Mountains contribute disproportionately to the terrestrial biodiversity of Earth, especially in the tropics, where they host hotspots of extraordinary and puzzling richness. With about 25% of all land area, mountain regions are home to more than 85% of the world’s species of amphibians, birds, and mammals, many entirely restricted to mountains. Biodiversity varies markedly among these regions. Together with the extreme species richness of some tropical mountains, this variation has proven challenging to explain under traditional climatic hypotheses. However, the complex climatic characteristics of rugged mountain regions differ fundamentally from those of lowland regions, likely playing a key role in generating and maintaining diversity. With ongoing global changes in climate and land use, the role of mountains as refugia for biodiversity may well come under threat.

The processes causing the latitudinal gradient in species richness remain elusive. Ecological theories for the origin of biodiversity gradients, such as competitive exclusion, neutral dynamics, and environmental filtering, make predictions for how functional diversity should vary at the alpha (within local assemblages), beta (among assemblages), and gamma (regional pool) scales. We test these predictions by quantifying hypervolumes constructed from functional traits representing major axes of plant strategy variation (specific leaf area, plant height, and seed mass) in tree assemblages spanning the temperate and tropical New World. Alpha-scale trait volume decreases with absolute latitude and is often lower than sampling expectation, consistent with environmental filtering theory. Beta-scale overlap decays with geographic distance fastest in the temperate zone, again consistent with environmental filtering theory. In contrast, gamma-scale trait space shows a hump-shaped relationship with absolute latitude, consistent with no theory. Furthermore, the overall temperate trait hypervolume was larger than the overall tropical hypervolume, indicating that the temperate zone permits a wider range of trait combinations or that niche packing is stronger in the tropical zone. Although there are limitations in the data, our analyses suggest that multiple processes have shaped trait diversity in trees, reflecting no consistent support for any one theory. S pecies richness increases toward the equator (1, 2) in major clades of both extant and extinct species of plants and animals (3, 4). The generality of the pattern hints at a correspondingly general explanation, yet the latitudinal gradient in species richness remains one of ecology's greatest unsolved puzzles. Long-running debates over the causes of the latitudinal gradient of species richness have focused on ecological, evolutionary, and geographic explanations (5-10). Although there has been some progress (11), it is also increasingly clear that there are numerous obstacles to understanding the primary drivers of the latitudinal gradient, including an ever-increasing number of hypotheses (12, 13), challenges in clearly separating their interdependencies (14, 15), and difficulties in rigorously falsifying their assumptions and predictions (16).More powerful tests of biodiversity theories need to move beyond species richness and instead explicitly focus on the mechanisms generating the gradient, by recasting the theories in terms of other measures of diversity, such as functional diversity (17-19). For example, explanations that assume species richness is limited by resource availability have often focused on the strength of species interactions, life history differences, and environmental constraints on how species pack into niche space (20). Evolutionary hypotheses have focused on differences in diversification rates, as well as the influence of species interactions on diversification rates (9). These interaction-based explanations implicitly refer to the degree of ecol...

Abstract1. There is an urgent need for large-scale botanical data to improve our understanding of community assembly, coexistence, biogeography, evolution, and many other fundamental biological processes. Understanding these processes is critical for predicting and handling human-biodiversity interactions and global change dynamics such as food and energy security, ecosystem services, climate change, and species invasions.2. The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data, containing roughly 81 million occurrence records from c. 375,000 species, c. 915,000 trait observations across 28 traits from c. 93,000 species, and co-occurrence records from 110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated phylogenies (each containing 81,274 species) for New World species. Here, we describe an r package that provides easy access to these data. K E Y W O R D S

BackgroundCalifornia is a world floristic biodiversity hotspot where the terms neo- and paleo-endemism were first applied. Using spatial phylogenetics, it is now possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism, by combining spatial information from museum collections and DNA-based phylogenies. Here we used a distributional dataset of 1.39 million herbarium specimens, a phylogeny of 1083 operational taxonomic units (OTUs) and 9 genes, and a spatial randomization test to identify regions of significant phylogenetic diversity, relative phylogenetic diversity, and phylogenetic endemism (PE), as well as to conduct a categorical analysis of neo- and paleo-endemism (CANAPE).ResultsWe found (1) extensive phylogenetic clustering in the South Coast Ranges, southern Great Valley, and deserts of California; (2) significant concentrations of short branches in the Mojave and Great Basin Deserts and the South Coast Ranges and long branches in the northern Great Valley, Sierra Nevada foothills, and the northwestern and southwestern parts of the state; (3) significant concentrations of paleo-endemism in Northwestern California, the northern Great Valley, and western Sonoran Desert, and neo-endemism in the White-Inyo Range, northern Mojave Desert, and southern Channel Islands. Multiple analyses were run to observe the effects on significance patterns of using different phylogenetic tree topologies (uncalibrated trees versus time-calibrated ultrametric trees) and using different representations of OTU ranges (herbarium specimen locations versus species distribution models).ConclusionsThese analyses showed that examining the geographic distributions of branch lengths in a statistical framework adds a new dimension to California floristics that, in comparison with climatic data, helps to illuminate causes of endemism. In particular, the concentration of significant PE in more arid regions of California extends previous ideas about aridity as an evolutionary stimulus. The patterns seen are largely robust to phylogenetic uncertainty and time calibration but are sensitive to the use of occurrence data versus modeled ranges, indicating that special attention toward improving geographic distributional data should be top priority in the future for advancing understanding of spatial patterns of biodiversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0435-x) contains supplementary material, which is available to authorized users.

A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth’s plant biodiversity that are rare. A large fraction, ~36.5% of Earth’s ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth’s plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.

Global climate change is driving species poleward and upward in high-latitude regions, but the extent to which the biodiverse tropics are similarly affected is poorly known due to a scarcity of historical records. In 1802, Alexander von Humboldt ascended the Chimborazo volcano in Ecuador. He recorded the distribution of plant species and vegetation zones along its slopes and in surrounding parts of the Andes. We revisited Chimborazo in 2012, precisely 210 y after Humboldt's expedition. We documented upward shifts in the distribution of vegetation zones as well as increases in maximum elevation limits of individual plant taxa of >500 m on average. These range shifts are consistent with increased temperatures and glacier retreat on Chimborazo since Humboldt's study. Our findings provide evidence that global warming is strongly reshaping tropical plant distributions, consistent with Humboldt's proposal that climate is the primary control on the altitudinal distribution of vegetation. T he biological impacts of ongoing climate change (1) are already apparent in species' poleward and upslope range shifts and earlier spring events (2-9). However, most studies stem from high-latitude areas and are generally restricted to dynamics across the past few decades (10). To our knowledge, only three previous resurveys have studied range shifts of tropical plant taxa, all at <4,000 m in elevation (7,8,11). Modeling (12) and paleoecological studies (13) suggest that tropical montane vegetation should be highly sensitive to climate change. However, researchers strongly debate whether tropical plants are tracking warming temperatures along elevation gradients, with most (although scarce) studies indicating they are lagging behind (cf. 14, 15). Such lags could have negative effects on the distributions of species dependent on certain plant taxa, e.g., as a food source (16). The question is particularly urgent given the growing evidence of systematically stronger warming rates in high-mountain environments (17).The legacy and works of Alexander von Humboldt (1769-1859) not only constitute the foundation of biogeography, but also what is likely the oldest dataset on altitudinal ranges of plant species. The observations recorded by Humboldt and Aimé Bonpland (1773-1858) during their travels in Central and South America, and synthesized in a Tableau of Mt. Chimborazo (summit 6,268 m above sea level) and accompanying essay (18), provide a unique opportunity to study tropical vegetation changes over a period of 210 y. To our knowledge, this period is more than twice as long as any previous resurvey study based on historical biodiversity records (11,19). We revisited the upper slopes of the Chimborazo volcano in June 2012. Our aim was to record the current elevational distribution of plants and test for upward shifts since Humboldt's expedition, as a response to anthropogenic global warming. We sampled plant species presence and abundance along transects every 100 m of elevation between 3,800 and 5,200 m. Three main findings, comparing ou...

Despite being a fundamental aspect of biodiversity, little is known about what controls species range sizes. This is especially the case for hyperdiverse organisms such as plants. We use the largest botanical data set assembled to date to quantify geographical variation in range size for ∼ 85 000 plant species across the New World. We assess prominent hypothesised range-size controls, finding that plant range sizes are codetermined by habitat area and long- and short-term climate stability. Strong short- and long-term climate instability in large parts of North America, including past glaciations, are associated with broad-ranged species. In contrast, small habitat areas and a stable climate characterise areas with high concentrations of small-ranged species in the Andes, Central America and the Brazilian Atlantic Rainforest region. The joint roles of area and climate stability strengthen concerns over the potential effects of future climate change and habitat loss on biodiversity.

Abstract. We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate change on New World forests, integrating data for climate niches of more than 14 000 species, community composition of 471 New World forest plots, and observed climate across the most recent glacial-interglacial interval. We show that a majority of communities have species compositions that are strongly filtered and are more in equilibrium with current climate than random samples from the regional pool. Variation in the level of current community disequilibrium can be predicted from Last Glacial Maximum climate and will increase with near-future climate change.