Molecular taxonomy: on way out?

[Robert Mesibov]

Jason de Koning wrote:

> Homoplasy is permitted, although assumptions about where and when it
> occurs come directly from the model of state transformation, which is
> integrated over branches.  In likelihood approaches, one uses a model  of
> character state transformation to produce a long probability  expression
> of one's observed data (usually) given a fixed tree.  That  expression
> depends on unobserved character states (for the ancestral  taxa), so it is
> typically integrated over all possible unobserved  states (e.g.,
> Probability(?->A) (t) = Probability(T->A) (t) +  Probability(C->A) (t) +
> Probability(A->A) (t) + Probability(G->A)  (t), where '+' in probability
> calculus corresponds to logical-OR and  't' is the 'time' one is
> integrating over (branch length) ).  The  relative rates of
> transformations and branch lengths are optimized so  that the joint
> likelihood of all characters is maximized (i.e.,  Maximum Likelihood).
> This treatment of unobserved states can be  thought of as weighting
> ancestral states by their probability under  the model.

Many thanks, Jason.
What interested me was the your suggestion that rates of molecular evolution
could be "tested". I'd thought that molecular evolution models typically
assumed a constant rate (clock-like evolution) of character transformation,
and that you only varied the probabilities of particular transformations. I
was therefore thinking that you meant transformation rates in a simulation
could be varied from branch to branch over a fixed, known phylogeny to see
whether particular rate combinations re-created the phylogeny more or less
efficiently after a fixed number of generations. Hence my question about
whether that fixed phylogeny had built-in homoplasy. Instead, you seem to be
saying that "rate" in the models is just the product (or integral) of
transformation probability and time. Have I got that right? If so, do you
know of any attempts to "demonstrate" using simulations that molecular
characters might have evolved at different rates along different branches of
particular phylogenies?
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Dr Robert Mesibov
Honorary Research Associate, Queen Victoria Museum and Art Gallery
and School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 6437 1195

Tasmanian Multipedes
http://www.qvmag.tas.gov.au/zoology/multipedes/mulintro.html
Spatial data basics for Tasmania
http://www.geog.utas.edu.au/censis/locations/index.html
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