Mark Holder wrote:
With respect to Jarrod's simulations, I have a few thoughts:
1. I don't understand the claim (in the original email) that "its
fairly straightforward to prove that asymmetric transition rates
cannot be identified using data collected on the tips of a
phylogeny" It seems like this is something that is routinely done
in phylogenetics, and proofs of identifiability of GTR exist
(demonstrating that this indeed feasible and not some
computational artifact).
I agree. This whole discussion may have started from a "fact" that
is *not* "fairly straightforward to prove". In which case it is not
necessary to bring speciation rates or priors into it.
A reversible two-state model should be able to have its parameters
estimated on a given tree, clocklike or not.
Joe
----
Joe Felsenstein, j...@gs.washington.edu
Dept. of Genome Sciences, Univ. of Washington
Box 355065, Seattle, WA 98195-5065 USA
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