This data package contains all data files necessary to conduct the macroevolutionary analyses of Greater Antillean Anolis lizard evolution presented in Mahler et al. 2013. These data comprise phylogenetic trees, phenotypic trait data, as well as biogeographic information and traditional ecomorph class assignments for the 100 species of Greater Antillean anoles investigated in this study.

The files "GA_Anolis_MCC.nex" and "GA_Anolis_MCC.tre" each contain the Bayesian maximum clade credibility chronogram for Greater Antillean Anolis used as the primary tree for the analyzed in this study. This tree was derived from a Bayesian analysis of mtDNA described in a previous study (Mahler et al. 2010) as well as in the supplementary materials of Mahler et al. 2013. It is pruned to the 100 Greater Antillean species used in this study. The two files contain the same tree, but in two different formats (Nexus and Newick, respectively).

The files "GA_Anolis_posterior_sample100.nex" and "GA_Anolis_posterior_sample100.tre" each contain 100 chronograms randomly sampled from posterior distribution of the above mentioned Bayesian analysis. The order of these trees matches the order in which they were analyzed for the Mahler et al. 2013 study. These files are also identical in content, but in Nexus and Newick formats, respectively.

The file "GA_Anolis_traits.csv" is a comma-delimited file that contains the Anolis trait values analysed in Mahler et al. 2013. These consist of natural log-transformed species averages for 11 phenotypic traits that are important for resource partitioning in anoles. These data derive from a slighly larger data set (including additional traits) reported in Mahler et al. 2010. Detailed trait descriptions are provided in that paper. Note that the trait "snout-to-vent length" occurs in two columns. The first column "AVG SVL" is the measure of body size that we used in our analyses. The column "Avg lnSVL2" contains SVL averages from a slightly smaller sample of individuals, and corresponds to the individuals for which we measured tail length. Because many anoles in museum collections (as well as in the wild) have missing or regenerated tails, we were unable to measure tail length for every specimen measured (although we did manage to measure an intact tail for every included species). Because tail length was based on a different sample, we include a corresponding SVL column for "size-correcting" that trait.

The file "GA_Anolis_biogeography.csv" is a comma-delimited file that reports the Greater Antillean island upon which each of the species in our study occurs. We treat all Greater Antillean anole species as endemics - none naturally occur on more than one large Greater Antillean island (some think that Anolis sagrei naturally colonized Jamaica within historical times, but this would have no bearing on anole macroevolution; Anolis sagrei is endemic to Cuba for our purposes). For each species, we provide a numerical code indicating island. Here is the key:
0 = Cuba
1 = Hispaniola
2 = Jamaica
3 = Puerto Rico

The file "GA_Anolis_trad_ecomorph_class.csv" is a comma-delimited file that indicates the traditional ecomorph assignments for each of the species in our study (see Losos 2009 for more information about these assignments). There are no column headers for this file. Ecomorph assignments played no role in the estimation of macroevolutionary adaptive peaks in Mahler et al. 2013, but in that paper we did examine the correspondence of our estimated peaks with these traditional assignments (see Figure S4). For each species, we provide a numerical code and a letter code indicating ecomorph class (these are redundant, but some analyses require a number). Here is the key:
0, TG = Trunk-Ground Ecomorph
1, TC = Trunk-Crown Ecomorph
2, CG = Crown-Giant Ecomorph
3, TW = Twig Ecomorph
4, GB = Grass-Bush Ecomorph
5, T = Trunk Ecomorph
10, U = "Unique" or "Non-ecomorph"


Please contact Luke Mahler (lmahler@gmail.com) with any questions about these data.
Also, here are a couple of references mentioned above:

Losos, J. B. (2009). Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. Berkeley, CA: University of California Press.

Mahler, D. L., Revell, L. J., Glor, R. E., & Losos, J. B. (2010). Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles. Evolution, 64(9), 2731–2745. doi:10.1111/j.1558-5646.2010.01026.x
