Estimating divergence times when branch lengths vary

Mike Syvanen syvanen at ucdavis.edu
Tue Jun 15 12:40:01 EST 1999



Thorsten Burmester wrote:

> Dear Evolutionists,
>
> Let us consider a phylogenetic tree of a superfamily of orthologous
> proteins. There are three or more distinct protein families, each with a
> rather constant evolution rate. I.e., the molecular clock assumption

>
> [snip tree]
>
> 1.) Do the different phylogenetic programs assign the branch lengths
> "correctly" to these internal branches (like a)? Are there different
> assumptions (apart from the general phylogenetic method used) that are
> implemented in the programs to calculate these lengths? I have the
> slight feeling that some programs (especially PAUP parsimony) tend to
> underestimate them.
>

I have found that PAUP phylograms cannot be used in this way, but that
corrected distance trees can.  I use the the GCG programs and in particular
their DISTANCES.  I use a reiteration of  a trifucation rate test to
construct the tree and estimate times.   This exercise is published in:

Syvanen (1999)" Temporal patterns of land plant evolution suggest extensive
polyphyly". to appear in Symbiosis to Eukaryotism ENDOCYTOBIOLOGY VII
E. Wagner, et al eds, University of Geneva

2.) Is there any statistical test to verify the estimated divergence

>

I present one, but I would like to see more extensive criticisms of this
test before it is recommended for general use.


Mike Syvanen






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