Methods and theory of phylogenetic inference
Salamin, Nicolas .
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
1 - University of Dublin, Trinity College, Department of Botany, College Green, Dublin, Dublin, 2, Ireland
birth and death
speciation and extinction rates
Markov chain Monte Carlo
Presentation Type: Symposium
Location: Alpine A (Snowbird Center)
Date: Tuesday, August 3rd, 2004
Time: 9:30 AM