Widespread mistaken identity in tropical plant collections

Musa species in mainland Southeast Asia: From wild to domesticate

Many species are defined in the Musa section within its natural diversification area in Southeast Asia. However, their actual number remains debated as botanical characterisation, distribution and intraspecific variability are still poorly known, compromising their preservation and their exploitation as crop wild relatives of cultivated forms. To address the underexplored Musa diversity in mainland Southeast Asia, at the northern edge of the natural range, 208 specimens were collected in Vietnam, Laos and China, mainly belonging to Musa balbisiana, M. itinerans, M. acuminata and M. yunnanensis. Data on location, morphology, environment and local knowledge were recorded, and leaf samples collected for high-throughput genotyping. This study combines geographical, morphological, and genomic diversity to clarify the taxonomic classification. The collected species exhibit highly distinctive morphologies and genomes, just as they differ in ranges and life traits. Intraspecific genomic diversity was also observed, although not necessarily morphologically perceptible. Mainland Southeast Asia is confirmed as a primary diversification centre for the Musa section. The diversity observed is only partially represented in major international ex situ collections, calling for their urgent enrichment and the promotion of in situ management procedures, for the protection of these threatened species and to better harness their potential in breeding programmes. Although considered wild, the species studied are all affected to varying extents by human use. Musa yunnanensis and M. acuminata subsp. burmannica are the most strictly wild forms, with spontaneous interspecific hybrids first described in this study. Although gathered as fodder, they were only occasionally dispersed outside their endemic zones. Musa itinerans is not cultivated per se, but natural populations are widely exploited, leading to a geographically structured diversity. The diversity of M. balbisiana is widely distributed and geographically structured by human activities. This species should be regarded as domesticated. These various stages, from simple opportunistic gathering to true domestication, shed light on the evolutionary history of today's cultivated varieties.

Guidelines for the effective and ethical sampling of herbaria

The use of herbaria for science and conservation is enabling greatly enhanced scopes and scales of discovery, exploration and protection of biodiversity. The availability of digital, open-access herbarium data is, perhaps counter-intuitively, expanding the use of physical collections by researchers who use digital collections to find specimens and then sample physical collections for multiomics investigations, including genomics, transcriptomics, metabolomics, proteomics and microbiomics. These investigations are leading to new scientific insights and supporting the development of conservation actions, but they come with a substantial cost: the partial or complete destruction of often irreplaceable specimens, which constitute a global heritage that should be permanently safeguarded for future reference. Here we provide a set of recommended best practices for the sustainable, equitable and ethical sampling of herbarium specimens. Our recommendations are intended for two complementary and partially overlapping audiences-users and stewards-who together build, use and protect herbarium collections.

The Tropical Andes Biodiversity Hotspot: A Comprehensive Dataset for the Mira-Mataje Binational Basins

We present a flora and fauna dataset for the Mira-Mataje binational basins. This is an area shared between southwestern Colombia and northwestern Ecuador, where both the Chocó and Tropical Andes biodiversity hotspots converge. We systematized data from 120 sources in the Darwin Core Archive (DwC-A) standard and geospatial vector data format for geographic information systems (GIS) (shapefiles). Sources included natural history museums, published literature, and citizen science repositories across 13 countries. The resulting database has 33,460 records from 6,821 species, of which 540 have been recorded as endemic, and 612 as threatened. The diversity represented in the dataset is equivalent to 10% of the total plant species and 26% of the total terrestrial vertebrate species in both hotspots. The dataset can be used to estimate and compare biodiversity patterns with environmental parameters and provide value to ecosystems, ecoregions, and protected areas. The dataset is a baseline for future assessments of biodiversity in the face of environmental degradation, climate change, and accelerated extinction processes.

Underground trees inhabit varied environmental extremes across the Afrotropics

BACKGROUND AND AIMS

Geoxyles, a distinctive feature of Afrotropical savannas and grasslands, survive recurrent disturbances by resprouting subshrub branches from large below-ground woody structures. Underground trees are a type of geoxyle that independently evolved within woody genera of at least 40 plant families in Africa. The environmental limits and determinants of underground tree biogeography are poorly understood, with the relative influence of frost and fire debated in particular. We aim to quantify variability in the niche of underground tree species relative to their taller, woody tree/shrub congeners.

METHODS

Using occurrence records of four Afrotropical genera, Parinari (Chrysobalanaceae), Ozoroa (Anacardiaceae), Syzygium (Myrtaceae) and Lannea (Anacardiaceae), and environmental data of nine climate and disturbance variables, the biogeography and niche of underground trees are compared with their open and closed ecosystem congeners.

KEY RESULTS

Along multiple environmental gradients and in a multidimensional environmental space, underground trees inhabit significantly distinct and extreme environments relative to open and closed ecosystem congeners. Niche overlap is low among underground trees and their congeners, and also among underground trees of the four genera. Of the study taxa, Parinari underground trees inhabit hotter, drier and more seasonal environments where herbivory pressure is greatest. Ozoroa underground trees occupy relatively more fire-prone environments, while Syzygium underground trees sustain the highest frost frequency and occur in relatively wetter conditions with seasonal waterlogging. Lannea underground trees are associated with the lowest temperatures, highest precipitation, and varying exposure to disturbance.

CONCLUSIONS

While underground trees exhibit repeated convergent evolution, varied environments shape the ecology and biogeography of this iconic plant functional group. The multiplicity of extreme environments related to fire, frost, herbivory and waterlogging that different underground tree taxa occupy, and the distinctiveness of these environments, should be recognized in the management of African grassy ecosystems.

Ex situ conservation of two rare oak species using microsatellite and SNP markers

Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.

Quantifying error in occurrence data: Comparing the data quality of iNaturalist and digitized herbarium specimen data in flowering plant families of the southeastern United States

iNaturalist has the potential to be an extremely rich source of organismal occurrence data. Launched in 2008, it now contains over 150 million uploaded observations as of May 2023. Based on the findings of a limited number of past studies assessing the taxonomic accuracy of participatory science-driven sources of occurrence data such as iNaturalist, there has been concern that some portion of these records might be misidentified in certain taxonomic groups. In this case study, we compare Research Grade iNaturalist observations with digitized herbarium specimens, both of which are currently available for combined download from large data aggregators and are therefore the primary sources of occurrence data for large-scale biodiversity/biogeography studies. Our comparisons were confined regionally to the southeastern United States (Florida, Georgia, North Carolina, South Carolina, Texas, Tennessee, Kentucky, and Virginia). Occurrence records from ten plant families (Gentianaceae, Ericaceae, Melanthiaceae, Ulmaceae, Fabaceae, Asteraceae, Fagaceae, Cyperaceae, Juglandaceae, Apocynaceae) were downloaded and scored on taxonomic accuracy. We found a comparable and relatively low rate of misidentification among both digitized herbarium specimens and Research Grade iNaturalist observations within the study area. This finding illustrates the utility and high quality of iNaturalist data for future research in the region, but also points to key differences between data types, giving each a respective advantage, depending on applications of the data.

Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation

Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.

A globally synthesised and flagged bee occurrence dataset and cleaning workflow

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and, we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.

Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex

PREMISE

Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts.

METHODS

Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries.

RESULTS

None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries.

CONCLUSIONS

Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high-throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes.

Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

Achieving zero extinction for land plants

Despite the importance of plants for humans and the threats to their future, plant conservation receives far less support compared with vertebrate conservation. Plants are much cheaper and easier to conserve than are animals, but, although there are no technical reasons why any plant species should become extinct, inadequate funding and the shortage of skilled people has created barriers to their conservation. These barriers include the incomplete inventory, the low proportion of species with conservation status assessments, partial online data accessibility, varied data quality, and insufficient investment in both in and ex situ conservation. Machine learning, citizen science (CS), and new technologies could mitigate these problems, but we need to set national and global targets of zero plant extinction to attract greater support.

Challenges and opportunities for using natural history collections to estimate insect population trends

Natural history collections (NHC) provide a wealth of information that can be used to understand the impacts of global change on biodiversity. As such, there is growing interest in using NHC data to estimate changes in species' distributions and abundance trends over historic time horizons when contemporary survey data are limited or unavailable. However, museum specimens were not collected with the purpose of estimating population trends and thus can exhibit spatiotemporal and collector-specific biases that can impose severe limitations to using NHC data for evaluating population trajectories. Here we review the challenges associated with using museum records to track long-term insect population trends, including spatiotemporal biases in sampling effort and sparse temporal coverage within and across years. We highlight recent methodological advancements that aim to overcome these challenges and discuss emerging research opportunities. Specifically, we examine the potential of integrating museum records and other contemporary data sources (e.g. collected via structured, designed surveys and opportunistic citizen science programs) in a unified analytical framework that accounts for the sampling biases associated with each data source. The emerging field of integrated modelling provides a promising framework for leveraging the wealth of collections data to accurately estimate long-term trends of insect populations and identify cases where that is not possible using existing data sources.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

Geographic distribution, conservation status and lectotypification of Pedersenia weberbaueri (Suess.) Holub (Amaranthaceae), an endemic and highly threatened shrub from the Marañón valley of Peru

The present study analyses the geographical distribution, conservation status, and nomenclature of Peruvian endemic Pedersenia weberbaueri. The species distribution was modelled using MaxEnt based on occurrence data and bioclimatic variables. The conservation status of the species was assessed against the categories and criteria of the IUCN Red List, and nomenclatural and typification issues were resolved. The potential distribution map of P. weberbaueri shows that the species is restricted to the seasonally dry tropical forests of the Marañón valley within a narrow latitudinal, longitudinal, and elevational range. Consequently, we propose to categorise the species as Endangered (EN) and provide the necessary information for its inclusion in the IUCN Red List. Finally, we resolve nomenclatural issues and designate a lectotype. The results contribute to the biological knowledge of P. weberbaueri and support subsequent conservation management plans.

Influence of different data cleaning solutions of point-occurrence records on downstream macroecological diversity models

Digital point-occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time-consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual-guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S-SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package-based pipelines reliably identified invalid coordinates. In contrast, the GBIF-filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application-filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high-quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.

Development of a system for the automated identification of herbarium specimens with high accuracy

Herbarium specimens are dried plants mounted onto paper. They are used by a limited number of researchers, such as plant taxonomists, as a source of information on morphology and distribution. Recently, digitised herbarium specimens have begun to be used in comprehensive research to address broader issues. However, some specimens have been misidentified, and if used, there is a risk of drawing incorrect conclusions. In this study, we successfully developed a system for identifying taxon names with high accuracy using an image recognition system. We developed a system with an accuracy of 96.4% using 500,554 specimen images of 2171 plant taxa (2064 species, 9 subspecies, 88 varieties, and 10 forms in 192 families) that grow in Japan. We clarified where the artificial intelligence is looking to make decisions, and which taxa is being misidentified. As the system can be applied to digitalised images worldwide, it is useful for selecting and correcting misidentified herbarium specimens.

MADS-box transcription factors determine the duration of temporary winter dormancy in closely related evergreen and deciduous Iris spp

Winter dormancy (WD) is a crucial strategy for plants coping with potentially deadly environments. In recent decades, this process has been extensively studied in economically important perennial eudicots due to changing climate. However, in evergreen monocots with no chilling requirements, dormancy processes are so far a mystery. In this study, we compared the WD process in closely related evergreen (Iris japonica) and deciduous (I. tectorum) iris species across crucial developmental time points. Both iris species exhibit a 'temporary' WD process with distinct durations, and could easily resume growth under warm conditions. To decipher transcriptional changes, full-length sequencing for evergreen iris and short read RNA sequencing for deciduous iris were applied to generate respective reference transcriptomes. Combining results from a multipronged approach, SHORT VEGETATIVE PHASE and FRUITFULL (FUL) from MADS-box was associated with a dormancy- and a growth-related module, respectively. They were co-expressed with genes involved in phytohormone signaling, carbohydrate metabolism, and environmental adaptation. Also, gene expression patterns and physiological changes in the above pathways highlighted potential abscisic acid and jasmonic acid antagonism in coordinating growth and stress responses, whereas differences in carbohydrate metabolism and reactive oxygen species scavenging might lead to species-specific WD durations. Moreover, a detailed analysis of MIKCCMADS-box in irises revealed common features described in eudicots as well as possible new roles for monocots during temporary WD, such as FLOWERING LOCUS C and FUL. In essence, our results not only provide a portrait of temporary WD in perennial monocots but also offer new insights into the regulatory mechanism underlying WD in plants.

Sharing taxonomic expertise between natural history collections using image recognition

Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.

Harnessing Large-Scale Herbarium Image Datasets Through Representation Learning

The mobilization of large-scale datasets of specimen images and metadata through herbarium digitization provide a rich environment for the application and development of machine learning techniques. However, limited access to computational resources and uneven progress in digitization, especially for small herbaria, still present barriers to the wide adoption of these new technologies. Using deep learning to extract representations of herbarium specimens useful for a wide variety of applications, so-called "representation learning," could help remove these barriers. Despite its recent popularity for camera trap and natural world images, representation learning is not yet as popular for herbarium specimen images. We investigated the potential of representation learning with specimen images by building three neural networks using a publicly available dataset of over 2 million specimen images spanning multiple continents and institutions. We compared the extracted representations and tested their performance in application tasks relevant to research carried out with herbarium specimens. We found a triplet network, a type of neural network that learns distances between images, produced representations that transferred the best across all applications investigated. Our results demonstrate that it is possible to learn representations of specimen images useful in different applications, and we identify some further steps that we believe are necessary for representation learning to harness the rich information held in the worlds' herbaria.

Coping with eccentricities of natural history collection data. A commentary on: 'Comparing fruiting phenology across two historical datasets: Thoreau's observations and herbarium specimens'

This article comments on: Tara K. Miller1, Amanda S. Gallinat, Linnea C. Smith and Richard B. Primack, Comparing fruiting phenology across two historical datasets: Thoreau’s observations and herbarium specimens, Annals of Botany, Volume 128, Issue 2, 23 July 2021, Pages 159–170, 10.1093/aob/mcab019

Biodiversity at the global scale: the synthesis continues

Traditionally, the generation and use of biodiversity data and their associated specimen objects have been primarily the purview of individuals and small research groups. While deposition of data and specimens in herbaria and other repositories has long been the norm, throughout most of their history, these resources have been accessible only to a small community of specialists. Through recent concerted efforts, primarily at the level of national and international governmental agencies over the last two decades, the pace of biodiversity data accumulation has accelerated, and a wider array of biodiversity scientists has gained access to this massive accumulation of resources, applying them to an ever-widening compass of research pursuits. We review how these new resources and increasing access to them are affecting the landscape of biodiversity research in plants today, focusing on new applications across evolution, ecology, and other fields that have been enabled specifically by the availability of these data and the global scope that was previously beyond the reach of individual investigators. We give an overview of recent advances organized along three lines: broad-scale analyses of distributional data and spatial information, phylogenetic research circumscribing large clades with comprehensive taxon sampling, and data sets derived from improved accessibility of biodiversity literature. We also review synergies between large data resources and more traditional data collection paradigms, describe shortfalls and how to overcome them, and reflect on the future of plant biodiversity analyses in light of increasing linkages between data types and scientists in our field.

Botanical Monography in the Anthropocene

Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs - comprehensive systematic treatments of a family or genus - have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity.

Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species

Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.

How FAIR are plant sciences in the twenty-first century? The pressing need for reproducibility in plant ecology and evolution

The need for open, reproducible science is of growing concern in the twenty-first century, with multiple initiatives like the widely supported FAIR principles advocating for data to be Findable, Accessible, Interoperable and Reusable. Plant ecological and evolutionary studies are not exempt from the need to ensure that the data upon which their findings are based are accessible and allow for replication in accordance with the FAIR principles. However, it is common that the collection and curation of herbarium specimens, a foundational aspect of studies involving plants, is neglected by authors. Without publicly available specimens, huge numbers of studies that rely on the field identification of plants are fundamentally not reproducible. We argue that the collection and public availability of herbarium specimens is not only good botanical practice but is also fundamental in ensuring that plant ecological and evolutionary studies are replicable, and thus scientifically sound. Data repositories that adhere to the FAIR principles must make sure that the original data are traceable to and re-examinable at their empirical source. In order to secure replicability, and adherence to the FAIR principles, substantial changes need to be brought about to restore the practice of collecting and curating specimens, to educate students of their importance, and to properly fund the herbaria which house them.

The role of digital herbarium collections in the taxonomic revision of complex plant families: Salicaceae sensu stricto

The importance of digitisation and digital resources in botanical research is underlined. Advantages and disadvantages of the use of digital herbaria in taxonomic research in Salicaceae sensu stricto are discussed and some suggestions on possible improvements are made.

Distribution of Ipomoea violacea (Convolvulaceae): patterns, gaps and reports for its occurrence in Brazil and West Tropical Africa

Abstract In 2015 a chance discovery of the beach moon flower in coastal Brazil led to an investigation of the global occurrence, distribution, and abundance of this pantropical littoral plant species. We here document new distribution records for coastal Brazil and West Tropical Africa; postulate a human-mediated long-distance dispersal for this species from the Indo-Pacific to the Atlantic, followed by local distribution via ocean currents; and provide historical context on the name confusion with other species. We also point out the risks inherent in using specimen information available on the internet without adequate verification for the identity of the specimens as a necessary first step.

Quantifying Tropical Plant Diversity Requires an Integrated Technological Approach

Tropical biomes are the most diverse plant communities on Earth, and quantifying this diversity at large spatial scales is vital for many purposes. As macroecological approaches proliferate, the taxonomic uncertainties in species occurrence data are easily neglected and can lead to spurious findings in downstream analyses. Here, we argue that technological approaches offer potential solutions, but there is no single silver bullet to resolve uncertainty in plant biodiversity quantification. Instead, we propose the use of artificial intelligence (AI) approaches to build a data-driven framework that integrates several data sources - including spectroscopy, DNA sequences, image recognition, and morphological data. Such a framework would provide a foundation for improving species identification in macroecological analyses while simultaneously improving the taxonomic process of species delimitation.

From leaf to label: A robust automated workflow for stomata detection

Plant leaf stomata are the gatekeepers of the atmosphere-plant interface and are essential building blocks of land surface models as they control transpiration and photosynthesis. Although more stomatal trait data are needed to significantly reduce the error in these model predictions, recording these traits is time-consuming, and no standardized protocol is currently available. Some attempts were made to automate stomatal detection from photomicrographs; however, these approaches have the disadvantage of using classic image processing or targeting a narrow taxonomic entity which makes these technologies less robust and generalizable to other plant species. We propose an easy-to-use and adaptable workflow from leaf to label. A methodology for automatic stomata detection was developed using deep neural networks according to the state of the art and its applicability demonstrated across the phylogeny of the angiosperms.We used a patch-based approach for training/tuning three different deep learning architectures. For training, we used 431 micrographs taken from leaf prints made according to the nail polish method from herbarium specimens of 19 species. The best-performing architecture was tested on 595 images of 16 additional species spread across the angiosperm phylogeny.The nail polish method was successfully applied in 78% of the species sampled here. The VGG19 architecture slightly outperformed the basic shallow and deep architectures, with a confidence threshold equal to 0.7 resulting in an optimal trade-off between precision and recall. Applying this threshold, the VGG19 architecture obtained an average F-score of 0.87, 0.89, and 0.67 on the training, validation, and unseen test set, respectively. The average accuracy was very high (94%) for computed stomatal counts on unseen images of species used for training.The leaf-to-label pipeline is an easy-to-use workflow for researchers of different areas of expertise interested in detecting stomata more efficiently. The described methodology was based on multiple species and well-established methods so that it can serve as a reference for future work.

New Guinea has the world's richest island flora

New Guinea is the world's largest tropical island and has fascinated naturalists for centuries^1,2. Home to some of the best-preserved ecosystems on the planet³ and to intact ecological gradients-from mangroves to tropical alpine grasslands-that are unmatched in the Asia-Pacific region^4,5, it is a globally recognized centre of biological and cultural diversity^6,7. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families-suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the 'Last Unknown'⁸.

Plant diversity in Yunnan: Current status and future directions

Yunnan, located in southwestern China, harbors more than 19,000 higher plants, which represents the highest plant diversity in the country. However, plant diversity in Yunnan faces enormous threats today, including habitat destruction and fragmentation, environmental pollution, and over-exploitation of natural resources. Despite recent efforts to protect biodiversity, there are still thousands of threatened species, some of which have become extinct. We analyzed available data to gain a greater understanding of plant diversity and the status of plant conservation in Yunnan. We found that southern, southeastern, and northwestern Yunnan are hotspots of total species, endemic species, specimens, new species and threatened species, whereas southeastern Yunnan is a hotspot for plant species with extremely small populations. Moreover, we found that there are still conservation gaps and poorly protected areas in central, eastern, and northeastern Yunnan. We conclude that conservation of plant diversity in Yunnan requires modern field investigation, systematic research, the development of comprehensive databases, and government support. We recommend that conservationists pay more attention to building and improving functional protection systems and popularizing science.

Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae)

Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.

Microscopic Authentication of Commercial Herbal Products in the Globalized Market: Potential and Limitations

Herbal products are marketed and used around the globe for their claimed or expected health benefits, but their increasing demand has resulted in a proportionally increase of their accidental contamination or intentional adulteration, as already confirmed with DNA-based methods. Microscopy is a traditional pharmacopoeial method used for plant identification and we systematically searched for peer-reviewed publications to document its potential and limitations to authenticate herbal medicines and food supplements commercially available on the global market. The overall authenticity of 508 microscopically authenticated herbal products, sold in 13 countries, was 59%, while the rest of 41% were found to be adulterated. This problem was extending over all continents. At the national level, there were conspicuous differences, even between neighboring countries. These microscopically authenticated commercial herbal products confirm that different magnifying instruments can be used to authenticate crude or processed herbal products traded in the global marketplace. The reviewed publications report the successful use of different magnifying instruments, single or in combinations with a second one, with or without a chemical or DNA-based technique. Microscopy is therefore a rapid and cost-efficient method, and can cope with mixtures and impurities. However, it has limited applicability for highly processed samples. Microscopic authentication of commercial herbal products will therefore contribute to raise public awareness for the extent of adulteration and the need to safeguard consumer safety against the challenges of globalization.

Using computer vision on herbarium specimen images to discriminate among closely related horsetails (Equisetum)

PREMISE

Equisetum is a distinctive vascular plant genus with 15 extant species worldwide. Species identification is complicated by morphological plasticity and frequent hybridization events, leading to a disproportionately high number of misidentified specimens. These may be correctly identified by applying appropriate computer vision tools.

METHODS

We hypothesize that aerial stem nodes can provide enough information to distinguish among Equisetum hyemale, E. laevigatum, and E . ×ferrissii, the latter being a hybrid between the other two. An object detector was trained to find nodes on a given image and to distinguish E. hyemale nodes from those of E. laevigatum. A classifier then took statistics from the detection results and classified the given image into one of the three taxa. Both detector and classifier were trained and tested on expert manually annotated images.

RESULTS

In our exploratory test set of 30 images, our detector/classifier combination identified all 10 E. laevigatum images correctly, as well as nine out of 10 E. hyemale images, and eight out of 10 E. ×ferrissii images, for a 90% classification accuracy.

DISCUSSION

Our results support the notion that computer vision may help with the identification of herbarium specimens once enough manual annotations become available.

Identifying factors that boost species discoveries of global reptiles

Most species remain unknown to science and might go extinct before we recognize their existence. Although specimens belonging to many of these unknown taxa may already be housed in scientific collections, they can remain ‘shelved’ for years bearing the wrong name or without a formal name. We investigate factors underlying variation in time lag between collection and description dates for 2356 reptile species described worldwide between 1992 and 2017. We modelled the time to description using biological and sociological variables in a time-to-event analysis. Time lag between collection and description varied from zero to 155 years (median = 5). More than one-quarter of species involved specimens ‘shelved’ for 12 years or more. The time lag was shorter when the collector of the holotype – specimen serving as the name-bearer of the species – was an author of the description, while taxonomic revisions uncovered species with longer time lags. Unknown species collected by non-taxonomists and ‘shelved’ in scientific collections remained incorrectly identified for a much longer time. Taxonomic revisions are crucial to reverse this trend and improve benefits of the collecting performed by non-taxonomists. Our findings reveal the kinds of preserved reptile specimens that most likely represent unknown species in scientific collections.

Molecular identification of Mazama species (Cervidae: Artiodactyla) from natural history collections

Natural history museum collections constitute an invaluable patrimony of biological diversity for analysing the taxa distribution and evolution. However, it is very common to discover taxonomic misidentification in museum collections based on incorrect data. The aim of this research was to identify brocket deer species (Mazama genus) using molecular markers. We collected 199 samples, performed DNA extraction and species identification using a specific mitochondrial marker based on a fragment of cytochrome b (Cytb) for Neotropical deer. We achieved the amplification and sequencing of 77 specimens and verified that 26% of the skulls were wrongly identified. Moreover, in the museum collections 57% of the specimens were only identified as Mazama sp, and we were able to identify them by molecular methods to the species level. Our findings clearly demonstrate the importance of integrating molecular analyses to identify Mazama species, since using only external morphology can result in a high probability of errors. We recommend the selection of non-convergent morphological characters, which together with the use of DNA collected from museum specimens should contribute to more accurate taxonomic identifications.

A foundation monograph of Ipomoea (Convolvulaceae) in the New World

A monograph of the 425 New World species of Ipomoea is presented. All 425 species are described and information is provided on their ecology and distribution, with citations from all countries from which they are reported. Notes are provided on salient characteristics and taxonomic issues related to individual species. A full synonymy is provided and 272 names are lectotypified. An extensive introduction discusses the delimitation and history of Ipomoea arguing that a broad generic concept is the only rational solution in the light of recent phylogenetic advances. Although no formal infrageneric classification is proposed, attention is drawn to the major clades of the genus and several morphologically well-defined clades are discussed including those traditionally treated under the names Arborescens, Batatas, Pharbitis, Calonyction and Quamoclit, sometimes as distinct genera, subgenera, sections or series. Identification keys are provided on a regional basis including multi-entry keys for the main continental blocks. Six species are described as new, Ipomoea nivea J.R.I. Wood & Scotland from Peru, I. apodiensis J.R.I. Wood & Scotland from Brazil, I. calcicola J.R.I. Wood & Scotland, I. pochutlensis J.R.I. Wood & Scotland, I. zacatecana J.R.I. Wood & Scotland and I. ramulosa J.R.I. Wood & Scotland from Mexico, while var. australis of I. cordatotriloba is raised to specific status as I. australis (O'Donell) J.R.I. Wood & P. Muñoz. New subspecies for I. nitida (subsp. krapovickasii J.R.I. Wood & Scotland) and for I. chenopodiifolia (subsp. bellator J.R.I. Wood & Scotland) are described. The status of previously recognized species and varieties is changed so the following new subspecies are recognized: I. amnicola subsp. chiliantha (Hallier f.) J.R.I. Wood & Scotland, I. chenopodiifolia subsp. signata (House) J.R.I. Wood & Scotland, I. orizabensis subsp. collina (House) J.R.I. Wood & Scotland, I. orizabensis subsp. austromexicana (J.A. McDonald) J.R.I. Wood & Scotland, I. orizabensis subsp. novogaliciana (J.A. McDonald) J.R.I. Wood & Scotland, I. setosa subsp. pavonii (Hallier f.) J.R.I. Wood & Scotland, I. setosa subsp. melanotricha (Brandegee) J.R.I. Wood & Scotland, I. setosa subsp. sepacuitensis (Donn. Sm.) J.R.I. Wood & Scotland, I. ternifolia subsp. leptotoma (Torr.) J.R.I. Wood & Scotland. Ipomoea angustata and I. subincana are treated as var. angustata (Brandegee) J.R.I. Wood & Scotland and var. subincana (Choisy) J.R.I. Wood & Scotland of I. barbatisepala and I. brasiliana respectively. Attention is drawn to a number of hitherto poorly recognized phenomena in the genus including a very large radiation centred on the Parana region of South America and another on the Caribbean Islands, a strong trend towards an amphitropical distribution in the New World, the existence of a relatively large number of species with a pantropical distribution and of many species in different clades with storage roots, most of which have never been evaluated for economic purposes. The treatment is illustrated with over 200 figures composed of line drawings and photographs.

Vascular plants of Victoria Island (Northwest Territories and Nunavut, Canada): a specimen-based study of an Arctic flora

Victoria Island in Canada's western Arctic is the eighth largest island in the world and the second largest in Canada. Here, we report the results of a floristic study of vascular plant diversity of Victoria Island. The study is based on a specimen-based dataset comprising 7031 unique collections from the island, including some 2870 new collections gathered between 2008 and 2019 by the authors and nearly 1000 specimens variously gathered by N. Polunin (in 1947), M. Oldenburg (1940s-1950s) and S. Edlund (1980s) that, until recently, were part of the unprocessed backlog of the National Herbarium of Canada and unavailable to researchers. Results are presented in an annotated checklist, including keys and distribution maps for all taxa, citation of specimens, comments on taxonomy, distribution and the history of documentation of taxa across the island, and photographs for a subset of taxa. The vascular plant flora of Victoria Island comprises 38 families, 108 genera, 272 species, and 17 additional taxa. Of the 289 taxa known on the island, 237 are recorded from the Northwest Territories portion of the island and 277 from the Nunavut part. Thirty-nine taxa are known on the island from a single collection, seven from two collections and three from three collections. Twenty-one taxa in eight families are newly recorded for the flora of Victoria Island: Artemisia tilesii, Senecio lugens, Taraxacum scopulorum (Asteraceae); Crucihimalaya bursifolia, Draba fladnizensis, D. juvenilis, D. pilosa, D. simmonsii (Brassicaceae); Carex bigelowii subsp. bigelowii, Eriophorum russeolum subsp. albidum (Cyperaceae); Anthoxanthum monticola subsp. monticola, Bromus pumpellianus, Deschampsia cespitosa subsp. cespitosa, D. sukatschewii, Festuca rubra subsp. rubra, Lolium perenne, Poa pratensis subsp. pratensis (Poaceae); Stuckenia filiformis (Potamogetonaceae); Potentilla × prostrata (Rosaceae); Galium aparine (Rubiaceae); and Salix ovalifolia var. ovalifolia (Salicaceae). Eight of these are new to the flora of the Canadian Arctic Archipelago: Senecio lugens, Draba juvenilis, D. pilosa, Anthoxanthum monticola subsp. monticola, Bromus pumpellianus, Deschampsia cespitosa subsp. cespitosa, Poa pratensis subsp. pratensis and Salix ovalifolia var. ovalifolia. One of these, Galium aparine, is newly recorded for the flora of Nunavut. Four first records for Victoria Island are introduced plants discovered in Cambridge Bay in 2017: three grasses (Festuca rubra subsp. rubra, Lolium perenne, and Poa pratensis subsp. pratensis) and Galium aparine. One taxon, Juncus arcticus subsp. arcticus, is newly recorded from the Northwest Territories. Of the general areas on Victoria Island that have been botanically explored the most, the greatest diversity of vascular plants is recorded in Ulukhaktok (194 taxa) and the next most diverse area is Cambridge Bay (183 taxa). The floristic data presented here represent a new baseline on which continued exploration of the vascular flora of Victoria Island - particularly the numerous areas of the island that remain unexplored or poorly explored botanically - will build.

Drivers of habitat partitioning among three Quercus species along a hydrologic gradient

A critical process that allows multiple, similar species to coexist in an ecological community is their ability to partition local habitat gradients. The mechanisms that underlie this separation at local scales may include niche differences associated with their biogeographic history, differences in ecological function associated with the degree of shared ancestry and trait-based performance differences, which may be related to spatial or temporal variation in habitat. In this study we measured traits related to water-use, growth and stress tolerance in mature trees and seedlings of three oak species (Quercus alba L., Quercus falcata Michx. and Quercus palustris Münchh). which co-occur in temperate forests across the eastern USA but tend to be found in contrasting hydrologic environments. The three species showed significant differences in their local distributions along a hydrologic gradient. We tested three possible mechanisms that influence their contrasting local environmental distributions and promote their long-term co-existence: (i) differences in their climatic distributions across a broad geographic range, (ii) differences in functional traits related to water use, drought tolerance and growth and (iii) contrasting responses to temporal variation in water availability. We identified key differences between the species in both their range-wide climatic distributions (especially aridity index and mean annual temperature) and physiological traits in mature trees and seedlings, including daily water loss, hydraulic conductance, stress responses, growth rate and biomass allocation. Taken together, these differences explain the habitat partitioning that allows three closely related species to co-occur locally.