Evolutionary models of phylogenetic trees

Proceedings of the Royal Society B: Biological Sciences

Volumn 270, Issue 1522, 2003, Pages 1425-1431

  Pinelis, Iosif ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Adaptability; Evolutionary models; Imbalance of phylogenetic trees; Prolonged stasis; Proportional to distinguishable arrangements model; Quasi stabilization

Indexed keywords

EVOLUTION; MODEL; PHYLOGENETICS;

ANALYSIS; ARTICLE; EVOLUTION; EVOLUTIONARY ADAPTATION; MODEL; PARAMETER; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROBABILITY; REPRODUCIBILITY;

EID: 0037816220     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2003.2374     Document Type: Article

References (34)

1. Aldous, D. J. 1996 Probability distributions on cladograms. In Random discrete structures (ed. D. Aldous & R. Pemantle), pp. 1-18. New York: Springer.
2. Aldous, D. J. 2001 Stochastic models and descriptive statistics for phylogenetic trees. Statist. Sci. 16, 23-34.
3. Cunningham, S. 1995 Problems with null models in the study of phylogenetic radiation. Evolution 49, 1292-1294.
4. Gould, J. S., Raup, D. M., Sepkoski Jr, J., Schopf, T. J. M. & Simberloff, D. S. 1977 The shape of evolution: a comparison of real and random clades. Paleobiology 3, 23-40.
5. Guyer, C. & Slowinski, J. B. 1991 Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages. Evolution 45, 340-350.
6. Guyer, C. & Slowinski, J. B. 1993 Adaptive radiation and the topology of large phylogenies. Evolution 47, 253-263.
7. Harcourt-Brown, K. G., Pearson, P. N. & Wilkinson, M. 2001 The imbalance of paleontological trees. Paleobiology 27, 188-204.
8. Harris, T. E. 1963 The theory of branching processes. Berlin: Springer.
9. Heard, S. B. 1992 Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees. Evolution 46, 1818-1826.
10. Heard, S. B. 1996 Patterns in phylogenetic tree balance with variable and evolving speciation rates. Evolution 50, 2141-2148.
11. Heard, S. B. & Mooers, A. Ø. 2002 Signatures of random and selective mass extinctions in phylogenetic tree balance. Syst. Biol. 51, 889-897.
12. Kendall, D. G. 1948 On the generalized 'birth-and-death' process. Ann. Math. Statist. 19, 1-15.
13. Losos, J. B. & Adler, F. R. 1995 Stumped by trees? A generalized null model for patterns of organismal diversity. Am. Nat. 145, 329-342.
14. Maddison, W. P. & Slatkin, M. 1991 Null models for the number of evolutionary steps in a character in a phylogenetic tree. Evolution 45, 1184-1197.
15. Mooers, A. Ø. 1995 Tree balance and tree completeness. Evolution 49, 379-384.
16. Mooers, A. Ø. & Heard, S. B. 1997 Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72, 31-54.
17. Nee, S. 2001 Inferring speciation rates from phylogenies. Evolution 55, 661-668.
18. Nee, S., Mooers, A. Ø. & Harvey, P. H. 1992 Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl Acad. Sci. USA 89, 8322-8326.
19. Nee, S., Holmes, E. C., May, R. M. & Harvey, P. H. 1994a Extinction rates can be estimated from molecular phylogenies. Phil. Trans. R. Soc. Lond. B 344, 77-82.
20. Nee, S., May, R. M. & Harvey, P. H. 1994b The reconstructed evolutionary process. Phil. Trans. R. Soc. Lond. B 344, 305-311.
21. Nee, S., Holmes, E. C., May, R. M. & Harvey, P. H. 1995 Estimating extinction from molecular phylogenies. In Extinction rates (ed. J. H. Lawton & R. M. May), pp. 164-182. Oxford University Press.
22. Rogers, J. S. 1993 Response of Colless's tree imbalance to number of terminal taxa. Syst. Biol. 42, 102-105.
23. Rogers, J. S. 1994 Central moments and probability distribution of Colless's coefficient of tree imbalance. Evolution 48, 2026-2036.
24. Rogers, J. S. 1996 Central moments and probability distributions of three measures of phylogenetic tree imbalance. Syst. Biol. 45, 99-110.
25. Rosen, D. E. 1978 Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27, 159-188.
26. Simberloff, D., Heck, K. L., McCoy, E. D. & Connor, E. F. 1981 There have been no statistical tests of cladistic biogeographical hypotheses (with discussion.). In Vicariance biogeography: a critique (ed. G. Nelson & D. E. Rosen), pp. 41-93. New York: Columbia University Press.
27. Slowinski, J. B. 1990 Probabilities of n-trees under two models: demonstration that asymmetrical interior nodes are not improbable. Syst. Zool. 39, 89-94.
28. Slowinski, J. B. & Guyer, C. 1989 Testing the stochasticity of patterns of organismal diversity: an improved null model. Am. Nat. 134, 907-920.
29. Soltis, P. S., Soltis, D. E., Savolainen, V., Crane, P. R. & Barraclough, T. G. 2002 Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc. Natl Acad. Sci. USA 99, 4430-4435.
30. Stanley, S. M., Signor III, P. W., Lidgard, S. & Karr, A. F. 1981 Natural clades differ from 'random' clades: simulations and analyses. Paleobiology 7, 115-127.
31. Steel, M. & McKenzie, A. 2001 Properties of phylogenetic trees generated by Yule-type speciation models. Math. Biosci. 170, 91-112.
32. Tamas, I., Klasson, L., Canbaeck, B., Naeslund, A. K., Eriksson, A.-S., Wernegreen, J. J., Sandstroem, J. P., Moran, N. A. & Andersson, S. G. E. 2002 50 Million years of genomic stasis in endosymbiotic bacteria. Nat. Rev. Genet. 3, 2376-2379.
33. Wernegreen, J. J. 2002 Genome evolution in bacterial endosymbionts of insects. Science 296, 850-861.
34. Yule, G. U. 1924 A mathematical theory of evolution, based on the conclusions of Dr J. C. Willis, F.R.S. Phil. Trans. R. Soc. Lond. B 213, 21-87.