[Mesquitelist] stochastic mapping

[Stefan Ekman]

Hello,

I  was wondering if someone could explain to me how stochastic mapping 
is implemented in Mesquite, and specifically how it compares to SIMMAP...

In SIMMAP, stochastic mapping is a Bayesian technique, which among other 
things means that you have to place a prior on tree length (i.e., the 
amount of morphological change in a tree).

In Mesquite, whether reconstructing ancestral states or summarizing 
change over trees (e.g., a posterior sample from MrBayes), I find no way 
of placing a prior on tree length (or any other proxy for rate). Does 
Mesquite use some kind of "implicit prior"? Or is stochastic mapping in 
Mesquite non-Bayesian, instead mapping the amount of change prescribed 
by the corresponding maximum likelihood reconstruction? If the latter, 
one would expect Summarize Change to give the same result with 
stochastic mapping as with maximum likelihood, but empiry indicates that 
this is not the case.

Many thanks in advance!

Sincerely,
Stefan Ekman
____________________________________________________
Museum of Evolution
Evolutionary Biology Centre
Uppsala University
Norbyvägen 16
SE-752 36  Uppsala, Sweden