You will want to try Bayesian mixed modeling which can handle your species
# problem by using “species” as a group level (i.e. “random”) effect. I
would recommend r packages brms and MCMCglmm and their vignettes. Both have
detailed “phylo” examples.
Maybe check out the r-sig-mixed-model listserv as well. Lots of similar
questions and good advice show up on there.
Jonathan A. Nations
Esselstyn Lab <http://www.museum.lsu.edu/esselstyn>
Museum of Natural Sciences <http://sites01.lsu.edu/wp/mns>
Louisiana State University
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