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The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here, we used an approach that integrates the rich fossil evidence of this group with phylogenies in biogeographic analysis to study the processes behind this distribution pattern. We first combined genome-skimming sequencing with existing molecular data to build a robust species-level phylogeny for c.130 Theaceae species, resolving most important unclarified relationships. We then developed an empirical Bayesian method to incorporate distribution evidence from fossil specimens into historical biogeographic analyses and used this method to account for the spatiotemporal history of Theaceae fossils. We compared our method with an alternative Bayesian approach and show that it provides consistent results while significantly reduces computational demands which allows analyses of much larger data sets. Our analyses revealed a circumboreal distribution of the family from the early Cenozoic to the Miocene and inferred repeated expansions and retractions of the modeled distribution in the Northern Hemisphere, suggesting that the current Theaceae distribution could be the remnant of a larger continuous distribution associated with the boreotropical forest that has been hypothesized to occupy most of the northern latitudes in the early Cenozoic. These results contradict with studies that only considered current species distributions and showcase the necessity of integrating fossil and molecular data in phylogeny-based parametric biogeographic models to improve the reliability of inferred biogeographical events. [Biogeography; genome skimming; phylogenomics; plastid genome; Theaceae.]

Functional traits can determine pairwise species interactions, such as those between plants and pollinators. However, the effects of biogeography and evolutionary history on trait-matching and trait-mediated resource specialization remain poorly understood.We compiled a database of 93 mutualistic hummingbird-plant networks (including 181 hummingbird and 1,256 plant species), complemented by morphological measures of hummingbird bill and floral corolla length. We divided the hummingbirds into their principal clades and used knowledge on hummingbird biogeography to divide the networks into four biogeographical regions: Lowland South America, Andes, North & Central America, and the Caribbean islands. We then tested: (a) whether hummingbird clades and biogeographical regions differ in hummingbird bill length, corolla length of visited flowers and resource specialization, and (b) whether hummingbirds' bill length correlates with the corolla length of their food plants and with their level of resource specialization.Hummingbird clades dominated by long-billed species generally visited longer flowers and were the most exclusive in their resource use. Bill and corolla length and the degree of resource specialization were similar across mainland regions, but the Caribbean islands had shorter flowers and hummingbirds with more generalized interaction niches. Bill and corolla length correlated in all regions and most clades, that is, trait-matching was a recurrent phenomenon in hummingbird-plant associations. In contrast, bill length did not generally mediate resource specialization, as bill length was only weakly correlated with resource specialization within one hummingbird clade (Brilliants) and in the regions of Lowland South America and the Andes in which plants and hummingbirds have a long co-evolutionary history. Supplementary analyses including bill curvature confirmed that bill morphology (length and curvature) does not in general predict resource specialization.These results demonstrate how biogeographical and evolutionary histories can modulate the effects of functional traits on species interactions, and that traits better predict functional groups of interaction partners (i.e. trait-matching) than resource specialization. These findings reveal that functional traits have great potential, but also key limitations, as a tool for developing more mechanistic approaches in community ecology.A free Plain Language Summary can be found within the Supporting Information of this article.

The question of whether migratory birds track a specific climatic niche by seasonal movements has important implications for understanding the evolution of migration, the factors affecting species' distributions, and the responses of migrants to climate change. Despite much research, previous studies of bird migration have produced mixed results. However, whether migrants track climate is only one half of the question, the other being why residents remain in the same geographic range year‐round. We provide a literature overview and test the hypothesis of seasonal niche tracking by evaluating seasonal climatic niche overlap across 437 migratory and resident species from eight clades of passerine birds. Seasonal climatic niches were based on a new global dataset of breeding and nonbreeding ranges. Overlap between climatic niches was quantified using ordination methods. We compared niche overlap of migratory species to two null expectations, (a) a scenario in which they do not migrate and (b) in comparison with the overlap experienced by closely related resident species, while controlling for breeding location and range size. Partly in accordance with the hypothesis of niche tracking, we found that the overlap of breeding versus nonbreeding climatic conditions in migratory species was greater than the overlap they would experience if they did not migrate. However, this was only true for migrants breeding outside the tropics and only relative to the overlap species would experience if they stayed in the breeding range year‐round. In contrast to the hypothesis of niche tracking, migratory species experienced lower seasonal climatic niche overlap than resident species, with significant differences between tropical and nontropical species. Our study suggests that in seasonal nontropical environments migration away from the breeding range may serve to avoid seasonally harsh climate; however, different factors may drive seasonal movements in the climatically more stable tropical regions., By examining seasonal niche overlap in migratory and resident bird species, we show that niche tracking varies depending on (a) the perspective in which the question was examined (i.e., from the perspective of the individual migrant or in comparison with resident species, (b) the direction of migration (i.e., whether the species is moving from the breeding or non‐breeding range), and (c) geographic location. Altogether, these results suggest that the drivers of migration vary depending on direction of migration as well as geographically, offering explanations for the mixed results from previous studies.

Animal pollinators are globally threatened by anthropogenic land use change and agricultural intensification. The yield of many food crops is therefore negatively impacted because they benefit from biotic pollination. This is especially the case in the tropics. For instance, fruit set of Coffea arabica has been shown to increase by 10–30% in plantations with a high richness of bee species, possibly influenced by the availability of surrounding forest habitat. Here, we performed a global literature review to (1) assess how much animal pollination enhances coffee fruit set, and to (2) examine the importance of the amount of forest cover, distance to nearby forest and forest canopy density for bee species richness and coffee fruit set. Using a systematic literature review, we identified eleven case studies with a total of 182 samples where fruit set of C. arabica was assessed. We subsequently gathered forest data for all study sites from satellite imagery. We modelled the effects of open (all forest with a canopy density of ≥25%), closed (≥50%) and dense (≥75%) forests on pollinator richness and fruit set of coffee. Overall, we found that animal pollination increases coffee fruit set by ~18% on average. In only one of the case studies, regression results indicate a positive effect of dense forest on coffee fruit set, which increased with higher forest cover and shorter distance to the forest. Against expectations, forest cover and distance to open forest were not related to bee species richness and fruit set. In summary, we provide strong empirical support for the notion that animal pollinators increase coffee fruit set. Forest proximity had little overall influence on bee richness and coffee fruit set, except when farms were surrounded by dense tropical forests, potentially because these may provide high-quality habitats for bees pollinating coffee. We, therefore, advocate that more research is done to understand the biodiversity value of dense forest for pollinators, notably assessing the mechanisms underlying the importance of forest for pollinators and their pollination services.

Knowledge of global patterns of biodiversity, ranging from intraspecific genetic diversity (GD) to taxonomic and phylogenetic diversity, is essential for identifying and conserving the processes that shape the distribution of life. Yet, global patterns of GD and its drivers remain elusive. Here we assess existing biodiversity theories to explain and predict the global distribution of GD in terrestrial mammal assemblages. We find a strong positive covariation between GD and interspecific diversity, with evolutionary time, reflected in phylogenetic diversity, being the best predictor of GD. Moreover, we reveal the negative effect of past rapid climate change and the positive effect of inter-annual precipitation variability in shaping GD. Our models, explaining almost half of the variation in GD globally, uncover the importance of deep evolutionary history and past climate stability in accumulating and maintaining intraspecific diversity, and constitute a crucial step towards reducing the Wallacean shortfall for an important dimension of biodiversity., The drivers of genetic diversity (GD) are poorly understood at the global scale. Here the authors show, for terrestrial mammals, that within-species GD covaries with phylogenetic diversity and is higher in locations with more stable past climates. They also interpolate GD for data-poor locations such as the tropics.

Climate stability leads to high levels of speciation and reduced extinction rates, shaping species richness patterns1–3. Hotspots of species diversity often overlap with regions that experienced stable temperatures and, perhaps, variable rates of precipitation during the late Quaternary4,5. These hotspots potentially harbour many species with low vagility and small geographical ranges6, making them more vulnerable to future ecoclimatic change4,7,8. By comparing global and regional patterns of climate stability during short periods of unusually large and widespread climate changes since the Last Glacial Maximum with twenty-first-century patterns, we show that human-driven climate change will disproportionally affect biodiversity in late Quaternary climate refugia, ultimately affecting the species, communities and ecosystems that are most vulnerable to climate change. Moreover, future changes in absolute temperature will probably erode the mechanisms that are theorized to sustain biodiversity hotspots across time. These impending shifts from stable to unstable temperatures—projected for the majority of the world’s biodiversity regions—threaten to reduce the size and extent of important climatic safe havens for diversity. Where climate refugia are forecast to persist until the end of this century, temperatures in these refuges are likely to exceed the acclimation capacity of many species, making them short-term hospices for biodiversity at best7–9. The stability of climatic conditions since the Last Glacial Maximum has contributed to current global patterns of species richness. Changes in patterns of climate stability this century reveal areas where climate change could reduce biodiversity, with largest losses in past climatic safe havens.

The causes of continental patterns in species richness continue to spur heated discussion. Hypotheses based on ambient energy have dominated the debate, but are increasingly being challenged by hypotheses that model richness as the overlap of species ranges, ultimately controlled by continental range dynamics of individual species. At the heart of this controversy lies the question of whether species richness of individual grid cells is controlled by local factors, or reflects larger-scale spatial patterns in the turnover of species’ ranges. Here, we develop a new approach based on assemblage dispersion fields, formed by overlaying the geographic ranges of all species co-occurring in a grid cell. We created dispersion fields for all tetrapods of South America, and characterized the orientation and shape of dispersion fields as a vector field. The resulting maps demonstrate the existence of macro-structures in the turnover of biotic similarity at continental scale that are congruent among vertebrate classes. These structures underline the importance of continental-scale processes for species richness in individual assemblages., Ecologists continue to debate whether local species assemblages result from habitat filtering or from turnover among the regional species pool. Here the authors develop a “dispersion field” method to mapping species range overlaps, showing that regional turnover processes are key to local assembly.

The numbers and impacts of non-native species (NNS) continue to grow. Multiple ranking protocols have been developed to identify and manage the most damaging species. However, existing protocols differ considerably in the type of impact they consider, the way evidence of impacts is included and scored, and in the way the precautionary principle is applied. These differences may lead to inconsistent impact assessments. Since these protocols are considered a main policy tool to promote mitigation efforts, such inconsistencies are undesirable, as they can affect our ability to reliably identify the most damaging NNS, and can erode public support for NNS management. Here we propose a broadly applicable framework for building a transparent NNS impact evidence base. First, we advise to separate the collection of evidence of impacts from the act of scoring the severity of these impacts. Second, we propose to map the collected evidence along a set of distinguishing criteria: where it is published, which methodological approach was used to obtain it, the relevance of the geographical area from which it originates, and the direction of the impact. This procedure produces a transparent and reproducible evidence base which can subsequently be used for different scoring protocols, and which should be made public. Finally, we argue that the precautionary principle should only be used at the risk management stage. Conditional upon the evidence presented in an impact assessment, decision-makers may use the precautionary principle for NNS management under scientific uncertainty regarding the likelihood and magnitude of NNS impacts. Our framework paves the way for an improved application of impact assessments protocols, reducing inconsistencies and ultimately enabling more effective NNS management.

Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.

AIM: The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of ‘supertramps’, ‘great speciators’ and relictualization. LOCATION: The Indo‐Pacific, Australia, Asia and Africa. TAXON: Corvoid passerine birds. METHODS: We constructed a new time‐calibrated molecular phylogeny of the core Campephagidae (cuckooshrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non‐independence. RESULTS: The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo‐Pacific, Australia, Southeast Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated (‘supertramps’) or show strong differentiation of local populations (‘great speciators’), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in ‘great speciators’ with intermediate levels of dispersal abilities (as per hand‐wing index). MAIN CONCLUSIONS: Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of ‘supertramps’, ‘great speciators’ and relictual palaeoendemics within the temporal stages of the taxon cycle.

AIM: We examined the geographical distribution of functional diversity for American amphibians and tested the relationship between functional diversity and environment. We also explored how the functional evenness of life‐history traits varies across biogeographical regions. LOCATION: Continental Americas. METHODS: We performed a trait classification based on an Eltonian approach and calculated functional diversity using Hill numbers, Shannon and Gini–Simpson indices. We tested the relationship between functional diversity and different axes of environmental variation by using a series of spatial autoregressive (SAR) models. RESULTS: Based on 212 different functional attributes for 2,776 species, we found that functional diversity has a latitudinal gradient consistent with that of species richness, regardless of the diversity index used. Evenness of functional diversity of amphibian assemblages varies depending on the region, but in general they are close to the maximum possible value. Areas with more functional richness relative to species richness are associated with high annual precipitation and low precipitation seasonality regardless of temperature; in contrast, areas with fewer functions than expected are associated with high aridity. MAIN CONCLUSIONS: The highest functional diversity is located in mountainous regions. Overall, functional diversity is positively correlated with humid environments with low precipitation seasonality and low aridity regardless of temperature. This is especially relevant for amphibians facing contemporary climate change because it suggests that future variation in rainfall patterns, but not in annual mean temperature, might interact with functional diversity to pose an imminent threat to amphibian functional diversity.

Aim We investigated the consistency between richness and trait-based diversity metrics in capturing the effects of management-related habitat factors on biodiversity. The choice of biodiversity metrics can substantially affect the evaluation of conservation tools. However, the relative sensitivity of different metrics is not well investigated, especially in a multi-taxon framework. Location European beech forests in Denmark. Methods We studied 20 beech stands comprising four management types (from intensively managed to long unmanaged stands). We analyzed how management-related environmental variables were reflected in the measure of: (i) species richness, (ii) number of conservation-relevant species (red-listed species and old-growth forest indicators) and (iii) functional diversity targeting five organism groups with different habitat requirements, i.e. vascular plants, epiphytic lichens and bryophytes, saproxylic fungi and breeding birds. Results Plain species richness at stand level was generally misleading, as it did not capture changes in the number of conservation relevant species with changes in management-related environmental variables. The interpretation of functional responses was most informative for the better known vascular plants, while responses were more fragmented for the other organism groups. Overall, however, functional responses were consistent with a loss of specialization and progressive simplification of species assemblages from long-unmanaged to intensively managed stands. Conclusions Our findings suggest that the occurrence of conservation-relevant species is a sound and relevant metric for planning and evaluating conservation actions, especially for less studied organism groups (e.g., saproxylic fungi and epiphytes). The functional approach is promising, but presupposes the availability of databases of relevant traits.

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.

Acknowledgements: Acknowledgements: We thank D. H. Mann for his detailed and constructive comments; and T. Ager, J. Austin, T. B. Brand, A. Cooper, S. Funder, M. T. P. Gilbert, T. Jørgensen, N. J. Korsgaard, S. Liu, M. Meldgaard, P. V. S. Olsen, M. L. Siggaard-Andersen, J. Stenderup, S. A. Woodroffe and staff at the GeoGenetics Sequencing Core and National Park Service-Western Arctic National Parklands for help and support. E.W. and D.J.M. thank the staff at St. John’s College, Cambridge, for providing a stimulating environment for scientific discussion of the project. E.W. thanks Illumina for collaboration. The Lundbeck Foundation GeoGenetics Centre is supported by the Carlsberg Foundation (CF18-0024), the Lundbeck Foundation (R302-2018-2155), the Novo Nordisk Foundation (NNF18SA0035006), the Wellcome Trust (UNS69906) and GRF EXC CRS Chair (44113220)—Cluster of Excellence. The PhyloNorway plant genome database is part of the Norwegian Barcode of Life Network (https://www.norbol.org) funded by the Research Council of Norway (226134/F50), the Norwegian Biodiversity Information Centre (14-14, 70184209) and The Arctic University Museum of Norway. Metabarcoding sequencing was funded by the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2017B001 and 2020A001). B.D.S. is supported by the Wellcome Trust programme in Mathematical Genomics and Medicine (WT220023); F.R. by a Villum Fonden Young Investigator award (no. 00025300); D.J.M. by the Quest Archaeological Research Fund; P.M. by the Swedish Research Council (VR); R.D. by the Wellcome Trust (WT207492); and A.R. by a Marie Skłodowska-Curie Actions Individual Fellowship (MSCA-IF, 703542) and the Research Council of Norway (KLIMAFORSK, 294929). L.O. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (no. 681605); I.G.A. and Y.L. from the ERC under the European Union’s Horizon 2020 research and innovation programme (no. 819192). J.I.S. and J.M. are supported by the Research Council of Norway. P.B.H. and N.R.E. acknowledge NERC funding (grant NE/P015093/1). D.W.B. was supported by a Marie Skłodowska-Curie Actions Incoming International Fellowship (MCIIF-40974). T.S.K. is funded by a Carlsberg Foundation Young Researcher Fellowship (CF19-0712)., During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

Aim: Across a variety of taxonomic scales, species diversity is unevenly distributed among its constituent units, and clades with few species are more common than expected assuming homogeneous rates of speciation and extinction among lineages. In order to explain the prevalence of species-poor families among a global and species-rich radiation of passerine birds, we test whether these groups share common eco-morphological, geographical and phylogenetic attributes. Location: Global. Time period: Late Oligocene to the present day. Major taxa studied: The Corvides (c. 790 species). Methods: We obtained 10 linear measurements of external morphology for 782 species of corvoid passerines. Using these measurements as a proxy for species ecology, we assessed the positioning of corvoid families in eco-morphological trait space and how these factors were associated with their species richness and rates of lineage diversification. Subsequently, we compared these same characteristics (species richness, morphological positioning and rates of lineage diversification) between families that are currently endemic to the Australasian ancestral area of the Corvides with those that have dispersed and diversified throughout other continental and insular landmasses. Results: Families with low species richness and rates of diversification tend to occupy the most peripheral positions in eco-morphological trait space, with almost all of these groups being endemic to Australasia. The peripheral eco-morphological positioning of the Australasian groupings is generally greater than expected upon accounting for differences in phylogenetic isolation and heterogeneity in rates of trait evolution, implying that species-poor corvoid families repeatedly evolved towards marginal areas of morphospace. Main conclusions: The over-representation of species-poor clades across diverse sets of organismal groups is consistent with their evolution towards, and the maintenance in, marginal areas of ecological niche space. The evolution of peripheral eco-morphological characters represents a potentially significant limit to rates of range expansion and lineage diversification.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Using the past to inform the future The late Quaternary paleorecord, within the past ∼130,000 years, can help to inform present-day management of the Earth's ecosystems and biota under climate change. Fordham et al. review when and where rapid climate transitions can be found in the paleoclimate record. They show how such events in Earth's history can shape our understanding of the consequences of future global warming, including rates of biodiversity loss, changes in ecosystem structure and function, and degradation in the goods and services that these ecosystems provide to humanity. They also highlight how recent developments at the intersection of paleoecology, paleoclimatology, and macroecology can provide opportunities to anticipate and manage the responses of species and ecosystems to changing climates in the Anthropocene. Science , this issue p. eabc5654

Despite improvements, studies assessing climate change effects on species range shifts fall short on aspects of data and methods., Studies have documented climate change–induced shifts in species distributions but uncertainties associated with data and methods are typically unexplored. We reviewed 240 reports of climate-related species-range shifts and classified them based on three criteria. We ask whether observed distributional shifts are compared against random expectations, whether multicausal factors are examined on equal footing, and whether studies provide sufficient documentation to enable replication. We found that only ~12.1% of studies compare distributional shifts across multiple directions, ~1.6% distinguish observed patterns from random expectations, and ~19.66% examine multicausal factors. Last, ~75.5% of studies report sufficient data and results to allow replication. We show that despite gradual improvements over time, there is scope for raising standards in data and methods within reports of climate-change induced shifts in species distribution. Accurate reporting is important because policy responses depend on them. Flawed assessments can fuel criticism and divert scarce resources for biodiversity to competing priorities.

Interactions between species are influenced by different ecological mechanisms, such as morphological matching, phenological overlap and species abundances. How these mechanisms explain interaction frequencies across environmental gradients remains poorly understood. Consequently, we also know little about the mechanisms that drive the geographical patterns in network structure, such as complementary specialization and modularity. Here, we use data on morphologies, phenologies and abundances to explain interaction frequencies between hummingbirds and plants at a large geographical scale. For 24 quantitative networks sampled throughout the Americas, we found that the tendency of species to interact with morphologically matching partners contributed to specialized and modular network structures. Morphological matching best explained interaction frequencies in networks found closer to the equator and in areas with low-temperature seasonality. When comparing the three ecological mechanisms within networks, we found that both morphological matching and phenological overlap generally outperformed abundances in the explanation of interaction frequencies. Together, these findings provide insights into the ecological mechanisms that underlie geographical patterns in resource specialization. Notably, our results highlight morphological constraints on interactions as a potential explanation for increasing resource specialization towards lower latitudes.

Speciation is thought to be predominantly driven by the geographical separation of populations of the ancestral species. Yet, in the marine realm, there is substantial biological diversity despite a lack of pronounced geographical barriers. Here, we investigate this paradox by considering the biogeography of marine mammals: cetaceans (whales and dolphins) and pinnipeds (seals and sea lions). We test for associations between past evolutionary diversification and current geographical distributions, after accounting for the potential effects of current environmental conditions. In general, cetacean lineages are widely dispersed and show few signs of geographically driven speciation, albeit with some notable exceptions. Pinnipeds, by contrast, show a more mixed pattern, with true seals (phocids) tending to be dispersed, whereas eared seals (otariids) are more geographically clustered. Both cetaceans and pinnipeds show strong evidence for environmental clustering of their phylogenetic lineages in relation to factors such as sea temperature, the extent of sea ice, and nitrate concentrations. Overall, current marine mammal biogeography is not indicative of geographical speciation mechanisms, with environmental factors being more important determinants of current taxonomic distributions. However, geographical isolation appears to have played a role in some important taxa, with evidence from the fossil record showing good support for these cases.

Natural environmental gradients encompass systematic variation in abiotic factors that can be exploited to test competing explanations of biodiversity patterns. The species–energy (SE) hypothesis attempts to explain species richness gradients as a function of energy availability. However, limited empirical support for SE is often attributed to idiosyncratic, local-scale processes distorting the underlying SE relationship. Meanwhile, studies are also often confounded by factors such as sampling biases, dispersal boundaries and unclear definitions of energy availability. Here, we used spatially structured observations of 8460 colonies of photo-symbiotic reef-building corals and a null-model to test whether energy can explain observed coral species richness over depth. Species richness was left-skewed, hump-shaped and unrelated to energy availability. While local-scale processes were evident, their influence on species richness was insufficient to reconcile observations with model predictions. Therefore, energy availability, either in isolation or in combination with local deterministic processes, was unable to explain coral species richness across depth. Our results demonstrate that local-scale processes do not necessarily explain deviations in species richness from theoretical models, and that the use of idiosyncratic small-scale factors to explain large-scale ecological patterns requires the utmost caution.

Aim: We derive a new phylogenetic framework of the Indo-Pacific avian genus Edolisoma based on a dense taxon sampling and use it in an explicit spatiotemporal framework to understand the history of intraspecific diversification dynamics in a ‘great speciator’, the Cicadabird Edolisoma tenuirostre/remotum complex. Location The Indo-Pacific island region, Australia and New Guinea. Taxon: Corvoid passerine birds (Passeriformes). Methods: We used Bayesian phylogenetic methods (beast) to construct a time-calibrated molecular phylogeny of all 19 species in the genus Edolisoma and 27 of 29 subspecies of the E. tenuirostre/remotum complex (previously Coracina tenuirostris) primarily based on one mitochondrial DNA marker. Ancestral area reconstruction methods (‘BioGeoBEARS’) were used to infer the historical biogeography of the genus. We used population-level analyses to assess intraspecific phylogeography and a molecular species delimitation test to evaluate the current taxonomy. A morphometric dataset was used to discuss differential dispersal ability among taxa. Results: Edolisoma originated in the late Miocene and diversification within the E. tenuirostre/remotum complex began in the Pleistocene. Within the North Melanesian and North Wallacean archipelagos, which have experienced several waves of diversification, we find significant patterns of genetic isolation by distance, but not within the Australo-Papuan ‘mainland’, which was recently back-colonized from these archipelagos. Based on the phylogeny, we suggest several taxonomic changes. We also discuss evidence of taxon cycles within Edolisoma based on correlations of species age, elevational ranges and dispersal ability. Main conclusions: The biogeographical history and patterns of differentiation between phylogroups within E. tenuirostre support the importance of barriers to gene flow in island systems. Examples of both recent genetic exchange across significant sea barriers and differentiation across much smaller water gaps suggest complex dispersal and diversification dynamics. The capacity for dispersal away from islands, and gradual shifts in dispersal ability in relation to the geographical setting, is supported as important factors in generating a ‘great speciator’. Phylogeography of a ‘great speciator’ (Aves: Edolisoma tenuirostre) reveals complex dispersal and diversification dynamics across the Indo-Pacific Locked until 7 February 2019 due to copyright restrictions. This is the peer reviewed version of an article, which has been published in final form at https://doi.org/10.1111/jbi.13182. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving

The archipelagos that form the transition between Asia and Australia were immortalized by Alfred Russel Wallace's observations on the connections between geography and animal distributions, which he summarized in what became the first major modern biogeographic synthesis. Wallace traveled the island region for eight years, during which he noted the marked faunal discontinuity across what has later become known as Wallace's Line. Wallace was intrigued by the bewildering diversity and distribution of life he discovered. But even today we ask ourselves how species formed within the region and why they are not evenly distributed. Biogeography, phylogeny, dispersal, biotic interactions, and abiotic factors affect the assembly of diversity. On the basis of a decade of research on the ecology, evolution, and systematics of corvoid passerine birds, we summarize what we have learned about the biogeography and assembly of island bird diversity. Corvoid passerine birds include nearly 800 species and 2,300 named taxa and thus represent a large, well-described, and globally distributed clade. Understanding the processes influencing biodiversity in this group is certain to deepen our general understanding of ecology and evolution in the context of biogeography and faunal assembly.

Macroecology has traditionally relied on descriptive characterization of large-scale ecological patterns to offer narrative explanations for the origin and maintenance of those patterns. Only recently have macroecologists begun to employ models termed ‘process-based’ and ‘mechanistic’, in contrast to other areas of ecology, where such models have a longer history. Here, we define and differentiate between process-based and mechanistic features of models, and we identify and discuss important advantages of working with models possessing such features. We describe some of the risks associated with process-based and mechanistic model-centered research programs, and we propose ways to mitigate these risks. Giving process-based and mechanistic models a more central role in research programs can reinvigorate macroecology by strengthening the link between theory and data.

Aim To identify key environmental factors associated with local fish species richness across a large tropical marine region. Location Wider Caribbean region. Methods Species richness estimates were based on a sightings database covering the wider Caribbean region. Environmental variables considered were distance to key habitats, habitat area, temperature, depth, salinity, nutrient concentration, as well as natural and anthropogenic disturbance. We test the significance of associations between these factors and species richness, establish the shape of these relationships and use spatial cross-validation to test the generality of these results. Species-specific environmental associations within these relationships were then tested. Results Five environmental variables showed significant associations with species richness, but only two, temperature and depth, proved robust to spatial cross-validation. Temperature was the best performing environmental predictor, showing a unimodal relationship with species richness and optimum temperatures consistent across analytical choices and data sets. Relationships between species richness and other environmental factors were also typically unimodal. Variation in species-specific temperature associations was significant within species richness gradients; with a higher number of species associated with optimal temperatures. Main conclusions Temperature represents the dominant environmental predictor of fish species richness identified by our study, showing a hump-shaped curve, peaking at around 27.4°C. This meant that the warmest sites within our study were not necessarily the most species rich. Variation in species thermal niches may play a key role in driving species richness gradients, with significant general positive trend for fish species to occur in locations exhibiting optimum sea surface temperatures.

With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time-calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3 Mya, 95% HPD 25.2–38.2 Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change.

Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c. 790 species) that are highly variable in the geographic and taxonomic distribution of species. Subsequently, we determine rates of historical dispersal between regions, the dynamics of diversification following regional colonization, and spatial variation in the distribution of species that differ in their rates of lineage diversification. The results of these analyses reveal spatiotemporal differences in the build-up of lineages across regions. The number of regions occupied and the rate of transition between regions both predict family richness well, indicating that the accumulation of high clade richness is associated with repeated expansion into new geographic areas. However, only the largest family (the Corvidae) had significantly heightened rates of both speciation and regional transition, implying that repeated regional colonization is not a general mechanism promoting lineage diversification among the Corvides.

Aim During the Late Pleistocene (c. 126–10 ka), modern humans (Homo sapiens) expanded their geographical range across Eurasia and eventually colonized the Americas. Although the routes by which they migrated have been intensively analysed, the dynamics of their realized climatic niche are still largely unknown. We assess temporal changes in the climatic niche of modern humans, the geographical distribution of their climatic niche and whether niche dynamics correlate with the magnitude of climate change and cultural advances, between 46 and 11 ka. Location Palaearctic. Methods Using the radiocarbon dated archaeological record and spatial palaeoclimatic simulations, we quantify different parameters of the realized climatic niche of modern humans (niche overlap, niche breadth and climatic marginality) between consecutive 1000–2000 year intervals. Moreover, using climate envelope models, we map the potential distributions of modern humans for each time interval and identify the regions that remained more climatically suitable and stable for modern humans through time. Results Between 46 and 22 ka the climatic niche of modern humans expanded, including periods of intense growth in niche breadth at 40 and 30 ka. Changes in seasonal water availability and technological innovations partly correlate with dynamics in niche parameters. We document a persistent climatically suitable mid-latitude belt in south Siberia linking western Europe to the Far East that may have facilitated human migration, and a potential climatic refugium in Beringia. Main conclusions The climatic niche of modern humans changed across the Late Pleistocene, as the result of both climatic and cultural changes. These populations of hunter-gatherers occupied novel climatic conditions but also remained in previously occupied areas under changing climates during the settlement of the Palaearctic. Our approach can provide clues as to where early modern humans may have overlapped in geographical and environmental space with Neanderthals or Denisovans, as evidenced by their contribution to the genetic heritage of some current populations.

Strong relationships between morphological and ecological characters are commonly predicted to reflect the association between form and function, with this hypothesis being well supported in restricted taxonomic and geographical contexts. Conversely, among broader sets of species, ecological variables have been shown to have limited power to explain morphological variation. To understand these apparent discrepancies, for a large and globally distributed passerine radiation, we test whether (a) the character states of four ecological variables (foraging mode, diet, strata and habitat) have different morphological optima, (b) ecological variables explain substantial variance in morphology and (c) ecological character states can be accurately predicted from morphology. We collected 10 linear morphological measurements for 782 species of corvoid passerines, and assessed (a) the fit of models of continuous trait evolution with different morphological optima for each ecological character state, (b) variation in morphological traits among ecological character states using phylogenetically corrected regressions and (c) the accuracy of morphological traits in predicting species-level membership of ecological character states using linear discriminant analysis (LDA). Models of morphological evolution with different ecological optima were well supported across numerous morphological axes, corresponding with significant differences in trait distributions among ecological character states. LDA also showed that membership of the ecological categories can be predicted with relatively high accuracy by morphology. In contrast to these findings, ecological variables explain limited amounts of variation in morphological traits. For a global radiation of passerine birds, we confirm that the generation of morphological variation is generally consistent with ecological selection pressures, but that ecological characters are of limited utility in explaining morphological differences among species. Although selection towards different optima means that membership of ecological character states tend to be well predicted by morphology, the overall morphospace of individual ecological character states tend to be broad, implying that morphology can evolve in multiple ways in response to similar selection pressures. Extensive variation in morphological adaptations among similar ecological strategies is likely to be a widespread phenomenon across the tree of life.

Aim: Although the effects of climate on species richness are known, regional pro‐ cesses may lead to different species richness–climate relationships across continents resulting in species richness anomalies, especially for tropical groups. Phylogenetic niche conservatism may also influence species richness–climate relationships of dif‐ ferent lineages. Here, we tested whether regional effects also exist for temperate lineages using the genus Quercus. Location: Northern Hemisphere. Time period: Present day. Major taxa studied: Quercus (Fagaceae). Methods: We used a dated phylogeny and distribution data for Quercus to evaluate its global species richness patterns and phylogenetic niche conservatism. To evaluate the consistency in species richness–climate relationships across continents of the genus Quercus as a whole and the temperate subgenus Quercus, we conducted analy‐ ses of covariance with continent as the categorical variable and climate variables as the covariate. We calibrated four widely used models using the global data or data from each continent separately and evaluated the predictive power of each model for different continents using the root mean squared error. Results: The relationships between species richness and climate were not signifi‐ cantly different among continents for both the genus Quercus as a whole and the subgenus Quercus. Unlike the models based on European data, those based on North American and eastern Asian data predicted both the global species richness and the richness in other continents. The species richness of a subtropical subgenus Cyclobalanopsis was most influenced by water availability, while that of a temperate subgenus Quercus was most influenced by environmental temperature. Main conclusions: In contrast to the subtropical subgenus Cyclobalanopsis, our results showed a consistent richness–climate relationship and absence of regional effects on species richness across continents for the temperate subgenus Quercus, likely suggest‐ ing that the species richness of temperate lineages, for example subgenus Quercus, may have reached equilibrium with the contemporary climate in the Northern Hemisphere.

Mountain regions are unusually biodiverse, with especially rich aggregations of small-30 ranged species that form centers of endemism. Mountains play an array of important roles for Earth's biodiversity, and impact neighboring lowlands through biotic interchange, changes in regional climate, and nutrient run-off. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with unique opportunities for co-existence and persistence of lineages, shaped by long-term climatic changes 35 interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology, notably areas comprising mafic and ultramafic lithologies—rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history worth preserving in the face of contemporary environmental changes.

Biodiversity assessments use a variety of data and models. We propose best-practice standards for studies in these assessments., Demand for models in biodiversity assessments is rising, but which models are adequate for the task? We propose a set of best-practice standards and detailed guidelines enabling scoring of studies based on species distribution models for use in biodiversity assessments. We reviewed and scored 400 modeling studies over the past 20 years using the proposed standards and guidelines. We detected low model adequacy overall, but with a marked tendency of improvement over time in model building and, to a lesser degree, in biological data and model evaluation. We argue that implementation of agreed-upon standards for models in biodiversity assessments would promote transparency and repeatability, eventually leading to higher quality of the models and the inferences used in assessments. We encourage broad community participation toward the expansion and ongoing development of the proposed standards and guidelines.

Abundant pollinators are often more generalised than rare pollinators. This could be because abundance drives generalisation: neutral effects suggest that more abundant species will be more generalised simply because they have more chance encounters with potential interaction partners. On the other hand, generalisation could drive abundance, as generalised species could have a competitive advantage over specialists, being able to exploit a wider range of resources and gain a more balanced nutrient intake. Determining the direction of the abundance-generalisation relationship is therefore a ‘chicken-and-egg’ dilemma. Here we determine the direction of the relationship between abundance and generalisation in plant-hummingbird pollination networks sampled from a variety of locations across the Americas. For the first time we resolve the direction of the abundance-generalisation relationship using independent data on animal abundance. We find evidence that hummingbird pollinators are generalised because they are abundant, and little evidence that hummingbirds are abundant because they are generalised. Additionally, a null model analysis suggests this pattern is due to neutral processes: most patterns of species-level abundance and generalisation were well explained by a null model that assumed interaction neutrality. These results suggest that neutral processes play a key role in driving broad patterns of generalisation in animal pollinators across large spatial scales.DeclarationsFunding – BIS is supported by the Natural Environment Research Council as part of the Cambridge Earth System Science NERC DTP [NE/L002507/1]. JVB was funded by CERL - Engineer Research and Development Center. PKM was funded by the São Paulo Research Foundation (FAPESP grant #2015/21457-4). PAC was funded by the David Lack studentship from the British Ornithologists’ Union and Wolfson College, University of Oxford. CL was funded by the ESDEPED-UAT grant. MAM acknowledges the Consejo Nacional para Investigaciones Científicas y Tecnológicas (Costa Rica), German Academic Exchange Service and the research funding program ‘LOEWE-Landes-Offensive zur Entwicklung Wissenschaftlichö konomischer Exzellenz’ of Hesse’s Ministry of Higher Education, Research, and the Arts (Germany). ROP was funded by CONACyT (project 258364). MAR was supported by the State of São Paulo Research Foundation (FAPESP) within the BIOTA/FAPESP, The Biodiversity Institute Program (www.biota.org.br) and the ‘Parcelas Permanentes’ project, as well as by Coordenação de Pessoal de Nível Superior (CAPES), Fundo de Apoio ao Ensino e à Pesquisa (FAEP)/Funcamp/Unicamp and The Nature Conservancy (TNC) of Brazil. LCR was supported by CNPq and Capes. MS was funded by CNPq (grant #302781/2016-1). AMMG is supported through a Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-2016-704409). LVD was supported by the Natural Environment Research Council (grants NE/K015419/1 and NE/N014472/1). AMMG, JS, CR and BD thank the Danish National Research Foundation for its support of the Center for Macroecology, Evolution and Climate (grant no. DNRF96). WJS is funded by Arcadia.

The accumulation of exceptional ecological diversity within a lineage is a key feature of adaptive radiation resulting from diversification associated with the subdivision of previously underutilized resources. The invasion of unoccupied niche space is predicted to be a key determinant of adaptive diversification, and this process may be particularly important if the diversity of competing lineages within the area, in which the radiation unfolds, is already high. Here, we test whether the evolution of nectarivory resulted in significantly higher rates of morphological evolution, more extensive morphological disparity, and a heightened build-up of sympatric species diversity in a large adaptive radiation of passerine birds (the honeyeaters, about 190 species) that have diversified extensively throughout continental and insular settings. We find that a large increase in rates of body size evolution and general expansion in morphological space followed an ancestral shift to nectarivory, enabling the build-up of large numbers of co-occurring species that vary greatly in size, compared to related and co-distributed nonnectarivorous clades. These results strongly support the idea that evolutionary shifts into novel areas of niche space play a key role in promoting adaptive radiation in the presence of likely competing lineages.

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.

Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.

The richness of saproxylic species is commonly found to be compromised in managed forests. However, it is often less clear if this reflects local scarcity of high quality deadwood objects or changes to the overall forest structure. Further, anthropogenic and natural drivers working at the landscape scale may have a strong impact. Hence, it is difficult to give detailed advice on how to conserve biodiversity in a cost-effective manner. Here we explored macrofungal richness on deadwood across a gradient of forest management intensity in Danish Fagus sylvatica forests. We aimed to disentangle the importance of habitat quality per se from the effects of variables recorded at the forest stand and landscape scales. Data was collected from 40 beech stands, each representing one of four broad management types: conventionally managed, near-to-nature managed, recently unmanaged and long unmanaged. Stands were aggregated within six larger forest clusters, to account for variation at the landscape scale. Fungal species were recorded as fruitbodies on deadwood at five decay stages. We found that the four management types showed strong differences in fungal richness, deadwood volume and forest structure, with long unmanaged stands having notably higher structural complexity and species richness. Fungal species richness and presence of red-listed fungi appeared to be mainly driven by deadwood volume, tree species and decay stage, but some stand-level variables such as canopy gaps, basal area and stand age were also of importance. Lying coarse deadwood had the highest species richness while standing coarse woody debris and fine deadwood had lower species density. Saproxylic fungal richness on individual deadwood objects was largely affected by resource quality and size, which is often limited in managed forests. Our results indicate that the best measure to increase fungal species richness, especially in managed stands, is to increase the amount of large diameter deadwood.

The Anthropocene is witnessing a loss of biodiversity, with well-documented declines in the diversity of ecosystems and species. For intraspecific genetic diversity, however, we lack even basic knowledge on its global distribution. We georeferenced 92,801 mitochondrial sequences for >4500 species of terrestrial mammals and amphibians, and found that genetic diversity is 27% higher in the tropics than in nontropical regions. Overall, habitats that are more affected by humans hold less genetic diversity than wilder regions, although results for mammals are sensitive to choice of genetic locus. Our study associates geographic coordinates with publicly available genetic sequences at a massive scale, yielding an opportunity to investigate both the drivers of this component of biodiversity and the genetic consequences of the anthropogenic modification of nature.

Aim Species richness is unevenly distributed among clades, reflecting differences in the extent to which species co-occur, their rates of geographical turnover and total area occupied. Here, we study richness variation among 10 large clades of New World passerine birds, assessing the dynamics of range expansion and diversification that led to the build-up of co-occurring species. Location New World. Methods We defined co-occurrence based on the presence in 1°×1° grid cells, an area substantially smaller than the geographical scale of speciation in birds, implying that range expansion is the main mechanism by which species accumulate within grid cells. For each species, we estimated its ‘diversification rate’, a measure of the extent to which it is a member of an actively diversifying lineage. Within each group, we ranked all species by this measure, before dividing them into quartiles. Results Neither clade age nor geographical area correlates with overall clade richness, but the maximum number of co-occurring species does. Within each group, locations supporting large numbers of species in actively diversifying lineages generally differ from those containing many species belonging to more ancient groups. The tropical Andes and Amazon are notable for continuously generating and maintaining species, such that the most species-rich clades have predominantly radiated in these areas. Based on the timing of their speciation events, we infer that a lack of reproductive isolation may limit the co-occurrence of species that are members of actively diversifying lineages, but not those that are generally long diverged. Main conclusions Spatiotemporal differences in the rates of range expansion and diversification are likely set by the capacity of regions to generate and maintain species. This, rather than the rate at which reproductive isolation accrues, area occupied, or time for diversification, appears to be the major factor underlying the disparity in clade richness between New World passerine groups.

Aim To understand how the integration of contextual spatial data on land cover and human infrastructure can help reduce spatial bias in sampling effort, and improve the utilization of citizen science-based species recording schemes. By comparing four different citizen science projects, we explore how the sampling design's complexity affects the role of these spatial biases. Location Denmark, Europe. Methods We used a point process model to estimate the effect of land cover and human infrastructure on the intensity of observations from four different citizen science species recording schemes. We then use these results to predict areas of under- and oversampling as well as relative biodiversity ‘hotspots’ and ‘deserts’, accounting for common spatial biases introduced in unstructured sampling designs. Results We demonstrate that the explanatory power of spatial biases such as infrastructure and human population density increased as the complexity of the sampling schemes decreased. Despite a low absolute sampling effort in agricultural landscapes, these areas still appeared oversampled compared to the observed species richness. Conversely, forests and grassland appeared undersampled despite higher absolute sampling efforts. We also present a novel and effective analytical approach to address spatial biases in unstructured sampling schemes and a new way to address such biases, when more structured sampling is not an option. Main conclusions We show that citizen science datasets, which rely on untrained amateurs, are more heavily prone to spatial biases from infrastructure and human population density. Objectives and protocols of mass-participating projects should thus be designed with this in mind. Our results suggest that, where contextual data is available, modelling the intensity of individual observation can help understand and quantify how spatial biases affect the observed biological patterns.

Island organisms often have wider feeding niches than mainland organisms, and migratory birds breeding on continents often widen their niches when overwintering on islands. Cuba's low hummingbird richness has puzzled ornithologists for decades. Here, we show that the Cuban hummingbird fauna is less rich than expected based on Cuba's elevation, when compared to the rest of the West Indian islands. Thereafter, we report nectar-feeding behaviour by 26 non-Trochilidae bird species in Cuba, encompassing pigeons/doves, woodpeckers and passerines, and endemic, resident and migratory species. We discuss if Cuba's speciose non-Trochilidae nectar-feeding avifauna may be associated with its depauperate hummingbird fauna.

Biodiversity conservation efforts in Europe have traditionally focused on farmland and open nature areas such as grasslands, heathlands and meadows, while little attention has been devoted to conservation actions in forest. Using detailed information on the geographical distribution of about 900 terrestrial species in Denmark we apply systematic conservation planning techniques to identify how to protect biodiversity at the lowest cost to society. The results suggest that conservation actions in forest should be given a higher priority. Thus, three to four times the number of forest species are protected per million € compared with species living in open land natural areas. Furthermore, a gap analysis finds the current designation of Natura 2000 and other protected areas is skewed toward open land natural areas, and insufficient to meet the conservation targets on forest species.

Insect responses to recent climate change are well documented, but the role of resource specialization in determining species vulnerability remains poorly understood. Uncovering local ecological effects of temperature change with high-quality, standardized data provides an important first opportunity for predictions about responses of resource specialists, and long-term time series are essential in revealing these responses. Here, we investigate temperature-related changes in local insect communities, using a sampling site with more than a quarter-million records from two decades (1992-2009) of full-season, quantitative light trapping of 1543 species of moths and beetles. We investigated annual as well as long-term changes in fauna composition, abundance and phenology in a climate-related context using species temperature affinities and local temperature data. Finally, we explored these local changes in the context of dietary specialization. Across both moths and beetles, temperature affinity of specialists increased through net gain of hot-dwelling species and net loss of cold-dwelling species. The climate-related composition of generalists remained constant over time. We observed an increase in species richness of both groups. Furthermore, we observed divergent phenological responses between cold- and hot-dwelling species, advancing and delaying their relative abundance, respectively. Phenological advances were particularly pronounced in cold-adapted specialists. Our results suggest an important role of resource specialization in explaining the compositional and phenological responses of insect communities to local temperature increases. We propose that resource specialists in particular are affected by local temperature increase, leading to the distinct temperature-mediated turnover seen for this group. We suggest that the observed increase in species number could have been facilitated by dissimilar utilization of an expanded growing season by cold- and hot-adapted species, as indicated by their oppositely directed phenological responses. An especially pronounced advancement of cold-adapted specialists suggests that such phenological advances might help minimize further temperature-induced loss of resource specialists. Although limited to a single study site, our results suggest several local changes in the insect fauna in concordance with expected change of larger-scale temperature increases.

Species attributes are commonly used to infer impacts of environmental change on multiyear species trends, e.g. decadal changes in population size. However, by themselves attributes are of limited value in global change attribution since they do not measure the changing environment. A broader foundation for attributing species responses to global change may be achieved by complementing an attributes-based approach by one estimating the relationship between repeated measures of organismal and environmental changes over short time scales. To assess the benefit of this multiscale perspective, we investigate the recent impact of multiple environmental changes on European farmland birds, here focusing on climate change and land use change. We analyze more than 800 time series from 18 countries spanning the past two decades. Analysis of long-term population growth rates documents simultaneous responses that can be attributed to both climate change and land-use change, including long-term increases in populations of hot-dwelling species and declines in long-distance migrants and farmland specialists. In contrast, analysis of annual growth rates yield novel insights into the potential mechanisms driving long-term climate induced change. In particular, we find that birds are affected by winter, spring, and summer conditions depending on the distinct breeding phenology that corresponds to their migratory strategy. Birds in general benefit from higher temperatures or higher primary productivity early on or in the peak of the breeding season with the largest effect sizes observed in cooler parts of species' climatic ranges. Our results document the potential of combining time scales and integrating both species attributes and environmental variables for global change attribution. We suggest such an approach will be of general use when high-resolution time series are available in large-scale biodiversity surveys.

Aim The water–energy dynamics hypothesis posits that species diversity is correlated with water availability and temperatures; diversity is lowest when water availability is reduced at low temperatures because few species can persist under such conditions. However, the relationship between water and energy availability and diversity likely varies geographically along environmental gradients. Here, we examined the drivers of such variability, using a global-scale data set on oaks. Location Global. Method To quantify spatial variation in both species diversity–water relationships and species diversity–energy relationships, we performed geographically weighted regressions (GWR) of (1) species diversity against energy availability, measured as potential evapotranspiration and temperature, and (2) species diversity against water availability, measured by precipitation and an aridity index. We then regressed the local slopes of these GWR models against water and energy separately, and water × energy combined to assess whether the regional-scale relationships among oak diversity, water and energy depended on climatic conditions at larger spatial extents. Results We found that the effects of low water availability and cold temperatures on oak diversity varied geographically. In particular, the effects of water and energy availability on oak diversity increased as water and energy availability decreased. Furthermore, the interaction between water and energy availability influenced regional-scale oak diversity–energy relationships but not oak diversity–water relationships. Main conclusion Our results suggest that the relationship between climate (and potentially climatic change) and oak diversity varies geographically, and that the effects of limiting water and temperature are likely to be most severe in arid environments.

A fundamental goal of ecological research is to understand and model how processes generate patterns so that if conditions change, changes in the patterns can be predicted. Different approaches have been proposed for modelling species assemblage, but their use to predict spatial patterns of species richness and other community attributes over a range of spatial and temporal scales remains challenging. Different methods emphasize different processes of structuring communities and different goals. In this review, we focus on models that were developed for generating spatially explicit predictions of communities, with a particular focus on species richness, composition, relative abundance and related attributes. We first briefly describe the concepts and theories that span the different drivers of species assembly. A combination of abiotic processes and biotic mechanisms are thought to influence the community assembly process. In this review, we describe four categories of drivers: (i) historical and evolutionary, (ii) environmental, (iii) biotic, and (iv) stochastic. We discuss the different modelling approaches proposed or applied at the community level and examine them from different standpoints, i.e. the theoretical bases, the drivers included, the source data, and the expected outputs, with special emphasis on conservation needs under climate change. We also highlight the most promising novelties, possible shortcomings, and potential extensions of existing methods. Finally, we present new approaches to model and predict species assemblages by reviewing promising 'integrative frameworks' and views that seek to incorporate all drivers of community assembly into a unique modelling workflow. We discuss the strengths and weaknesses of these new solutions and how they may hasten progress in community-level modelling.

The global loss of biodiversity threatens unique biota and the functioning and services of ecosystems essential for human wellbeing. To safeguard biodiversity and ecosystem services, designating protected areas is crucial; yet the extent to which the existing placement of protection is aligned to meet these conservation priorities is questionable, especially in the oceans. Here we investigate and compare global patterns of multiple biodiversity components (taxonomic, phylogenetic and functional), ecosystem services and human impacts, with the coverage of marine protected areas across a nested spatial scale. We demonstrate a pronounced spatial mismatch between the existing degree of protection and all the conservation priorities above, highlighting that neither the world’s most diverse, nor the most productive ecosystems are currently the most protected ecosystems. Furthermore, we show that global patterns of biodiversity, ecosystem services and human impacts are poorly correlated, hence complicating the identification of generally applicable spatial prioritization schemes. However, a hypothetical “consensus approach” would have been able to address all these conservation priorities far more effectively than the existing degree of protection, which at best is only marginally better than a random expectation. Therefore, a holistic perspective is needed when designating an appropriate degree of protection of marine conservation priorities worldwide.