Estimating speciation and extinction rates for phylogenies of higher taxa

Systematic Biology

Volumn 62, Issue 2, 2013, Pages 220-230

  Stadler, Tanja ^a   Bokma, Folmer ^b  

^a ETH ZURICH   (Switzerland)

^b UMEÅ UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIRD; CLASSIFICATION; COMPUTER SIMULATION; MAMMAL; METHODOLOGY; PHYLOGENY; SPECIES DIFFERENTIATION; SPECIES EXTINCTION;

ANIMALS; BIRDS; CLASSIFICATION; COMPUTER SIMULATION; EXTINCTION, BIOLOGICAL; GENETIC SPECIATION; MAMMALS; MODELS, BIOLOGICAL; PHYLOGENY;

EID: 84873600078     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys087     Document Type: Article

References (39)

1. Aldous D., Popovic L. 2005. A critical branching process model for biodiversity. Adv. Appl. Probab. 37: 1094-1115.
2. Alfaro M., Santini F., Brock C., Alamillo H., Dornburg A., Rabosky D., Carnevale G., Harmon L. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. USA 106: 13410.
3. Bininda-Emonds O.R., Cardillo M., Jones K.E., MacPhee R.D., Beck R.M., Grenyer R., Price S.A., Vos R.A., Gittleman J.L., PurvisA. 2007. The delayed rise of present-day mammals. Nature 446: 507-512.
4. Bokma F. 2003. Testing for equal rates of cladogenesis in diverse taxa. Evolution 57: 2469-2474.
5. Bokma F. 2008. Bayesian estimation of speciation and extinction probabilities from (in) complete phylogenies. Evolution 62: 2441-2445.
6. Brock C., Harmon L., Alfaro M. 2011. Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom. Syst. Biol. 60: 410-419.
7. Crisp M., Cook L. 2009. Explosive radiation or cryptic mass extinction? Interpreting signatures in molecular phylogenies. Evolution 63: 2257-2265.
8. Cusimano N., Renner S. 2010. Slowdowns in diversification rates from real phylogenies may not be real. Syst. Biol. 59: 458-464.
9. Drummond A., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
10. Etienne R., Haegeman B., Stadler T., Aze T., Pearson P., Purvis A., Phillimore A. 2012. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. Roy. Soc. B. 279: 1300-1309.
11. Farris J. 1976. Expected asymmetry of phylogenetic trees. Syst. Biol. 25: 196-198.
12. Feller W. 1968. An introduction to probability theory and its applications. 3rd ed. Vol. I. New York: John Wiley & Sons Inc.
13. FitzJohn R., Maddison W., Otto S. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst. Biol. 58: 595.
14. Foote M., Hunter J., Janis C., Sepkoski J. Jr. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283: 1310.
15. GernhardT. 2008. The conditioned reconstructed process. J. Theor. Biol. 253: 769-778.
16. Harvey P.H., May R.M., Nee S. 1994. Phylogenies without fossils. Evolution 48: 523-529.
17. Höhna S., Stadler T., Ronquist F., Britton T. 2011. Inferring speciation and extinction rates under different sampling schemes. Mol. Biol. Evol. 28: 2577-2589.
18. Kendall D.G. 1948a. On some modes of population growth leading to R. A. Fisher's logarithmic series distribution. Biometrika 35: 6-15.
19. Kendall D.G. 1948b. On the generalized "birth-and-death" process. Ann. Math. Statist. 19: 1-15.
20. Kendall D.G. 1949. Stochastic processes and population growth. J. Roy. Statist. Soc. Ser. B 11: 230-264.
21. Kubo T., Iwasa Y. 1995. Inferring the rates of branching and extinction from molecular phylogenies. Evolution 49: 694-704.
22. Magallon S., Sanderson M. 2001. Absolute diversification rates in angiosperm clades. Evolution 55: 1762-1780.
23. Morlon H., Parsons T., Plotkin J. 2011. Reconciling molecular phylogenies with the fossil record. Proc. Natl. Acad. Sci. USA 108: 16327-16332.
24. Nee S.C., May R.M., Harvey P. 1994. The reconstructed evolutionary process. Philos. Trans. Roy. Soc. Lond. Ser. B 344: 305-311.
25. Paradis E. 2003. Analysis of diversification: combining phylogenetic and taxonomic data. Proc. Roy. Soc. B 270: 2499.
26. Pommier T., Canbäck B., Lundberg P., Hagström Å., Tunlid A. 2009. Rami: a tool for identification and characterization of phylogenetic clusters in microbial communities. Bioinformatics 25: 736-742.
27. Purvis A., Nee S., Harvey P. 1995. Macroevolutionary inferences from primate phylogeny. Proc. Roy. Soc. Lond. Ser. B 260: 329-333.
28. Rabosky D. 2009. Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils. Syst. Biol. 58: 629.
29. Rabosky D., Donnellan S., Talaba A., Lovette I. 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade. Proc. Roy. Soc. B 274: 2915.
30. Rabosky D., Lovette I. 2008. Density-dependent diversification in North American wood warblers. Proc. Roy. Soc. B 275: 2363.
31. Raup D.M., Gould S.J., Schopf T.J.M., Simberloff D.S. 1973. Stochastic models of phylogeny and the evolution of diversity. J. Geol. 81: 449-452.
32. Ricklefs R. 2003. Global diversification rates of passerine birds. Proc. Roy. Soc. B 270: 2285.
33. Ricklefs R. 2006. Global variation in the diversification rate of passerine birds. Ecology 87: 2468-2478.
34. Sibley C., Ahlquist J. 1990. Phylogeny and classification of birds: a study in molecular evolution. New Haven: Yale University Press.
35. Stadler T. 2009. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theor. Biol. 261: 58-66.
36. Stadler T. 2011a. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Natl. Acad. Sci. USA 108: 6187-6192.
37. Stadler T. 2011b. Simulating trees with a fixed number of extant species. Syst. Biol. 60: 676-684.
38. Yang Z. 2007. Paml 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
39. Yang Z., Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 17: 717-724.