Global patterns of vascular plant alpha diversity

Efficient estimation of plant species diversity in desert regions using UAV-based quadrats and advanced machine learning techniques

Understanding the distribution of plant species diversity(PSD) along spatial and environmental gradients is essential for implementing effective conservation strategies. However, effective monitoring of large-scale PSD in desert regions remain challenging. In this study, traditional and unmanned aerial vehicle (UAV) quadrat surveys were employed to monitor the vegetation composition in the desert regions of the Junggar Basin, China. By combining multi-source data, two variable selection methods (elastic net regression and Boruta) and two machine learning algorithms (support vector machines and boosted regression trees) were used to develop PSD estimation models. This study aimed to investigate spatiotemporal variations in PSD and their driving factors. The results are as follows. (1) UAV method is more efficient and accurate than traditional methods in investigating PSD in desert areas. (2) The model combining variables selected by Elastic Net Regression and the Boosted Regression Trees algorithm is the optimal model for estimating PSD in desert areas(R2 = 0.476-0.613, RMSE = 0.135-2.2, MAE = 0.1-1.72). (3) The central region of the basin exhibited lower PSD, whereas the peripheral regions demonstrated higher PSD but were more heavily impacted by external disturbances. Over the past 20 years, 5.99 %-13.87 % of the area has shown a significant decline in PSD. (4) Cumulative precipitation and soil organic carbon are the primary drivers of PSD's spatial patterns, while human disturbance dictates its temporal dynamics. This study introduced a novel method for estimating PSD, providing a theoretical foundation for ecological restoration, and biodiversity conservation in the study region.

Does the abiotic environment influence the distribution of flower and fruit colors?

PREMISE

Color in flowers and fruits carries multiple functions, from attracting animal partners (pollinators, dispersers) to mitigating environmental stress (cold, drought, UV-B). With research historically focusing on biotic interactions as selective agents, however, it remains unclear whether abiotic stressors impact flower and fruit colors across large spatial scales and shape their global distribution. Moreover, although flowers and fruits are developmentally linked and exposed to the same macroclimatic conditions, whether they have similar (correlated) responses to environmental stress remains unknown.

METHODS

Leveraging a data set of 2815 animal-pollinated and animal-dispersed species from 51 plant clades, we tested whether the diversity and distribution of flower and fruit colors (scored into eight categories) is shaped by temperature, aridity, and UV-B irradiance.

RESULTS

Global diversity of flower and fruit colors was uncoupled, with flower color diversity generally lower than fruit color diversity and peaking in areas of high abiotic stress. Fruit color diversity peaked in tropical areas where the diversity of animal mutualists is highest. These distinct patterns were shaped by different responses of individual flower and fruit colors to abiotic stressors (for flowers, pink and red to cold temperatures, yellow and purple to UV-B irradiance; for fruits, red to cold and wet conditions, black to warm, and yellow, green, and orange to UV-B).

CONCLUSIONS

Our results challenge the paradigm that flower and fruit colors are primarily shaped by animal partners but instead indicate that abiotic factors may set the macroecological stage for color evolution, with different selective factors acting on flowers and fruits.

Global impoverishment of natural vegetation revealed by dark diversity

Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity1. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region2. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.

High-throughput protein crystallography to empower natural product-based drug discovery

Nature is a rich and largely untapped reservoir of small molecules, the latter historically being the main source of new drugs. Three-dimensional structures of proteins in complex with small-molecule ligands represent key information to progress drug-discovery projects, in particular in the hit-to-lead phase. High-throughput crystallography has been of extensive use in recent years, especially to obtain crystallographic complexes of synthetic ligands and fragments. However, the process of discovering novel bioactive natural products has experienced limitations that have long prevented large drug-discovery programs using this outstanding source of molecules. Recent technologies have contributed to the re-emergence of natural products in modern drug discovery. We present the use of high-throughput protein crystallography to directly capture bioactive natural products from unpurified biota chemical samples using protein crystals. These routines, which are currently in use at the Brazilian Centre for Research in Energy and Materials (CNPEM), are introduced with a description of crystal preparation, automated data collection and processing at the MANACÁ beamline (Sirius, LNLS, CNPEM), along with case examples of bioactive natural product capture using protein crystals. The usefulness of this pipeline, which accelerates the discovery and structural elucidation of both known and previously unknown bioactive natural products, paves the way for the development of innovative therapeutic agents, thus contributing to the new era of natural product-based drug discovery.

Millennial Floristic Diversity and Land Management as Inferred from Archaeo-Palynological Research in Southern Italy

Palynology is an invaluable tool for reconstructing past biodiversity in agrarian and cultural landscapes and for understanding present-day environmental assets. By analysing past evidence, rooted in botanical knowledge, we can foresee future environmental trends. Italy, at the centre of the Mediterranean, is one of the richest countries in terms of pollen analyses from archaeological sites and therefore is particularly suited to reconstructing human-environment relationships and anthropogenic impacts on flora over time. We selected data filled in the database BRAIN. This paper presents new elaboration on pollen data from 14 published and unpublished archaeological sites, showing past plant diversity and land management in prehistorical and historical contexts of southern Italy. Overall, the research demonstrates that the floristic palaeodiversity, as revealed through the group-equalised indicator species analysis, supports and validates the palynological data on the flora of Campania, Basilicata, and Sicily. The study highlights the presence of ubiquitous pollen taxa in anthropogenic environments and explores the connection between past and present plant diversity.

Exceptional concentration of fish diversity in Yasuní National Park, Ecuador (Napo River Basin)

Background

Despite limited access and rather deficient sampling in many lowland areas of eastern Ecuador, scientists have been able to demonstrate that this specific region of Amazonia houses extraordinarily high concentrations of species within several taxa - terrestrial and aquatic, plant and animal, vertebrate and invertebrate.

New information

In this work, we developed an updated list of the ichthyofauna of the Yasuní National Park (YNP), based on an extensive literature review and databases of the most representative ichthyological collections from Ecuador. Our results yielded 458 species of freshwater fishes distributed in 47 families and 13 orders. This number exceeded previous fish lists from YNP and accounts for a considerable proportion of species inhabiting the Napo River Basin as well as the entire Amazon River Basin.The higher-than-previously-reported species diversity within this protected area, the services these species provide to humans and the absence of invasive species underscore the need for greater efforts and investment in protecting and managing western Amazonian lands and waters.

Dung predicts the global distribution of herbivore grazing pressure in drylands

Dryland grazing sustains millions of people worldwide but, when poorly managed, threatens food security. Here we combine livestock and wild herbivore dung mass data from surveys at 760 dryland sites worldwide, representing independent measurements of herbivory, to generate high-resolution maps. We show that livestock and wild herbivore grazing is globally disconnected, and identify hotspots of herbivore activity across Africa, the Eurasian grasslands, India, Australia and the United States. Wild herbivore dung mass was negatively correlated with total organic nitrogen, yet strong site-level correlations exist between our livestock dung estimates and total soil organic nitrogen. Using dung mass as a proxy of herbivore abundance enables standardized, field-based measures of grazing pressure that account for different herbivore types. This can improve herbivore density modelling and guide better management practices for populations that rely on dryland-grazing livestock for food.

Identifying the combined impact of human activities and natural factors on China's avian species richness using interpretable machine learning methods

With human activities-derived escalating climate change and rapid urbanization, avian species face significant survival challenges. Understanding the impact of human activities and environmental drivers on avian species richness is critical for effective biodiversity conservation. Unlike prior studies on avian biodiversity modeling that often rely on traditional statistical or single-model approaches, this study introduces a novel combination of Extreme Gradient Boosting (XGBoost), SHapley Additive exPlanations (SHAP) and Structural Equation Modeling (SEM) to both predict and interpret avian species richness in China. Using data from the most comprehensive citizen science bird database available in the country, we explore how both natural and human-driven factors affect avian species richness. Our results showed that: (1) The number of bird species categorized as rare or endangered underscores the urgent need for bird conservation. (2) The XGBoost model outperformed the other four models in predicting avian species richness, achieving a testing R2 of 0.84 and a testing MSE of 2379. (3) Interpretable machine learning indicated that key factors influencing avian species richness include GDP, wind speed, longitude, farmland area, sewage treatment ratio, GDP growth, forest area, and secondary industry ratio. (4) The SEM revealed the interactive effects of natural and human factors on bird species richness, supporting the results obtained from interpretable machine learning. Based on these findings, we recommend leveraging GDP for stronger biodiversity policies, implementing afforestation to mitigate wind and enhance bird habitats, optimizing agriculture to reduce habitat destruction, and improving sewage treatment to enhance water quality for avian ecosystems. This study offers new insights for biodiversity conservation strategies by integrating economic development and environmental management, marking a pioneering effort in avian biodiversity modeling in China through the application of this novel combination of methods, which distinguishes it from earlier research approaches.

Contrasting environmental drivers of tree community variation within heath forests in Brunei Darussalam, Borneo

Understanding how abiotic factors influence Bornean tropical tree communities and diversity is a key aspect in elucidating the mechanisms of species co-existence and habitat preferences in these biodiverse forests. We focused on investigating forest structure, tree diversity and community composition of lowland Bornean heath forests in Brunei Darussalam, within two 0.96 ha permanent forest plots at Bukit Sawat Forest Reserve and Badas Forest Reserve. All trees with stem diameter ≥ 5 cm were tagged, identified and measured for their stem diameter and basal area. Soil physiochemical properties (pH, gravimetric water content and concentrations of total carbon, nitrogen, phosphorus, potassium, calcium and magnesium in topsoil) and environmental factors (relative humidity, canopy openness, litter depth and topographic variables of elevation, slope and aspect) were quantified as potential drivers of tree community differences. A total of 2,368 trees were recorded, representing 229 tree species in 211 genera and 58 families. Significant between-site differences in forest structure and tree community compositions were detected, despite limited differences in environmental and soil properties. Tree community composition at Bukit Sawat appeared to be influenced by topographic variables, while those at Badas were influenced by canopy openness. Our results showed that small-scale soil and environmental variation appeared to shape the local tree communities at Bukit Sawat and Badas. We recorded numerous Bornean endemic and tree species of high conservation values. We thus highlight the necessity of conducting long-term research on the forest dynamics of Bornean heath forests to effectively manage these high conservation value habitats which are currently experiencing changes driven by disturbances.

Global patterns of species diversity and distribution in the biomedically and biotechnologically important fungal genus Aspergillus

Aspergillus fungi are key producers of pharmaceuticals, enzymes, and food products and exhibit diverse lifestyles, ranging from saprophytes to opportunistic pathogens. To improve understanding of Aspergillus species diversity, identify key environmental factors influencing their geographic distributions, and estimate the impact of future climate change, we trained a random forest machine learning classifier on 30,542 terrestrial occurrence records for 176 species (~40% of known species in the genus) and 96 environmental variables. We found that regions with high species diversity are concentrated in temperate forests, which suggests that areas with mild seasonal variation may serve as diversity hotspots. Species range estimates revealed extensive variability, both within and across taxonomic sections; while some species are cosmopolitan, others have more restricted ranges. Furthermore, range overlap between species is generally low. The top predictors of mean species richness were the index of cumulative human impact and five bioclimatic factors, such as temperature and temperate vs non-temperate ecoregions. Our future climate analyses revealed considerable variation in species range estimates in response to changing climates; some species ranges are predicted to expand (e.g., the food spoilage and mycotoxin-producing Aspergillus versicolor), and others are predicted to contract or remain stable. Notably, the predicted range of the major pathogen Aspergillus fumigatus was predicted to decrease in response to climate change, whereas the range of the major pathogen Aspergillus flavus was predicted to increase and gradually decrease. Our findings reveal how both natural and human factors influence Aspergillus species ranges and highlight their ecological diversity, including the diversity of their responses to changing climates, which is of relevance to pathogen and mycotoxin risk assessment.

Enhanced effects of species richness on resistance and resilience of global tree growth to prolonged drought

The increasing duration of drought induced by global climate change has reduced forest productivity. Biodiversity is believed to mitigate the effects of drought, thereby enhancing the stability of tree growth. However, the effects of species richness on tree growth stability under droughts with different durations remain uncertain. Here, we used tree ring data from 4,072 sites globally, combined with climate and plant richness data, to evaluate the effects of species richness on the resistance and resilience of trees to short-term and prolonged droughts. We found that species richness enhanced resistance but weakened resilience of trees to drought globally. Compared to short-term drought, species richness further increased tree growth during prolonged drought but reduced the growth afterward, resulting in stronger effects on resistance and resilience. In addition, as the degree of drought intensified and regional aridity levels increased, the effects of richness on resistance and resilience under short-term drought were enhanced, but these trends were reduced or even reversed under prolonged drought. These results reveal the global effects of species richness on resistance and resilience of tree growth to droughts with different durations and highlight that species richness plays a crucial role in resisting prolonged drought.

Characterizing the structural complexity of the Earth's forests with spaceborne lidar

Forest structural complexity is a key element of ecosystem functioning, impacting light environments, nutrient cycling, biodiversity, and habitat quality. Addressing the need for a comprehensive global assessment of actual forest structural complexity, we derive a near-global map of 3D canopy complexity using data from the GEDI spaceborne lidar mission. These data show that tropical forests harbor most of the high complexity observations, while less than 20% of temperate forests reached median levels of tropical complexity. Structural complexity in tropical forests is more strongly related to canopy attributes from lower and middle waveform layers, whereas in temperate forests upper and middle layers are more influential. Globally, forests exhibit robust scaling relationships between complexity and canopy height, but these vary geographically and by biome. Our results offer insights into the spatial distribution of forest structural complexity and emphasize the importance of considering biome-specific and fine-scale variations for ecological research and management applications. The GEDI Waveform Structural Complexity Index data product, derived from our analyses, provides researchers and conservationists with a single, easily interpretable metric by combining various aspects of canopy structure.

Predicting undetected native vascular plant diversity at a global scale

Vascular plants are diverse and a major component of terrestrial ecosystems, yet their geographic distributions remain incomplete. Here, I present a global database of vascular plant distributions by integrating species distribution models calibrated to species' dispersal ability and natural habitats to predict native range maps for 201,681 vascular plant species into unsurveyed areas. Using these maps, I uncover unique patterns of native vascular plant diversity, endemism, and phylogenetic diversity revealing hotspots in underdocumented biodiversity-rich regions. These hotspots, based on detailed species-level maps, show a pronounced latitudinal gradient, strongly supporting the theory of increasing diversity toward the equator. I trained random forest models to extrapolate diversity patterns under unbiased global sampling and identify overlaps with modeled estimations but unveiled cryptic hotspots that were not captured by modeled estimations. Only 29% to 36% of extrapolated plant hotspots are inside protected areas, leaving more than 60% outside and vulnerable. However, the unprotected hotspots harbor species with unique attributes that make them good candidates for conservation prioritization.

Land use modulates resistance of grasslands against future climate and inter-annual climate variability in a large field experiment

Climate and land-use change are key drivers of global change. Full-factorial field experiments in which both drivers are manipulated are essential to understand and predict their potentially interactive effects on the structure and functioning of grassland ecosystems. Here, we present 8 years of data on grassland dynamics from the Global Change Experimental Facility in Central Germany. On large experimental plots, temperature and seasonal patterns of precipitation are manipulated by superimposing regional climate model projections onto background climate variability. Climate manipulation is factorially crossed with agricultural land-use scenarios, including intensively used meadows and extensively used (i.e., low-intensity) meadows and pastures. Inter-annual variation of background climate during our study years was high, including three of the driest years on record for our region. The effects of this temporal variability far exceeded the effects of the experimentally imposed climate change on plant species diversity and productivity, especially in the intensively used grasslands sown with only a few grass cultivars. These changes in productivity and diversity in response to alterations in climate were due to immigrant species replacing the target forage cultivars. This shift from forage cultivars to immigrant species may impose additional economic costs in terms of a decreasing forage value and the need for more frequent management measures. In contrast, the extensively used grasslands showed weaker responses to both experimentally manipulated future climate and inter-annual climate variability, suggesting that these diverse grasslands are more resistant to climate change than intensively used, species-poor grasslands. We therefore conclude that a lower management intensity of agricultural grasslands, associated with a higher plant diversity, can stabilize primary productivity under climate change.

Landform and lithospheric development contribute to the assembly of mountain floras in China

Although it is well documented that mountains tend to exhibit high biodiversity, how geological processes affect the assemblage of montane floras is a matter of ongoing research. Here, we explore landform-specific differences among montane floras based on a dataset comprising 17,576 angiosperm species representing 140 Chinese mountain floras, which we define as the collection of all angiosperm species growing on a specific mountain. Our results show that igneous bedrock (granitic and karst-granitic landforms) is correlated with higher species richness and phylogenetic overdispersion, while the opposite is true for sedimentary bedrock (karst, Danxia, and desert landforms), which is correlated with phylogenetic clustering. Furthermore, we show that landform type was the primary determinant of the assembly of evolutionarily older species within floras, while climate was a greater determinant for younger species. Our study indicates that landform type not only affects montane species richness, but also contributes to the composition of montane floras. To explain the assembly and differentiation of mountain floras, we propose the 'floristic geo-lithology hypothesis', which highlights the role of bedrock and landform processes in montane floristic assembly and provides insights for future research on speciation, migration, and biodiversity in montane regions.

Predicting the responses of European grassland communities to climate and land cover change

European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

The global pattern of epiphytic liverwort disparity: insights from Frullania

The geographical and ecological patterns of morphological disparity are crucial to understand how species are assembled within communities in the context of the evolutionary history, morphological evolution and ecological interactions. However, with limited exceptions, rather few studies have been conducted on the global pattern of disparity, particularly in early land plants. Here we explored the spatial accumulation of disparity in a morphologically variable and species rich liverwort genus Frullania in order to test the hypothesis of latitude disparity gradient. We compiled a morphological data set consisting of eight continuous traits for 244 currently accepted species, and scored the species distribution into 19 floristic regions worldwide. By reconstructing the morphospace of all defined regions and comparisons, we identified a general Gondwana-Laurasia pattern of disparity in Frullania. This likely results from an increase of ecological opportunities and / or relaxed constraints towards low latitudes. The lowest disparity occurred in arid tropical regions, largely due to a high extinction rate as a consequence of paleoaridification. There was weak correlation between species diversity and disparity at different spatial scales. Furthermore, long-distance dispersal may have partially shaped the present-day distribution of Frullania disparity, given its frequency and the great contribution of widely distributed species to local morphospace. This study not only highlighted the crucial roles of paleoenvironmental changes, ecological opportunities, and efficient dispersal on the global pattern of plant disparity, but also implied its dependence on the ecological and physiological function of traits.

Variation in xylem vulnerability to cavitation shapes the photosynthetic legacy of drought

Increased drought conditions impact tree health, negatively disrupting plant water transport which, in turn, affects plant growth and survival. Persistent drought legacy effects have been documented in many diverse ecosystems, yet we still lack a mechanistic understanding of the physiological processes limiting tree recovery after drought. Tackling this question, we exposed saplings of a common Australian evergreen tree (Eucalyptus viminalis) to a cycle of drought and rewatering, seeking evidence for a link between the spread of xylem cavitation within the crown and the degree of photosynthetic recovery postdrought. Individual leaves experiencing >35% vein cavitation quickly died but this did not translate to a rapid overall canopy damage. Rather, whole canopies showed a gradual decline in mean postdrought gas exchange rates as water stress increased. This gradual loss of canopy function postdrought was due to a significant variation in cavitation vulnerability of leaves within canopies leading to diversity in the capacity of leaves within a single crown to recover function after drought. These results from the evergreen E. viminalis emphasise the importance of within-crown variation in xylem vulnerability as a central character regulating the dynamics of canopy death and the severity of drought legacy through time.

Global multifaceted biodiversity patterns, centers, and conservation needs in angiosperms

The Convention on Biological Diversity seeks to conserve at least 30% of global land and water areas by 2030, which is a challenge but also an opportunity to better preserve biodiversity, including flowering plants (angiosperms). Herein, we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species. Using this database, we constructed biodiversity-environment models to predict global patterns of taxonomic, phylogenetic, and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets. We further evaluated the current protection status of the biodiversity centers of these diversity facets. Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities. Idiosyncratic centers of functional diversity, particularly of herbaceous species, were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets. Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms (woody vs. herbaceous), thus providing directions for guiding the future conservation of global plant diversity.

Transnational conservation to anticipate future plant shifts in Europe

To meet the COP15 biodiversity framework in the European Union (EU), one target is to protect 30% of its land by 2030 through a resilient transnational conservation network. The European Alps are a key hub of this network hosting some of the most extensive natural areas and biodiversity hotspots in Europe. Here we assess the robustness of the current European reserve network to safeguard the European Alps' flora by 2080 using semi-mechanistic simulations. We first highlight that the current network needs strong readjustments as it does not capture biodiversity patterns as well as our conservation simulations. Overall, we predict a strong shift in conservation need through time along latitudes, and from lower to higher elevations as plants migrate upslope and shrink their distribution. While increasing species, trait and evolutionary diversity, migration could also threaten 70% of the resident flora. In the face of global changes, the future European reserve network will need to ensure strong elevation and latitudinal connections to complementarily protect multifaceted biodiversity beyond national borders.

Variations in species diversity patterns and community assembly rules among vegetation types in the karst landscape

The various vegetation types in the karst landscape have been considered the results of heterogeneous habitats. However, the lack of a comprehensive understanding of regional biodiversity patterns and the underlying ecological processes limits further research on ecological management. This study established forest dynamic plots (FDPs) of the dominant vegetation types (shrubland, SL; mixed tree and shrub forest, MTSF; coniferous forest, CF; coniferous broadleaf mixed forest, CBMF; and broadleaf forest, BF) in the karst landscape and quantified the species diversity patterns and potential ecological processes. The results showed that in terms of diversity patterns, the evenness and species richness of the CF community were significantly lower than other vegetation types, while the BF community had the highest species richness. The other three vegetation types showed no significant variation in species richness and evenness. However, when controlling the number of individuals of FDPs, the rarefied species richness showed significant differences and ranked as BF > SL > MTSF > CBMF > CF, highlighting the importance of considering the impacts of abundance. Additionally, the community assembly of climax communities (CF or BF) was dominated by stochastic processes such as species dispersal or species formation, whereas deterministic processes (habitat filtering) dominated the secondary forests (SL, MTSF, and CBMF). These findings proved that community assembly differs mainly between the climax community and other communities. Hence, it is crucial to consider the biodiversity and of the potential underlying ecological processes together when studying regional ecology and management, particularly in heterogeneous ecosystems.

Mapping wild vascular plant species diversity in urban areas in California using crowdsourcing data by regression kriging: Examining socioeconomic disparities

Biodiversity is crucial for human health, but previous methods of measuring biodiversity require intensive resources and have other limitations. Crowdsourced datasets from citizen scientists offer a cost-effective solution for characterizing biodiversity on a large spatial scale. This study has two aims: 1) to generate fine-resolution plant species diversity maps in California urban areas using crowdsourced data and extrapolation methods; and 2) to examine their associations with sociodemographic factors and identify subpopulations with low biodiversity exposure. We used iNaturalist observations from 2019 to 2022 to calculate species diversity metrics by exploring the sampling completeness in a 5 × 5-km2 grid and then computing species diversity metrics for grid cells with at least 80 % sample completeness (841 out of 4755 grid cells). A generalized additive model with ordinary kriging (GAM OK) provided moderately reliable estimates, with correlations of 0.64-0.66 between observed and extrapolated metrics, relative mean absolute errors of 21 %-23 %, and relative root mean squared errors of 27 %-30 % for grid cells with ≥80 % sample completeness from 10-fold cross-validation. GAM OK was further applied to extrapolate species diversity metrics from saturated grid cells (N = 841) to the remaining grid cells with <80 % sample completeness (N = 3914) and generate diversity maps that cover the grid. Further, generalized linear mixed models were used to examine the associations between species diversity and sociodemographic indicators at census tract level. The wild vascular plant species diversity metrics were inversely associated with neighborhood socioeconomic status (i.e., unemployment, linguistic isolation, educational attainment, and poverty rate). Minority populations (i.e., African American, Asian American, and Hispanic) and children had significantly lower diversity exposure in their neighborhoods. Crowdsourcing data offers a cost-effective solution for characterizing large-scale biodiversity in urban areas.

Floristic Richness in a Mediterranean Hotspot: A Journey across Italy

Species richness is a fundamental property of biodiversity patterns and is properly expressed by the species-area relationship (SAR), namely the increase in the number of species with the area. Here, we studied and explored the species-area relationship with respect to vascular plant species in Italy and compared vascular plant richness among Italian administrative regions. Concerning the entire vascular flora (native and alien), the best-performing formula is the Arrhenius' Power function: S = c Az. The constants of this function are c = 241.2 and z = 0.281. The best-performing formula concerning just native (c = 245.2 and z = 0.263) and alien (c = 10.1 and z = 0.404) richness is the Power function as well. The floristically richest Italian regions considering the entire flora are Liguria, Friuli Venezia Giulia, and Trentino-Alto Adige, which are also the regions that are richest in alien flora unfortunately. Regions of particular naturalistic interest are Abruzzo, Valle d'Aosta, and Molise, because only these three regions exhibit native floristic richness that is higher than expected, and this is coupled with an alien floristic richness that is lower than expected. On the contrary, four regions (Lombardia, Veneto, Toscana, and Emilia-Romagna) show potentially severe conservation problems due to biological invasions since they experience native floristic richness that is lower than expected, with an alien floristic richness that is higher than expected. This study offers for the first time the 'c' and 'z' constants specifically calibrated at the national level for Italian vascular flora. The availability of such constants allows the calculation of the number of expected species for a given area to be investigated, providing a robust starting hypothesis for floristic studies.

Identifying hotspots of woody plant diversity and their relevance with home ranges of the critically endangered gibbon (Nomascus hainanus) across forest landscapes within a tropical nature reserve

Introduction

To achieve effective conservation objectives, it is crucial to map biodiversity patterns and hotspots while considering multiple influencing factors. However, focusing solely on biodiversity hotspots is inadequate for species conservation on a landscape scale. This emphasizes the importance of integrating hotspots with the home ranges of species to identify priority conservation areas.

Methods

Compiling the vegetation data with environmental and anthropogenic disturbance data collected from kilometer-grid plots in Bawangling Nature Reserve, Hainan, China, we analyzed the spatial distribution of plant diversity (species richness and Shannon-Wiener index), as well as the main drivers affecting these patterns. We also investigated the spatial distribution of hotspots using a threshold approach and compared them with the home ranges of the flagship species, Hainan gibbon (Nomascus hainanus).

Result

Climate and soil are predominant drivers shaping the spatial pattern of plant diversity in Bawangling Nature Reserve, surpassing the influence of anthropogenic disturbance and topographic factors. Both diversity indices exhibit a generally similar pattern with exceptions in surrounding areas of Futouling and Elongling. The hotspots identified by the Shannon-Wiener index showed a higher spatial overlap with the home ranges of Hainan gibbon compared to the species richness hotspots. The recently established Hainan gibbon Group E in 2019, located 8 km away from the original Futouling habitat, does not coincide with identified hotspots.

Discussion

Our findings indicate that the hotspots of plant diversity within the habitat of Hainan gibbon Group E are relatively limited, emphasizing the necessity of giving precedence to its conservation. Integrating hotspots with the home ranges of critically endangered species offers decision-makers valuable information to establish rational conservation networks in the context of changing environments, as well as a reference for habitat restoration of species.

Magnitude and direction of green-up date in response to drought depend on background climate over Mongolian grassland

Increasing drought is one major consequence of ongoing global climate change and is expected to cause significant changes in vegetation phenology, especially for naturally vulnerable ecosystems such as grassland. However, the linkage between the response characteristic of green-up date (GUD) to drought and background climate remains largely unknown. Here, we focused on how the GUD of Mongolian grassland responds to extreme drought events (EDE). We first extracted the GUD from the MODIS Enhanced Vegetation Index data during 2001-2020 and identified the preseason EDE using the standardized precipitation evapotranspiration index data. Subsequently, we quantified the response of GUD to preseason EDE (DGUD) in each pixel as the difference in GUD between drought and normal years. The effect of 12 factors on DGUD was analyzed using the random forest algorithm. The results showed that the GUD under EDE may delay or advance by > 20 days compared to normal years. For the regions with mean annual temperature > -2 °C, the GUD was delayed under EDE due to the dominant role of water restriction on GUD, while the GUD was advanced under EDE in colder areas due to the warmer temperature during drought. However, the magnitude of delay in GUD under drought was greater in regions with less precipitation and more severe droughts. Our results could help to develop appropriate management strategies to mitigate the impacts of drought on grasslands.

Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Is there a massive glacial-Holocene flora continuity in Central Europe?

The prevailing paradigm about the Quaternary ecological and evolutionary history of Central European ecosystems is that they were repeatedly impoverished by regional extinctions of most species during the glacial periods, followed by massive recolonizations from southern and eastern refugia during interglacial periods. Recent literature partially contradicts this view and provides evidence to re-evaluate this Postglacial Recolonization Hypothesis and develop an alternative one. We examined the long-term history of the flora of the Carpathian (Pannonian) Basin by synthesising recent advances in ecological, phylogeographical, palaeoecological and palaeoclimatological research, and analysing the cold tolerance of the native flora of a test area (Hungary, the central part of the Carpathian Basin). We found that (1) many species have likely occurred there continuously since before the Last Glacial Maximum (LGM); (2) most of the present-day native flora (1404 species, about 80%) can occur in climates as cold as or colder than the LGM (mean annual temperature ≤+3.5°C); and (3) grasslands and forests can be species-rich under an LGM-like cold climate. These arguments support an alternative hypothesis, which we call the Flora Continuity Hypothesis. It states that long-term continuity of much of the flora in the Carpathian Basin is more plausible than regional extinctions during the LGM followed by massive postglacial recolonizations. The long-term continuity of the region's flora may have fundamental implications not only for understanding local biogeography and ecology (e.g. the temporal scale of processes), but also for conservation strategies focusing on protecting ancient species-rich ecosystems and local gene pools.

Mapping density, diversity and species-richness of the Amazon tree flora

Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.

Impacts of landscape patterns on plant species diversity at a global scale

Landscape patterns are important drivers of biodiversity. Owing to differences in vegetation types, sampling methods, diversity measures, spatial scales, and landscape levels, the impact of landscape patterns on biodiversity remains widely debated. Using a global standardized plant community database and land use and land cover maps at 30-m resolution, for the period 1990-2017, we calculated plant species α- and β-diversity, and landscape metrics at patch- and landscape-levels, and discerned the direct and indirect impacts of landscape patterns on plant species diversity based on environmental factors, namely climate, spatial features, and human disturbance. We found that landscape patterns exhibited the main indirect effects, whereas climate factors exhibited dominant direct effects on plant α-diversity via the direct effects of patch patterns and functional traits. With respect to β-diversity, landscape-level patterns exerted more direct than indirect effects. These effects are strongly dependent on scale. Landscape- and patch-level patterns had opposite effects on plant diversity, depending on their composition and spatial structure, demonstrating that their effects could be mediated by one another. The adaptation of plants to landscape patterns is mainly through variations in leaf area, plant height, specific leaf area, stem density, seed biomass, and other seed-dispersal traits, which vary across vegetation types. Our findings highlight the importance of functional traits and diversity in understanding the mechanism by which landscape patterns influence plant species diversity; accordingly, we recommend balancing the spatial structure of patch- and landscape-level patterns to enhance variation in functional traits, and, ultimately, to maintain global plant diversity.

Mycorrhizal feedbacks influence global forest structure and diversity

One mechanism proposed to explain high species diversity in tropical systems is strong negative conspecific density dependence (CDD), which reduces recruitment of juveniles in proximity to conspecific adult plants. Although evidence shows that plant-specific soil pathogens can drive negative CDD, trees also form key mutualisms with mycorrhizal fungi, which may counteract these effects. Across 43 large-scale forest plots worldwide, we tested whether ectomycorrhizal tree species exhibit weaker negative CDD than arbuscular mycorrhizal tree species. We further tested for conmycorrhizal density dependence (CMDD) to test for benefit from shared mutualists. We found that the strength of CDD varies systematically with mycorrhizal type, with ectomycorrhizal tree species exhibiting higher sapling densities with increasing adult densities than arbuscular mycorrhizal tree species. Moreover, we found evidence of positive CMDD for tree species of both mycorrhizal types. Collectively, these findings indicate that mycorrhizal interactions likely play a foundational role in global forest diversity patterns and structure.

Global diversity and biogeography of potential phytopathogenic fungi in a changing world

Phytopathogenic fungi threaten global food security but the ecological drivers of their global diversity and biogeography remain unknown. Here, we construct and analyse a global atlas of potential phytopathogenic fungi from 20,312 samples across all continents and major oceanic island regions, eleven land cover types, and twelve habitat types. We show a peak in the diversity of phytopathogenic fungi in mid-latitude regions, in contrast to the latitudinal diversity gradients observed in aboveground organisms. Our study identifies climate as an important driver of the global distribution of phytopathogenic fungi, and our models suggest that their diversity and invasion potential will increase globally by 2100. Importantly, phytopathogen diversity will increase largely in forest (37.27-79.12%) and cropland (34.93-82.51%) ecosystems, and this becomes more pronounced under fossil-fuelled industry dependent future scenarios. Thus, we recommend improved biomonitoring in forests and croplands, and optimised sustainable development approaches to reduce potential threats from phytopathogenic fungi.

Occurrence-based diversity estimation reveals macroecological and conservation knowledge gaps for global woody plants

Incomplete sampling of species' geographic distributions has challenged biogeographers for many years to precisely quantify global-scale biodiversity patterns. After correcting for the spatial inequality of sample completeness, we generated a global species diversity map for woody angiosperms (82,974 species, 13,959,780 occurrence records). The standardized diversity estimated more pronounced latitudinal and longitudinal diversity gradients than the raw data and improved the spatial prediction of diversity based on environmental factors. We identified areas with potentially high species richness and rarity that are poorly explored, unprotected, and threatened by increasing human pressure: They are distributed mostly at low latitudes across central South America, Central Africa, subtropical China, and Indomalayan islands. These priority areas for botanical exploration can help to efficiently fill spatial knowledge gaps for better describing the status of biodiversity and improve the effectiveness of the protected area network for global woody plant conservation.

Animal and plant space-use drive plant diversity-productivity relationships

Plant community productivity generally increases with biodiversity, but the strength of this relationship exhibits strong empirical variation. In meta-food-web simulations, we addressed if the spatial overlap in plants' resource access and animal space-use can explain such variability. We found that spatial overlap of plant resource access is a prerequisite for positive diversity-productivity relationships, but causes exploitative competition that can lead to competitive exclusion. Space-use of herbivores causes apparent competition among plants, resulting in negative relationships. However, space-use of larger top predators integrates sub-food webs composed of smaller species, offsetting the negative effects of exploitative and apparent competition and leading to strongly positive diversity-productivity relationships. Overall, our results show that spatial overlap of plants' resource access and animal space-use can greatly alter the strength and sign of such relationships. In particular, the scaling of animal space-use effects opens new perspectives for linking landscape processes without effects on biodiversity to productivity patterns.

Winds of change. A commentary on 'Demographic trade-offs and functional shifts in a hurricane-impacted tropical forest'

This article comments on:

María Natalia Umaña, Jessica Needham, Jimena Forero-Montaña, Christopher J. Nytch, Nathan G. Swenson, Jill Thompson, María Uriarte and Jess K. Zimmerman. Demographic trade-offs and functional shifts in a hurricane-impacted tropical forest, Annals of Botany, Volume 131, Issue 7, 6 June 2023, Pages 1051–1060, https://doi.org/10.1093/aob/mcad004

Double stress of waterlogging and drought drives forest-savanna coexistence

Forest-savanna boundaries are ecotones that support complex ecosystem functions and are sensitive to biotic/abiotic perturbations. What drives their distribution today and how it may shift in the future are open questions. Feedbacks among climate, fire, herbivory, and land use are known drivers. Here, we show that alternating seasonal drought and waterlogging stress favors the dominance of savanna-like ecosystems over forests. We track the seasonal water-table depth as an indicator of water stress when too deep and oxygen stress when too shallow and map forest/savanna occurrence within this double-stress space in the neotropics. We find that under a given annual precipitation, savannas are favored in landscape positions experiencing double stress, which is more common as the dry season strengthens (climate driver) but only found in waterlogged lowlands (terrain driver). We further show that hydrological changes at the end of the century may expose some flooded forests to savanna expansion, affecting biodiversity and soil carbon storage. Our results highlight the importance of land hydrology in understanding/predicting forest-savanna transitions in a changing world.

Effects of drought, disturbance, and biotic neighborhood on experimental tree seedling performance

Forest biodiversity is likely maintained by a complex suite of interacting drivers that vary in importance across both space and time. Contributing factors include disturbance, interannual variation in abiotic variables, and biotic neighborhood effects. To probe ongoing uncertainties and potential interactions, we investigated tree seedling performance in a temperate mid-Atlantic forest ecosystem. We planted seedlings of five native tree species in mapped study plots, half of which were subjected to disturbance, and then monitored seedling survival, height growth, and foliar condition. The final year of data collection encompassed a drought, enabling comparison between intervals varying in water availability. Seedling performance was analyzed as a function of canopy cover and biotic neighborhood (conspecific and heterospecific abundance), including interactions, with separate generalized linear mixed models fit for each interval. All species exhibited: (a) pronounced declines in height growth during the drought year, (b) detrimental effects of adult conspecifics, and (c) beneficial effects of canopy openness. However, despite these consistencies, there was considerable variation across species in terms of the relevant predictors for each response variable in each interval. Our results suggest that drought may strengthen or reveal conspecific inhibition in some instances while weakening it or obscuring it in others, and that some forms of conspecific inhibition may manifest only under particular canopy conditions (although given the inconsistency of our findings, we are not convinced that conspecific inhibition is critical for diversity maintenance in our study system). Overall, our work reveals a complex forest ecosystem that appears simultaneously and interactively governed by biotic neighborhood structure (e.g., conspecific and/or heterospecific abundance), local habitat conditions (e.g., canopy cover), and interannual variability (e.g., drought).

Geography of Indian Butterflies: Patterns Revealed by Checklists of Federal States

Butterflies are widely used to analyze biogeographical patterns, both at the global and regional scales. Thus far, most of the latter originated from well-surveyed northern regions, while the species-rich tropical areas lag due to a lack of appropriate data. We used checklists of 1379 butterfly species recorded in 36 federal states of the Republic of India (1) to explore the basic macroecological rules, and (2) to relate species richness and the distribution of endemics and geographic elements to geography, climate, land covers and socioeconomic conditions of the states. The area, land covers diversity and latitude did not affect species richness, whereas topographic diversity and the precipitation/temperature ratio (energy availability) were positive predictors. This is due the geographic and climatic idiosyncrasies of the Indian subcontinent, with its highest species richness in the small, densely forested mountainous northeast that receives summer monsoons. The peninsular effect that decreases the richness towards the tip of subcontinent is counterbalanced by the mountainous forested Western Ghats. Afrotropical elements are associated with savannahs, while Palearctic elements are associated with treeless habitats. The bulk of Indian butterfly richness, and the highest conservation priorities, overlap with global biodiversity hotspots, but the mountainous states of the Western Himalayas and the savannah states of peninsular India host distinctive faunas.

Flora of Northeast Asia

As a component of the MAP project, the study of the flora in Northeast Asia (comprising Japan, South Korea, North Korea, Northeast China, and Mongolia) convincingly underscores the indispensability of precise and comprehensive diversity data for flora research. Due to variations in the description of flora across different countries in Northeast Asia, it is essential to update our understanding of the region's overall flora using the latest high-quality diversity data. This study employed the most recently published authoritative data from various countries to conduct a statistical analysis of 225 families, 1782 genera, and 10,514 native vascular species and infraspecific taxa in Northeast Asia. Furthermore, species distribution data were incorporated to delineate three gradients in the overall distribution pattern of plant diversity in Northeast Asia. Specifically, Japan (excluding Hokkaido) emerged as the most prolific hotspot for species, followed by the Korean Peninsula and the coastal areas of Northeast China as the second richest hotspots. Conversely, Hokkaido, inland Northeast China, and Mongolia constituted species barren spots. The formation of the diversity gradients is primarily attributed to the effects of latitude and continental gradients, with altitude and topographic factors within the gradients modulating the distribution of species.

Climate-trait relationships exhibit strong habitat specificity in plant communities across Europe

Ecological theory predicts close relationships between macroclimate and functional traits. Yet, global climatic gradients correlate only weakly with the trait composition of local plant communities, suggesting that important factors have been ignored. Here, we investigate the consistency of climate-trait relationships for plant communities in European habitats. Assuming that local factors are better accounted for in more narrowly defined habitats, we assigned > 300,000 vegetation plots to hierarchically classified habitats and modelled the effects of climate on the community-weighted means of four key functional traits using generalized additive models. We found that the predictive power of climate increased from broadly to narrowly defined habitats for specific leaf area and root length, but not for plant height and seed mass. Although macroclimate generally predicted the distribution of all traits, its effects varied, with habitat-specificity increasing toward more narrowly defined habitats. We conclude that macroclimate is an important determinant of terrestrial plant communities, but future predictions of climatic effects must consider how habitats are defined.

Global models and predictions of plant diversity based on advanced machine learning techniques

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is still incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, and neural networks) and conventional statistical methods (generalized linear models and generalized additive models) to test environment-related hypotheses of broad-scale vascular plant diversity gradients and to model and predict species richness and phylogenetic richness worldwide. To this end, we used 830 regional plant inventories including c. 300 000 species and predictors of past and present environmental conditions. Machine learning showed a superior performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness, illustrating the great potential of such techniques for disentangling complex and interacting associations between the environment and plant diversity. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modeling techniques (ensemble predictions) to reveal global patterns and centers of plant diversity at multiple resolutions down to 7774 km² . Our predictive maps provide accurate estimates of global plant diversity available at grain sizes relevant for conservation and macroecology.

Metabarcoding of soil environmental DNA to estimate plant diversity globally

Introduction

Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods.

Methods

We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data.

Results

Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region.

Discussion

eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.