Mammalian evolution: Timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition

Systematic Biology

Volumn 48, Issue 1, 1999, Pages 76-93

  Penny, David ^a   Hasegawa, Masami ^b   Waddell, Peter J ^a,b   Hendy, Michael D ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

Author keywords

Amino acid compos ition; Constant site removal LogDeterminant; K T boundary; Mammalian evolution; Mitochondrial DNA genomes; Rodent monophyly

Indexed keywords

AVES; CETACEA; DINOSAURIA; EQUUS CABALLUS; MAMMALIA; PRIMATES; RHINOCEROS; RODENTIA;

AMINO ACID; MITOCHONDRIAL DNA; PROTEIN;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; COMPUTER PROGRAM; EVOLUTION; GENETICS; HUMAN; MAMMAL;

AMINO ACIDS; ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION; HUMANS; MAMMALS; PROTEINS; SOFTWARE;

EID: 0033085036     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/106351599260454     Document Type: Article

References (72)

1. ADACHI, J., AND M. HASEGAWA. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459-468.
2. ARCHIBALD, J. D. 1996. Fossil evidence or a Late Cretaceous origin of "hoofed" mammals. Science 272:1150-1153.
3. BAR-HEN, A., AND D. PENNY. 1996. Estimating the bias on the LogDeterminant transformation for evolutionary trees. Appl. Math. Lett. 9:1-5.
4. BARRY, D., AND J. A. HARTIGAN. 1987. Asynchronous distance between homologous DNA sequences. Biometrics 43:261-276.
5. BENTON, M. J. 1997. Vertebrate paleontology. Chapman and Hall, New York.
6. BROMHAM, L. D., M. J. PHILLIPS, AND D. PENNY. In press. Growing up with dinosaurs: Molecular dates and the mammalian radiation. Trends Ecol. Evol.
7. BROMHAM, L. D., A. RAMBAUGH, A. COOPER, R. FORTEY, AND D. PENNY 1998. Testing the Cambrian explosion hypothesis by using a molecular dating technique. Proc. Natl. Acad. Sci. USA 95:12386-12389.
8. CAO, Y., A. JANKE A., P. J. WADDELL, M. WESTERMAN, O. TAKENAKA, S. MURATA, N. OKADA, S. PÄÄBO, AND M. HASEGAWA. 1998. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47:307-322.
9. CAO, Y., N. OKADA, AND M. HASEGAWA. 1997. Phylogenetic position of guinea pig revisited. Mol. Biol. Evol. 14:461-164.
10. CHANG, J.T. 1996. Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency. Math. Biosci. 137:51-93.
11. CHARLESTON, M. 1998. Spectrum. Available from http: //taxonomy.zoology.gla.ac.uk/∼mac/spectrum/.
12. COOPER, A., AND D. PENNY. 1997. Mass survival of birds across the Cretaceous/Tertiary boundary. Science 275:1109-1113.
13. CREE, A., C H. DAUGHERTY, AND J. M. HEY. 1995. Reproduction of a rare New Zealand reptile, the tuatara Sphenodon punctatus, on rat-free and rat-inhabited islands. Conserv. Biol. 9:373-383.
14. D'ERCHIA, A. M., C. GISSI, G. PESOLE, C. SACCONE, AND U. ARNASON 1996. The guinea-pig is not a rodent. Nature 381:597-600.
15. FEDUCCIA, A. 1995. Explosive evolution in Tertiary birds and mammals. Science 267:63-64.
16. FELSENSTEIN, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
17. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
18. FOSTER, P.G. 1997. Phylogenetic implications of the effect of nucleotide bias on amino acid composition. Ph.D. Thesis, University of Ottawa, Ottawa, Canada.
19. FOSTER, P. G., L. S. JERMIIN, AND D. A. HICKEY. 1997. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44:282-288.
20. GRAUR, D., W. A. HIDE, AND W.-H. LI. 1991. Is the guinea-pig a rodent? Nature 351:649-652.
21. GRAUR, D., L. DURET, and M. GOUY. 1996. Phylogenetic position of the order Lagomorpha. Nature. 379:333-335.
22. GU, X., AND W.-H. LI. 1996. Bias-corrected paralinear and LogDet distances and tests of molecular clocks and phylogenies under nonstationary nucleotide frequencies. Mol. Biol. Evol. 13:1375-1382.
23. HASEGAWA, M., AND Y. HASHIMOTO. 1993. Ribosomal RNA trees misleading? Nature 361:23.
24. HASEGAWA, M.,H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:160-174.
25. HEDGES, S.B., P.H. PARKER, C.G. SIBLEY, AND S. KUMAR. 1996. Continental breakup and the diversification of birds and mammals. Nature 381:226-229.
26. HENDY, M. D., AND D. PENNY. 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38:297-309.
27. HENDY, M. D., AND D. PENNY. 1993. Spectral analysis of phylogenetic data. J. Class. 10:5-24.
28. HOLMES, B. 1997. When we were worms. New Sci. 18th Oct: 30-35.
29. HÖSS, H. M, A. DILLING, A. CURRANT, AND S. PÄÄBO. 1996. Molecular phylogeny of the extinct ground sloth (Mylodon darwinii). Proc. Natl. Acad. Sci. USA 93:181-185.
30. HUSON, D. 1998. SplitsTree: Analysing and visualising evolutionary data. Bioinformatics 14:68-73.
31. JANKE, A., X. FU, AND U. ARNASON. 1997. The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria. Proc. Natl. Acad. Sci. USA 94:1276-1281.
32. KUMAR, S., AND S. B. HEDGES. 1998. A molecular timescale for vertebrate evolution. Nature 392:917-920.
33. LAKE, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances. Proc. Natl. Acad. Sci. USA 91:1455-1459.
34. LAKE, J. A. 1996. Phylogenetic inference: How much of evolutionary history is knowable? Mol. Biol. Evol. 14:213-219.
35. LENTO, G. M., R. E. HICKSON, G. K. CHAMBERS, AND D. PENNY. 1994. Use of spectral analysis to test hypotheses on the evolutionary origin of the pinnipeds. Mol. Biol. Evol. 12:28-52.
36. LOCKHART, P. J., A. W. D. LARKUM, M. A. STEEL, P. J. WADDELL, AND D. PENNY. 1996. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93:1930-1934.
37. LOCKHART, P. J., M. A. STEEL, M. A. HENDY, AND D. PENNY. 1994. Recovering evolutionary trees under a more general model of sequence evolution. Mol. Biol. Evol. 11:605-612.
38. MIYAMOTO, M., AND W. M. FITCH. 1995. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12:503-513.
39. NESSOV, L. A., J. D. ARCHIBALD, AND Z. KIELAN-JAWOROWSKA. 1998. Ungulate-like mammals from the Late Cretaceous of Uzbekistan and a phylogenetic analysis of Ungulomorpha. Bull. Carnegie Mus. Nat. Hist. 34:40-88.
40. OLSEN, G. J. 1987. Earliest phylogenetic branchings: Comparing rRNA-based evolutionary trees inferred with several techniques. Cold Spring Harbor Symp. Quant. Biol. 52:825-837.
41. PENNY, D. 1998. Combining molecules, fossils and theory in evolutionary biology. Pages 59-62 in Geology and genes (R. A. Cooper and C. M. Jones, eds.). Geological Society of New Zealand, Wellington.
42. PENNY, D., AND M. HASEGAWA. 1997. The platypus put in its place. Nature 387:549-550.
43. PENNY, D., M. D. HENDY, P. J. LOCKHART, AND M. A. STEEL. 1996. Corrected parsimony, minimum evolution and Hadamard conjugations. Syst. Biol. 45:593-603.
44. PHILLIPE, H. 1997. Rodent monophyly: Pitfalls of molecular phylogenies. J. Mol. Evol. 45:712-715.
45. PHILLIPS, M.J., AND D. PENNY. 1998. Mass survival of tetrapods across the Cretaceous-Tertiary boundary. Pages 63-65 in Geology and genes (R. A. Cooper and C. M. Jones, eds.). Geological Society of New Zealand, Wellington.
46. PRESS, W. H., B. P. FLANNERY, S. A. TEUKOLSKY, AND W.T. VETTERLING. 1989. Numerical recipes: The art of scientific computing. Cambridge Univ. Press, Cambridge, England.
47. PUMO, D. E., P. S. FINAMORE, W. R. FRANEK, C. J. PHILLIPS, S. TARZAMI, AND D. BALZARANO. 1998. Complete mitochondrial genome of a neotropical fruit bat, Artibeus jamaicensis, and a new hypothesis of the relationships of bats to other eutherian mammals. J. Mol. Evol. 47:709-712.
48. REYES, A., G. PESOLE, AND C. SACCONE. 1998. Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: Further evidence for rodent paraphyly. J. Mol. Evol. 15:499-505.
49. RICH, T. H., P. VICKERS-RICH, A. CONSTANTINE, T. F. FLANNERY, L. KOOL, AND N. VAN KLAVEREN. 1997. A tribosphenic mammal from the Mesozoic of Australia. Science 278:1438-1442.
50. SAITOU, N., AND M. NEI. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 183:584-598.
51. SIDOW, A., T. NGUYEN, AND T. P. SPEED. 1992. Estimating the fraction of invariable codons with a capture-recapture method. J. Mol. Evol. 35:253-260.
52. SIMPSON, G. G. 1945. The principles of classification and the classification of mammals. Bull. Am. Mus. Nat. Hist. 85:1-350.
53. SPRINGER, M. S. 1997. Molecular clocks and the timing of the placental and marsupial radiations in relation to the Cretaceous-Tertiary boundary. J. Mammal. Evol. 4:285-302.
54. SPRINGER, M. S., G. C. CLEVEN, O. MADSEN, W. W. DE JONG, V. G. WADDELL, H. M. AMRINE, AND M. J. STANHOPE. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388:61-64.
55. STANHOPE, M. J., V. G. WADDELL, O. MADSEN, W. DE JONG, C. B. HEDGES, G. C. CLEVEN, D. KAO, AND M. S. SPRINGER. 1998. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Natl. Acad. Sci. USA 95:9967-9972.
56. STEEL, M. A. 1994. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7:19-23.
57. STEEL, M. A., M. D. HENDY, AND D. PENNY. 1993. Parsimony can be consistent! Syst. Biol. 42:581-587.
58. SULLIVAN, J., AND D. L. SWOFFORD. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol. 4:77-86.
59. SWOFFORD, D. L. 1998. PAUP *: Phylogentic analysis under parsimony, version 4.0 (d62-64). Sinauer, Sunderland, Massachusetts.
60. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
61. TOWNS, D. R. 1991. Response of lizard assemblages in the Mercury Islands, New Zealand, to removal of an introduced rodent: The kiore (Rattus exulans). J. R. Soc. N.Z. 21:119-136.
62. TUFFLEY, C., AND M. A. STEEL. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:63-91.
63. WADDELL, P. J. 1995. Statistical methods of phylogenetic analysis: Including Hadamard conjugations, LogDet transforms, and maximum likelihood. Ph.D. Thesis, Massey University, Palmerston North, New Zealand.
64. WADDELL, P. J., Y. CAO, J. HAUF, AND M. HASEGAWA. 1999 Using novel methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet and site stripping to detect internal conflicts in the data, with special reference to the position of elephant, armadillo, and hedgehog. Syst. Biol. 48:31-53 (this issue).
65. WADDELL, P. J., Y. CAO, M. HASEGAWA, AND D. P. MINDELL. 1999 Assessing the Cretaceous superordinal divergence times in birds and placental mammals using whole mitochondrial protein sequences and an extended statistical framework. Syst. Biol. 48:119-137 (this issue).
66. WADDELL, P. J., P. O. LEWIS, AND D. L. SWOFFORD. In press. Distance-based methods of inferring evolutionary trees (Manual chapter 4). In PAUP *: Phylogenetic analysis under parsimony, version 4.0 (D. L. Swofford). Sinauer Associates, Sunderland, Massachusetts.
67. WADDELL, P. J., AND D. PENNY. 1996. Evolutionary trees of apes and humans from DNA sequences. Pages 53-73 in Handbook of human symbolic evolution (A. J. Lock and C. R. Peters, eds.), Oxford Univ. Press, Oxford, England.
68. WADDELL, P. J., D. PENNY, AND T. MOORE. 1997. Hadamard conjugations and modeling sequence evolution with unequal rates across sites. Mol. Phylogenet. Evol. 8:33-50.
69. WADDELL, P. J., AND M. A. STEEL. 1997. General time reversible distances with unequal rates across sites: Mixing Γ and inverse Gaussian distributions with invariant sites. Mol. Phylogenet. Evol. 8:398-414.
70. WESTERMAN, M., AND D. EDWARDS. 1991. The divergence time between echidna (Monotremata: Tachyglossidae) and platypus (Monotremata: Ornithorhynchidae) - New data from DNA studies. Aust. Mammal. 14:115-120.
71. XU, X., A. JANKE, AND U. ARNASON. 1996. The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea). Mol. Biol. Evol. 13:1167-1173.
72. YANG, Z. 1996. Among-site rate variation and its impact on phylogenetic analysis. Trends Ecol. Evol. 11:367-372.