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A large number of published ecological studies fail to include basic information about the climate data used. In the interest of reproducibility and transparency, we offer recommendations for best practices that we urge Editors, authors, and reviewers to adopt in future publications.

As most life-forms exist as holobionts, reduction of host-level biodiversity drives parallel habitat losses to their host-adapted microorganisms. The holobiont concept helps us to understand how species are habitats for - often ignored - coevolved microorganisms also worthy of conservation. Indeed, loss of host-associated microbial biodiversity may accelerate the extinction risks of their host., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Classic ecological research into the determinants of biodiversity patterns emphasised the important role of three-dimensional (3D) vegetation heterogeneity. Yet, measuring vegetation structure across large areas has historically been difficult. A growing focus on large-scale research questions has caused local vegetation heterogeneity to be overlooked compared with more readily accessible habitat metrics from, for example, land cover maps. Using newly available 3D vegetation data, we investigated the relative importance of habitat and vegetation heterogeneity for explaining patterns of bird species richness and composition across Denmark (42,394 km 2 ). We used standardised, repeated point counts of birds conducted by volunteers across Denmark alongside metrics of habitat availability from land-cover maps and vegetation structure from rasterised LiDAR data (10 m resolution). We used random forest models to relate species richness to environmental features and considered trait-specific responses by grouping species by nesting behaviour, habitat preference and primary lifestyle. Finally, we evaluated the role of habitat and vegetation heterogeneity metrics in explaining local bird assemblage composition. Overall, vegetation structure was equally as important as habitat availability for explaining bird richness patterns. However, we did not find a consistent positive relationship between species richness and habitat or vegetation heterogeneity; instead, functional groups displayed individual responses to habitat features. Meanwhile, habitat availability had the strongest correlation with the patterns of bird assemblage composition. Our results show how LiDAR and land cover data complement one another to provide insights into different facets of biodiversity patterns and demonstrate the potential of combining remote sensing and structured citizen science programmes for biodiversity research. With the growing coverage of LiDAR surveys, we are witnessing a revolution of highly detailed 3D data that will allow us to integrate vegetation heterogeneity into studies at large spatial extents and advance our understanding of species' physical niches., (© 2023 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Land-use change is considered the greatest threat to nature, having caused worldwide declines in the abundance, diversity, and health of species and ecosystems. Despite increasing research on this global change driver, there are still challenges to forming an effective synthesis. The estimated impact of land-use change on biodiversity can depend on location, research methods, and taxonomic focus, with recent global meta-analyses reaching disparate conclusions. Here, we critically appraise this research body and our ability to reach a reliable consensus. We employ named entity recognition to analyze more than 4000 abstracts, alongside full reading of 100 randomly selected papers. We highlight the broad range of study designs and methodologies used; the most common being local space-for-time comparisons that classify land use in situ. Species metrics including abundance, distribution, and diversity were measured more frequently than complex responses such as demography, vital rates, and behavior. We identified taxonomic biases, with vertebrates well represented while detritivores were largely missing. Omitting this group may hinder our understanding of how land-use change affects ecosystem feedback. Research was heavily biased toward temperate forested biomes in North America and Europe, with warmer regions being acutely underrepresented despite offering potential insights into the future effects of land-use change under novel climates. Various land-use histories were covered, although more research in understudied regions including Africa and the Middle East is required to capture regional differences in the form of current and historical land-use practices. Failure to address these challenges will impede our global understanding of land-use change impacts on biodiversity, limit the reliability of future projections and have repercussions for the conservation of threatened species. Beyond identifying literature biases, we highlight the research priorities and data gaps that need urgent attention and offer perspectives on how to move forward., (© 2021 John Wiley & Sons Ltd.)

To meet the ambitious objectives of biodiversity and climate conventions, the international community requires clarity on how these objectives can be operationalized spatially and how multiple targets can be pursued concurrently. To support goal setting and the implementation of international strategies and action plans, spatial guidance is needed to identify which land areas have the potential to generate the greatest synergies between conserving biodiversity and nature's contributions to people. Here we present results from a joint optimization that minimizes the number of threatened species, maximizes carbon retention and water quality regulation, and ranks terrestrial conservation priorities globally. We found that selecting the top-ranked 30% and 50% of terrestrial land area would conserve respectively 60.7% and 85.3% of the estimated total carbon stock and 66% and 89.8% of all clean water, in addition to meeting conservation targets for 57.9% and 79% of all species considered. Our data and prioritization further suggest that adequately conserving all species considered (vertebrates and plants) would require giving conservation attention to ~70% of the terrestrial land surface. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to meet conservation targets for 81.3% of the terrestrial plant and vertebrate species considered. Our results provide a global assessment of where land could be optimally managed for conservation. We discuss how such a spatial prioritization framework can support the implementation of the biodiversity and climate conventions., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

The tropical conservatism hypothesis (TCH) posits that the latitudinal gradient in biological diversity arises because most extant clades of animals and plants originated when tropical environments were more widespread and because the colonization of colder and more seasonal temperate environments is limited by the phylogenetically conserved environmental tolerances of these tropical clades. Recent studies have claimed support of the TCH, indicating that temperate plant diversity stems from a few more recently derived lineages that are nested within tropical clades, with the colonization of the temperate zone being associated with key adaptations to survive colder temperatures and regular freezing. Drought, however, is an additional physiological stress that could shape diversity gradients. Here, we evaluate patterns of evolutionary diversity in plant assemblages spanning the full extent of climatic gradients in North and South America. We find that in both hemispheres, extratropical dry biomes house the lowest evolutionary diversity, while tropical moist forests and many temperate mixed forests harbor the highest. Together, our results support a more nuanced view of the TCH, with environments that are radically different from the ancestral niche of angiosperms having limited, phylogenetically clustered diversity relative to environments that show lower levels of deviation from this niche. Thus, we argue that ongoing expansion of arid environments is likely to entail higher loss of evolutionary diversity not just in the wet tropics but in many extratropical moist regions as well., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Geographic range size has long fascinated ecologists and evolutionary biologists, yet our understanding of the factors that cause variation in range size among species and across space remains limited. Not only does geographic range size inform decisions about the conservation and management of rare and nonindigenous species due to its relationship with extinction risk, rarity, and invasiveness, but it also provides insights into fundamental processes such as dispersal and adaptation. There are several features unique to plants (e.g. polyploidy, mating system, sessile habit) that may lead to distinct mechanisms explaining variation in range size. Here, we highlight key studies testing intrinsic and extrinsic hypotheses about geographic range size under contrasting scenarios where species' ranges are static or change over time. We then present results from a meta-analysis of the relative importance of commonly hypothesized determinants of range size in plants. We show that our ability to infer the relative importance of these determinants is limited, particularly for dispersal ability, mating system, ploidy, and environmental heterogeneity. We highlight avenues for future research that merge approaches from macroecology and evolutionary ecology to better understand how adaptation and dispersal interact to facilitate niche evolution and range expansion., (© 2020 The Authors. New Phytologist © 2020 New Phytologist Trust.)

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., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

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., (Copyright © 2019, American Association for the Advancement of Science.)

The functional composition of plant communities is commonly thought to be determined by contemporary climate. However, if rates of climate-driven immigration and/or exclusion of species are slow, then contemporary functional composition may be explained by paleoclimate as well as by contemporary climate. We tested this idea by coupling contemporary maps of plant functional trait composition across North and South America to paleoclimate means and temporal variation in temperature and precipitation from the Last Interglacial (120 ka) to the present. Paleoclimate predictors strongly improved prediction of contemporary functional composition compared to contemporary climate predictors, with a stronger influence of temperature in North America (especially during periods of ice melting) and of precipitation in South America (across all times). Thus, climate from tens of thousands of years ago influences contemporary functional composition via slow assemblage dynamics., (© 2018 John Wiley & Sons Ltd.)

Background: California 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)., Results: We 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)., Conclusions: These 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.

Premise of the Study: California's vascular flora is the most diverse and threatened in temperate North America. Previous studies of spatial patterns of Californian plant diversity have been limited by traditional metrics, non-uniform geographic units, and distributional data derived from floristic descriptions for only a subset of species., Methods: We revisited patterns of sampling intensity, species richness, and relative endemism in California based on equal-area spatial units, the full vascular flora, and specimen-based distributional data. We estimated richness, weighted endemism (inverse range-weighting of species), and corrected weighted endemism (weighted endemism corrected for richness), and performed a randomization test for significantly high endemism., Key Results: Possible biases in herbarium data do not obscure patterns of high richness and endemism at the spatial resolution studied. High species richness was sometimes associated with significantly high endemism (e.g., Klamath Ranges) but often not. In Stebbins and Major's (1965) main endemism hotspot, Southwestern California, species richness is high across much of the Peninsular and Transverse ranges but significantly high endemism is mostly localized to the Santa Rosa and San Bernardino mountains. In contrast, species richness is low in the Channel Islands, where endemism is significantly high, as also found for much of the Death Valley region., Conclusions: Measures of taxonomic richness, even with greater weighting of range-restricted taxa, are insufficient for identifying areas of significantly high endemism that warrant conservation attention. Differences between our findings and those in previous studies appear to mostly reflect the source and scale of distributional data, and recent analytical refinements., (© 2017 Botanical Society of America.)

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.

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 14000 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.

Macro-scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as mislead conservation prioritization. In recent years, this has resulted in an increased focus on developing methods to correct for sampling bias. In this study, we use sample-size-correcting methods to examine patterns of tropical plant diversity in Ecuador, one of the most species-rich and climatically heterogeneous biodiversity hotspots. Species richness estimates were calculated based on 205,735 georeferenced specimens of 15,788 species using the Margalef diversity index, the Chao estimator, the second-order Jackknife and Bootstrapping resampling methods, and Hill numbers and rarefaction. Species richness was heavily correlated with sampling effort, and only rarefaction was able to remove this effect, and we recommend this method for estimation of species richness with "big data" collections.