MAGALLON, SUSANA A. Instituto de Biologia, Universidad Nacional Autonoma de Mexico, A.P. 70-233, Mexico D.F. 04510, Mexico. - Phylogenies, molecules, clocks, the fossil record, and their role in inferring rates of evolution and timing of lineage divergence.
The study of geographic disjunctions is inextricably linked with the
timing of lineage splitting. This presentation will summarize some of
the principal issues and methods pertaining the inference of
evolutionary rates and timing of lineage divergence on the basis of
molecular sequence data, and in the context of an explicit
phylogenetic hypothesis. The adequacy of substitution models should be
assessed, particularly regarding the need to include parameters to
accommodate among-site rate variation. Rate variation among lineages
is an important source of error in age estimates. The assumption of
rate constancy should be tested either through relative rate tests, or
through global tests, which may rely on a comparison of observed vs.
estimated branch lengths, or on the likelihood values of models of
evolution that differ only in the presence/absence of rate constancy.
Information from geological events or the fossil record can be
incorporated into a phylogeny to provide a general chronological
calibration, or minimum- or maximum-age constrains to nodes. Fossils
should be evaluated as to whether they provide the stem group or crown
group age of a given clade. Reconstruction of divergence times among
lineages under rate constancy may be straightforwardly achieved
through predictions from a weighted linear regression analysis of
inferred distances against calibration times, or through the use of
maximum likelihood and a rate-constant substitution model on a given
phylogeny. Promising approaches to estimating divergence times in the
absence of rate constancy have been recently developed. A
non-parametric method, based on the assumption of rate
autocorrelation, minimizes local shifts in rates from branch to
branch. A semi-parametric method combines a different substitution
rate in each branch with a penalization for excessive variation.
Examples of some of these methods and of the effect of node
constrains, based on lineage divergence among major seed plant clades,
will be presented.
Key words: branch lengths, fossil record, lineage-effects, non-parametric rate smoothing, penalized likelihood, rate variation