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.

Good luck!
Jonathan A. Nations
PhD Candidate
Esselstyn Lab <>
Museum of Natural Sciences <>
Louisiana State University

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