Phylogenetic trees

Birds. Given the list of species at the regional pool (21), we obtained 100 phylogenetic trees inferred from the BirdTree.org online database using the “Stage2 MayrParSho Ericson” source tree as birds’ master phylogeny (available at http://birdtree.org/methods/). Trees’ topology is resolved with a combination of genetic and taxonomic information and dated with a relaxed molecular clock [see (6, 41) for details]. A few species that were identified at genus level in the field (i.e., Elaenia sp., Myiarchus sp., Patagioenas sp., Penelope sp., and Turdus sp.) therefore could not be found in the master phylogeny. We randomly grafted these species in their correspondent clades using the “add.species.to.genus” function in the phytools package version 0.6-00 in R (42).

Plants. Given the list of plant species at the regional pool (21), we used the megaphylogeny of trees (43) with the “S.PhyloMaker” function (41) to obtain the initial plant tree. The initial tree was based on “scenario 1” in which missing genera and/or species are added as basal polytomies within their higher taxonomic level (44). Then, we simultaneously resolved the polytomies and adjusted the branch lengths using an evolutionary birth-death model with the help of “PolytomyResolver” function (45) and BEAST version 1.5.4 (46). Markov Chain Monte Carlo analyses were run for 10⁶ iterations, and trees were sampled every 10³ iterations. After discarding the 25% first trees, we randomly selected 100 trees for subsequent analyses.