rWCVP: a companion R package for the World Checklist of Vascular Plants

Tracking hidden dimensions of plant biogeography from herbaria

Plants are diverse, but investigating their ecology and evolution in nature across geographic and temporal scales to predict how species will respond to global change is challenging. With their geographic and temporal breadth, herbarium data provide physical evidence of the existence of a species in a place and time. The remarkable size of herbarium collections along with growing digitization efforts around the world and the possibility of extracting functional traits and geographic data from preserved plant specimens makes them invaluable resources for advancing our understanding of changing species distributions over time, functional biogeography, and conserving plant communities. Here, I synthesize core aspects of plant biogeography that can be gleaned from herbaria along changing distributions, attributes (functional biogeography), and conservation biogeography across the globe. I advocate for a collaborative, multisite, and multispecies research to harness the full potential of these collections while addressing the inherent challenges of using herbarium data for biogeography and macroecological investigations. Ultimately, these data present untapped resources and opportunities to enable predictions of plant species' responses to global change and inform effective conservation planning.

PNSS: An online plant name service system

Biodiversity plays a vital role in human survival and development. Consequently, the protection of biodiversity has become a global concern. Biological names serve as biological identifiers and the use of correct biological names helps promote biodiversity conservation research. At present, there are numerous taxonomic databases and software tools available worldwide for processing plant names. However, these resources are scattered across various database websites or personal computers. Users must invest a significant amount of time collecting these resources and expend substantial effort to learn, use and maintain them, consequently leading to high user learning and usage costs. Here, we propose a solution to address the above problem. We collected mainstream and freely available taxonomic datasets from around the world, integrated them into an extensive taxonomic dataset and subsequently mapped the data in this summary database to Solr search engine. Then, based on these taxonomic datasets, we designed database, algorithms and system, developed the system and finally established an online plant name service system (PNSS). The PNSS not only integrates the mainstream taxonomic datasets, but also offers free plant name retrieval, matching, search, parsing and application programming interface (API) services to help biologists conduct more effective research on biodiversity conservation.

Climate space, traits, and the spread of nonnative plants in North America

The future distribution of invading species depends on the climate space available and certain life history traits that facilitate invasion. Here, to predict the spread potential of plant species introduced in North America north of Mexico (NAM), we compiled distribution and life history data (i.e., seed size, life form, and photosynthetic pathways) for 3021 exotic plant species introduced to NAM. We comparatively examined the species' range size and climate space in both native and exotic regions and the role of key life history traits. We found that large climate space for most exotic plants is still available in NAM. The range sizes in global exotic regions could better predict the current range sizes in NAM than those in global native regions or global native plus exotic regions. C3 species had larger ranges on average than C4 and CAM plants, and herbaceous species consistently showed stronger relationships in range size between native and exotic regions than woody species, as was the case within the C3 species group. Seed size was negatively related to range size both in native regions and in NAM. However, seed size surprisingly showed a positive correlation with global exotic range size and no correlation with the current actual global (native plus exotic) range size. Our findings underline the importance of species' native distribution and life history traits in predicting the spread of exotic species. Future studies should continue to identify potential climate space and use underappreciated species traits to better predict species invasions under changing climate.

mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images

Premise

Recent advances in imaging herbarium specimens have enhanced their use in biodiversity studies. However, user-friendly tools that facilitate the assembly of customized sets of herbarium specimen images on personal devices are still lacking.

Methods and Results

Here we present the R package mvh ("my virtual herbarium"), which includes functions designed to search and download metadata and openly available images associated with herbarium specimens based on taxon or geography. We tested the functionalities of mvh by searching metadata associated with five sets of 10 vascular plant species and five sets of 10 terrestrial coordinates. The download function had a success rate of 99%, downloading 291 out of the 293 images found in the search. Possible reasons for download failure are discussed.

Conclusions

As long as an internet connection is available, mvh simplifies the assembly and organization of virtual herbaria, thereby facilitating the investigation of novel empirical questions as well as trends in digitization efforts.

Climb forest, climb: diverse disperser communities are key to assist plants tracking climate change on altitudinal gradients

Climate change is forcing species to shift their distribution ranges. Animal seed dispersers might be particularly important in assisting plants tracking suitable climates to higher elevations. However, this role is still poorly understood due to a lack of comprehensive multi-guild datasets along elevational gradients. We compiled seed dispersal networks for the five altitudinal vegetation belts of the Tenerife Island (0-3718 m above sea level) to explore how plant and animal species might facilitate the mutual colonisation of uphill habitats under climate change. The overall network comprised 283 distinct interactions between 73 plant and 27 animal species, with seed dispersers offering viable pathways for plants to colonise upper vegetation belts. A pivotal role is played by a lizard as island-level hub, while four birds and one introduced mammal (rabbit) are also important connectors between belts. Eleven plant species were empirically found to be actively dispersed to elevations beyond their current known range, with observed vertical dispersal distances largely surpassing those required to escape climate change. Furthermore, over half of the plants arriving at higher elevations were exotic. Functionally diverse disperser communities are crucial for enabling plants tracking climate change on mountains, but exotic plants might particularly benefit from this upward lift.

An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species

•We present 'U.Taxonstand Online', a user-friendly web application for scientific name matching of both plants and animals.•U.Taxonstand Online provides a solution for the users with limited abilities of programming and data mining.•We add several new functions to clean and format the data for R package U.Taxonstand.

expowo: An R package for mining global plant diversity and distribution data

Premise

Data on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open-source package that facilitates extracting and using botanical data from POWO.

Methods and Results

The expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species-discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy-to-handle outputs, we also show empirical examples from a set of biodiverse countries and representative species-rich and ecologically important angiosperm families.

Conclusions

By harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.

florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil

Premise

The Flora e Funga do Brasil project is the most comprehensive effort to reliably document Brazilian plant and fungal diversity. It involves the collaborative work of hundreds of taxonomists, integrating detailed and standardized morphological descriptions, nomenclatural status, and geographic distribution information of plants, algae, and fungi collected throughout Brazil. Despite the extensive information available, managing the information from the Flora e Funga do Brasil website poses certain challenges.

Methods and Results

florabr is an R package developed to facilitate the exploration and geographical analysis of species information derived from the Flora e Funga do Brasil. Unique to florabr is its ability to interact with the latest, or any other version of the dataset, which undergoes weekly updates. I illustrate the practical application of florabr in common tasks in biogeography and conservation studies.

Conclusions

florabr is anticipated to be of significant interest to biogeographers, ecologists, curators of biological collections, and taxonomists actively contributing to the Flora e Funga do Brasil.

Evidence of a European seed dispersal crisis

Seed dispersal is crucial for ecosystem persistence, especially in fragmented landscapes, such as those common in Europe. Ongoing defaunation might compromise effective seed dispersal, but the conservation status of pairwise interactions remains unknown. With a literature review, we reconstructed the first European-wide seed dispersal network and evaluated the conservation status of interactions by assessing each interacting partner's IUCN (International Union for Conservation of Nature) conservation status and population trends. We found that a third of the disperser species and interactions face potential extinction and that 30% of the plant species have most of their dispersers threatened or declining. Our study reveals a developing seed dispersal crisis in Europe and highlights large knowledge gaps regarding the dispersers and conservation status of zoochorous plants, urging further scrutiny and action to conserve the seed dispersal service.

Previously unmeasured genetic diversity explains part of Lewontin's paradox in a k -mer-based meta-analysis of 112 plant species

At the molecular level, most evolution is expected to be neutral. A key prediction of this expectation is that the level of genetic diversity in a population should scale with population size. However, as was noted by Richard Lewontin in 1974 and reaffirmed by later studies, the slope of the population size-diversity relationship in nature is much weaker than expected under neutral theory. We hypothesize that one contributor to this paradox is that current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads to a reference genome underestimate levels of genetic diversity in many species. To test this idea, we calculated nucleotide diversity ( π ) and k -mer-based metrics of genetic diversity across 112 plant species, amounting to over 205 terabases of DNA sequencing data from 27,488 individual plants. We then compared how these different metrics correlated with proxies of population size that account for both range size and population density variation across species. We found that our population size proxies scaled anywhere from about 3 to over 20 times faster with k -mer diversity than nucleotide diversity after adjusting for evolutionary history, mating system, life cycle habit, cultivation status, and invasiveness. The relationship between k -mer diversity and population size proxies also remains significant after correcting for genome size, whereas the analogous relationship for nucleotide diversity does not. These results suggest that variation not captured by common SNP-based analyses explains part of Lewontin's paradox in plants.

Genome size is positively correlated with extinction risk in herbaceous angiosperms

Angiosperms with large genomes experience nuclear-, cellular-, and organism-level constraints that may limit their phenotypic plasticity and ecological niche, which could increase their risk of extinction. Therefore, we test the hypotheses that large-genomed species are more likely to be threatened with extinction than those with small genomes, and that the effect of genome size varies across three selected covariates: life form, endemism, and climatic zone. We collated genome size and extinction risk information for a representative sample of angiosperms comprising 3250 species, which we analyzed alongside life form, endemism, and climatic zone variables using a phylogenetic framework. Genome size is positively correlated with extinction risk, a pattern driven by a signal in herbaceous but not woody species, regardless of climate and endemism. The influence of genome size is stronger in endemic herbaceous species, but is relatively homogenous across different climates. Beyond its indirect link via endemism and climate, genome size is associated with extinction risk directly and significantly. Genome size may serve as a proxy for difficult-to-measure parameters associated with resilience and vulnerability in herbaceous angiosperms. Therefore, it merits further exploration as a useful biological attribute for understanding intrinsic extinction risk and augmenting plant conservation efforts.

Disturbance and vegetational structure in an urban forest of Indian Siwaliks: an ecological assessment

Urban forests face multiple human-mediated pressures leading to compromised ecosystem structure and functioning. Therefore, understanding ecosystem structure in response to ongoing pressures is crucial for sustaining ecological integrity and human well-being. We aim to assess the disturbance and its effects on the vegetation structure of urban forests in Chandigarh using a combination of remote sensing techniques and vegetation surveys. The disturbance was evaluated as a change in NDVI (Normalised Difference Vegetation Index) from 2001 to 2021 by applying the BFAST (Breaks For Additive Season and Trend) algorithm to the MODIS satellite imagery data. A vegetation survey was conducted to compare the species composition, taxonomic and phylogenetic diversity as measures of forest vegetational structure. While signals of disturbance were evident, the changes in vegetation structure were not well established from our study. Further, this analysis indicated no significant differences in vegetation composition due to disturbance (F1,12 = 0.91, p = 0.575). However, the phylogenetic diversity was substantially lower for disturbed plots than undisturbed plots, though the taxonomic diversity was similar among the disturbed and undisturbed plots. Our results confirmed that disturbance effects are more prominent on the phylogenetic than taxonomic diversity. These findings can be considered early signals of disturbance and its impact on the vegetation structure of urban forests and contribute to the knowledge base on urban ecosystems. Our study has implications for facilitating evidence-based decision-making and the development of sustainable management strategies for urban forest ecosystems.

O armário: Fruiting phenology data for 4,462 plant taxa in Portugal (1926-2013)

Species phenology - the timing of key life events - is being altered by ongoing climate changes with yet underappreciated consequences for ecosystem stability. While flowering is generally occurring earlier, we know much less about other key processes such as the time of fruit ripening, largely due to the lack of comprehensive long-term datasets. Here we provide information on the exact date and site where seeds of 4,462 taxa were collected for the Index Seminum (seed exchange catalogue) of the Botanic Garden of the University of Coimbra, between 1926 and 2013. Seeds were collected from spontaneous and cultivated individuals across Portugal, including both native and introduced taxa. The database consists of 127,747 curated records with information on the species, or infraspecific taxa (including authority), and the day and site where seeds were collected. All records are georeferenced and provided with a confidence interval for the collection site. Taxonomy was first curated manually by in-house botanists and then harmonized according to the GBIF backbone taxonomy.

Extinction risk predictions for the world's flowering plants to support their conservation

More than 70% of all vascular plants lack conservation status assessments. We aimed to address this shortfall in knowledge of species extinction risk by using the World Checklist of Vascular Plants to generate the first comprehensive set of predictions for a large clade: angiosperms (flowering plants, c. 330 000 species). We used Bayesian Additive Regression Trees (BART) to predict the extinction risk of all angiosperms using predictors relating to range size, human footprint, climate, and evolutionary history and applied a novel approach to estimate uncertainty of individual species-level predictions. From our model predictions, we estimate 45.1% of angiosperm species are potentially threatened with a lower bound of 44.5% and upper bound of 45.7%. Our species-level predictions, with associated uncertainty estimates, do not replace full global, or regional Red List assessments, but can be used to prioritise predicted threatened species for full Red List assessment and fast-track predicted non-threatened species for Least Concern assessments. Our predictions and uncertainty estimates can also guide fieldwork, inform systematic conservation planning and support global plant conservation efforts and targets.

Spatial heterogeneity of neo- and paleo-endemism for plants in Madagascar

Madagascar is a biogeographically unique island with a remarkably high level of endemism. However, endemic taxa in Madagascar are massively threatened due to unprecedented pressures from anthropogenic habitat modification and climate change. A comprehensive phylogeny-based biodiversity evaluation of the island remains lacking. Here, we identify hotspots of taxonomic and phylogenetic plant diversity and neo- and paleo-endemism by generating a novel dated tree of life for the island. The tree is based on unprecedented sampling of 3,950 species (33% of the total known species) and 1,621 genera (93% of the total known genera and 69% of endemic genera) of Malagasy vascular plants. We find that island-endemic genera are concentrated in multiple lineages combining high taxonomic and phylogenetic diversity. Integrating phylogenetic and geographic distribution data, our results reveal that taxon richness and endemism are concentrated in the northern, eastern, and southeastern humid forests. Paleo-endemism centers are concentrated in humid eastern and central regions, whereas neo-endemism centers are concentrated in the dry and spiny forests in western and southern Madagascar. Our statistical analysis of endemic genera in each vegetation region supports a higher proportion of ancient endemic genera in the east but a higher proportion of recent endemic genera in the south and west. Overlaying centers of phylogenetic endemism with protected areas, we identify conservation gaps concentrated in western and southern Madagascar. These gaps should be incorporated into conservation strategies to aid the protection of multiple facets of biodiversity and their benefits to the Malagasy people.

Global patterns and ecological drivers of taxonomic and phylogenetic endemism in angiosperm genera

Endemism of lineages lies at the core of understanding variation in community composition among geographic regions because it reflects how speciation, extinction, and dispersal have influenced current distributions. Here, we investigated geographic patterns and ecological drivers of taxonomic and phylogenetic endemism of angiosperm genera across the world. We identify centers of paleo-endemism and neo-endemism of angiosperm genera, and show that they are mostly located in the Southern Hemisphere in tropical and subtropical regions, particularly in Asia and Australia. Different categories of phylogenetic endemism centers can be differentiated using current climate conditions. Current climate, historical climate change, and geographic variables together explained ∼80% of global variation in taxonomic and phylogenetic endemism, while 42-46%, 1%, and 15% were independently explained by these three types of variables, respectively. Thus our findings show that past climate change, current climate, and geography act together in shaping endemism, which are consistent with the findings of previous studies that higher temperature and topographic heterogeneity promote endemism. Our study showed that many centers of phylogenetic endemism of angiosperms, including regions in Amazonia, Venezuela, and west-central tropical Africa that have not previously been identified as biodiversity hotspots, are missed by taxon-based measures of endemism, indicating the importance of including evolutionary history in biodiversity assessment.

Ukrainian Plant Trait Database: UkrTrait v. 1.0

Background

Considering the growing demand for plant trait data and taking into account the lack of trait data from Eastern Europe, especially from its steppic region, we launched a new Ukrainian Plant Trait Database (UkrTrait v. 1.0) aiming at collecting all the available plant trait data from Ukraine.To facilitate further use of this database, we linked the trait terminology to the TRY Plant Trait Database, Thesaurus of Plant Characteristics (TOP) and Plant Trait Ontology (TO). For taxa names, we provide the crosswalks between the Ukrainian checklist and international sources, i.e. GBIF Backbone Taxonomy, World Checklist of Vascular Plants (World Checklist of Vascular Plants (World Checklist of Vascular Plants (WCVP), World Flora Online (WFO) and Euro+Med PlantBase. We aim to integrate our data into the relevant global (TRY Plant Trait Database) and pan-European (FloraVeg.EU) databases. The current version of the database is freely available at the Zenodo repository and will be updated in the future.

New information

Until now, plant traits for the Ukrainian flora were scattered across literature, often focusing on single species and written mainly in Ukrainian. Additionally, many traits were in grey literature or remained non-digitised, which rendered them inaccessible to the global scientific community. Addressing this gap, our Ukrainian Plant Trait Database (UkrTrait v. 1.0) represents a significant step forward. We compiled and digitised plant traits from local Ukrainian literature sources. Furthermore, we performed our own field and laboratory measurements of various plant traits that were not previously available in literature. In the current version of the UkrTrait, we focus on vascular plant species that are absent from the other European trait databases, with emphasis on species that are representative for the steppe vegetation. Traits assembled from literature include life span (annuals, biennials, perennials), plant height, flowering period (flowering months), life form (by Raunkiaer), plant growth form and others. Our own measured traits include seed mass, seed shape, leaf area, leaf nitrogen concentration and leaf phosphorus concentration. The current version, i.e. UkrTrait v. 1.0, comprises digitised literature data of 287,948 records of 75 traits for 6,198 taxa and our own trait measurements of 2,390 records of 12 traits for 388 taxa.

Effects of climate and environmental heterogeneity on the phylogenetic structure of regional angiosperm floras worldwide

The tendency of species to retain ancestral ecological distributions (phylogenetic niche conservatism) is thought to influence which species from a species pool can persist in a particular environment. Thus, investigating the relationships between measures of phylogenetic structure and environmental variables at a global scale can help understand the variation in species richness and phylogenetic structure in biological assemblages across the world. Here, we analyze a comprehensive data set including 341,846 species in 391 angiosperm floras worldwide to explore the relationships between measures of phylogenetic structure and environmental variables for angiosperms in regional floras across the world and for each of individual continental (biogeographic) regions. We find that the global phylogenetic structure of angiosperms shows clear and meaningful relationships with environmental factors. Current climatic variables have the highest predictive power, especially on phylogenetic metrics reflecting recent evolutionary relationships that are also related to current environmental heterogeneity, presumably because this favors plant speciation in various ways. We also find evidence that past climatic conditions, and particularly refugial conditions, play an important role in determining the phylogenetic structure of regional floras. The relationships between environmental conditions and phylogenetic metrics differ between continents, reflecting the different evolutionary histories of their floras.

Three in four undescribed plant species are threatened with extinction

This article is part of the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

Global distribution, climatic preferences and photosynthesis-related traits of C4 eudicots and how they differ from those of C4 grasses

C₄ is one of three known photosynthetic processes of carbon fixation in flowering plants. It evolved independently more than 61 times in multiple angiosperm lineages and consists of a series of anatomical and biochemical modifications to the ancestral C3 pathway increasing plant productivity under warm and light-rich conditions. The C4 lineages of eudicots belong to seven orders and 15 families, are phylogenetically less constrained than those of monocots and entail an enormous structural and ecological diversity. Eudicot C4 lineages likely evolved the C4 syndrome along different evolutionary paths. Therefore, a better understanding of this diversity is key to understanding the evolution of this complex trait as a whole. By compiling 1207 recognised C4 eudicots species described in the literature and presenting trait data among these species, we identify global centres of species richness and of high phylogenetic diversity. Furthermore, we discuss climatic preferences in the context of plant functional traits. We identify two hotspots of C4 eudicot diversity: arid regions of Mexico/Southern United States and Australia, which show a similarly high number of different C4 eudicot genera but differ in the number of C4 lineages that evolved in situ. Further eudicot C4 hotspots with many different families and genera are in South Africa, West Africa, Patagonia, Central Asia and the Mediterranean. In general, C4 eudicots are diverse in deserts and xeric shrublands, tropical and subtropical grasslands, savannas and shrublands. We found C4 eudicots to occur in areas with less annual precipitation than C4 grasses which can be explained by frequently associated adaptations to drought stress such as among others succulence and salt tolerance. The data indicate that C4 eudicot lineages utilising the NAD-ME decarboxylating enzyme grow in drier areas than those using the NADP-ME decarboxylating enzyme indicating biochemical restrictions of the later system in higher temperatures. We conclude that in most eudicot lineages, C4 evolved in ancestrally already drought-adapted clades and enabled these to further spread in these habitats and colonise even drier areas.

Why plant diversity and distribution matter

This article is the Editorial for the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

Geographic patterns of taxonomic and phylogenetic β-diversity of angiosperm genera in regional floras across the world

Beta diversity (β-diversity) is the scalar between local (α) and regional (γ) diversity. Understanding geographic patterns of β-diversity is central to ecology, biogeography, and conservation biology. A full understanding of the origin and maintenance of geographic patterns of β-diversity requires exploring both taxonomic and phylogenetic β-diversity, as well as their respective turnover and nestedness components, and exploring phylogenetic β-diversity at different evolutionary depths. In this study, we explore and map geographic patterns of β-diversity for angiosperm genera in regional floras across the world. We examine both taxonomic and phylogenetic β-diversity and their constituent components, and both tip-weighted and basal-weighted phylogenetic β-diversity, and relate them to latitude. On the one hand, our study found that the global distribution of β-diversity is highly heterogeneous. This is the case for both taxonomic and phylogenetic β-diversity, and for both tip-weighted and basal-weighted phylogenetic β-diversity. On the other hand, our study found that there are highly consistent geographic patterns among different metrics of β-diversity. In most cases, metrics of β-diversity are negatively associated with latitude, particularly in the Northern Hemisphere. Different metrics of taxonomic β-diversity are strongly and positively correlated with their counterparts of phylogenetic β-diversity.

Neophytes may promote hybridization and adaptations to a changing planet

Human activities erode geographic barriers, facilitating hybridization among previously isolated taxa. However, limited empirical research exists on the consequences of introduced species (neophytes) for hybridization and subsequent evolutionary outcomes. To address this knowledge gap, we employed a macroecological approach. First, we examined the spatial and phylogenetic overlap between neophytes and hybrids by integrating the Plants of the World Online database with the Global Naturalized Alien Flora database. Second, leveraging the largest dated plant phylogeny available, we compared diversification rates between genera containing hybrids and neophytes versus those without. Third, focusing on the extensively studied hybrid flora of Britain, we studied the spatial distributions of hybrids in relation to neophyte and native parents, assessing potential adaptations to anthropogenic disturbances and impacts on native species. Overall, our findings highlight positive ties between contemporary biodiversity redistribution and hybridization. Spatially (across countries) and phylogenetically (across genera), neophyte incidence was positively associated with hybrid incidence. Genera comprising both hybrids and neophytes displayed significantly higher diversification rates. Neophyte hybrids primarily occupied areas with a higher human footprint, with limited evidence of hybrids threatening native species throughout their range in more natural habitats. These results challenge the notion that species naturalizations and hybridizations exclusively yield negative outcomes for biodiversity. While it is conceivable that anthropogenic hybridization may facilitate recombination of genetic variation and contribute to conserving genetic diversity in disturbed environments, further research is needed to fully understand these processes.