Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny

Evolution

Volumn 54, Issue 2, 2000, Pages 397-405

  Oakley, Todd H ^a   Cunningham, Clifford W ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Ancestral reconstruction; Comparative methods; Computer simulation; Independent contrasts; Known phylogeny; Squared change parsimony

Indexed keywords

BACTERIOPHAGE; EVOLUTION; PHYLOGENY; RECONSTRUCTION;

ARTICLE; BACTERIOPHAGE T7; CLASSIFICATION; COMPUTER SIMULATION; GENETICS; PHENOTYPE; PHYLOGENY;

BACTERIOPHAGE T7; COMPUTER SIMULATION; PHENOTYPE; PHYLOGENY;

EID: 0034061046     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2000.tb00042.x     Document Type: Article

References (57)

1. Ackerly, D. D. 1998. Leaf size, sapling allometry, and Corner's rules: a phylogenetic study of correlated evolution in maples (Acer). Am. Nat. 152:767-791.
2. Brooks, D. R., and D. A. McLennan. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Univ. of Chicago Press, Chicago.
3. Bull, J. J., C. W. Cunningham, I. J. Molineux. M. R. Badgett, and D. M. Hillis. 1993. Experimental molecular evolution of bacteriophage T7. Syst. Biol. 47:993-1007.
4. Bull, J. J., M. R. Badgett, H. A. Wichman, J. P. Huelsenbeck, D. M. Hillis, A. Gulati, C. Ho, and I. J. Molineux. 1997. Exceptional convergent evolution in a virus. Genetics 147:1497-1507.
5. Charlesworth, D., M. T. Morgan, and B. Charlesworth. 1993. Mutation accumulation in finite outbreeding and inbreeding populations. Genet. Res. 61:39-56.
6. Coddington, J. A. 1988. Cladistic tests of adaptational hypotheses. Cladistics 4:3-22.
7. Cunningham, C. W., K. O. Omland, and T. H. Oakley. 1998. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13:361-366.
8. Diaz-Uriarte, R., and T. Garland. 1996. Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from Brownian motion. Syst. Biol. 45: 27-47.
9. Donoghue, M. J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43: 1137-1156.
10. Duarte, E. A., D. K. Clarke, A. Moya, S. F. Elena, E. Domingo, and J. Holland. 1993. Many-trillion-fold amplification of single RNA virus particles fails to overcome the Muller's ratchet effect. J. Virol. 67:3620-3623.
11. Dunn, J. J., and F. W. Studier. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166:477-535.
12. Escarmis, C., M. Davila, and E. Domingo. 1999. Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet. J Mol Biol 285:495-505.
13. Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
14. _. 1988. Phylogenies and quantitative characters. Annu. Rev. Ecol. Syst. 19:445-471.
15. _. 1995. PHYLIP: phylogeny inference package. Vers. 3.5c. Distributed by the author, University of Washington, Seattle.
16. Foote, M. 1996. On the probability of ancestors in the fossil record. Paleobiology 22:141-151.
17. Frumhoff, P. C., and H. K. Reeve. 1994. Using phylogenies to test hypotheses of adaptation: a critique of some current proposals. Evolution 48:172-180.
18. Garland, T., P. H. Harvey, and A. R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically indpendent contrasts. Syst. Biol. 41:18-32.
19. Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993. Phylogenetic analysis of covariance by compter simulation. Syst. Biol. 42:265-292.
20. Garland, T., Jr., P. E. Midford, and A. R. Ives. 1999. An introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values. Am. Zool. 39: 347-388.
21. Grafen, A. 1989. The phylogenetic regression. Phil. Trans. R. Soc. Lond. 326:119-157.
22. Greene, H. W. 1986. Diet and arboreality in the emerald monitor, Varanus prasinus, with comments on the study of adaptation. Fieldiana Zool. N.S. 31:1-12.
23. Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341-1351.
24. Harvey, P. H., and M. D. Pagel. 1991. The comparative Method in evolutionary biology. Oxford Univ. Press, Oxford.
25. Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett, and I. J. Molineux. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592.
26. Holmquist, R. 1979. The method of parsimony: an experimental test and theoretical analysis of the adequacy of molecular restoration studies. J. Mol. Biol. 135:939-958.
27. Huey, R. B., and A. F. Bennett. 1987. Phylogenetic studies of co-adaptation: preferred temperatures versus optimal performance temperatures of lizards. Evolution 40:1098-1115.
28. Losos, J. B. 1990. Ecomorphology, performance capability, and scaling of West Indian Anolis lizards: An evolutionary analysis. Ecol. Monogr. 60:369-388.
29. _. 1992. The evolution of convergent structure in Caribbean Anolis communities. Syst. Biol. 41:403-420.
30. _. 1996. Phylogenies and comparative biology, stage II: testing causal hypotheses derived from phylogenies with data from extant taxa. Syst. Biol. 45:259-260.
31. Maddison, D. R. 1995. Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees. Syst. Biol. 44:474-481.
32. Maddison, W. P. 1991. Squared-change parsimony reconstructions of ancestral states for continuous valued characters on a phylogenetic tree. Syst. Zool. 40:304-314.
33. Maddison, W. P., and D. R. Maddison. 1992. MacClade: analysis of phylogeny and character evolution. Sinauer, Sunderland, MA.
34. Martins, E. P., and T. Garland, Jr. 1991. Phylogenetic analysis of the correlated evolution of continuous characters: a simulation study. Evolution 45:534-557.
35. Martins, E. P., and T. F Hansen. 1996. Phylogenetic comparative methods: the statistical analysis of interspecific data. Pp. 22-75 in E. P. Martins, ed. Phylogenies and the comparative method in animal behavior. Oxford Univ. Press, Oxford.
36. _. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat. 149:646-667.
37. Mitani, J. C., J. Gros-Louis, and J. H. Manson. 1996. Number of males in primate groups: comparative tests of competing hypotheses. Am. J. Primatol. 38:315-332.
38. Møller, A. P., and T. R. Birkhead. 1992. A pairwise comparative method as illustrated by copulation frequency in birds. Am. Nat. 139:644-656.
39. Nelson, G. 1989. Species and taxa: systematics and evolution. Pp. 60-81 in D. Otto and J. A. Endler, eds. Speciation and its consequences. Sinauer, Sunderland, MA.
40. Omland, K. E. 1997. Examining two standard assumptions of ancestral reconstructions: repeated loss of dichromatism in dabbling ducks (Anatini). Evolution 51:1636-1646.
41. Pagel, M. D. 1993. Seeking the evolutionary regression coefficient: an analysis of what comparative methods measure. J. Theor. Biol 164:191-205.
42. _. 1998. Inferring evolutionary processes from phylogenies. Zool. Scr. 26:331-348.
43. Pagel, M. D., and P. H. Harvey. 1988. The taxon-level problem in the evolution of mammalian brain size: facts and artifacts. Am. Nat. 132:344-359.
44. _. 1989. Taxonomic differences in the sealing of brain on body weight among mammals. Science 244(4912):1589-1593.
45. Parker, A. R., D. R. McKenzie, and S. T. Ahyong. 1998. A unique form of light reflector and the evolution of signalling in Ovalipes (Crustacea: Decapoda: Portunidae). Proc. R. Soc. Lond. B Biol. Sci. 265:861-867.
46. Ryan, M. J., and A. S. Rand. 1995. Female responses to ancestral advertisement calls in Tungara frogs. Science 269:390-392.
47. _. 1999. Phylogenetic influence on mating call preferences in female tungara frogs, Physalaemus pustulosus. Anim. Behav. 57: 945-956.
48. Saitou, N. 1989. A theoretical study of the underestimation of branch lengths by the maximum parsimony principle. Syst. Zool. 38:1-6.
49. Sambrook, E., F. Fritsch, and T. Maniatis. 1989. Molecular Cloning. Cold Spring Harbor Press, Cold Spring Harbor, NY.
50. Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711.
51. Schultz, T. R., R. B. Cocroft, and G. A. Churchill. 1996. The reconstruction of ancestral character states. Evolution 50:504-511.
52. Smith, A. B. 1994. Systematics and the fossil record. Blackwell Scientific Publications, London.
53. Strathmann, R. R., and D. J. Eernisse. 1994. What molecular phylogenies tell us about the evolution of larval forms. Am. Zool. 34:502-512.
54. Tateno, Y. 1990. A method for molecular phylogeny construction by direct use of nucleotide sequence data. J. Mol. Evol. 30: 85-93.
55. Wang, I. N., D. E. Dykhuizen, and L. B. Slobodkin. 1996. The evolution of phage lysis timing. Evol. Ecol. 10:545-558.
56. White, M. E., J. J. Bull, I. J. Molineaux, and D. M. Hillis. 1991. Experimental phylogenies from T7 bacteriophage. Dioscorides Press, Portland, OR.
57. Yin. J. 1991. A quantifiable phenotype of viral propagation. Biochem. Biophys. Res. Comm. 174:1009-1014.