Abstract
The estimation of diversification rates using phylogenetic data has attracted a lot of attention in the past decade. In this context, the analysis of incomplete phylogenies (e.g. phylogenies resolved at the family level but unresolved at the species level) has remained difficult. I present here a likelihood-based method to combine partly resolved phylogenies with taxonomic (species-richness) data to estimate speciation and extinction rates. This method is based on fitting a birth-and-death model to both phylogenetic and taxonomic data. Some examples of the method are presented with data on birds and on mammals. The method is compared with existing approaches that deal with incomplete phylogenies. Some applications and generalizations of the approach introduced in this paper are further discussed.
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Selected References
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- Barraclough T. G., Nee S. Phylogenetics and speciation. Trends Ecol Evol. 2001 Jul 1;16(7):391–399. doi: 10.1016/s0169-5347(01)02161-9. [DOI] [PubMed] [Google Scholar]
- Mayhew Peter J. Shifts in hexapod diversification and what Haldane could have said. Proc Biol Sci. 2002 May 7;269(1494):969–974. doi: 10.1098/rspb.2002.1957. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nee S., Holmes E. C., May R. M., Harvey P. H. Extinction rates can be estimated from molecular phylogenies. Philos Trans R Soc Lond B Biol Sci. 1994 Apr 29;344(1307):77–82. doi: 10.1098/rstb.1994.0054. [DOI] [PubMed] [Google Scholar]
- Nee S., Holmes E. C., Rambaut A., Harvey P. H. Inferring population history from molecular phylogenies. Philos Trans R Soc Lond B Biol Sci. 1995 Jul 29;349(1327):25–31. doi: 10.1098/rstb.1995.0087. [DOI] [PubMed] [Google Scholar]
- Nee S., May R. M., Harvey P. H. The reconstructed evolutionary process. Philos Trans R Soc Lond B Biol Sci. 1994 May 28;344(1309):305–311. doi: 10.1098/rstb.1994.0068. [DOI] [PubMed] [Google Scholar]
- doi: 10.1098/rspb.1997.0158. [DOI] [PMC free article] [Google Scholar]
- Paton Tara, Haddrath Oliver, Baker Allan J. Complete mitochondrial DNA genome sequences show that modern birds are not descended from transitional shorebirds. Proc Biol Sci. 2002 Apr 22;269(1493):839–846. doi: 10.1098/rspb.2002.1961. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Purvis A., Nee S., Harvey P. H. Macroevolutionary inferences from primate phylogeny. Proc Biol Sci. 1995 Jun 22;260(1359):329–333. doi: 10.1098/rspb.1995.0100. [DOI] [PubMed] [Google Scholar]
- Pybus O. G., Harvey P. H. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc Biol Sci. 2000 Nov 22;267(1459):2267–2272. doi: 10.1098/rspb.2000.1278. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sims Hallie J., McConway Kevin J. Nonstochastic variation of species-level diversification rates within angiosperms. Evolution. 2003 Mar;57(3):460–479. doi: 10.1111/j.0014-3820.2003.tb01538.x. [DOI] [PubMed] [Google Scholar]