Data from: Diversification rates have declined in the Malagasy herpetofauna

The evolutionary origins of Madagascar's biodiversity remain mysterious despite the fact that relative to land area, there is no other place with consistently high levels of species richness and endemism across a range of taxonomic levels. Most efforts to explain diversification on the island have focused on geographical models of speciation, but recent studies have begun to address the island's accumulation of species through time, although with conflicting results. Prevailing hypotheses for diversification on the island involve either constant diversification rates or scenarios where rates decline through time. Using relative-time-calibrated phylogenies for seven endemic vertebrate clades and a model-fitting framework, I find evidence that diversification rates have declined through time on Madagascar. I show that diversification rates have clearly declined throughout the history of each clade, and models invoking diversity-dependent reductions to diversification rates best explain the diversification histories for each clade. These results are consistent with the ecological theory of adaptive radiation, and, coupled with ancillary observations about ecomorphological and life-history evolution, strongly suggest that adaptive radiation was an important formative process for one of the most species-rich regions on the Earth. These results cast the Malagasy biota in a new light and provide macroevolutionary justification for conservation initiatives. MCC and Posterior Trees - output from BEASTThis compressed file contains the posterior distribution of trees as well as the MCC tree (with mean node heights) for each clade.rawtrees.zipTrees pruned of extraneous taxa for diversification analysesThese are the MCC and posterior trees of each clade that have been pruned of inappropriate taxa for the diversification analyses. Pruned tips are not from Madagascar, are intraspecific samples, and/or are not valid species.droptip_trees.zipModel fitting results and summariesThis file contains the results of the HMM model fits for each clade. Each clade was analyzed at two levels of taxonomic sampling completeness - 100% and 50%. Thus, the files that include "_1_Complete" or "_0.5_Complete" refer to 100% or 50% complete respectively. The files with "AnalyzedTrees" in their names are the randomly selected trees from the posterior distributions that were analyzed. Note that in producing these lists, the MCC tree was placed on top of all posterior trees. Thus, the first row in all refers to the MCC tree (1), and the remaining 49 rows are the number of the randomly selected posterior tree plus 1.modelstats.zipR code and functions to run this analysisThis contains relevant functions and the code I used to collect these data. See the README within for more details.Rcode.zip