Documented living plant collections distinguish botanic gardens from other green spaces and horticultural landscapes. With more than 3,500 collections worldwide, these institutions steward at least 105,634 species-around 30% of all land plant diversity-while fulfilling amenity, educational, scientific and conservation roles. However, twenty-first-century challenges demand a re-evaluation of how these collections are documented and managed. We argue that meeting these emerging needs requires higher standards of coordinated information management and innovation in data infrastructures across the global network. This Perspective critically examines data management practices of living collections supporting scientific research and conservation, from institutional to global levels. We identify the renewed demands on living collections, highlight exemplar global data infrastructures, define data challenges inherent to living collections and explore how current systems fall short in enabling a connected global system. Finally, we outline a vision for high-performance collections, fully integrated into a robust global data ecosystem.

Background and aims – The newly described species Arcytophyllum leymebambense sp. nov. (Rubiaceae) from the Amazonas department of northern Peru represents an isolated lineage within the monophyletic genus Arcytophyllum. This study aims to describe its distinctive morphological features and ecological context, assess its phylogenetic position, and discuss its implications for the diversification of the genus in the Andes. Material and methods – Morphological observations were conducted on herbarium specimens and field collections from the type locality. Phylogenetic analyses were performed using nuclear and plastid DNA sequences from the tribe Spermacoceae, with particular emphasis on Arcytophyllum. Key results – Arcytophyllum leymebambense sp. nov. is morphologically distinct from its congeners by its acuminate leaf and sepal apices, hirsute-lanuginose seeds, and the presence of protective hooks surrounding the ovary. It inhabits humid, high-elevation grasslands known as “Jalca,” where it coexists with a diverse assemblage of montane species. The species appears to be endemic to the region and is currently known from only three populations. Its restricted distribution, combined with potential threats such as overgrazing and fire, supports a preliminary conservation assessment as Critically Endangered (CR). Conclusion – The discovery of Arcytophyllum leymebambense sp. nov. highlights the underestimated diversity of Andean Rubiaceae and provides evidence that Andean species form a grade within the diversification of Arcytophyllum. This pattern suggests a historical northward expansion of the lineage into the high mountains of Panama and Costa Rica.

In phylogeographic studies, genetic distances between individuals are typically small: In the European endemic, declining medicinal plant Arnica montana L., range-wide biogeographic patterns so far remained obscure as sequence diversity in plastome marker regions is very low. While entire chloroplast genomes promise higher resolution, comparing them in great detail is a technical challenge, requiring high accuracy and repeatability in sequencing, assembly and annotation, automated across large sample sets. Using A. montana as our working example, we developed the PlastidPipeline, which consistently and repeatably provides structurally standardized and annotated, ready-to-analyze plastomes from short-read sequences. The PlastidPipeline combines well-tested standard software tools with own scripts, from data cleanup through plastome assembly, structural standardization, annotation, to quality control and raw read backmapping. Using publicly available read data of diverse provenance, we obtained plastid genomes for eight A. montana accessions across Europe, four further species of Arnica and three outgroup species. All A. montana plastomes formed a well-supported clade, split further into an Iberian and a Central/Northern European geographic group, which are, however, connected by patterns of potential heteroplasmy. Beyond demonstrating that pan-plastome phylogeography is both feasible and useful, we recommend the analysis of within-sample read variation, and improved standardization of newly reported plastomes.

Drymaria (Caryophyllaceae) is here considered to contain 56 species plus 19 infraspecific taxa, excluding autonyms. In the current study, all effectively published names of Drymaria were compiled, and information about their taxonomy, distribution, and nomenclatural types is provided. In addition, an overview of the taxonomic history of Drymaria is presented. As a result, one neotype, 15 lectotypes, and the type for the genus Mollugophytum are newly designated. Altogether, 188 names were treated, of which 52 are heterotypic and 50 are homotypic synonyms. An additional 10 names were either unresolved or are now considered to belong to other genera. A brief assessment of the distribution of the respective taxa is also provided, including the examination of herbarium specimens and specimen images, which indicates that two regions possess high levels of endemism—Mexico with 20 species and the Andes with 14 species. There are few studies that assess the conservation status of Drymaria species, and only 10 species and two varieties have had IUCN Red List assessments.

The tribe Cunonieae comprises five genera and 214 species of shrubs and trees currently distributed in the Southern Hemisphere and the tropics, exhibiting an amphi-Pacific disjunct distribution shared with Araucariaceae, Myrtaceae, Nothofagaceae, Podocarpaceae, and Proteaceae, among others. To address the central question of how historical geological forces have shaped the distribution of plant diversity in the southern hemisphere, we aimed to provide evidence from the biogeographical history of Cunonieae. We generated the most densely sampled phylogenetic trees of Cunonieae available to date, with 121 samples and 81 species, based on 404 new sequences of plastid and nuclear DNA regions with high hierarchical phylogenetic signal (matK, trnL-F, rpl16, and internal transcribed spacer (ITS)). We included 184 samples of Rosids to estimate divergence times using fossil calibration points. For biogeographic inference, we employed a time-stratified model including fossils as tips. Cunonia and Pterophylla were paraphyletic in the ITS tree, and Cunonia was paraphyletic in the plastid tree. Pancheria, Vesselowskya, and Weinmannia were monophyletic, the latter with conflicting nuclear and plastid phylogenies. The crown group Cunonieae was dated at similar to 56 Ma, and its ancestral areas were Antarctica and Patagonia. Antarctica acted as a bridge between Australia and South America before the consolidation of the Antarctic Ice Sheet and the extinction of the lineage in Antarctica from the Oligocene to the Miocene. Following that, Cunonieae spread to lower latitudes via Zealandia/Oceania and Patagonia/South America. Geological changes during the Pliocene facilitated a further burst in diversification along the Andes, in Madagascar, and in New Caledonia, where at least three colonization events occurred.

Background and Aims The parietal clade is one of the major lineages of the angiosperm order Malpighiales. Several nodes in the phylogenetic trees inferred from concatenated chloroplast genes exhibited low support, and various Malpighiales genera were found to have highly altered plastid genomes.Methods Here we newly generated seven complete plastid genomes to represent the major lineages of the pantropical genus Casearia using genome skimming. Together with published genome sequences of various sources, we comparatively analysed the genome structure of all major lineages of the Salicaceae and their putative relatives across the parietal clade.Key Results All plastid genomes, including those of the Rhizophoraceae outgroup, were syntenous, with the exception of Passifloraceae, which exhibited accelerated pseudogenization, gene loss and major structural rearrangements. Although rpl32 is absent from all Salicaceae, this is not a synapomorphy for the family, due to other losses in genera such as Hydnocarpus and Viola. Apart from the exons, we found sequences of all introns and most spacers to be alignable, except short and hypervariable stem-loop elements. We could therefore explore the phylogenetic signal of complete plastid genomes.Conclusions All three partitions, exons, introns and spacers, presented congruent topologies with maximum support for the Samydoideae being sister to a clade of Salicoideae and Scyphostegioideae within the monophyletic Salicaceae. Our results underscore the potential of complete plastid genomes to further explore the evolutionary diversification of the Malpighiales.

BACKGROUND AND AIMS:Philodendron is one of the largest genera in the Neotropics with well over 600 species in three subgenera (Meconostigma, Philodendron and Pteromischum). Following an early Oligocene origin, it was considered to have colonized Central America only late, in the Pliocene. However, molecular phylogenetic trees so far were short in species from Central America, which is now recognized as the second center of diversity. We aimed at elucidating the evolutionary origin of Philodendron diversity in this area, exploring relationships between Central and South American species, and assessing the role of the Isthmus of Panama in their diversification. METHODS:Fieldwork was conducted across Mexico, Costa Rica, Panama, and Colombia. To maximize coverage of tree space, 319 new samples were added to an existing alignment of three plastid regions (petD, rpl16, and trnK/matK). Phylogenetic trees from a total of 302 taxa were inferred using Maximum Likelihood approaches. Divergence times were estimated with BEAST, and diversification dynamics were assessed with BAMM. KEY RESULTS:Philodendron and its three subgenera were monophyletic, with the largest subgenus Philodendron comprising 15 major lineages. Two significant diversification rate shifts within subgenus Philodendron associated with the uplift of the Northern Andes and the emergence of montane cloud forests in southern Central America were observed. Most of the diversification events of Central American lineages apparently aligns with the last phases of the Isthmus and the formation of Talamanca mountain range. South American ancestors highlight the role of the Isthmus as a biogeographic corridor that enabled migrations of Philodendron into Central America. CONCLUSIONS:The diversification of Philodendron in Central America aligns with major geological events and the emergence of novel habitats. Compared to previous studies, our findings highlight the importance of a geographically and taxonomically comprehensive sampling for accurately reconstructing the evolutionary history of large plant genera.

Collections’ digitisation is a priority in many natural history collections, and publicly available datasets are expanding rapidly. The potential value of collections remains largely untapped even in modern research, because the vast scope of collections dwarfs current efforts at data mobilisation. Collections are continually expanding, and there are an estimated 3 billion undigitised specimen records worldwide. In this review, we use a simple model to illustrate that current efforts at global digitisation will not succeed until the late 21 st century at the earliest, unless new technologies are harnessed and commitments by funding bodies and society are made. As we advance toward specimen digitisation, an equally important consideration is that the majority of these digital records only represent a fraction of the information potentially available from the collection objects. The term “collectomics” was coined in discussions within the Senckenberg institution as a phrase for digital frameworks that embrace all current and future data and knowledge derived from specimens. This expands on the concept of museomics, which was originally defined to focus on molecular data generated from museum specimens. Rooted in the concept of the extended specimen, collectomics encompasses metadata, images, traits, DNA, and further data extracted in the future with yet unknown applications, all of which are connected to environmental data and other historical contextual information. Thus, a view of digitisation under the collectomics concept is not limited to natural history collections but directly integrates evolutionary, ecosystem and social sciences, including the human contributions of collectors, donors, and researchers in the past and future. A “collectomics” view envisions seamless integration of multidimensional specimen-based data, with interoperability among historical, artistic, ethnographic, and natural history collections, to generate knowledge that is needed to tackle global challenges.

Biodiversity knowledge, from genes to ecosystems, is crucial for addressing the biodiversity crisis. However, even in well-explored countries like Germany, much biodiversity remains unknown. Therefore, several research institutions are joining forces to conduct a comprehensive biodiversity inventory, combining broad taxonomic expertise with advanced technologies. By consolidating data across many organismic groups, the Unknown Germany initiative will significantly enhance conservation strategies and may serve as a model for similar efforts worldwide.

Background: Shrubs recognized as I. hartmanii were known from the northern Mexican deserts, whereas I. cassiniiformis is considered to occur throughout the Mexican highlands. Morphologically similar individuals were reported under both names also south beyond the Isthmus of Tehuantepec to Guatemala. Question: Are I. hartmanii and I. cassiniiformis distinct species, or do they represent widespread taxa exhibiting clinal variation due to adaptation along a gradient spanning desert to evergreen tropical forest? Taxon: Amaranthaceae, Iresine. Study site: Mexico and Central America. Method: Field and herbarium work, molecular phylogenetics, morphology, palynology, distribution mapping. Results: Plastid and nuclear phylogenetic trees suggest a complex speciation scenario in Iresine, revealing new lineages in the mountains of Chiapas, Oaxaca and Guatemala that also differ by morphological characters. Iresine cassiniiformis appears monophyletic and occurs in the Trans-Mexican Volcanic Belt whereas I. hartmanii comprises a core clade of individuals confined to the northern deserts. Specimens morphologically intermediate to I. cassiniiformis, and part of the I. hartmanii species clade in nrITS, occur directly south of the desert zone, either representing ancestral types in the speciation of I. hartmanii or introgression from I. cassiniiformis. Conclusion: Our results underscore the importance of an integrative taxonomy approach including molecular phylogenetics and morphology with a dense sampling of putative species from throughout the geographical range in order to arrive at explicit hypotheses on species limits. Here this supports the description and naming of two new species.

A taxonomic backbone of the Plumbaginaceae is presented and the current state of knowledge on phylogenetic relationships and taxon limits is reviewed as a basis for the accepted taxon concepts. In total, 4,476 scientific names and designations are treated of which 30 are not in the family Plumbaginaceae. The Plumbaginaceae are subdivided in three tribes with 26 genera and 1,179 accepted species. Two subgenera, 17 sections, two subsections and 187 infraspecific taxa are accepted. At the species and infraspecific level 2,782 synonyms were assigned to accepted taxa, whereas 194 names were excluded from the core checklist (i.e., unplaced taxa, infrageneric subdivisions with still uncertain application, names of verified uncertain application, invalid horticultural names, excluded names from other families, other excluded designations, and unresolved names). The EDIT Platform for Cybertaxonomy was utilized as the tool to compile and manage the names and further taxonomic data under explicit taxon concepts. Secundum references are given in case taxon concepts were taken from the literature, whereas this study serves as reference for newly circumscribed taxa. The family’s division into the tribes Aegialitideae, Limonieae, and Plumbagineae departs from earlier two-subfamily classifications, prompted by recent phylogenetic findings that challenge the subfamilial affinity of Aegialitis. The genus Acantholimon was extended to include Gladiolimon, as currently available phylogenetic and morphological data support this merger. In Limonium, all accepted species could be assigned to sections and subsections or the “Mediterranean lineage”, respectively, making use of the phylogenetic distribution of their morphological characters and states. A new combination and/or status is proposed for Dyerophytum socotranum, Limonium thymoides, Limonium × fraternum, Limonium × rossmaessleri, and Limonium sect. Jovibarba. Special attention is given to nomenclatural issues, particularly for Statice nomen ambiguum to resolve the names under accepted names. The use of artificial groupings like “aggregates”, “complexes” and “species groups” in alpha-taxonomic treatments is discussed. The taxonomic backbone will receive continued updates and through the Caryophyllales Taxonomic Expert Network, it contributes the treatment of the Plumbaginaceae for the World Flora Online.

The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.

Campanula L. is among the genera with the highest number of endemics in the Caucasus ecoregion. A group of attractive alpine and subalpine perennial rosette plants with short single-flowered stems centred in the Caucasus has been treated as Campanula subg. Scapiflorae or at other ranks, with considerably varying circumscription and classification. Molecular phylogenetic analysis of three plastid DNA regions (trnK/matK, petD, rpl16) of a strongly extended sampling, comprising 23 of the 27 commonly accepted taxa (85%) with 330 accessions built on and guided by the results of our previous study of the group, confirmed the polyphyly of C. subg. Scapiflorae in any of its circumscriptions. The core clade of the group comprises exclusively endemics and near-endemics of the Caucasus and is treated here as C. sect. Tridentatae in a revised circumscription. The phylogenetic relationships of the disparate other elements of the Scapiflorae group are outlined.

Background: Shrubs recognized as I. hartmanii were known from the northern Mexican deserts, whereas I. cassiniiformis is considered to occur throughout the Mexican highlands. Morphologically similar individuals were reported under both names also south beyond the Isthmus of Tehuantepec to Guatemala. Question: Are I. hartmanii and I. cassiniiformis distinct species, or do they represent widespread taxa exhibiting clinal variation due to adaptation along a gradient spanning desert to evergreen tropical forest? Taxon: Amaranthaceae, Iresine. Study site: Mexico and Central America. Method: Field and herbarium work, molecular phylogenetics, morphology, palynology, distribution mapping. Results: Plastid and nuclear phylogenetic trees suggest a complex speciation scenario in Iresine, revealing new lineages in the mountains of Chiapas, Oaxaca and Guatemala that also differ by morphological characters. Iresine cassiniiformis appears monophyletic and occurs in the Trans-Mexican Volcanic Belt whereas I. hartmanii comprises a core clade of individuals confined to the northern deserts. Specimens morphologically intermediate to I. cassiniiformis, and part of the I. hartmanii species clade in nrITS, occur directly south of the desert zone, either representing ancestral types in the speciation of I. hartmanii or introgression from I. cassiniiformis. Conclusion: Our results underscore the importance of an integrative taxonomy approach including molecular phylogenetics and morphology with a dense sampling of putative species from throughout the geographical range in order to arrive at explicit hypotheses on species limits. Here this supports the description and naming of two new species.

The achyranthoid clade constitutes the second most species-rich lineage of the Amaranthaceae after the gomphrenoid clade. The Achyranthoids are mostly African, in contrast to the largely Neotropical Gomphrenoids, and comprise a large number of genera, many of which were revealed as non-monophyletic. Here were focus on subclade II of the Achyranthoids with the so far accepted genera Achyranthes, Achyropsis, Centrostachys, Cyathula, Nelsia, Nototrichium, Pandiaka, Sericocomopsis, and Sericostachys. Building upon an earlier dataset, we extended taxon and character sampling, both for molecular and morphological characters. Our plastid and nuclear trees converge on several highly supported clades, one comprising most species of Cyathula, Nelsia, Pandiaka and two highly divergent lineages of plants hitherto identified as Sericocomopsis hildebrandtii. Morphologically, individuals within these lineages are similar, with one of them matching the type of Sericocomopsis meruensis. This name was formerly considered a synonym and is resurrected at species level. Cymous partial florescences are ancestral in this clade, which corresponds to the genus Cyathula as re-circumscribed here. To the contrary, sterile flowers and bracteoles or tepals modified to hooks serving dispersal by animals appear multiple times within and outside this clade, indicating how their use as diagnostic characters for genera led to non-monophyletic entities. For the phylogenetically isolated and morphologically distinct Cyathula orthacantha the new genus Sebsebea is described, and for Sericocomopsis pallida the new genus Evelynastra. The Achyranthes clade is characterized by solitary, fertile flowers including the genera Achyropsis and Nototrichium both of which are merged to make Achyranthes monophyletic. In addition to a treatment to establish all required nomenclatural changes and typifications, we also provide a taxonomic backbone with full synonymy for the achyranthoid subclade II.

The Gynoxyoid clade of the Senecioneae (Asteraceae) until now included the five genera Aequatorium, Gynoxys, Nordenstamia, Paracalia and Paragynoxys as diagnosed using selected morphological characters. In their pre-phylogenetic circumscription, the genera Aequatorium and Paragynoxys were considered to inhabit the northern Andes in contrast to Nordenstamia and Paracalia that occur in the central Andes. The most species-rich genus, Gynoxys, was believed to be distributed throughout the Andes. We use a recently established plastid phylogenomic framework that rendered Gynoxys paraphyletic to further evaluate the delimitation of genera in the Gynoxyoid clade. We examine the morphological variation of all members of the Gynoxyoid to identify characters potentially informative at genus level. This results in a matrix of eleven, mostly multistate characters, including those originally used to diagnose these genera. The ancestral character state inference displays a high level of homoplasy, but nevertheless supports the recognition of four genera. Aequatorium is characterised by white radiate capitula. Paracalia and Paragynoxys share white flowers and floral characteristics, such as flower opening and length of disc flowers lobes, as plesiomorphic states, but differ in habit (scandent shrubs vs. trees). Paracalia also retained white flowers, but its two species are characterised by the absence of outer phyllaries. The genera Gynoxys and Nordenstamia comprise species with yellow capitula which appear to be a derived feature in the Gynoxyoids. The genus Nordenstamia, with eight species, is synonymised under Gynoxys since molecular evidence shows its species nested within various parts of the Gynoxys subclade and the morphological variation of Nordenstamia falls well within that of Gynoxys. With the goal to assign all species to four genera (Aequatorium, Gynoxys, Paracalia and Paragynoxys), we assess the states for the eleven characters for all members of the Gynoxyoids and generate new ETS and ITS sequences for 171 specimens belonging to 49 species to further support their generic placement. We provide a taxonomic treatment for the four genera recognised here including amended diagnoses and morphological descriptions. Furthermore, a species-level taxonomic backbone is elaborated for all genera using electronic tools that list 158 currently accepted names and synonyms (209 names in total) with the respective protologue and type information, as well as notes on the current understanding of species limits. Eleven names are newly synonymised, two are lectotypified and eight are newly transferred to other genera.

DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high‐quality sequences to maximize identification success. BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence and associated metadata. It is free, open‐source and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location. BarKeeper offers features to collect and manage data and metadata about specimens, taxa and DNA sequences from Sanger sequencing and high‐throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy‐based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats. BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error‐prone manual steps and enabling efficient collaborative workflows.

Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well-distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy.