[Mesquitelist] stochastic mapping
stefan.ekman at evolmuseum.uu.se
Thu Feb 5 00:57:16 PST 2009
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!
Museum of Evolution
Evolutionary Biology Centre
SE-752 36 Uppsala, Sweden
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