Testing the relationship between morphological and molecular rates of change along phylogenies

Evolution

Volumn 56, Issue 10, 2002, Pages 1921-1930

  Bromham, Lindell ^a,b   Woolfit, Megan ^a,b   Lee, Michael S Y ^b,c   Rambaut, Andrew ^d  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c SOUTH AUSTRALIAN MUSEUM   (Australia)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Maximum likelihood; Molecular clock; Node density effect; Phylogenetic independence; Relative rates; Substitution rate

Indexed keywords

EVOLUTION; PHYLOGENY;

ANIMALIA; VERTEBRATA;

EID: 0036808040     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2002.tb00118.x     Document Type: Article

References (43)

1. Austin, O. L. 1961. Birds of the World: A Survey of the Twenty-seven Orders and One Hundred and Fifty-five Families. Golden Press, New York.
2. Barraclough, T. G., and V. Savolainen. 2001. Evolutionary rates and species diversity in flowering plants. Evolution 55:677-683.
3. Barraclough, T. G., P. H. Harvey, and S. Nee. 1996. Rate of rbcL gene sequence evolution and species diversification in flowering plants (angiosperms). Proc. R. Soc. Lond. B 263:589-591.
4. Bousquet, J., S. H. Strauss, and P. Li. 1992. Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae). Mol. Biol. Evol. 9:1076-1088.
5. Briggs, D. E., R. A. Fortey, and M. A. Wills. 1992. Morphological disparity in the Cambrian. Science 256:1670-1673.
6. Brochu, C. A. 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Syst. Biol. 46:479-522.
7. Bromham, L. D., and M. D. Hendy. 2000. Can fast early rates reconcile molecular dates to the Cambrian explosion? Proc. R. Soc. Lond. B 267:1041-1047.
8. Bryant, H. N. 1995. Why autapomorphies should be removed: A reply to Yeates. Cladistics 11:381-384.
9. Chippindale, P. T., L. K. Ammerman, and J. A. Campbell. 1998. Molecular approaches to phylogeny of Abronia (Anguidae: Gerrhonotinae), with emphasis on relationships in subgenus Auriculabronia. Copeia 1998:883-892.
10. Conway Morris, S. 1998. Early metazoan evolution: Reconciling paleontology and molecular biology. Am. Zool. 38:867-877.
11. Cotgreave, P., and P. H. Harvey. 1994. Phylogeny and the relationship between body-size and abundance in bird communities. Funct. Ecol. 8:219-228.
12. Flynn, J. J., and M. A. Nedbal. 1998. Phylogeny of the Carnivora (Mammalia): Congruence vs. incompatibility among multiple datasets. Mol. Phylog. Evol. 9:414-426.
13. Fortey, R. A., D. E. G. Briggs, and M. A. Wills. 1996. The Cambrian evolutionary "explosion": Decoupling cladogenesis from morphological disparity. Biol. J. Linn. Soc. 57:13-33.
14. Funk, D., D. Futuyma, G. Orti, and A. Meyer. 1995. Mitochondrial DNA sequences and multiple datasets: A phylogenetic analysis of phytophagous beetles (Ophraella: Chrysomelidae). Mol. Biol. Evol. 12:627-640.
15. Gillespie, J. H. 1991. The Causes of Molecular Evolution. Oxford Univ. Press, Oxford, U.K.
16. Harris, D. J., E. N. Arnold, and R. H. Thomas. 1998a. Rapid speciation, morphological evolution, and adaptation to extreme environments in South African sand lizards (Meroles) as revealed by mitochondrial gene sequences. Mol. Phylog. Evol. 10:37-48.
17. _. 1998b. Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. Roy. Soc. Lond. B 265:1939-1948.
18. Harvey, P. H., and A. Purvis. 1991. Comparative methods for explaining adaptations. Nature 351:619-624.
19. 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.
20. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge Univ. Press, Cambridge, U.K.
21. Knoll, A. H., and S. B. Carroll. 1999. Early animal evolution: Emerging views from comparative biology. Science 284:2129-2137.
22. Lee, M. S. Y. 1999. Shortening the phylogenetic fuse. Trends Ecol. Evol. 13:323.
23. Messenger, S. L., and J. A. McGuire. 1998. Morphology, molecules and the phylogenetics of cetaceans. Syst. Biol. 47:90-124.
24. Montgelard, C., S. Ducrocq, and E. Douzery. 1998. What is a suiforme (Artiodactyla)? Mol. Phylog. Evol. 9:528-532.
25. Omland, K. E. 1997. Correlated rates of molecular and morphological evolution. Evolution 51:1381-1393.
26. Rambaut, A. E. 1996. Se-Al: Sequence Alignment Editor. Available via http://evolve.zoo.ox.ac.uk/software/Se-Al.
27. Sanderson, M. J. 1990. Estimating rates of speciation and evolution: A bias due to homoplasy. Cladistics 6:387-391.
28. _. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. J. Mol. Evol. 14:1218-1231.
29. Schulte, J. A., II, J. R. Macey, A. Larson, and T. J. Papenfuss. 1998. Molecular tests of phylogenetic taxonomies: A general procedure and example using four subfamilies of the lizard family Iguanidae. Mol. Phylog. Evol. 10:367-376.
30. Shaffer, H. B., P. Meylan, and M. L. McKnight. 1997. Tests of turtle phylogeny: Molecular, morphological, and paleontological approaches. Syst. Biol. 46:235-268.
31. Sites, J. W., Jr., S. K. Davis, T. Guerra, J. B. Iverson, and H. L. Snell. 1996. Character congruence and phylogenetic signal in molecular and morphological datasets: A case study in the living iguanas (Squamata, Iguanidae). Mol. Biol. Evol. 13:1087-1105.
32. Smith, A. B., L. Lafay, and R. Christen. 1992. Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids. Phil. Trans. R. Soc. Lond. B 338:365-382.
33. Sokal, R. R., and F. J. Rohlf. 1995. Biometry: The Principles and Practice of Statistics in Biological Research. W. H. Freeman, San Francisco, CA.
34. Swofford, D. L. 1999. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods). Ver. 4. Sinauer Associates, Sunderland, MA.
35. Valentine, J., D. Jablonski, and D. Erwin. 1999. Fossils, molecules and embryos: New perspectives on the Cambrian explosion. Development 126:851-859.
36. Vermeij, G. 1996. Animal origins. Science 274:525-526.
37. Wayne, R. K., E. Geffen, D. J. German, K. P. Koepfli, L. M. Lau, and C. R. Marshall. 1997. Molecular systematics of the Canidae. Syst. Biol. 46:622-653.
38. Wiens, J. J., and T. W. Reeder. 1997. Phylogeny of the spiny lizards (Sceloporus) based on molecular and morphological evidence. Herpetological Monographs 11:1-101.
39. Wills, M. A. 1998. Cambrian and Recent disparity: The picture from priapulids. Paleobiology 24:177-199.
40. Wills, M. A., D. E. G. Briggs, and R. A. Fortey. 1994. Disparity as an evolutionary index: A comparison of Cambrian and Recent arthropods. Palaeobiology 20:93-130.
41. Yang, Z. 1994. Maximum likelihood phylogenetic estimate from DNA sequences with variable rates over sites: Approximate methods. J Mol. Evol. 39:306-314.
42. Yeates, D. 1992. Why remove autapomorphies? Cladistics 8:387-389.
43. Yoder, A. D., M. Cartmill, M. Ruvolo, K. Smith, and R. Vilgalys. 1996. Ancient single origin for Malagasy primates. Proc. Natl. Acad. Sci. USA 93:5122-5126.