On transition bias in mitochondrial genes of pocket gophers

Journal of Molecular Evolution

Volumn 43, Issue 1, 1996, Pages 32-40

  Xia, Xuhua ^a   Hafner, Mark S ^a   Sudman, Philip D ^a,b  

^a LOUISIANA STATE UNIVERSITY   (United States)

^b W O Farber Center for Civic Leadership   (United States)

Author keywords

Mitochondrial protein gene; Molecular evolution; Purifying selection; Transition bias

Indexed keywords

ARTICLE; EVOLUTION; GENETIC ANALYSIS; GENETIC SELECTION; MITOCHONDRION; MUTATION;

EID: 0029819269     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02352297     Document Type: Article

References (36)

1. Aquadro CF, Greenberg BD (1983) Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics 103:287-312
2. Bechkenhach AT, Thomas WK, Homayoun S (1990) Intraspecific sequence variation in the mitochondrial genome of rainbow trout (Oncorhynchus mykiss). Genome 33:13-15
3. Brown WM (1985) The mitochondrial genome of animals. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum Press, New York, p 95
4. Brown GG, Simpson MV (1982) Novel features of animal mtDNA evolution as shown by sequences of two rate cytochrome oxidase subunit II genes. Proc Natl Acad Sci USA 79:3246-3250
5. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: the tempo and mode of evolution. J Mol Evol 18:225-239
6. Curtis SE, Clegg MT (1984) Molecular evolution of chloroplast DNA sequences. Mol Biol Evol 1:291-301
7. DeSalle R Freedman T, Prager EM, Wilston AC (1987) Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J Mol Evol 26:157-164
8. DeWalt TS, Sudman PD, Hafner MS, Davis SK (1993) Phylogenetic relationship of pocket gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochrome b sequences. Mol Phylogen Evol 2:193-204
9. Edwards SV, Wilson AC (1990) Phylogcnetically informative length polymorphisms and sequence variability in mitochondrial DNA of Australian songbirds (Pomatostomus). Genetics 126:695-711
10. Felsenstein J (1993) PHYLIP 3.5 (phylogeny inference package). Department of Genetics, University of Washington, Seattle
11. Fitch W (1980) Estimating the total number of nuclcotide substitutions since the common ancestor of a pair of homologous genes: comparison of several methods and three beta hemoglobin messenger RNAs. J Mol Evol 16:153-209
12. Gojobori T, Li WH, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360-369
13. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736
14. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864
15. Hafner MS, Sudman PD, Villablanca FX, Spradling TA, Demastes JW, Nadler SA (1994) Disparate rates of molecular evolution in cospeciating hosts and parasites. Science 265:1087-1090
16. Irwin DM, Kocher TD, Wilson AC (1991) Evolution of the cytochrome h gene of mammals. J Mol Evol 32:128-144
17. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
18. Kishino H, Miyata T, Hasegawa M (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 31:151-160
19. Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96-99
20. Li WH, Wu CI, Luo CH (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions and its evolutionary implications. J Mol Evol 21:58-71
21. Li WH, Wu CI, Luo CH (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150-174
22. Miyata T, Miyazawa S, Yasunaga T (1979) Two types of amino acid substitution in protein evolution. J Mol Evol 12:219-236
23. Myers KA, Raffhill R, O'Conner PJ (1988) Repair of alkylated purines in the hepatic DNA of mitochondria and nuclei in the rat. Carcinogenesis 9:285-292
24. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
25. SAS Institute (1994) SAS/STAT User's guide, version 6, 4th ed, vol I. p 222
26. Satta Y, Ishiwa H, Chigusa SI (1987) Analysis of nucleotide substitutions of mitochondrial DNAs in Drosophila melanogaster and its sibling species. Mol Biol Evol 4:638-650
27. Satoh MS, Huh N, Rajewsky MF, Turoki T (1988) Enzymatic removal of O-ethylguanine from mitochondrial DNA in rat tissues exposed to N-ethyl-N-nitrosourea in vivo. J Biol Chem 263:6854-6856
28. Swofford DL (1993) Phylogenetic analysis using parsimony (PAUP). version 3.2. University of Illinois, Champaign
29. Thomas WK, Beckenbach AT (1989) Variation in Salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution. J Mol Evol 29:233-245
30. Thomas WK, Wilson AC (1991) Mode and tempo of molecular evolution in the nematode Caenorhabditis: cytochrome oxidase II and calmodulin sequences. Genetics 128:269-279
31. Thomas WK, Maa J, Wilson AC (1989) Shifting constraints on tRNA genes during mitochondrial DNA evolution in animals. New Biol 1:93-100
32. van Ooyen A, van den Berg J, Mantel N, Weissmann C (1979) Comparison of total sequence of a cloned rabbit β-globin gene and its flanking regions with a homologous mouse sequence. Science 206: 337-344
33. Vogel F, Kopun M (1977) Higher frequencies of transitions among point mutations. J Mol Evol 9:159-180
34. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial. chloroplast and nuclear DNAs. Proc Natl Acad Sci USA 84:9054-9058
35. Yang Z, (1994) Maximum likelihood phlogenetic estimation from DNA sequences with variable rates over sites: approximately methods. J Mol Evol 39:306-314
36. Yang Z (1995) Phylogenetic analysis by maximum likelihood (PAML), version 1.1. Institute of Molecular Evolutionary Genetics. The Pennsylvania State University