R-Sig-Phylo (listserv for R-phylogenetics, worth checking out!)
evoldir (listserv for evolutionary biology)
Liam Revell's "Comparative methods in R" blog (focused on implementing comparative methods in R)
--->specific post: http://blog.phytools.org/2013/02/a-comment-on-distribution-of-residuals.html
--->discussed homework: http://www.phytools.org/mpma/hw_2.1/
The R for Phylogenetics Hackathon (NESCent resource on R for Phylogenetics)
Phyloseminar (online talks about phylogenetics, including comparative methods)
Bodega Bay Phylogenetics Workshop (lectures and problem sets)
The Comparative Primatology Research Group (Charlie's lab web pages)
Time Tree (divergence times)
10kTrees (primate phylogeny)
Phylogenetic targeting (identifying species to study in the future)
PhyloDiversity (various researchers and resources)
Brian O'Meara's site (comparison of packages, other info)
Journal, Methods in Ecology and Evolution
Center for Ecology and Evolution Symposium videos, "Ecology and Macroevolution"
AnthroTree Website (examples to accompany Charlie's book)
The Comprehensive R Archive network
BE-r-phylo.org (NESCent tutorial for phylogenetics in R)
NESCent - National Evolutionary Synthesis Center
R Graph Gallery - all the beautiful things you can do with R!
PanTHERIA - “a species-level database of life history, ecology, and geography of extant and recently extinct mammals.”
Podcasts for R beginners: http://www.tcd.ie/Zoology/research/research/theoretical/Rpodcasts.php