Summary1. Understanding the dynamics of speciation, extinction and phenotypic evolution is a central challenge in evolutionary biology. Here, we present BAMMtools, an R package for the analysis and visualization of macroevolutionary dynamics on phylogenetic trees. BAMMtools is a companion package to BAMM, an open-source program for reversible-jump MCMC analyses of diversification and trait evolution. 2. Functions in BAMMtools operate directly on output from the BAMM program. The package is oriented towards reconstructing and visualizing changes in evolutionary rates through time and across clades in a Bayesian statistical framework. 3. BAMMtools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximum a posteriori probability. Users can compare the fit of alternative diversification models using Bayes factors and by directly comparing model posterior probabilities. 4. By providing a robust framework for quantifying uncertainty in macroevolutionary dynamics, BAMMtools will facilitate inference on the complex mixture of processes that have shaped the distribution of species and phenotypes across the tree of life.

The correlation between species diversification and morphological evolution has long been of interest in evolutionary biology. We investigated the relationship between these processes during the radiation of 250+scincid lizards that constitute Australia's most species-rich clade of terrestrial vertebrates. We generated a time-calibrated phylogenetic tree for the group that was more than 85% complete at the species level and collected multivariate morphometric data for 183 species. We reconstructed the dynamics of species diversification and trait evolution using a Bayesian statistical framework (BAMM) that simultaneously accounts for variation in evolutionary rates through time and among lineages. We extended the BAMM model to accommodate time-dependent phenotypic evolution, and we describe several new methods for summarizing and visualizing macroevolutionary rate heterogeneity on phylogenetic trees. Two major clades (Lerista, Ctenotus; >90 spp. each) are associated with high rates of species diversification relative to the background rate across Australian sphenomorphine skinks. The Lerista clade is characterized by relatively high lability of body form and has undergone repeated instances of limb reduction, but Ctenotus is characterized by an extreme deceleration in the rate of body shape evolution. We estimate that rates of phenotypic evolution decreased by more than an order of magnitude in the common ancestor of the Ctenotus clade. These results provide evidence for a modal shift in phenotypic evolutionary dynamics and demonstrate that major axes of morphological variation can be decoupled from species diversification. More generally, the Bayesian framework described here can be used to identify and characterize complex mixtures of dynamic processes on phylogenetic trees. [Bayesian; diversification; evolvability; lizard; macroevolution, punctuated equilibrium, speciation.].

Living vertebrates vary drastically in body size, yet few taxa reach the extremely minute size of some frogs and teleost fish. Here we describe two new species of diminutive terrestrial frogs from the megadiverse hotspot island of New Guinea, one of which represents the smallest known vertebrate species, attaining an average body size of only 7.7 mm. Both new species are members of the recently described genus Paedophryne, the four species of which are all among the ten smallest known frog species, making Paedophryne the most diminutive genus of anurans. This discovery highlights intriguing ecological similarities among the numerous independent origins of diminutive anurans, suggesting that minute frogs are not mere oddities, but represent a previously unrecognized ecological guild.

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Ecological and phenotypic convergence is a potential outcome of adaptive radiation in response to ecological opportunity. However, a number of factors may limit convergence during evolutionary radiations, including interregional differences in biogeographic history and clade-specific constraints on form and function. Here, we demonstrate that a single clade of terrestrial snakes from Australia-the oxyuranine elapids-exhibits widespread morphological convergence with a phylogenetically diverse and distantly related assemblage of snakes from North America. Australian elapids have evolved nearly the full spectrum of phenotypic modalities that occurs among North American snakes. Much of the convergence appears to involve the recurrent evolution of stereotyped morphologies associated with foraging mode, locomotion and habitat use. By contrast, analysis of snake diets indicates striking divergence in feeding ecology between these faunas, partially reflecting regional differences in ecological allometry between Australia and North America. Widespread phenotypic convergence with the North American snake fauna coupled with divergence in feeding ecology are clear examples of how independent continental radiations may converge along some ecological axes yet differ profoundly along others.

The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees.

Public databases in taxonomy, phylogenetics and geographic and fossil occurrence records are key research tools that provide raw materials, on which broad-scale analyses and synthesis in their respective fields are based. Comparable repositories for natural history observations are rare. Publicly available natural history data on traits like diet, habitat and reproduction are scattered across an extensive primary literature and remain relatively inaccessible to researchers interested in using these data for broad-scale analyses in macroecology and macroevolution. In this paper, I introduce SquamataBase, an open-source R package and database of predator-prey records involving the world’s snakes. SquamataBase facilitates the discovery of natural history observations for use in comparative analyses and synthesis and, in its current form, contains observations of at least 18,304 predator individuals comprising 1,227 snake species and at least 58,633 prey items comprising 3,231 prey taxa. To facilitate integration with comparative analysis workflows, the data are distributed inside an R package, which also provides basic functionality for common data manipulation and filtering operations. Moving forward, the continued development of public natural history databases and their integration with existing digitisation efforts in biodiversity science should become a priority.