Analysis of diversification: Combining phylogenetic and taxonomic data

Proceedings of the Royal Society B: Biological Sciences

Volumn 270, Issue 1532, 2003, Pages 2499-2505

  Paradis, Emmanuel ^a  

^a INSTITUT DES SCIENCES DE L EVOLUTION   (France)

Author keywords

Diversity; Estimation; Extinction; Maximum likelihood; Phylogeny; Speciation

Indexed keywords

ESTIMATION METHOD; EXTINCTION; MAXIMUM LIKELIHOOD ANALYSIS; PHYLOGENY; SPECIATION (BIOLOGY); SPECIES DIVERSITY; TAXONOMY;

ARTICLE; BIRD; DATA BASE; FAMILY; GENETIC VARIABILITY; MAMMAL; MAXIMUM LIKELIHOOD METHOD; PHYLOGENY; PRIORITY JOURNAL; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; SPECIES EXTINCTION; STATISTICAL MODEL; TAXONOMIC DATA; TAXONOMIC IDENTIFICATION;

AVES; MAMMALIA;

EID: 0345170676     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2003.2513     Document Type: Article

References (28)

1. Barraclough, T. G. & Nee, S. 2001 Phylogenetics and speciation. Trends Ecol. Evol. 16, 391-399.
2. Douzery, E. J. P., Delsue, F., Stanhope, M. J. & Duchon, H. 2003 Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals, and incompatibility among fossil calibrations. J. Mol. Evol. (In the press.)
3. Edwards, A. W. F. 1992 Likelihood, expanded edn. Baltimore, MD: Johns Hopkins University Press.
4. Harvey, P. H., May, R. M. & Nee, S. 1994 Phylogenies without fossils. Evolution 48, 523-529.
5. Hey, J. 1992 Using phylogenetic trees to study speciation and extinction. Evolution 46, 627-640.
6. Hudson, D. J. 1971 Interval estimation from the likelihood function. J. R. Statist. Soc. B 33, 256-262.
7. Ihaka, R. & Gentleman, R. 1996 R: a language for data analysis and graphics. J. Comput. Graphical Statist. 5, 299-314.
8. Kendall, D. G. 1948 On the generalized "birth-and-death" process. Ann. Math. Stat. 19, 1-15.
9. Mayhew, P. J. 2002 Shifts in hexapod diversification and what Haldane could have said. Proc. R. Soc. Lond. B 269, 969-974. (DOI 10.1098/rspb.2002. 1957.)
10. Mooers, A. Ø. & Heard, S. B. 1997 Evolutionary process from phylogenetic tree shape. Q. Rev. Biol 72, 31-54.
11. Nee, S., May, R. M. & Harvey, P. H. 1994a The reconstructed evolutionary process. Phil. Trans. R. Soc. Lond. B 344, 305-311.
12. Nee, S., Holmes, E. C., May, R. M. & Harvey, P. H. 1994b Extinction rates can be estimated from molecular phylogenies. Phil. Trans. R. Soc. Lond. B 344, 77-82.
13. Nee, S., Holmes, E. C., Rambaut, A. & Harvey, P. H. 1995 Inferring population history from molecular phylogenies. Phil. Trans. R. Soc. Lond. B 349, 25-31.
14. Paradis, E. 1997 Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proc. R. Soc. Lond. B 264, 1141-1147. (DOI 10.1098/rspb.1997.0158.)
15. Paradis, E. 1998a Testing for constant diversification rates using molecular phylogenies: a general approach based on statistical tests for goodness of fit. Mol. Biol. Evol. 15, 476-479.
16. Paradis, E. 1998b Detecting shifts in diversification rates without fossils. Am. Nat. 152, 176-187.
17. Paradis, E., Claude, J. & Strimmer, K. 2003 APE: an R package for analyses of phylogenetics and evolution. Bioinformatics (In the press.)
18. Paton, T., Haddrath, O. & Baker, A. J. 2002 Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc. R. Soc. Lond. B 269, 839-846. (DOI 10.1098/rspb.2002.1961.)
19. Purvis, A., Nee, S. & Harvey, P. H. 1995 Macroevolutionary inferences from primate phylogeny. Proc. R. Soc. Lond. B 260, 329-333.
20. Pybus, O. G. & Harvey, P. H. 2000 Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B 267, 2267-2272. (DOI 10.1098/rspb.2000.1278.)
21. Sanderson, M. J. 1997 A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14, 1218-1231.
22. Sanderson, M. J. & Donoghue, M. J. 1996 Reconstructing shifts in diversification rates on phylogenetic trees. Trends Ecol. Evol. 11, 15-20.
23. Schnabel, R. B., Koontz, J. E. & Weiss, B. E. 1985 A modular system of algorithms for unconstrained minimization. ACM Trans. Math. Software 11, 419-440.
24. Sibley, C. G. & Ahlquist, J. E. 1990 Phylogeny and classification of birds: a study in molecular evolution. New Haven, CT: Yale University Press.
25. Sibley, C. G. & Monroe Jr, B. L. 1990 Distribution and taxonomy of birds of the world. New Haven, CT: Yale University Press.
26. Sims, H. J. & McConway, K. J. 2003 Nonstochastic variation of species-level diversification rates within angiosperms. Evolution 57, 460-479.
27. Slowinski, J. B. & Guyer, C. 1993 Testing whether certain traits have caused amplified diversification: an improved method based on a model of random speciation and extinction. Am. Nat. 142, 1019-1024.
28. Wilson, D. E. & Reeder, D. M. (eds) 1993 Mammal species of the world. A taxonomic and geographic reference, 2nd edn. Washington, DC: Smithsonian Institution Press.