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 inferences.
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 observations. 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 ---- Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
