Global geodiversity components are not equally represented in UNESCO Global Geoparks

The aim of UNESCO Global Geoparks (UGGs) is to protect globally significant geoheritage and geodiversity, but quantitative evidence on the global representativeness of geodiversity components (i.e. geology, soils, geomorphology and hydrology) in these geoparks is in short supply. Here, we provide a first assessment by deriving a global map of geodiversity to test whether the presence of geodiversity components in UGGs is representative for the global availability and distribution of geodiversity. Using openly accessible global datasets and a newly developed workflow, we have calculated metrics for each geodiversity component and a global geodiversity index; we then quantified whether UGGs represent global geodiversity and then compared their components to a randomized spatial distribution of geoparks. Our results show that lithological and topographical diversity are more represented in UGGs than outside these sites, while soil type and hydrological diversity are not significantly different. Furthermore, individual soil types and lithological classes are under-represented and unevenly distributed in Asian and European UGGs. This is probably caused by the concentration of geoparks in Asian and European mountains. To better conserve geodiversity, we suggest an initiative to consider the protection and representation of all geodiversity components in their global context. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.

The status and future of essential geodiversity variables

Rapid environmental change, natural resource overconsumption and increasing concerns about ecological sustainability have led to the development of 'Essential Variables' (EVs). EVs are harmonized data products to inform policy and to enable effective management of natural resources by monitoring global changes. Recent years have seen the instigation of new EVs beyond those established for climate, oceans and biodiversity (ECVs, EOVs and EBVs), including Essential Geodiversity Variables (EGVs). EGVs aim to consistently quantify and monitor heterogeneity of Earth-surface and subsurface abiotic features, including geology, geomorphology, hydrology and pedology. Here we assess the status and future development of EGVs to better incorporate geodiversity into policy and sustainable management of natural resources. Getting EGVs operational requires better consensus on defining geodiversity, investments into a governance structure and open platform for curating the development of EGVs, advances in harmonizing in situ measurements and linking heterogeneous databases, and development of open and accessible computational workflows for global digital mapping using machine-learning techniques. Cross-disciplinary collaboration and partnerships with governmental and private organizations are needed to ensure the successful development and uptake of EGVs across science and policy. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.

Africa as an evolutionary arena for large fruits

Strong paleoclimatic change and few Late Quaternary megafauna extinctions make mainland Africa unique among continents. Here, we hypothesize that, compared with elsewhere, these conditions created the ecological opportunity for the macroevolution and geographic distribution of large fruits. We assembled global phylogenetic, distribution and fruit size data for palms (Arecaceae), a pantropical, vertebrate-dispersed family with > 2600 species, and integrated these with data on extinction-driven body size reduction in mammalian frugivore assemblages since the Late Quaternary. We applied evolutionary trait, linear and null models to identify the selective pressures that have shaped fruit sizes. We show that African palm lineages have evolved towards larger fruit sizes and exhibited faster trait evolutionary rates than lineages elsewhere. Furthermore, the global distribution of the largest palm fruits across species assemblages was explained by occurrence in Africa, especially under low canopies, and extant megafauna, but not by mammalian downsizing. These patterns strongly deviated from expectations under a null model of stochastic (Brownian motion) evolution. Our results suggest that Africa provided a distinct evolutionary arena for palm fruit size evolution. We argue that megafaunal abundance and the expansion of savanna habitat since the Miocene provided selective advantages for the persistence of African plants with large fruits.

Country-wide data of ecosystem structure from the third Dutch airborne laser scanning survey

The third Dutch national airborne laser scanning flight campaign (AHN3, Actueel Hoogtebestand Nederland) conducted between 2014 and 2019 during the leaf-off season (October-April) across the whole Netherlands provides a free and open-access, country-wide dataset with ∼700 billion points and a point density of ∼10(-20) points/m². The AHN3 point cloud was obtained with Light Detection And Ranging (LiDAR) technology and contains for each point the x, y, z coordinates and additional characteristics (e.g. return number, intensity value, scan angle rank and GPS time). Moreover, the point cloud has been pre-processed by 'Rijkswaterstraat' (the executive agency of the Dutch Ministry of Infrastructure and Water Management), comes with a Digital Terrain Model (DTM) and a Digital Surface Model (DSM), and is delivered with a pre-classification of each point into one of six classes (0: Never Classified, 1: Unclassified, 2: Ground, 6: Building, 9: Water, 26: Reserved [bridges etc.]). However, no detailed information on vegetation structure is available from the AHN3 point cloud. We processed the AHN3 point cloud (∼16 TB uncompressed data volume) into 10 m resolution raster layers of ecosystem structure at a national extent, using a novel high-throughput workflow called 'Laserfarm' and a cluster of virtual machines with fast central processing units, high memory nodes and associated big data storage for managing the large amount of files. The raster layers (available as GeoTIFF files) capture 25 LiDAR metrics of vegetation structure, including ecosystem height (e.g. 95^th percentiles of normalized z), ecosystem cover (e.g. pulse penetration ratio, canopy cover, and density of vegetation points within defined height layers), and ecosystem structural complexity (e.g. skewness and variability of vertical vegetation point distribution). The raster layers make use of the Dutch projected coordinate system (EPSG:28992 Amersfoort / RD New), are each ∼1 GB in size, and can be readily used by ecologists in a geographic information system (GIS) or analytical open-source software such as R and Python. Even though the class '1: Unclassified' mainly includes vegetation points, other objects such as cars, fences, and boats can also be present in this class, introducing potential biases in the derived data products. We therefore validated the raster layers of ecosystem structure using >180,000 hand-labelled LiDAR points in 100 randomly selected sample plots (10 m × 10 m each) across the Netherlands. Besides vegetation, objects such as boats, fences, and cars were identified in the sampled plots. However, the misclassification rate of vegetation points (i.e. non-vegetation points that were assumed to be vegetation) was low (∼0.05) and the accuracy of the 25 LiDAR metrics derived from the AHN3 point cloud was high (∼90%). To minimize existing inaccuracies in this country-wide data product (e.g. ships on water bodies, chimneys on roofs, or cars on roads that might be incorrectly used as vegetation points), we provide an additional mask that captures water bodies, buildings and roads generated from the Dutch cadaster dataset. This newly generated country-wide ecosystem structure data product provides new opportunities for ecology and biodiversity science, e.g. for mapping the 3D vegetation structure of a variety of ecosystems or for modelling biodiversity, species distributions, abundance and ecological niches of animals and their habitats.

Global raster dataset on historical coastline positions and shelf sea extents since the Last Glacial Maximum

MOTIVATION

Historical changes in sea level caused shifting coastlines that affected the distribution and evolution of marine and terrestrial biota. At the onset of the Last Glacial Maximum (LGM) 26 ka, sea levels were >130 m lower than at present, resulting in seaward-shifted coastlines and shallow shelf seas, with emerging land bridges leading to the isolation of marine biota and the connection of land-bridge islands to the continents. At the end of the last ice age, sea levels started to rise at unprecedented rates, leading to coastal retreat, drowning of land bridges and contraction of island areas. Although a growing number of studies take historical coastline dynamics into consideration, they are mostly based on past global sea-level stands and present-day water depths and neglect the influence of global geophysical changes on historical coastline positions. Here, we present a novel geophysically corrected global historical coastline position raster for the period from 26 ka to the present. This coastline raster allows, for the first time, calculation of global and regional coastline retreat rates and land loss rates. Additionally, we produced, per time step, 53 shelf sea rasters to present shelf sea positions and to calculate the shelf sea expansion rates. These metrics are essential to assess the role of isolation and connectivity in shaping marine and insular biodiversity patterns and evolutionary signatures within species and species assemblages.

MAIN TYPES OF VARIABLES CONTAINED

The coastline age raster contains cells with ages in thousands of years before present (bp), representing the time since the coastline was positioned in the raster cells, for the period between 26 ka and the present. A total of 53 shelf sea rasters (sea levels <140 m) are presented, showing the extent of land (1), shelf sea (0) and deep sea (NULL) per time step of 0.5 kyr from 26 ka to the present.

SPATIAL LOCATION AND GRAIN

The coastline age raster and shelf sea rasters have a global representation. The spatial resolution is scaled to 120 arcsec (0.333° × 0.333°), implying cells of c. 3,704 m around the equator, 3,207 m around the tropics (±30°) and 1,853 m in the temperate zone (±60°).

TIME PERIOD AND TEMPORAL RESOLUTION

The coastline age raster shows the age of coastline positions since the onset of the LGM 26 ka, with time steps of 0.5 kyr. The 53 shelf sea rasters show, for each time step of 0.5 kyr, the position of the shelf seas (seas shallower than 140 m) and the extent of land.

LEVEL OF MEASUREMENT

Both the coastline age raster and the 53 shelf sea rasters are provided as TIFF files with spatial reference system WGS84 (SRID 4326). The values of the coastline age raster per grid cell correspond to the most recent coastline position (in steps of 0.5 kyr). Values range from 0 (0 ka, i.e., present day) to 260 (26 ka) in bins of 5 (0.5 kyr). A value of "no data" is ascribed to pixels that have remained below sea level since 26 ka.

SOFTWARE FORMAT

All data processing was done using the R programming language.

Human impacts on the world’s raptors

Raptors are emblematic of the global biodiversity crisis because one out of five species are threatened with extinction and over half have declining populations due to human threats. Yet our understanding of where these “threats” impact raptor species is limited across terrestrial Earth. This is concerning because raptors, as apex predators, are critically positioned in ecological food webs, and their declining populations can undermine important ecosystem services ranging from pest control to disease regulation. Here, we map the distribution of 15 threats within the known ranges of 172 threatened and near threatened raptor species globally as declared by the International Union for the Conservation of Nature. We analyze the proportion of each raptor range that is exposed to threats, identify global hotspots of impacted raptor richness, and investigate how human impacts on raptors vary based on several intrinsic (species traits) and extrinsic factors. We find that humans are potentially negatively affecting at least one threatened raptor species across three quarters of Earth’s terrestrial area (78%; 113 million km2). Our results also show that raptors have 66% of their range potentially impacted by threats on average (range 2.7–100%). Alarmingly, critically endangered species have 90% of their range impacted by threats on average. We also highlight 57 species (33%) of particular concern that have &gt; 90% of their ranges potentially impacted. Without immediate conservation intervention, these 57 species, including the most heavily impacted Forest Owlet (Athene blewitti), the Madagascar Serpent-eagle (Eutriorchis astur), and the Rufous Fishing-owl (Scotopelia ussheri), will likely face extinction in the near future. Global “hotspots” of impacted raptor richness are ubiquitous, with core areas of threat in parts of the Sahel and East Africa where 92% of the assessed raptors are potentially impacted per grid cell (10 species on average), and in Northern India where nearly 100% of raptors are potentially impacted per grid cell (11 species). Additionally, “coolspots” of unimpacted richness that represent refuges from threats occur in Greenland and Canada, where 98 and 58% of raptors are potentially unimpacted per grid cell, respectively (nearly one species on average), Saharan Africa, where 21% of raptors are potentially unimpacted per grid cell (one species on average), and parts of the Amazon, where 12% of raptors are potentially unimpacted per grid cell (0.6 species on average). The results provide essential information to guide conservation planning and action for the world’s imperiled raptors.

The minimum land area requiring conservation attention to safeguard biodiversity

Ambitious conservation efforts are needed to stop the global biodiversity crisis. In this study, we estimate the minimum land area to secure important biodiversity areas, ecologically intact areas, and optimal locations for representation of species ranges and ecoregions. We discover that at least 64 million square kilometers (44% of terrestrial area) would require conservation attention (ranging from protected areas to land-use policies) to meet this goal. More than 1.8 billion people live on these lands, so responses that promote autonomy, self-determination, equity, and sustainable management for safeguarding biodiversity are essential. Spatially explicit land-use scenarios suggest that 1.3 million square kilometers of this land is at risk of being converted for intensive human land uses by 2030, which requires immediate attention. However, a sevenfold difference exists between the amount of habitat converted in optimistic and pessimistic land-use scenarios, highlighting an opportunity to avert this crisis. Appropriate targets in the Post-2020 Global Biodiversity Framework to encourage conservation of the identified land would contribute substantially to safeguarding biodiversity.

The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms

The Cretaceous-Palaeogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this 'Palaeocene megaherbivore gap' (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature and increased evolution of megafaunal (≥4 cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but the absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by simultaneously rising temperatures, rainforest expansion, and the subsequent radiation of seed-dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess diversification and adaptation during one of the most enigmatic periods in angiosperm history.

Scaling Notebooks as Re-configurable Cloud Workflows

Literate computing environments, such as the Jupyter (i.e., Jupyter Notebooks, JupyterLab, and JupyterHub), have been widely used in scientific studies; they allow users to interactively develop scientific code, test algorithms, and describe the scientific narratives of the experiments in an integrated document. To scale up scientific analyses, many implemented Jupyter environment architectures encapsulate the whole Jupyter notebooks as reproducible units and autoscale them on dedicated remote infrastructures (e.g., highperformance computing and cloud computing environments). The existing solutions are still limited in many ways, e.g., 1) the workflow (or pipeline) is implicit in a notebook, and some steps can be generically used by different code and executed in parallel, but because of the tight cell structure, all steps in the Jupyter notebook have to be executed sequentially and lack of the flexibility of reusing the core code fragments, and 2) there are performance bottlenecks that need to improve the parallelism and scalability when handling extensive input data and complex computation.

In this work, we focus on how to manage the workflow in a notebook seamlessly. We 1) encapsulate the reusable cells as RESTful services and containerize them as portal components, 2) provide a composition tool for describing workflow logic of those reusable components, and 3) automate the execution on remote cloud infrastructure. Empirically, we validate the solution's usability via a use case from the Ecology and Earth Science domain, illustrating the processing of massive Light Detection and Ranging (LiDAR) data. The demonstration and analysis show that our method is feasible, but that it needs further improvement, especially on integrating distributed workflow scheduling, automatic deployment, and execution to develop as a mature approach.

Global plant-frugivore trait matching is shaped by climate and biogeographic history

Species interactions are influenced by the trait structure of local multi‐trophic communities. However, it remains unclear whether mutualistic interactions in particular can drive trait patterns at the global scale, where climatic constraints and biogeographic processes gain importance. Here we evaluate global relationships between traits of frugivorous birds and palms (Arecaceae), and how these relationships are affected, directly or indirectly, by assemblage richness, climate and biogeographic history. We leverage a new and expanded gape size dataset for nearly all avian frugivores, and find a positive relationship between gape size and fruit size, that is, trait matching, which is influenced indirectly by palm richness and climate. We also uncover a latitudinal gradient in trait matching strength, which increases towards the tropics and varies among zoogeographic realms. Taken together, our results suggest trophic interactions have consistent influences on trait structure, but that abiotic, biogeographic and richness effects also play important, though sometimes indirect, roles in shaping the functional biogeography of mutualisms.

The mutualism-antagonism continuum in Neotropical palm-frugivore interactions: from interaction outcomes to ecosystem dynamics

Frugivory, that is feeding on fruits, pulp or seeds by animals, is usually considered a mutualism when interactions involve seed dispersal, and an antagonism when it results in the predation and destruction of seeds. Nevertheless, most frugivory interactions involve both benefits and disadvantages for plants, and the net interaction outcomes thus tend to vary along a continuum from mutualism to antagonism. Quantifying outcome variation is challenging and the ecological contribution of frugivorous animals to plant demography thus remains little explored. This is particularly true for interactions in which animals do not ingest entire fruits, that is in seed‐eating and pulp‐eating. Here, we provide a comprehensive review of Neotropical palm–frugivore interactions, with a focus on how frugivore consumption behaviour (i.e. digestive processing, fruit‐handling ability and caching behaviour) and feeding types (fruit‐eating, pulp‐eating and seed‐eating) influence interaction outcomes at different demographic stages of palms. We compiled a total of 1043 species‐level palm–frugivore interaction records that explicitly captured information on which parts of palm fruits are eaten by animals. These records showed consumption of fruits of 106 Neotropical palm species by 273 vertebrate species, especially birds (50%) and mammals (45%), but also fish (3%) and reptiles (2%). Fruit‐eating involved all four taxonomic vertebrate classes whereas seed‐eating and pulp‐eating were only recorded among birds and mammals. Most fruit‐eating interactions (77%) resulted in positive interaction outcomes for plants (e.g. gut‐passed seeds are viable or seeds are successfully dispersed), regardless of the digestive processing type of vertebrate consumers (seed defecation versus regurgitation). The majority of pulp‐eating interactions (91%) also resulted in positive interaction outcomes, for instance via pulp removal that promoted seed germination or via dispersal of intact palm seeds by external transport, especially if animals have a good fruit‐handling ability (e.g. primates, and some parrots). By contrast, seed‐eating interactions mostly resulted in dual outcomes (60%), where interactions had both negative effects on seed survival and positive outcomes through seed caching and external (non‐digestive) seed dispersal. A detailed synthesis of available field studies with qualitative and quantitative information provided evidence that 12 families and 27 species of mammals and birds are predominantly on the mutualistic side of the continuum whereas five mammalian families, six mammal and one reptile species are on the antagonistic side. The synthesis also revealed that most species can act as partial mutualists, even if they are typically considered antagonists. Our review demonstrates how different consumption behaviours and feeding types of vertebrate fruit consumers can influence seed dispersal and regeneration of palms, and thus ultimately affect the structure and functioning of tropical ecosystems. Variation in feeding types of animal consumers will influence ecosystem dynamics via effects on plant population dynamics and differences in long‐distance seed dispersal, and may subsequently affect ecosystem functions such as carbon storage. The quantification of intra‐ and inter‐specific variation in outcomes of plant–frugivore interactions – and their positive and negative effects on the seed‐to‐seedling transition of animal‐dispersed plants – should be a key research focus to understand better the mutualism–antagonism continuum and its importance for ecosystem dynamics.

Ecological and evolutionary significance of primates' most consumed plant families

Angiosperms have been essential components of primate diets for millions of years, but the relative importance of different angiosperm families remains unclear. Here, we assess the contribution and ecological and evolutionary significance of plant families to diets of wild primates by compiling an unprecedented dataset of almost 9000 dietary records from 141 primary sources covering 112 primate species. Of the 205 angiosperm plant families recorded in primate diets, only 10 were consumed by more than half of primate species. Plants of the Moraceae and Fabaceae families were the most widely and frequently consumed, and they likely represent keystone resources for primates. Over 75% of species fed on these two families, and together they made up a median of approximately 13% of primate diets. By analysing the relative proportion of different plant parts consumed, we found that Moraceae was mainly eaten as fruit and Fabaceae as non-fruit parts, with the consumption of these two families not showing a significant phylogenetic signal across primate species. Moraceae consumption was associated with small home range sizes, even though more frugivorous primates tended to have larger home ranges compared to more folivorous species, possibly due to the year-round availability of moraceous fruits and the asynchrony in their phenology. Our results suggest that primates may be intricately and subtly shaped by the plant families that they have consumed over millions of years, and highlight the importance of detailed dietary studies to better understand primate ecology and evolution.

Frugivore-fruit size relationships between palms and mammals reveal past and future defaunation impacts

Mammalian frugivores are critical seed dispersers, but many are under threat of extinction. Futhermore, the impact of past and future defaunation on plant assemblages has yet to be quantified at the global scale. Here, we integrate palm and mammalian frugivore trait and occurrence data and reveal a global positive relationship between fruit size and frugivore body size. Global variation in fruit size is better explained by present-day frugivore assemblages than by Late Pleistocene assemblages, suggesting ecological and evolutionary reorganization after end-Pleistocene extinctions, except in the Neotropics, where some large-fruited palm species may have outlived their main seed dispersers by thousands of years. Our simulations of frugivore extinction over the next 100 years suggest that the impact of defaunation will be highest in the Old World tropics, and an up to 4% assemblage-level decrease in fruit size would be required to maintain the global body size–fruit size relationship. Overall, our results suggest that while some palm species may be able to keep pace with future defaunation through evolutionary changes in fruit size, large-fruited species may be especially vulnerable to continued defaunation.

Extinctions of megafauna can have cascading effects on their ecological communities. Here, Lim et al. investigate the relationships of historical and current mammalian frugivore body size with palm fruit size, then project how further mammal extinctions are likely to affect palm communities.

Associated evolution of fruit size, fruit colour and spines in Neotropical palms

Understanding how ecological interactions have shaped the evolutionary dynamics of species traits remains a challenge in evolutionary ecology. Combining trait evolution models and phylogenies, we analysed the evolution of characters associated with seed dispersal (fruit size and colour) and herbivory (spines) in Neotropical palms to infer the role of these opposing animal-plant interactions in driving evolutionary patterns. We found that the evolution of fruit colour and fruit size was associated in Neotropical palms, supporting the adaptive interpretation of seed-dispersal syndromes and highlighting the role of frugivores in shaping plant evolution. Furthermore, we revealed a positive association between fruit size and the presence of spines on palm leaves, bracteas and stems. We hypothesize that interactions between palms and large-bodied frugivores/herbivores may explain the evolutionary relationship between fruit size and spines. Large-bodied frugivores, such as extinct megafauna, besides consuming the fruits and dispersing large seeds, may also have consumed the leaves or damaged the plants, thus simultaneously favouring the evolution of large fruits and defensive structures. Our findings show how current trait patterns can be understood as the result of the interplay between antagonistic and mutualistic interactions that have happened throughout the evolutionary history of a clade.

Palm fruit colours are linked to the broad-scale distribution and diversification of primate colour vision systems

A long-standing hypothesis in ecology and evolution is that trichromatic colour vision (the ability to distinguish red from green) in frugivorous primates has evolved as an adaptation to detect conspicuous (reddish) fruits. This could provide a competitive advantage over dichromatic frugivores which cannot distinguish reddish colours from a background of green foliage. Here, we test whether the origin, distribution and diversity of trichromatic primates is positively associated with the availability of conspicuous palm fruits, i.e. keystone fruit resources for tropical frugivores. We combine global data of colour vision, distribution and phylogenetic data for more than 400 primate species with fruit colour data for more than 1700 palm species, and reveal that species richness of trichromatic primates increases with the proportion of palm species that have conspicuous fruits, especially in subtropical African forests. By contrast, species richness of trichromats in Asia and the Americas is not positively associated with conspicuous palm fruit colours. Macroevolutionary analyses further indicate rapid and synchronous radiations of trichromats and conspicuous palms on the African mainland starting 10 Ma. These results suggest that the distribution and diversification of African trichromatic primates is strongly linked to the relative availability of conspicuous (versus non-conspicuous) palm fruits, and that interactions between primates and palms are related to the coevolutionary dynamics of primate colour vision systems and palm fruit colours.

Trait-Based Assessments of Climate-Change Impacts on Interacting Species

Plant-animal interactions are fundamentally important in ecosystems, but have often been ignored by studies of climate-change impacts on biodiversity. Here, we present a trait-based framework for predicting the responses of interacting plants and animals to climate change. We distinguish three pathways along which climate change can impact interacting species in ecological communities: (i) spatial and temporal mismatches in the occurrence and abundance of species, (ii) the formation of novel interactions and secondary extinctions, and (iii) alterations of the dispersal ability of plants. These pathways are mediated by three kinds of functional traits: response traits, matching traits, and dispersal traits. We propose that incorporating these traits into predictive models will improve assessments of the responses of interacting species to climate change.

Research questions to facilitate the future development of European long-term ecosystem research infrastructures: A horizon scanning exercise

Distributed environmental research infrastructures are important to support assessments of the effects of global change on landscapes, ecosystems and society. These infrastructures need to provide continuity to address long-term change, yet be flexible enough to respond to rapid societal and technological developments that modify research priorities. We used a horizon scanning exercise to identify and prioritize emerging research questions for the future development of ecosystem and socio-ecological research infrastructures in Europe. Twenty research questions covered topics related to (i) ecosystem structures and processes, (ii) the impacts of anthropogenic drivers on ecosystems, (iii) ecosystem services and socio-ecological systems and (iv), methods and research infrastructures. Several key priorities for the development of research infrastructures emerged. Addressing complex environmental issues requires the adoption of a whole-system approach, achieved through integration of biotic, abiotic and socio-economic measurements. Interoperability among different research infrastructures needs to be improved by developing standard measurements, harmonizing methods, and establishing capacities and tools for data integration, processing, storage and analysis. Future research infrastructures should support a range of methodological approaches including observation, experiments and modelling. They should also have flexibility to respond to new requirements, for example by adjusting the spatio-temporal design of measurements. When new methods are introduced, compatibility with important long-term data series must be ensured. Finally, indicators, tools, and transdisciplinary approaches to identify, quantify and value ecosystem services across spatial scales and domains need to be advanced.

PalmTraits 1.0, a species-level functional trait database of palms worldwide

Plant traits are critical to plant form and function -including growth, survival and reproduction- and therefore shape fundamental aspects of population and ecosystem dynamics as well as ecosystem services. Here, we present a global species-level compilation of key functional traits for palms (Arecaceae), a plant family with keystone importance in tropical and subtropical ecosystems. We derived measurements of essential functional traits for all (>2500) palm species from key sources such as monographs, books, other scientific publications, as well as herbarium collections. This includes traits related to growth form, stems, armature, leaves and fruits. Although many species are still lacking trait information, the standardized and global coverage of the data set will be important for supporting future studies in tropical ecology, rainforest evolution, paleoecology, biogeography, macroecology, macroevolution, global change biology and conservation. Potential uses are comparative eco-evolutionary studies, ecological research on community dynamics, plant-animal interactions and ecosystem functioning, studies on plant-based ecosystem services, as well as conservation science concerned with the loss and restoration of functional diversity in a changing world.

The potential importance of unburned islands as refugia for the persistence of wildlife species in fire-prone ecosystems

The persistence of wildlife species in fire-prone ecosystems is under increasing pressure from global change, including alterations in fire regimes caused by climate change. However, unburned islands might act to mitigate negative effects of fire on wildlife populations by providing habitat in which species can survive and recolonize burned areas. Nevertheless, the characteristics of unburned islands and their role as potential refugia for the postfire population dynamics of wildlife species remain poorly understood.We used a newly developed unburned island database of the northwestern United States from 1984 to 2014 to assess the postfire response of the greater sage-grouse (Centrocercus urophasianus), a large gallinaceous bird inhabiting the sagebrush ecosystems of North America, in which wildfires are common. Specifically, we tested whether prefire and postfire male attendance trends at mating locations (leks) differed between burned and unburned areas, and to what extent postfire habitat composition at multiple scales could explain such trends.Using time-series of male counts at leks together with spatially explicit fire history information, we modeled whether male attendance was negatively affected by fire events. Results revealed that burned leks often exhibit sustained decline in male attendance, whereas leks within unburned islands or >1.5 km away from fire perimeters tend to show stable or increasing trends.Analyses of postfire habitat composition further revealed that sagebrush vegetation height within 0.8 km around leks, as well elevation within 0.8 km, 6.4 km, and 18 km around leks, had a positive effect on male attendance trends. Moreover, the proportion of the landscape with cheatgrass (Bromus tectorum) cover >8% had negative effects on male attendance trends within 0.8 km, 6.4 km, and 18 km of leks, respectively. Synthesis and applications. Our results indicate that maintaining areas of unburned vegetation within and outside fire perimeters may be crucial for sustaining sage-grouse populations following wildfire. The role of unburned islands as fire refugia requires more attention in wildlife management and conservation planning because their creation, protection, and maintenance may positively affect wildlife population dynamics in fire-prone ecosystems.

To adapt or go extinct? The fate of megafaunal palm fruits under past global change

Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes.

Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature

Background

A considerable portion of primary biodiversity data is digitally locked inside published literature which is often stored as pdf files. Large-scale approaches to biodiversity science could benefit from retrieving this information and making it digitally accessible and machine-readable. Nonetheless, the amount and diversity of digitally published literature pose many challenges for knowledge discovery and retrieval. Text mining has been extensively used for data discovery tasks in large quantities of documents. However, text mining approaches for knowledge discovery and retrieval have been limited in biodiversity science compared to other disciplines.

New information

Here, we present a novel, open source text mining tool, the Biodiversity Observations Miner (BOM). This web application, written in R, allows the semi-automated discovery of punctual biodiversity observations (e.g. biotic interactions, functional or behavioural traits and natural history descriptions) associated with the scientific names present inside a corpus of scientific literature. Furthermore, BOM enable users the rapid screening of large quantities of literature based on word co-occurrences that match custom biodiversity dictionaries. This tool aims to increase the digital mobilisation of primary biodiversity data and is freely accessible via GitHub or through a web server.

Towards global data products of Essential Biodiversity Variables on species traits

Essential Biodiversity Variables (EBVs) allow observation and reporting of global biodiversity change, but a detailed framework for the empirical derivation of specific EBVs has yet to be developed. Here, we re-examine and refine the previous candidate set of species traits EBVs and show how traits related to phenology, morphology, reproduction, physiology and movement can contribute to EBV operationalization. The selected EBVs express intra-specific trait variation and allow monitoring of how organisms respond to global change. We evaluate the societal relevance of species traits EBVs for policy targets and demonstrate how open, interoperable and machine-readable trait data enable the building of EBV data products. We outline collection methods, meta(data) standardization, reproducible workflows, semantic tools and licence requirements for producing species traits EBVs. An operationalization is critical for assessing progress towards biodiversity conservation and sustainable development goals and has wide implications for data-intensive science in ecology, biogeography, conservation and Earth observation.

Frugivory-related traits promote speciation of tropical palms

Animal-mediated seed dispersal by frugivorous birds and mammals is central to the ecology and functioning of ecosystems, but whether and how frugivory-related traits have affected plant speciation remains little explored. Fruit size is directly linked to plant dispersal capacity and therefore influences gene flow and genetic divergence of plant populations. Using a global species-level phylogeny with comprehensive data on fruit sizes and plant species distributions, we test whether fruit size has affected speciation rates of palms (Arecaceae), a plant family characteristic of tropical rainforests. Globally, the results reveal that palms with small fruit sizes have increased speciation rates compared with those with large (megafaunal) fruits. Speciation of small-fruited palms is particularly high in the understory of tropical rainforests in the New World, and on islands in the Old World. This suggests that frugivory-related traits in combination with geography and the movement behaviour of frugivores can influence the speciation of fleshy-fruited plants.

Functionally specialised birds respond flexibly to seasonal changes in fruit availability

Interactions between resource and consumer species result in complex ecological networks. The overall structure of these networks is often stable in space and time, but little is known about the temporal stability of the functional roles of consumer species in these networks. We used a trait-based approach to investigate whether consumers (frugivorous birds) show similar degrees of functional specialisation on resources (plants) in ecological networks across seasons. We additionally tested whether closely related bird species have similar degrees of functional specialisation and whether birds that are functionally specialised on specific resource types within a season are flexible in switching to other resource types in other seasons. We analysed four seasonal replicates of two species-rich plant-frugivore networks from the tropical Andes. To quantify fruit preferences of frugivorous birds, we projected their interactions with plants into a multidimensional plant trait space. To measure functional specialisation of birds, we calculated a species' functional niche breadth (the extent of seasonal plant trait space utilised by a particular bird) and functional originality (the extent to which a bird species' fruit preference functionally differs from those of other species in a seasonal network). We additionally calculated functional flexibility, i.e. the ability of bird species to change their fruit preference across seasons in response to variation in plant resources. Functional specialisation of bird species varied more among species than across seasons, and phylogenetically similar bird species showed similar degrees of functional niche breadth (phylogenetic signal λ = 0·81) and functional originality (λ = 0·89). Additionally, we found that birds with high functional flexibility across seasons had narrow functional niche breadth and high functional originality per season, suggesting that birds that are seasonally specialised on particular resources are most flexible in switching to other fruit resources across seasons. The high flexibility of functionally specialised bird species to switch seasonally to other resources challenges the view that consumer species rely on functionally similar resources throughout the year. This flexibility of consumer species may be an important, but widely neglected mechanism that could potentially stabilise consumer-resource networks in response to human disturbance and environmental change.

Fundamental species traits explain provisioning services of tropical American palms

The well-being of the global human population rests on provisioning services delivered by 12% of the Earth's ∼400,000 plant species¹. Plant utilization by humans is influenced by species traits^2-4, but it is not well understood which traits underpin different human needs⁵. Here, we focus on palms (Arecaceae), one of the most economically important plant groups globally⁶, and demonstrate that provisioning services related to basic needs, such as food and medicine, show a strong link to fundamental functional and geographic traits. We integrate data from 2,201 interviews on plant utilization from three biomes in South America-spanning 68 communities, 43 ethnic groups and 2,221 plant uses-with a dataset of 4 traits (leaf length, stem volume, fruit volume, geographic range size) and a species-level phylogeny⁷. For all 208 palm species occurring in our study area, we test for relations between their traits and perceived value. We find that people preferentially use large, widespread species rather than small, narrow-ranged species, and that different traits are linked to different uses. Further, plant size and geographic range size are stronger predictors of ecosystem service realization for palm services related to basic human needs than less-basic needs (for example, ritual). These findings suggest that reliance on plant size and availability may have prevented our optimal realization of wild-plant services, since ecologically rare yet functionally important (for example, chemically) clades may have been overlooked. Beyond expanding our understanding of how local people use biodiversity in mega-diverse regions, our trait- and phylogeny-based approach helps to understand the processes that underpin ecosystem service realization, a necessary step to meet societal needs in a changing world with a growing human population^5,8.

Historical colonization and dispersal limitation supplement climate and topography in shaping species richness of African lizards (Reptilia: Agaminae)

To what extent deep-time dispersal limitation shapes present-day biodiversity at broad spatial scales remains elusive. Here, we compiled a continental dataset on the distributions of African lizard species in the reptile subfamily Agaminae (a relatively young, Neogene radiation of agamid lizards which ancestors colonized Africa from the Arabian peninsula) and tested to what extent historical colonization and dispersal limitation (i.e. accessibility from areas of geographic origin) can explain present-day species richness relative to current climate, topography, and climate change since the late Miocene (~10 mya), the Pliocene (~3 mya), and the Last Glacial Maximum (LGM, 0.021 mya). Spatial and non-spatial multi-predictor regression models revealed that time-limited dispersal via arid corridors is a key predictor to explain macro-scale patterns of species richness. In addition, current precipitation seasonality, current temperature of the warmest month, paleo-temperature changes since the LGM and late Miocene, and topographic relief emerged as important drivers. These results suggest that deep-time dispersal constraints — in addition to climate and mountain building — strongly shape current species richness of Africa’s arid-adapted taxa. Such historical dispersal limitation might indicate that natural movement rates of species are too slow to respond to rates of ongoing and projected future climate and land use change.

Functional traits help to explain half-century long shifts in pollinator distributions

Changes in climate and land use can have important impacts on biodiversity. Species respond to such environmental modifications by adapting to new conditions or by shifting their geographic distributions towards more suitable areas. The latter might be constrained by species’ functional traits that influence their ability to move, reproduce or establish. Here, we show that functional traits related to dispersal, reproduction, habitat use and diet have influenced how three pollinator groups (bees, butterflies and hoverflies) responded to changes in climate and land-use in the Netherlands since 1950. Across the three pollinator groups, we found pronounced areal range expansions (>53%) and modelled range shifts towards the north (all taxa: 17–22 km), west (bees: 14 km) and east (butterflies: 11 km). The importance of specific functional traits for explaining distributional changes varied among pollinator groups. Larval diet preferences (i.e. carnivorous vs. herbivorous/detritivorous and nitrogen values of host plants, respectively) were important for hoverflies and butterflies, adult body size for hoverflies, and flight period length for all groups. Moreover, interactions among multiple traits were important to explain species’ geographic range shifts, suggesting that taxon-specific multi-trait analyses are needed to predict how global change will affect biodiversity and ecosystem services.

Global patterns and drivers of phylogenetic structure in island floras

Islands are ideal for investigating processes that shape species assemblages because they are isolated and have discrete boundaries. Quantifying phylogenetic assemblage structure allows inferences about these processes, in particular dispersal, environmental filtering and in-situ speciation. Here, we link phylogenetic assemblage structure to island characteristics across 393 islands worldwide and 37,041 vascular plant species (representing angiosperms overall, palms and ferns). Physical and bioclimatic factors, especially those impeding colonization and promoting speciation, explained more variation in phylogenetic structure of angiosperms overall (49%) and palms (52%) than of ferns (18%). The relationships showed different or contrasting trends among these major plant groups, consistent with their dispersal- and speciation-related traits and climatic adaptations. Phylogenetic diversity was negatively related to isolation for palms, but unexpectedly it was positively related to isolation for angiosperms overall. This indicates strong dispersal filtering for the predominantly large-seeded, animal-dispersed palm family whereas colonization from biogeographically distinct source pools on remote islands likely drives the phylogenetic structure of angiosperm floras. We show that signatures of dispersal limitation, environmental filtering and in-situ speciation differ markedly among taxonomic groups on islands, which sheds light on the origin of insular plant diversity.

Global diversification of a tropical plant growth form: environmental correlates and historical contingencies in climbing palms

Tropical rain forests (TRF) are the most diverse terrestrial biome on Earth, but the diversification dynamics of their constituent growth forms remain largely unexplored. Climbing plants contribute significantly to species diversity and ecosystem processes in TRF. We investigate the broad-scale patterns and drivers of species richness as well as the diversification history of climbing and non-climbing palms (Arecaceae). We quantify to what extent macroecological diversity patterns are related to contemporary climate, forest canopy height, and paleoclimatic changes. We test whether diversification rates are higher for climbing than non-climbing palms and estimate the origin of the climbing habit. Climbers account for 22% of global palm species diversity, mostly concentrated in Southeast Asia. Global variation in climbing palm species richness can be partly explained by past and present-day climate and rain forest canopy height, but regional differences in residual species richness after accounting for current and past differences in environment suggest a strong role of historical contingencies in climbing palm diversification. Climbing palms show a higher net diversification rate than non-climbers. Diversification analyses of palms detected a diversification rate increase along the branches leading to the most species-rich clade of climbers. Ancestral character reconstructions revealed that the climbing habit originated between early Eocene and Miocene. These results imply that changes from non-climbing to climbing habits may have played an important role in palm diversification, resulting in the origin of one fifth of all palm species. We suggest that, in addition to current climate and paleoclimatic changes after the late Neogene, present-day diversity of climbing palms can be explained by morpho-anatomical innovations, the biogeographic history of Southeast Asia, and/or ecological opportunities due to the diversification of high-stature dipterocarps in Asian TRFs.