Jonathan Rolland and colleagues show that the gradient of increased mammalian diversity towards the tropics is driven by both faster speciation and reduced extinction.

The study of islands as model systems has played an important role in the development of evolutionary and ecological theory. The 50th anniversary of MacArthur and Wilson's (December 1963) article, 'An equilibrium theory of insular zoogeography', was a recent milestone for this theme. Since 1963, island systems have provided new insights into the formation of ecological communities. Here, building on such developments, we highlight prospects for research on islands to improve our understanding of the ecology and evolution of communities in general. Throughout, we emphasise how attributes of islands combine to provide unusual research opportunities, the implications of which stretch far beyond islands. Molecular tools and increasing data acquisition now permit reassessment of some fundamental issues that interested MacArthur and Wilson. These include the formation of ecological networks, species abundance distributions, and the contribution of evolution to community assembly. We also extend our prospects to other fields of ecology and evolution -understanding ecosystem functioning, speciation and diversification -frequently employing assets of oceanic islands in inferring the geographic area within which evolution has occurred, and potential barriers to gene flow. Although island-based theory is continually being enriched, incorporating non-equilibrium dynamics is identified as a major challenge for the future.

The latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the 'diversification rate hypothesis' with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs.

Summary The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade.We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model.We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr.Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.

SignificanceAmazonia is not only the world’s most diverse rainforest but is also the region in tropical America that has contributed most to its total biodiversity. We show this by estimating and comparing the evolutionary history of a large number of animal and plant species. We find that there has been extensive interchange of evolutionary lineages among different regions and biomes, over the course of tens of millions of years. Amazonia stands out as the primary source of diversity, which can be mainly explained by the total amount of time Amazonian lineages have occupied the region. The exceedingly rich and heterogeneous diversity of the American tropics could only be achieved by high rates of dispersal events across the continent.

Summary1. A number of approaches for studying macroevolution using phylogenetic trees have been developed in the last few years. Here, we present RPANDA, an R package that implements model-free and model-based phylogenetic comparative methods for macroevolutionary analyses. 2. The model-free approaches implemented in RPANDA are recently developed approaches stemming from graph theory that allow summarizing the information contained in phylogenetic trees, computing distances between trees, and clustering them accordingly. They also allow identifying distinct branching patterns within single trees. 3. RPANDA also implements likelihood-based models for fitting various diversification models to phylogenetic trees. It includes birth-death models with i) constant, ii) time-dependent and iii) environmental-dependent speciation and extinction rates. It also includes models with equilibrium diversity derived from the coalescent process, as well as a likelihood-based inference framework to fit the individual-based model of Speciation by Genetic Differentiation, which is an extension of Hubbell's neutral theory of biodiversity. 4. RPANDA can be used to (i) characterize trees by plotting their spectral density profiles (ii) compare trees and cluster them according to their similarities, (iii) identify and plot distinct branching patterns within trees, (iv) compare the fit of alternative diversification models to phylogenetic trees, (v) estimate rates of speciation and extinction, (vi) estimate and plot how these rates have varied with time and environmental variables and (vii) deduce and plot estimates of species richness through geological time. 5. RPANDA provides investigators with a set of tools for exploring patterns in phylogenetic trees and fitting various models to these trees, thereby contributing to the ongoing development of phylogenetics in the life sciences.

Predicting how biodiversity will be affected and will respond to human-induced environmental changes is one of the most critical challenges facing ecologists today. Here, we put current environmental changes and their effects on biodiversity in a macroevolutionary perspective. We build on research in palaeontology and recent developments in phylogenetic approaches to ask how macroevolution can help us understand how environmental changes have affected biodiversity in the past, and how they will affect biodiversity in the future. More and more paleontological and phylogenetic data are accumulated, and we argue that much of the potential these data have for understanding environmental changes remains to be explored.

BackgroundBayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads.ResultsUsing Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior.ConclusionsThese results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.