Inferring evolutionary processes from phylogenies

Zoologica Scripta

Volumn 26, Issue 4, 1997, Pages 331-348

  Pagel, Mark ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIODIVERSITY; EVOLUTION; PHYLOGENY;

EID: 0031421806     PISSN: 03003256     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1463-6409.1997.tb00423.x     Document Type: Article

References (44)

1. Collinge, J., Sidle, K. C. L., Meads, J., Ironside, J. & Hill, A. F. 1996. Molecular analysis of prion strain variation and the etiology of New Variant CJD. - Nature 383 (6602), 685-690.
2. Cotgreave, P. & Pagel, M. 1997. Predicting and understanding rarity: the comparative approach. In The Biology of Rarity: the causes and consequences of rare-common differences (eds. W. Kunin and K. Gaston): Chapman and Hall, 237-261.
3. Edwards, A. W. F. 1972. Likelihood. The John Hopkins University Press.
4. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. - J. Mol. Evol. 17, 368-376.
5. Felsenstein, J. 1985. Phytogenies and the comparative method. - Am. Nat. 125, 1-15.
6. Fitch, W. M., Leiter, J. M. E., Li, X. & Palese, P. 1991. Positive Darwinian evolution in human influenza A viruses. - Proc. Natl. Acad. Sci. USA 88, 4270-4274.
7. Friday, A. 1989. Quantitative aspects of the estimation of evolutionary trees. - Folia Primat. 53, 221-234.
8. Garland, T. 1992. Rate tests for phenotypic evolution using phylogenetically independent contrasts. - Am. Nat. 140, 509-519.
9. Gartand, T., Harvey, P. H. & Ives, A. R. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. -Syst. Biol. 41, 18-32.
10. Gillespie, J. H. 1991. The causes of molecular evolution. Oxford: Oxford University Press.
11. Goldman, N. 1990. Maximum likelihood inference of phylogenetic trees. - Syst. Zool. 39, 345-361.
12. Grafen, A. 1989. The phylogenetic regression. - Phil. Tran. R. Soc. Lond. B 326, 119-157.
13. Grafen, A. & Ridley, M. 1996. Statistical tests for discrete cross-species data. - J. Theor. Biol. 183, 255-267.
14. Hansen, T. & Martins, E. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. - Evolution 50, 1404-1417.
15. Harvey P. H. & Pagel, M. 1991. The comparative method in evolutionary biology. Oxford University Press.
16. Hillis, D., Moritz, M. & Mable, B. K. 1996. Molecular Systematics (2nd Edition). Sunderland, Mass: Sinauer.
17. Holden, C. & Mace, R. 1997. A phylogenetic analysis of the evolution of lactose digestion in adults. - Hum. Biol. 69, 605-628.
18. Huey, R. B. 1987. Phylogeny, history and the comparative method. In New directions in ecological physiology (eds M. E. Feder, A. F. Bennett, W. Burgren, & R. B. Huey). Cambridge University Press.
19. Huey, R. B. & Bennett, A. F. 1987. Phylogenetic studies of co-adaptation: preferred temperatures versus optimal performance temperatures of lizards. - Evolution 41, 1098-1115.
20. Jermiin, L. S., Graur, D., Lowe, R. M. & Crozier, R. 1994. Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes. - J. Mol. Evol. 39, 160-173.
21. Johnston, J. 1963. Econometric Methods. New York: McGraw Hill.
22. Kimura, M. 1968. Evolutionary rate at the molecular level. - Nature 217, 624-626.
23. Krakauer, D. C., Pagel, M., Southwood, T. R. E. & Zanotto, P. M. de A. 1996. Phylogenesis of prion protein. - Nature 380, 675.
24. Krakauer, D. C. & Pagel, M. 1996. The genealogy of a toxic protein and the case of BSE. - Soc. Biol. Hum. Aff. 61, 45-54.
25. Krakauer, D. C., Zanotto, P. de A. & Pagel, M. 1998. Prion's progress: patterns and rates of molecular evolution in relation to spongiform disease. J. Mol. Evol., in press.
26. Lutzoni, F. & Pagel, M. 1997. Accelerated molecular evolution as a consequence of transitions to mutualism. - Proc. Natl. Acad. Sci. USA 94, 11422-11427.
27. Mace, R., & Pagel, M. 1997. Tips, branches, and nodes: seeking adaptation through comparative studies. In Human Nature: a critical reader (ed. L. Betzig): 297-310. New York: Oxford University Press.
28. Nee, S., Holmes, E. C., Rambaut, A. & Harvey, P. H. 1996. Inferring population history from molecular phylogenies. In New uses for new phytogenies (eds P. H. Harvey, A. Leigh-Brown, J. Maynard Smith & S. Nee). Oxford University Press.
29. Pagel, M. 1992. A method for the analysis of comparative data. - J. Theor. Biol. 156, 431-442.
30. Pagel, M. 1993. Seeking the evolutionary regression coefficient: an analysis of what comparative methods measure. - J. Theor. Biol. 164, 191-205.
31. Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. -Proc. R. Soc. Lond. B 255, 375, 37-45.
32. Pagel, M. & Harvey, P. H. 1989a. Comparative methods for investigating adaptation depend upon evolutionary models. - Folia Primat. 53, 203-220.
33. Pagel, M. & Harvey, P. H. 1989b. Taxonomic differences in the scaling of brain on body weight among mammals. - Science 244, 1589-1593.
34. Price, T. & Birch, G. L. 1996. Repeated evolution of sexual color dimorphism in passerine birds. - Auk 113, 842-848.
35. Purvis, A. 1995 A composite estimate of primate phylogeny. - Phil. Trans. R. Soc. Lond. B 348, 405-421.
36. Rao, C. R. & Kleffe, J. 1988. Estimation of rariance components and applications. North Holland: Amsterdam.
37. Read, A. & Nee, S. 1995. Inference from binary comparative data. -J. Theor. Biol. 173: 99-108.
38. Riek, R., Hornemann, S., Wider, G., Billeter, M., Glockshuber, R. & Wüthrich, K. 1996. NMR structure of the mouse prion protein domain PrP(121-231). - Nature 382, 180-182.
39. Schluter, D. 1995. Uncertainty in ancient phylogenies. - Nature 377, 108-109.
40. Sueoka, N. 1962. On thegenetic basis of variation and heterogeneity of DNA base composition. - Proc. Natl. Acad. Sci. USA 48, 582-592.
41. Sueoka, N. 1988. Directional mutation pressure and neutral molecular evolution. - Proc. Natl. Acad. Sci. USA 85, 2653-2657.
42. Vilá, C. et al. 1997. Multiple and ancient origins of the domestic dog. -Science 276, 1687.
43. Ward, D. & Seely, M. K. 1996. Adaptation and constraint in the evolution of the physiology and behaviour of the Namib Desert Tenebrionid beetle genus Onymacris. - Evolution 50, 1231-1240.
44. Weisberg, S. 1985. Applied linear regression. 2nd edition. Wiley.