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Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.
Richard G FitzJohn1, Wayne P Maddison, Sarah P Otto
1Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada. fitzjohn@zoology.ubc.ca
Systematic Biology
|June 8, 2010
Summary
New methods infer trait effects on speciation and extinction rates using incomplete phylogenetic data. This advances evolutionary biology research by enabling analysis even without fully resolved phylogenies.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Speciation Research
Background:
- Species traits influence diversification patterns and trait distributions.
- Existing methods for detecting differential diversification require complete phylogenies.
- Incomplete phylogenetic information limits the study of trait-influenced evolutionary rates.
Purpose of the Study:
- To develop novel likelihood methods for inferring trait effects on speciation and extinction rates.
- To generalize existing binary-state speciation and extinction methods for incomplete phylogenies.
- To enable evolutionary rate analysis with partially resolved or incompletely sampled phylogenies.
Main Methods:
- Developed two likelihood methods generalizing the binary-state speciation and extinction approach.
- Applied Bayesian framework with simulated phylogenies to assess method performance under varying phylogenetic resolution.
- Utilized an "unresolved clade" method for analyses with incomplete phylogenetic data.
Main Results:
- The new methods effectively infer trait effects on speciation and extinction rates without complete phylogenetic information.
- Differential diversification due to speciation rate asymmetry was detected robustly even with 50% phylogenetic resolution.
- The unresolved clade method was successfully demonstrated using shorebird (Charadriiformes) sexual dimorphism and diversification.
Conclusions:
- The developed methods allow direct estimation of trait impacts on speciation and extinction rates using incompletely resolved phylogenies.
- These approaches significantly expand the applicability of diversification analyses in evolutionary biology.
- Enables robust inference of evolutionary dynamics when complete phylogenetic data is unavailable.
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