Tree models for macroevolution and phylogenetic analysis

Systematic Biology

Volumn 60, Issue 6, 2011, Pages 735-746

  Jones, Graham R ^a  

^a NONE   (United Kingdom)

Author keywords

Bellman Harris models; branching processes; phylogenetic analysis; tree balance; TreeBASE

Indexed keywords

EID: 80054944961     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr086     Document Type: Article

References (29)

1. Agapow P.M., Purvis A. 2002. Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis. Syst. Biol. 51:866-872. (Pubitemid 36111101)
2. Aldous D. 1996. Probability distributions on cladograms. Random discrete structures, The IMA Volumes in Mathematics and its Applications. Aldous D., Pemantle R., editors. Volume 76. Minneapolis (MN): Springer. p. 1-18.
3. Aldous D.J. 2001. Stochastic models and descriptive statistics for phy-logenetic trees, from Yule to today. Statist. Sci. 16:23-34. (Pubitemid 33632845)
4. Alfaro M.E., Santini F., Brock C., Alamillo H., Dornburg A., Rabosky D.L., Carnevale G., Harmon L.J. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. U.S.A. 106:13410-13414.
5. Athreya K.B., Ney P.E. 1972. Branching processes. Berlin (Germany): Springer-Verlag.
6. Bellman R., Harris T.E. 1952. On age-dependent binary branching processes. Ann. Math. 55:280-295.
7. Berger J.O. 1985. Statistical decision theory and Bayesian analysis. 2nd ed. New York (NY): Springer-Verlag.
8. Blum M.G.B., François O. 2007. Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance. Syst. Biol. 55:685-691.
9. Chan K.M.A., Moore B.R. 1999. Accounting for mode of speciation increases power and realism of tests of phylogenetic asymmetry. Am. Nat. 153:332-346. (Pubitemid 29186640)
10. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
11. Edwards A.W.F. 1970. Estimation of the branch points of a branching diffusion process (with discussion). J. R. Statist. Soc. B. 32: 155-174.
12. Ford D. 2006. Probabilities on cladogram: introduction to the alpha model [Ph. D. thesis]. Stanford (CA): Stanford University.
13. Gernhard T., Hartmann K., Steel M. 2008. Stochastic properties of generalised yule models, with biodiversity applications. J. Math. Biol. 57:713-735.
14. Hartmann K. 2008. Biodiversity conservation and evolutionary models [PhD Thesis]. Christchurch (New Zealand): University of Canterbury.
15. Heath T.A., Zwickl D.J., Kim J., Hillis D.M. 2008. Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst. Biol. 57:160-166.
16. Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754-755. (Pubitemid 32851390)
17. Kirkpatrick M., Slatkin M. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution. 47:1171-1181.
18. Kontoleon N. 2006. The Markovian binary tree: a model of the macroevolutionary process [PhD Thesis]. Adelaide (South Australia): The University of Adelaide.
19. Losos J.B., Adler F.R. 1995. Stumped by trees? A generalized null model for patterns of organismal diversity. Am. Nat. 145: 329-342.
20. McCullagh P., Pitman J., Winkel M. 2008. Gibbs fragmentation trees. Bernoulli 14:988-1002.
21. McPeek M.A., Brown J.M. 2007. Clade age and not diversification rate explains species richness among animal taxa. Am. Nat. 169: 97-106.
22. Mooers A., Heard S.B. 1997. Inferring evolutionary process from phy-logenetic tree shape. Q. Rev. Biol. 72:31-54. (Pubitemid 127681333)
23. Pinelis I. 2003. Evolutionary models of phylogenetic trees. Proc. Biol. Sci. 270:1425-1431. (Pubitemid 36833291)
24. R Development Core Team. 2008. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. ISBN 3-900051-07-0.
25. Sanderson M.J., Donoghue M.J., Piel W., Eriksson T. 1994. Tree-BASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Am. J. Bot. 81: 183-189.
26. Stadler T. 2008. Evolving trees-models for speciation and extinction in phylogenetics [PhD Thesis]. Munich (Germany): Technische Uni-versität München, Zentrum Mathematik.
27. Steel M., McKenzie A. 2001. Properties of phylogenetic trees generated by Yule-type speciation models. Math. Biosci. 170:91-112. (Pubitemid 32230649)
28. Yang Z., Rannala B. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311. (Pubitemid 26315133)
29. Yang Z., Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724. (Pubitemid 27287292)