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Time-dependent speciation and extinction from phylogenies: a least squares approach
1Institut de Recherche pour le Développement, UR175 CAVIAR, BP 5095, 361 rue Jean-François Breton, F-34196 Montpellier Cédex 5, France. Emmanuel.Paradis@ird.fr
Evolution; International Journal of Organic Evolution
|November 9, 2010
Summary
This study introduces a time-dependent birth-death model to analyze molecular phylogenies, enabling the estimation of speciation and extinction rates over time. It offers new methods for fitting models and assessing uncertainty in evolutionary analyses.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Computational Biology
Background:
- Molecular phylogenies offer insights into macroevolutionary patterns and processes.
- However, reconstructing past evolutionary events from phylogenies alone is challenging due to the absence of fossil data.
Purpose of the Study:
- To develop and apply a general time-dependent birth-death model for analyzing phylogenies.
- To derive methods for fitting models of temporal variation in speciation and extinction rates.
- To assess the uncertainty of parameter estimates and provide tree simulation algorithms.
Main Methods:
- Utilized a general time-dependent birth-death model to fit phylogenies.
- Derived formulae for the expected cumulative distribution function of branching times.
- Developed maximum likelihood and least squares estimators for model fitting.
- Implemented parametric and nonparametric bootstrap procedures for uncertainty assessment.
- Presented algorithms for continuous-time phylogenetic tree simulation.
Main Results:
- Established formulae for computing branching time distributions under various speciation/extinction models.
- Derived maximum likelihood estimators and proposed a least squares fitting procedure to overcome limitations.
- Developed bootstrap methods for robust uncertainty quantification, with nonparametric bootstrap offering faster computation and narrower intervals.
- Demonstrated the approach using simulated data and real phylogenies of primates and lizards.
Conclusions:
- The time-dependent birth-death model provides a flexible framework for macroevolutionary inference from phylogenies.
- The developed statistical methods, including least squares fitting and bootstrap procedures, enhance the reliability of evolutionary rate estimations.
- This approach facilitates a deeper understanding of macroevolutionary dynamics by integrating phylogenetic data with temporal variation in speciation and extinction.
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