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Methods and theory of phylogenetic inference

Salamin, Nicolas [1].

Estimating speciation and extinction rates from phylogenetic trees: A Markov chain Monte Carlo approach.

Phylogenetic trees based on molecular data contain a temporal dimension associated with the branch lengths defining the trees. The tempo of evolution of lineages can then be estimated from those trees using stochastic processes, such as the birth and death process, resulting in estimates of speciation and extinction rates. Here, a full maximum-likelihood approach is described to estimate the speciation and extinction rates from molecular phylogenetic trees. Uncertainties in the estimation of the branch lengths and the topology were taken into account using Markov chain Monte Carlo. In contrast to a Bayesian approach, no prior distributions were assumed on the parameters, and an importance sampling scheme was used instead. Computer simulations were performed and showed that accurate estimates of speciation and extinction rates can be obtained using the method, as long as large DNA matrices and a comprehensive set of taxa have been sampled. Finally, the Gesneriaceae, a tropical plant family with multiple pollination syndromes, was used to illustrate the use of the method.


1 - University of Dublin, Trinity College, Department of Botany, College Green, Dublin, Dublin, 2, Ireland

Keywords:
birth and death
speciation and extinction rates
Markov chain Monte Carlo
importance sampling
macroevolution
phylogenetics.

Presentation Type: Symposium
Session: 31-3
Location: Alpine A (Snowbird Center)
Date: Tuesday, August 3rd, 2004
Time: 9:30 AM
Abstract ID:174


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