Let me add more warnings to Marguerite and Thomas's excellent
responses.   People may be tempted to infer ancestral states and then
treat those inferences as data (and also to infer ancestral
environments and then treat those inferences as data).  In fact, I
wonder whether that is not the main use people make of these

But not only are those inferences very noisy, they are correlated with
each other.  So if you infer the ancestral state for the clade (Old
World Monkeys, Apes) and also the ancestral state for the clade (New
World Monkeys, (Old World Monkeys, Apes)) the two will typically not
only be error-prone, but will also typically be subject to strongly
correlated errors.  Using them as data for further inferences is very
dubious.  It is better to figure out what your hypothesis is and then
test it on the data from the tips of the tree, without the
intermediate step of taking ancestral state inferences as

The popular science press in particular demands a fly-on-the-wall
account of what happened in evolution, and giving them the ancestral
state inferences as if they were known precisely is a mistake.

Joe Felsenstein         j...@gs.washington.edu
 Department of Genome Sciences and Department of Biology,
 University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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