Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates

Molecular Biology and Evolution

Volumn 13, Issue 7, 1996, Pages 933-942

  Zardoya, Rafael ^a   Meyer, Axel ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

maximum likelihood; maximum parsimony; mtDNA; protein coding genes; vertebrate phylogeny

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; EVOLUTION; GENETIC ANALYSIS; NONHUMAN; PHYLOGENY; VERTEBRATE;

MAMMALIA; TETRAPODA; VERTEBRATA;

EID: 0029834015     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025661     Document Type: Article

References (54)

1. ADACHI, J., and M. HASEGAWA. 1992. MOLPHY: programs for molecular phylogenetics I-PROTML: maximum likelihood inference of protein phylogeny. Computer science monographs, 27, Institute of Statistical Mathematics, Tokyo.
2. _. 1995. Phylogeny of whales: dependence of the inference on species sampling. Mol. Biol. Evol. 12:177-179.
3. ANDERSON, S., A. T. BANKIER, B. G. BARRELL et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-464.
4. ANDERSON, S., M. H. DE BRUIJN, A. R. COULSON, I. C. EPERON, F. SANGER, and I. G. YOUNG. 1982. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian genome. J. Mol. Biol. 156:683-717.
5. ARNASON, U., and A. GULLBERG. 1993. Comparison between the complete mitochondrial sequences of the blue and the fin whale, two species that can hybridize in nature. J. Mol. Evol. 37:312-322.
6. ARNASON, U., A. GULLBERG, E. JOHNSSON, and C. LEDJE. 1993. The nucleotide sequence of the mitochondrial DNA molecule of the Grey seal, Halichoerus grypus, and a comparison with mitochondrial sequences of other true seals. J. Mol. Evol. 37:323-330.
7. ARNASON, U., A. GULLBERG, and B. WIDEGREN. 1991. The complete nucleotide sequence of the mitochondrial DNA of the Fin whale, Balaenoptera physalus. J. Mol. Evol. 33: 556-568.
8. ARNASON, U., and E. JOHNSSON. 1992. The complete mitochondrial DNA sequence of the Harbor seal, Phoca vitulina. J. Mol. Evol. 43:493-505.
9. AVISE, J. C. 1994. Molecular markers, natural history, and evolution. Chapman and Hall, New York.
10. BENTON, M. J. 1990. Phylogeny of the major tetrapod groups: Morphological data and divergence dates. J. Mol. Evol. 30: 409-424.
11. BIBB, M. J., R. A. VAN ETTEN, C. T. WRIGHT, M. W. WALBERG, and D. A. CLAYTON. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167-180.
12. CAO, Y., J. ADACHI, A. JANKE, S. PAABO, and M. HASEGAWA. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 39:519-527.
13. CHANG, Y. S., F. L. HUANG, and T. B. LO. 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38:138-155.
14. CUMMINGS, M. P., S. P. OTTO, and J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
15. DEGLI ESPOSTI, M., S. DE VRIES, M. CRIMI, A. GHELLI, T. PATARNELLO, and A. MEYER. 1993. Mitochondrial cytochrome b: evolution and structure of the protein. Biochim. Biophys. Acta. (Bioenergetics) 1143:243-271.
16. DESJARDINS, P., and R. MORAIS. 1990, Sequence and gene organization of the chicken mitochondrial genome. J. Mol. Biol. 212:599-634.
17. DEVEREUX, J., P. HAEBERLI, and O. SMITHIES. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
18. EDWARDS, A. W. F., M. NEI, N. TAKEZAKI, and T. SITNIKOVA. 1995. Assessing molecular phylogenies. Science 267:253.
19. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
20. _. 1989. PHYLIP - phylogeny inference package (version 3.4.). Cladistics 5:164-166.
21. GADALETA G., G. PEPE, G. DE CANDIA, C. QUAGLIARIELLO, E. SBISA, and C. SACCONE. 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.
22. GRAYBEAL, A. 1994. Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Syst. Biol. 43:174-193.
23. HILLIS, D. M., and J. J. BULL. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
24. HILLIS, D. M., J. P. HUELSENBECK, and C. W. CUNNINGHAM. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
25. HILLIS, D. M., J. P. HUELSENBECK, and D. L. SWOFFORD. 1994. Hobgoblin of phylogenetics? Nature 369:363-364.
26. HORAI, S., K. HAYASAKA, R. KONDO, K. TSUGANE, and N. TAKAHATA. 1995. Recent african origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. USA 92:532-536.
27. JANKE, A., G. FELDMAIER-FUCHS, K. THOMAS, A. VON HAESELER, and S. PAÄBO. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256.
28. KISHINO, H., and M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
29. KOCHER, T. D., W. K. THOMAS, A. MEYER, S. V. EDWARDS, S. PAABO, F. X. VILLABLANCA, and A. C. WILSON. 1989. Dynamics of mitochondrial DNA evolution in animals. Proc. Natl. Acad. Sci. USA 86:6196-6200.
30. KRETTEK, A., A. GULLBERG, and U. ARNASON. 1995. Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla. J. Mol. Evol. 41:952-957.
31. LYNCH, M., and P. E. JARRELL. 1993. A method for calibrating molecular clocks and its application to animal mitochondrial DNA. Genetics 135:1197-1208.
32. MARTIN, M. J., E GONZALEZ-CANDELAS, F. SOBRINO, and J. DOPAZO. 1995. A method for determining the position and size of optimal sequence regions for phylogenetic analysis. J. Mol. Evol. 41:1128-1138.
33. MEYER, A. 1993. Evolution of mitochondrial DNA in fishes. Pp. 1-38 in P. W. HOCHACHKA and T. P. MOMMSEN, eds. Molecular biology frontiers, biochemistry and molecular biology of fishes. Vol. 2. Elsevier Science Publishers, Amsterdam.
34. _. 1994a. DNA technology and phylogeny of fish: molecular phylogenetic studies of fish. Pp. 219-249 in A. R. BEAUMONT, ed. Genetics and evolution of aquatic organisms. Chapman and Hall, London.
35. _. 1994b. Shortcomings of the cytochrome b gene as a molecular marker. Trends Ecol. Evol. 9:278-280.
36. MEYER, A. and A. C. WILSON. 1990. Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J. Mol. Evol. 31:359-364.
37. MILINKOVITCH, M. C., G. ORTI, and A. MEYER. 1995. Novel phylogeny of whales revisited but not revised. Mol. Biol. Evol. 12:518-520.
38. MOORE, W. S. 1995. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49:718-726.
39. NAYLOR, G. J., T. M. COLLINS, and W. M. BROWN. 1995. Hydrophobicity and phylogeny. Nature 373:555-556.
40. ORTI, G., and A. MEYER. 1996. Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleostean fishes. Mol. Biol. Evol. 13:556-573.
41. ROE, B. A., M. DIN-POW, R. K. WILSON, and J. F. WONG. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260:9759-9774.
42. RUSSO, C. A. M., N. TAKEZAKI, and M. NEI. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.
43. RZHETSKY, A, and M. NEI. 1994. Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J. Mol. Evol. 38:295-299.
44. SAIKI, R. K., D. H. GELFAND, S. STOFFEL, S. SCHARF, R. HIGUCHI, G. T. HORN, K. B. MULLIS, and H. A. ERLICH. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
45. SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
46. STEWART, C. B. 1993. The powers and pitfalls of parsimony. Nature 361:603-607.
47. SWOFFORD, D. L. 1993. PAUP: phylogenetic analysis using parsimony. Version 3.1.1. Illinois Natural History Survey, Champaign, Ill.
48. TAJIMA, F. 1991. Determination of window size for analyzing DNA sequences. J. Mol. Evol. 33:470-473.
49. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of human and the apes. Evolution 37: 221-244.
50. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 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.
51. TZENG, C. S., C. F. HUI, S. C. SHEN, and P. C. HUANG. 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Res. 20:4853-4858.
52. XU, X., and A. ARNASON. 1994. The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region. Gene 148:357-362.
53. ZARDOYA, R., A. GARRIDO-PERTIERRA, and J. M. BAUTISTA. 1995. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 41:942-951.
54. ZARDOYA, R., and A. MEYER. 1996. The complete nucleotide sequence of the mitochondrial genome of the lungfish (Protopterus dolloi), supports its phylogenetic position as a close relative of land vertebrates. Genetics 142:1249-1263.