Simulating trees with a fixed number of extant species

Systematic Biology

Volumn 60, Issue 5, 2011, Pages 676-684

  Stadler, Tanja ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Birth death model; mass extinction; phylogenetic tree; rate shift; simulation

Indexed keywords

ARTICLE; BAYES THEOREM; BIODIVERSITY; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; EVALUATION; EVOLUTION; METHODOLOGY; PALEONTOLOGY; SPECIES DIFFERENTIATION; SPECIES EXTINCTION; STATISTICAL MODEL;

BAYES THEOREM; BIODIVERSITY; BIOLOGICAL EVOLUTION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EXTINCTION, BIOLOGICAL; GENETIC SPECIATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; PALEONTOLOGY;

EID: 80051988868     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syr029     Document Type: Article

References (31)

1. Aldous D.J. 2001. Stochastic models and descriptive statistics for phy-logenetic trees, from Yule to today. Stat. Sci. 16:23-34. (Pubitemid 33632845)
2. Aldous D.J., Popovic L. 2005. A critical branching process model for biodiversity. Adv. Appl. Probab. 37:1094-1115. (Pubitemid 43186362)
3. Crisp M., Cook L. 2009. Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies. Evolution. 63:2257-2265.
4. Cusimano N., Renner S. 2010. Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 59:458-464.
5. Day J., Cotton J., Barraclough T. 2008. Tempo and mode of diversification of Lake Tanganyika cichlid fishes. PloS one. 3:1730.
6. FitzJohn R., Maddison W., Otto S. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylo-genies. Syst. Biol. 58:595-611.
7. Gernhard T. 2008. The conditioned reconstructed process. J. Theor. Biol. 253:769-778.
8. Harmon L., Weir J., Brock C., Glor R., Challenger W., Hunt G. 2007. GEIGER in R-running macroevolutionary simulation, and estimating parameters related to diversification from comparative phylogenetic data [Internet]. Available from: http://cran. r-project.org/web/packages/geiger/index.html.
9. Hartmann K. 2007. TreeSample [Internet]. Available from: http://www.tb.ethz.ch/people/tstadler.
10. Hartmann K., Wong D., Stadler T. 2010. Sampling trees from evolutionary models. Syst. Biol. 59:465-476.
11. Harvey P.H., May R.M., Nee S. 1994. Phylogenies without fossils. Evolution. 48:523-529.
12. Heard S., Mooers A. 2002. Signatures of random and selective mass extinctions in phylogenetic tree balance. Syst. Biol. 51:889.
13. Maddison W. 2007. Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56:701-710. (Pubitemid 47402904)
14. Marjoram P., Molitor J., Plagnol V., Tavaré S. 2003. Markov chain Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. U.S.A. 100: 15324.
15. Nee S.C., May R.M., Harvey P. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. Lond. Ser. B. 344:305-311. (Pubitemid 2092171)
16. Paradis E. 1997. Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proc. R. Soc. B Biol. Sci. 264:1141.
17. Paradis E. 1998. Detecting shifts in diversification rates without fossils. Am. Nat. 152:176-187. (Pubitemid 28349038)
18. Paradis E., Claude J., Strimmer K. 2004. Ape: analyses of phylogenetics and evolution in R language. Bioinformatics. 20:289-290. (Pubitemid 38195693)
19. Phillimore A., Price T. 2008. Density-dependent cladogenesis in birds. PLoS Biol. 6:e71.
20. Popovic L. 2004. Asymptotic genealogy of a critical branching process. Ann. Appl. Probab. 14:2120-2148. (Pubitemid 41449208)
21. Pybus O.G., Harvey P.H. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. 267:2267-2272.
22. Rabosky D. 2006. Likelihood methods for detecting temporal shifts in diversification rates. Evolution. 60:1152-1164. (Pubitemid 44804474)
23. Rabosky D. 2009a. Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol. Lett. 12:735-743.
24. Rabosky D. 2009b. Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils. Syst. Biol. 58:629.
25. Rabosky D. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution. 64:1816-1824.
26. Rabosky D., Lovette I. 2008. Density-dependent diversification in North American wood warblers. Proc. R. Soc. B Biol. Sci. 275:2363.
27. Rambaut A. 2002. PhyloGen: phylogenetic tree simulator package. Department of Zoology, University of Oxford. Available from: http://tree.bio.ed.ac.uk/software/.
28. Stadler T. 2006-2009. Cass [Internet]. Available from: http://www .tb.ethz.ch/people/tstadler.
29. Stadler T. 2009. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theor. Biol. 261:58-66.
30. Stadler T. 2010. TreeSim in R-simulating trees under the birth-death model [Internet]. Available from: http://cran.r-project.org/web/packages/ TreeSim/index.html.
31. Yule G.U. 1924. A mathematical theory of evolution: based on the conclusions of Dr. J.C. Willis. Philos. Trans. R. Soc. Lond. Ser. B. 213: 21-87.