the cytochrome bcl complex from bovine heart mitochondria. Science 277:60-66
43. Yang Z (1997) Phylogenetic analysis by maximum likelihood (PAML). Version 1.3. Department of Integrative Biology, University of California at Berkeley, Berkeley
44. Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650
45. Yoder AD, Cartmill M, Ruvolo M, Smith K, Vilgalys R (1996) Ancient single origin for Malagasy primates. Proc Natl Acad Sci USA 93: 5122-5126
46. Yokoyama R, Yokoyama S (1990) Convergent evolution of the red-and green-like visual pigment genes in fish, Astyanax fasciatus, and human. Proc Natl Acad Sci USA 87:9315-9318
47. Yokoyama S (1995) Amino acid replacements and wavelength absorption of visual pigments in vertebrates. Mol Biol Evol 12:53-61