Climate change may be a major threat to biodiversity in the next 100 years. Although there has been important work on mechanisms of decline in some species, it generally remains unclear which changes in climate actually cause extinctions, and how many species will likely be lost. Here, we identify the specific changes in climate that are associated with the widespread local extinctions that have already occurred. We then use this information to predict the extent of future biodiversity loss and to identify which processes may forestall extinction. We used data from surveys of 538 plant and animal species over time, 44% of which have already had local extinctions at one or more sites. We found that locations with local extinctions had larger and faster changes in hottest yearly temperatures than those without. Surprisingly, sites with local extinctions had significantly smaller changes in mean annual temperatures, despite the widespread use of mean annual temperatures as proxies for overall climate change. Based on their past rates of dispersal, we estimate that 57–70% of these 538 species will not disperse quickly enough to avoid extinction. However, we show that niche shifts appear to be far more important for avoiding extinction than dispersal, although most studies focus only on dispersal. Specifically, considering both dispersal and niche shifts, we project that only 16–30% of these 538 species may go extinct by 2070. Overall, our results help identify the specific climatic changes that cause extinction and the processes that may help species to survive.

The latitudinal diversity gradient is Earth’s foremost biodiversity pattern, persistent across clades and geologic time. Several recent studies have shown that diversification rates are similar among latitudes, and therefore cannot explain the latitudinal diversity gradient. An alternative explanation is that the tropics were colonized earlier than the temperate zone, allowing more time for speciation to build richness. Here we test the diversification-rate and colonization time hypotheses in freshwater ray-finned fishes, a group comprising nearly a quarter of all living vertebrate species and with a longer evolutionary history than other vertebrates. To build a global timeline for colonization and diversification, we performed ancestral area reconstructions on a time-calibrated phylogeny of all ray-finned fishes using occurrence records from over 3,000 freshwater habitats. We found that diversification rates are not systematically related to latitude, consistent with analyses in other groups. Instead, the timing of colonization to continental regions had 2–5 times more explanatory power for species richness than diversification rates. Earlier colonization explains high richness in the tropics, with the Neotropics in particular supporting the most diverse fauna for the past 100 million years. Most extratropical fish lineages colonized shortly after the end-Cretaceous mass extinction, leaving limited time to build diversity even in places where diversification rates are high. Our results demonstrate that evolutionary time, reflecting colonization and long-term persistence of lineages, is a powerful driver of biodiversity gradients.

In a previous paper, we used simulations and empirical data to show that BAMM (Bayesian Analysis of Macroevolutionary Mixtures) can give misleading estimates of rates and rate shifts. In simulations, BAMM underestimated rate shifts across every tree analyzed, and assigned incorrect rates to most clades in most trees. In empirical analyses, BAMM behaved as expected from simulations, and assigned different rates to clades when clades were analyzed alone versus across the tree (i.e., with rate heterogeneity). Rabosky recently criticized our paper, focusing primarily on the idea that our comparison of BAMM to another approach (method-of-moments estimators of Magallón and Sanderson, or MS estimators) was unfair to BAMM. Here, we provide further evidence that BAMM gives misleading rate estimates in empirical studies. We then describe how Rabosky's rown method comparisons were either acknowledged as being problematic or were described inaccurately (to favor BAMM). Finally, we show that the MS estimators can perform well when rates vary over time, despite untested assertions that they require constant rates to be accurate. Many other methods are available for analyzing diversification rates: we argue that BAMM should be avoided for estimating both diversification rates and rate shifts.

Aim The evolutionary causes of the latitudinal diversity gradient are debated. Hypotheses have ultimately invoked either faster rates of diversification in the tropics or more time for diversification owing to the tropical origins of higher taxa. Here, we perform the first test of the diversification rate and time hypotheses in freshwater ray‐finned fishes, a group comprising nearly a quarter of all living vertebrates. Location Global. Time period 368–0 Ma. Major taxa studied Extant freshwater ray‐finned fishes. Methods Using a mega‐phylogeny of actinopterygian fishes and a global database of occurrence records, we estimated net diversification rates, the number of colonizations and regional colonization times of co‐occurring species in freshwater drainage basins. We used generalized additive models to test whether these factors were related to latitude. We then compared the influence of diversification rates, numbers of colonizations, colonization times and surface area on species richness, and how these factors are related to each other. Results Although both diversification rates and time were related to richness, time had greater explanatory power and was more strongly related to latitude than diversification rates. Other factors (basin surface area and number of colonizations) also helped to explain richness but were unrelated to latitude. The most diverse freshwater basins of the world (Amazon and Congo rivers) were dominated by lineages having Mesozoic origins. The temperate groups dominant today arrived near the Cretaceous–Palaeogene boundary, leaving comparatively less time to build richness. Diversification rates and colonization times were inversely related: recently colonized basins had the fastest rates, whereas ancient species‐rich faunas had slower rates. Main conclusions We concluded that time is the leading driver of latitudinal disparities in richness in freshwater fish faunas. We suggest that the most likely path to building very high species richness is through diversification over long periods of time, rather than through rapid diversification.

What an animal eats is a fundamental aspect of its biology, but the evolution of diet has not been studied across animal phylogeny. Here, we performed a large‐scale phylogenetic analysis to address three unresolved questions about the evolution of animal diets. (i) Are diets conserved across animal phylogeny? (ii) Does diet influence rates of species proliferation (diversification) among animal phyla? (iii) What was the ancestral diet of animals and major animal clades? We analyzed diet data for 1087 taxa, proportionally sampled among animal phyla based on the relative species richness of phyla. Our survey suggests that across animals, carnivory is most common (∼63%), herbivory less common (∼32%), and omnivory relatively rare (∼3%). Despite considerable controversy over whether ecological traits are conserved or labile, we found strong conservatism in diet over extraordinarily deep timescales. We found that diet is unrelated to rates of species diversification across animal phyla, contrasting with previous studies showing that herbivory increased diversification within some important groups (e.g., crustaceans, insects, and mammals). Finally, we estimated that the ancestor of all animals was most likely carnivorous, as were many major phyla (e.g., arthropods, molluscs, and chordates). Remarkably, our results suggest that many carnivorous species living today may have maintained this diet through a continuous series of carnivorous ancestors for >800 million years.