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Workflows for dealing with new names coming with content or backbone data for WFO. TEN, Taxonomic Expert Network.
Source publication
It is time to synthesize the knowledge that has been generated through more than 260 years of botanical exploration, taxonomic and, more recently, phylogenetic research throughout the world. The adoption of an updated Global Strategy for Plant Conservation (GSPC) in 2011 provided the essential impetus for the development of the World Flora Online (...
Contexts in source publication
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... is already harmonized with the Botanical Database of Southern Africa (BODATSA; SANBI, 2016). The Euro+Med PlantBase (Euro+Med, 2006-) covers Europe, the Mediterranean region and the Caucasus, which is a biogeographically consistent region. It includes ca. ...
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... the content treatment with those in the Taxonomic Backbone. Ideally, this will be done by the contributor, so that the content comes in with WFOIDs already assigned. The name matching otherwise presents several challenges, which have to be resolved in the staging area -inter alia the treatment of homonyms and the incorporation of new names (see Fig. ...
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... two-step process can be repeated if additional data are added to the Caryophyllales database. The second step will also be used for data provision from other databases maintained using the EDIT Platform, e.g., Flora de la República de Cuba ( Greuter & al. 1998-) and Euro+ Med PlantBase (Euro+Med 2006-). ...
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... is already harmonized with the Botanical Database of Southern Africa (BODATSA; SANBI, 2016). The Euro+Med PlantBase (Euro+Med, 2006-) covers Europe, the Mediterranean region and the Caucasus, which is a biogeographically consistent region. It includes ca. ...
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... the content treatment with those in the Taxonomic Backbone. Ideally, this will be done by the contributor, so that the content comes in with WFOIDs already assigned. The name matching otherwise presents several challenges, which have to be resolved in the staging area -inter alia the treatment of homonyms and the incorporation of new names (see Fig. ...
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... two-step process can be repeated if additional data are added to the Caryophyllales database. The second step will also be used for data provision from other databases maintained using the EDIT Platform, e.g., Flora de la República de Cuba ( Greuter & al. 1998-) and Euro+ Med PlantBase (Euro+Med 2006-). ...
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At present, there are 115 botanical gardens and arboreta of various departmental affiliations operating in Russia, which are united in a single network ‘The Council of Botanical Gardens of Russia’. The biodiversity conservation in situ and ex situ has become one of the key mainstreams and a third of the national flora has been preserved in living c...
Citations
... These specimens were then dried, pressed, and finally identified using the Flora of Ethiopia and Eritrea in the Herbarium of the University of Gondar. The recent scientific name changes for plant species were verified using The World Flora Online (Borsch et al. 2020). ...
Ethiopia has gained recognition in Africa for its biological diversity. Sadly, the destructive actions of humans for centuries have resulted in fragmented forests, causing them to be scattered in patches. The Central Gondar Zone, located in northwestern Ethiopia, is known for its diverse forest patches that are crucial for conservation. The objective of this work was to evaluate the conservation status of a sample of these forest patches distributed across government managed and church managed forests. Data on woody species were collected, systematically, in 520 nested plots (20 m × 20 m) across 65 transects distributed in the 10 sampled forest patches. A total of 146 woody plant species (63 families, 6 endemics) were recorded, with Fabaceae being the most dominant (16.7%).The inverted J-shape pattern of trees in the forest patches suggests healthy conditions with active regeneration and recruitment of forest species. Comparative analyses of the forest patches revealed significant differences in species richness, similarity, structure, and regeneration among the three growth forms. Targeted conservation strategies should prioritize species with low IVI, threatened endemics, and poor regeneration, while engaging local communities and religious institutions as key stakeholders to enhance ecological integrity and sustainable management of these forest patches.
... Manniophyton fulvum (Euphorbiaceae) was by far the most abundant species, accounting for nearly one-third of the lianas at our study site. It is a geographically widespread species (Borsch et al. 2020) and found to be the most dominant species in two other studies in the Democratic Republic of Congo (DRC; Ewango et al. 2015;Mumbanza et al. 2020). Although these two studies considered this species to be a habitat generalist, we found that it was associated with open-canopy and short-stature forests. ...
Lianas are important components of tropical forest diversity and dynamics, yet little is known about the drivers of their community structure and composition. Combining extensive field and LiDAR data, we investigated the influence of local topography, forest structure, and tree composition on liana community structure, and their floristic and functional composition, in a moist forest in northern Republic of Congo. We inventoried all lianas ≥ 1 cm in diameter in 144 20 × 20‐m quadrats located in four 9‐ha permanent plots, where trees and giant herbs were inventoried. We characterized the functional strategies of selected representatives of the main liana taxa using a set of resource‐use leaf and wood traits. Finally, we used complementary statistical analyses, including multivariate and randomization approaches, to test whether forest structure, topography, and tree composition influence the structure, floristic composition, and functional composition of liana communities. The structure of liana communities was strongly shaped by local forest structure, with higher abundances and total basal areas in relatively open‐canopy forests, where lianas competed with giant herbs. Liana floristic composition exhibited a weak spatial structure over the study site but was marginally influenced by the local forest structure and topography. Only forest structure had a weak but significant effect on liana functional composition, with more conservative strategies—higher stem tissue density and lower PO4 leaf concentration and SLA values—in tall and dense forests. Finally, we found evidence of host specificity with significant attraction/repulsion for 19% of the tested liana and tree species associations, suggesting that the unexplained floristic variation may be partly attributed to these host‐species‐specific associations, although the underlying mechanisms behind remain elusive. Overall, our findings demonstrate that liana communities' structure can be much better predicted than their composition, calling for a better understanding of the implications of the large functional diversity observed in liana communities.
... Identifcation was performed using the fora of Ethiopia and Eritrea, with support from experts at the University of Gondar. Te recent scientifc name change for a plant species will be verifed using the World Flora Online [32]. Additionally, the endemic status and conservation assessments of the identifed plant species were cross-referenced and validated against the comprehensive works of Vivero, et al. [33], Awas [34], Dagne [35], Ayalew, et al. [36], and the IUCN Red List of Treatened Species online database (https:// www.iucnredlist.org/), ...
Identifying plant communities has been a central aspect of vegetation science for centuries, with emphasis on the distribution, composition, and classification of plant communities. This study aimed to assess how environmental variables influence plant community formation and vegetation dynamics in northwest Ethiopia. A systematic random sampling technique was employed to gather vegetation data from 50 plots, each measuring 20 × 20 m, arranged at 100-m intervals along seven transects. In each plot, the encountered species and their percentage cover-abundance were recorded, which were subsequently transformed into a modified Braun–Blanquet scale. Additionally, composite soil samples collected from 15 × 15 cm subplots were analyzed for 20 soil parameters. The Shannon–Wiener index was used to measure species diversity. Hierarchical clustering and ordination analyses (DCA and RDA) were conducted on the floristic and environmental data, respectively, using R software. A total of 69 woody plant species from 64 genera and 44 families were recorded at altitudes ranging from 2485 to 2747 m above sea level. The Shannon–Wiener diversity index (H) was 3.74, and the evenness index (J) was 0.90. These high species diversity indices showed ecosystem health, stability, reflecting effective species interactions, and resource utilization. Among 6 terrain variables and 14 edaphic factors, 12 of these environmental factors (altitude, slope, aspect, cutting, silt, pH, sand, organic carbon, organic matter, total nitrogen, phosphorus, and calcium) were found significantly to (p≤0.05) explain the variation in species composition and community formation of four plant communities in the study area. The observed patterns of community formation underscore the need to design different conservation measures tailored to the specific environmental conditions at different elevations.
... This broader classification has been widely adopted in botanical literature, including floras, atlases, species descriptions, and research studies globally (Jongkind, 2004;Perveen & Qaiser, 2009;Wilkie, 2009;LaFrankie, 2010;Xie & al., 2014;Cardoso & al., 2017;Christenhusz & al., 2017;Ulloa Ulloa & al., 2017;Figueiredo & al., 2020;Dang & al., 2022;Walker & Eggli, 2023;Hanes & al., 2024). Moreover, it has been standardised in major global biodiversity databases (e.g., Borsch & al., 2020;Govaerts & al., 2021) and referenced in textbooks on plant systematics (Simpson, 2010;Judd & al., 2015), ensuring familiarity among students and researchers alike. Therefore, reverting to an alternative concept could risk reintroducing confusion and undermining the stability achieved over the past two decades. ...
Malvales is a diverse order of flowering plants, economically and ecologically relevant, and it is known for its broad morphological variability. Recent phylogenomic studies have revealed a complex evolutionary history for the order, including localised phylogenetic discordances among nuclear loci. However, since the late 1990s, Malvales classification has largely been neglected. This study aims to address this gap by revisiting the classification of Malvales, with a focus on its largest family, Malvaceae. By integrating phylogenomic and morphological datasets, our primary goals are to provide an updated phylogeny for the order and to map key traits supporting a revised suprageneric classification, while accounting for gene and species tree conflicts. Our molecular dataset included 194 genera and 309 nuclear genes, obtained through target sequence capture using Angiosperms353 probes. This dataset covers approximately half of the known genera in the order, representing all families and subfamilies, as well as nearly all tribes, and all subtribes. A coalescent approach utilising nuclear gene trees was used to infer phylogenetic relationships. A morphological matrix with 50 characters relevant for suprageneric classification was compiled, and character‐state distributions for selected traits were mapped against the phylogenetic tree to identify and discuss diagnostic features for clades. Phylogenetic relationships and the monophyly of most groups aligned closely with previous studies. Morphological traits that define key clades varied significantly across Malvales, with differences observed in growth habit, leaf structure, pollen type, floral features, and fruit/seed morphology. In Malvaceae, we resolved uncertainties in the early Malvoideae lineages, and we describe a new tribe, Pentaplareae tr. nov., which clarifies the taxonomic placement of a previously uncertain genus. Additionally, we propose the recognition of a new subfamily, Matisioideae subfam. nov., elevated from its former status as a tribe, and positioned as the sister group to Malvoideae. This study highlights how taxonomic frameworks can be refined even in the face of conflicting phylogenomic data, demonstrating the importance of integrating molecular and morphological evidence in revising classifications.
... During July 2021 and 2022, within each of the 30 m × 30 m quadrats we recorded the presence and projected cover abundance (%) of all vascular understory (height ≤ 1.3 m) species, including woody plants, herbaceous plants, and ferns. Nomenclature follows 'World Flora Online' (Borsch et al., 2020). We classified the recorded species (Table S1) using the definition of 'specialist forest species that can be found mainly in the closed-canopy forest' (i.e., category 1.1 in Heinken et al., 2022). ...
Protected areas are supposed to mitigate the loss of diversity caused by human activities in forests. However, different management strategies applied across protected areas affect diversity in various ways. This study compares the taxonomic, functional, and phylogenetic diversity, and the species composition of understory plants, between sustainably managed forests and strictly protected forests. From temperate beech (Fagus sylvatica L.) forests within the Foreste Casentinesi National Park (Northern Apennine, Italy), we selected 28 quadrats in strictly protected and managed zones. In each quadrat, we recorded the cover abundance of vascular plant species and measured two functional traits (specific leaf area and clonal lateral spread) on the most abundant understory species. We used generalized linear models to test for differences in taxonomic (species richness and the percentage of forest specialist species), functional (functional richness for single and multiple traits), and phylogenetic diversity (mean pairwise distance) between protection zones. Lastly, we evaluated differences in species composition between protection zones using non-metric multidimensional scaling, supported by PER-MANOVA and indicator species analyses. Species richness and phylogenetic diversity did not differ between strictly protected and managed zones. Strictly protected forests had a significantly higher percentage of forest specialist species and functional richness of clonal lateral spread than forests allowing sustainable logging. Species composition was significantly different between strictly protected and managed forests; the most important indicator species detected within managed zones were Sanicula europaea and Aremonia agrimonoides, while Veronica montana, Oxalis acetosella, and Salvia glutinosa were indicator species within strictly protected forests. The difference between strictly protected forests and forests managed with sustainable logging is reflected in the proportion of forest specialist species and the diversity of belowground space occupation and resource acquisition strategies. Instead, species richness and phylogenetic diversity do not discriminate between the two protection zones. We suggest incorporating specialist species, functional and compositional diversity metrics into the evaluation framework to guide future conservation and management practices.
... Where multiple records existed for a single species, we computed the species median trait value. We validated each record name against World Flora Online (WFO), a comprehensive list of plant species 31 with the R package 'WorldFlora' . TRY species names that did not match WFO were corrected. ...
We present a dataset of plant hydraulic and structural traits imputed for 55,779 tree species based on TRY plant trait dataset observations and phylogenetic relationships. We collected plant trait values for maximum stomatal conductance (gsMAX), xylem pressure at 12%, 50%, and 88% conductance loss (P12, P50, P88), maximum observed rooting depth (rdMAX), photosynthetic Water Use Efficiency (WUE), maximum plant height (height), Specific Leaf Area (SLA), and leaf Nitrogen content (LeafN). We demonstrated that each of these traits exhibited remarkably large phylogenetic signals across all land plants. Based on the strength of this signal we then developed random forest (RF) models trained on TRY trait data to impute the traits of previously unstudied tree species using Phylogenetic Eigenvector Maps. We quantified imputed trait uncertainty by fitting RF model test dataset residuals to skew exponential power distributions accounting for heteroscedasticity, demonstrating encouraging lack of biases in the imputed dataset. The resulting dataset of imputed trait values can support global analyses of plant trait variations and species-level parameterization of earth systems models.
... For example, the Global Root Traits (GRooT) (10) provides a complete database specializing in the characteristics of the plant's roots, while the Global Naturalized Alien Flora (GloNAF) provides data on plant species that were introduced to regions outside their native range (11). The Global tree portal search offers a searchable database of tree species by scientific name and country (12), while World Flora Online (WFO) provides global taxonomic data, including images of species (13). As a final example Global Inventory of Floras and Traits (GIFT), adds a geographical component, allowing users to explore plant species and traits through a map-based interface (14). ...
DATABASE URL: https://forestforward.udl.cat
Mitigating the effects of environmental exploitation on forests requires robust data analysis tools to inform sustainable management strategies and enhance ecosystem resilience. Access to extensive, integrated plant biodiversity data, spanning decades, is essential for this purpose. However, such data is often fragmented across diverse datasets with varying standards, posing two key challenges: first, integrating these datasets into a unified, well-structured data warehouse, and second, handling the vast volume of data using big data technologies to analyze and monitor the temporal evolution of ecosystems. To address these challenges, we developed and used an ETL (Extract, Transform, Load) protocol that curated and integrates 4,482 forestry datasets from around the world, dating back to the 18th century, into a 100GB data warehouse containing over 172 million records sourced from the GBIF (Global Biodiversity Information Facility) repository. We implemented Python scripts and a NoSQL MongoDB database to streamline and automate the ETL process, using the data warehouse to create the ForestForward web platform. ForestForward is a free, user-friendly application developed using the Django framework, which enables users to consult, download, and visualize the curated data. The platform allows users to explore data layers by year and observe the temporal evolution of ecosystems through visual representations.
... The information contained in biological archives, such as herbaria, comprises a knowledge base that is fundamental to research related to biodiversity, conservation, and restoration. A collaborative research infrastructure is necessary that provides wide and free access to the information in these collections, which can be done by digitizing specimens and the respective associated data (Borsch et al. 2020), as well as by establishing governance strategies and actions for validated species (Garnett et al. 2020). Currently, with the public availability of digital information and images of specimens in biological collections, combined with fast access to biodiversity data provided by information technology devices, machine knowledge, and the adequate use of artificial intelligence, significant advances have been made, especially in the last two decades. ...
The program “REFLORA - Brazilian Plants: Historic Rescue and Virtual Herbarium for Knowledge and Conservation of the Brazilian Flora” was established by the National Council for Scientific and Technological Development (CNPq) in 2010, involved numerous participants at the international, federal, state, and private company levels, and included approximately 24.5 million reais in investments over a period of 5 years. It had the objective of rescuing and making available images and information about herbarium specimens of Brazilian plants deposited in foreign collections. Under the auspices of this program, research projects were financed with consumable, durable, and grant resources that covered aspects of taxonomy, evolution and phytogeographic adaptation, molecular biology, conservation, use, and historical details of expeditions and their relationship to the colonization of Brazil. Additionally, using subsidies from the REFLORA Program, the REFLORA Virtual Herbarium was created allowing the program to fulfill its initial objectives of receiving 500 thousand images and repatriating data from the RBG-Kew and MNHN-Paris herbaria, as well as data and images from other national and foreign herbaria that were subsequently added. This article describes the historical context of creating and implementing the REFLORA Virtual Herbarium, which has become one of the most important tools for research and advancing knowledge about the biodiversity of plants and fungi, in addition to being fundamental to fulfill international goals and agreements assumed by Brazil, such as Flora of Brazil 2020.
... Numerous recent efforts have been directed toward compiling more than two centuries of taxonomic studies into comprehensive databases [21,39,46]. The focus has been on address ing taxonomic impediments, which refer to the lack of taxonomic information such as descrip [37] and cities with more than 1 million inhabitants (gray dots) and those with more than 10 million people, known as megacities (black dots) [38]. ...
... Numerous recent efforts have been directed toward compiling more than two centuries of taxonomic studies into comprehensive databases [21,39,46]. The focus has been on addressing taxonomic impediments, which refer to the lack of taxonomic information such as description, identification, recognition, and classification. ...
... For instance, online plant information is available for geographic areas, such as Australia, Tropical and Temperate Asia, Africa, Europe, Northern and Southern America, and the Pacific. In the future, databases of these regions will be consolidated into the World Flora Online platform [46], fostering the development of global research in diverse fields [43]. All these initiatives are now either complete or in progress mainly because a significant number of herbarium specimens are available online, owing to extensive digitization efforts worldwide [39]. ...
Cities are particularly vulnerable to climate change for their intrinsic characteristics. Imperviousness, heat islands, and pervasive pollution are common urban problems that challenge the current status quo in decision-making. As an alternative, Nature-based Solutions (NbS) arose from the need to tackle environmental issues through multifunctional solutions. Plant biodiversity is at the core of NbS, but such solutions are constrained by the limited knowledge of species benefits for cities, particularly in the biodiverse Global South. In this review, we stress the potential use of morphological characters from taxonomic studies as a shortcut to assess the ecosystem services of plant species. Species description and identification keys can be translated into ecosystem services to support the use of species not yet listed in cities. Bridging the potential for ecosystem service provision and morphological characters like life form, bark, leaf phenology and morphology, and reproductive morphology based on the comprehensive literature will allow decision-makers to widen their options to promote urban biodiversity. Building a platform requires summarizing plants’ ecosystem service knowledge and subsequently validating models’ predictive power. Still, this approach holds great potential to promote urban biodiversity for more resilient and enjoyable urban environments.
... and other sources with a set of content terms associated with those labels. 2. We also assembled some key corpi (e.g., names of known plant taxa from Kew Plants of the World Online [https:// powo.science.kew.org/], the World Flora Online plant list [Borsch et al., 2020], and the Integrated Taxonomic Information System [ITIS] database [https://www.itis. gov/]) to help with matching to key fields (e.g., dwc: scientificName). ...
Premise
One of the slowest steps in digitizing natural history collections is converting labels associated with specimens into a digital data record usable for collections management and research. Here, we address how herbarium specimen labels can be converted into digital data records via extraction into standardized Darwin Core fields.
Methods
We first showcase the development of a rule‐based approach and compare outcomes with a large language model–based approach, in particular ChatGPT4. We next quantified omission and commission error rates across target fields for a set of labels transcribed using optical character recognition (OCR) for both approaches. For example, we find that ChatGPT4 often creates field names that are not Darwin Core compliant while rule‐based approaches often have high commission error rates.
Results
Our results suggest that these approaches each have different strengths and limitations. We therefore developed an ensemble approach that leverages the strengths of each individual method and documented that ensembling strongly reduced overall information extraction errors.
Discussion
This work shows that an ensemble approach has particular value for creating high‐quality digital data records, even for complicated label content. While human validation is still needed to ensure the best possible quality, automated approaches can speed digitization of herbarium specimen labels and are likely to be broadly usable for all natural history collection types.
