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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Caryophyllaceae with a cushion-like life form occur with a large number of species at the higher altitudes of the Andes (3500–5000 m) and have evolved convergently in several different lineages. Based on molecular phylogenetic analysis it is shown that members of the former genera Plettkea and Pycnophyllopsis, but also certain species previously classified as Arenaria constitute a subclade nested within the monophyletic genus Stellaria. Both plastid (trnK-matK-psbA + trnL-F) and nuclear (nrITS) trees converged on such a highly supported 'Plettkea' clade. Morphologically, the members of the 'Plettkea' subclade of Stellaria are further characterized by reduced to completely absent petals and seeds with a more or less conspicuous tuberculate testa. This clade is described as S. sect. Plettkea (Mattf.) Montesinos & Borsch. Species-level relationships within S. sect. Plettkea are also congruently inferred by plastid and nuclear genomic compartments, with three further sublineages recognized: Altogether, our detailed taxonomic revision showed that the 'Plettkea' clade in fact constitutes an Andean radiation of 21 species within Stellaria, four of which are described as new to science. Earlier treatments indicated just a few species with a putative placement. The results of this investigation underscore the importance of fieldwork and integrated molecular-morphological approaches to assess the species diversity in Andean plant groups. In addition to the phylogenetic analysis, we provide a taxonomic backbone including all names and types, descriptions and information on distribution and ecology and a key for identification. Regarding the next relatives of the S. sect. Plettkea clade, our plastid trees depict the 'Nitentes' clade of Stellaria as sister, whereas nrITS instead suggests a sister group relationship of the 'Nitentes' with the speciose 'Larbreae' clade. Our inferred relationships of major clades further deviate from published molecular trees by indicating an early branching position of the 'Petiolares' clade. Citation: Montesinos-Tubée D. B. & Borsch T. 2023: Molecular phylogenetics and morphology reveal the Plettkea lineage including several members of Arenaria and Pycnophyllopsis to be a clade of 21 South American species nested within Stellaria (Caryophyllaceae, Alsineae) Version of record first published online on 21 December 2023 ahead of inclusion in December 2023 issue. Las Caryophyllaceae, con forma de vida en matas o almohadillas, se encuentran en las mayores altitudes de los Andes (3500–5000 m) con un gran número de especies y han tenido una evolución convergente en diversos linajes. Análisis filogenéticos moleculares, recuperan un subclado anidado dentro del género monofilético Stellaria, constituido por los miembros previamente clasificados en Plettkea y Pycnophyllopsis y especies clasificadas hasta ahora en Arenaria. Tanto los árboles de plástidos (trnK-matK-psbA + trnL-F) como los nucleares (nrITS) convergen en un clado de 'Plettkea' altamente apoyado estadísticamente. Morfológicamente, los miembros del subclado 'Plettkea' de Stellaria se caracterizan, además, por compartir pétalos reducidos o completamente ausentes y semillas con un tegumento tuberculado más o menos conspicuo. El subclado se valida como S. sect. Plettkea (Mattf.) Montesinos & Borsch. Las relaciones a nivel de especie dentro de esta sección también se infieren congruentemente por compartimentos genómicos plastidiales y nucleares, con tres sublinajes. En conjunto, nuestra detallada revisión taxonómica mostró que el clado Plettkea constituye una radiación andina de 21 especies dentro de Stellaria, cuatro de las cuales se describen como nuevas para la ciencia. Tratamientos anteriores indicaban sólo unas pocas especies con una ubicación putativa. Los resultados de esta investigación destacan la importancia del trabajo de campo y la integración de métodos moleculares y morfológicos para evaluar la diversidad de especies en los grupos de plantas andinas. Además del análisis filogenético, proporcionamos una columna vertebral taxonómica que incluye todos los nombres y datos de los tipos nomenclaturales. Se proporcionan descripciones e información sobre distribución y ecología así como una clave para identificarlas. Con respecto a los parientes próximos del clado de S. sect. Plettkea, nuestros árboles de plástidos muestran al clado 'Nitentes' de Stellaria como hermano, mientras que nrITS sugiere más bien una relación de grupo hermano de los 'Nitentes' con el clado 'Larbreae'. Las relaciones inferidas de los clados principales se desvían aún más de los árboles moleculares publicados previamente, al indicar una posición de ramificación temprana del clado 'Petiolares'. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background and Aims The genus Buxus has high levels of endemism in the Caribbean flora, with ~ 50 taxa. In Cuba, 82 % grow on ultramafic substrates and 59 % are nickel (Ni) accumulators or Ni hyperaccumulators. Hence it is an ideal model group to study if this diversification could be related to adaptation to ultramafic substrates and to Ni hyperaccumulation. Methods We generated a well-resolved molecular phylogeny, including nearly all of the Neotropical and Caribbean Buxus taxa. To obtain robust divergence times we tested for the effects of different calibration scenarios, and we reconstructed ancestral areas and ancestral character states. Phylogenetic trees were examined for trait-independent shifts in diversification rates and we used multi-state models to test for state-dependent speciation and extinction rates. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America'. Key Results We found a Caribbean Buxus clade with Mexican ancestors, encompassing three major subclades, which started to radiate during the middle Miocene (13.25 Mya). Other Caribbean islands and northern South America were reached from ~3 Mya onwards. Conclusions An evolutionary scenario is evident in which Buxus plants able to grow on ultramafic substrates by exaptation became ultramafic substrate endemics and evolved stepwise from Ni tolerance through Ni accumulation to Ni hyperaccumulation, which has triggered species diversification of Buxus in Cuba. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America'. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Field observations of morphologically intermediate water lilies in central Canada suggested a hybrid origin involving the parents Nymphaea odorata Aiton and Nymphaea leibergii Morong despite the fertile nature of these plants. Sequencing of the nrlTS and the plastid rps4-trnT-trnF regions further including all members of the north temperate Nymphaea subg. Nymphaea clade, and samples from other hybrids occurring in North America in the wild, allowed us to determine that individuals of N. leibergii and of N. odorata were the maternal and paternal parents, respectively. Hybrids of New England have all proven to be sterile, are genetically variable, and probably are F1. By comparison, the plants of east-central Saskatchewan and west-central Manitoba are fully fertile and genetically uniform based on ISSR and sequence data. On the basis of this evidence, the latter are here described as a new species, Nymphaea loriana sp. nov., which may have originated during the Holocene climatic optimum about 6000 years ago in a past contact zone of the parents. Further hybrids detected between N. odorata and Nymphaea tetragona Georgi, as well as between N. leibergii and N. tetragona, were always sterile. Gene trees of the temperate clade of Nymphaea converge onaclade of small-flowered water lilies (sect. Chamaenymphaea), including N. leibergii, N. tetragona, and Nymphaea pygmaea. Nuclear ITS further resolves an American clade (Nymphaea mexicana Zucc.--N. odorata) sister to all remaining species. This split into two major subclades also appears in the otherwise less resolved rps4-trnT-trnF tree. Thus the origin of N. loriana is a reticulation between long-separated parental lineages. Key words: Nymphaea subg. Nymphaea, phylogeny, divergent ITS copies, hybridization, post-glacial migration, species monophyly. Les observations de terrain des nenuphars du centre du Canada dont la morphologie est intermediaire ont suggere qu'ils emaneraient d'un hybride dont Nymphaea odorata Aiton et Nymphaea leibergii Morong seraient les parents, malgre la nature fertile de ces vegetaux. Le sequencage des regions de l'ETI-nr et du plastide rps4-trnT-trnF incluant tous les membres du clade tempere Nymphaea subg. Nymphaea, et des echantillons d'autres hybrides presents dans la nature en Amerique du Nord, ont permis aux auteurs de determiner que les individus N. leibergii et N. odorata constituaient les parents maternels et paternels, respectivement. Les hybrides de Nouvelle-Angleterre se sont tous reveles steriles et genetiquement variables, constituant probablement la F1. En comparaison, les plantes du centre-est de la Saskatchewan et du centre-ouest du Manitoba sont pleinement fertiles et genetiquement uniformes selon des donnees d'ISSR et de sequences. Sur le base de ces elements probants, ces dernieres sont decrites ici comme constituant une espece nouvelle, Nymphaea loriana sp. nov., qui pourrait avoir emerge durant l'optimum climatique holocene il y a environ 6000 ans, dans une zone de contact passee des parents. D'autres hybrides detectes entre N. odorata et Nymphaea tetragona Georgi ainsi qu'entre N. leibergii et N. tetragona etaient toujours steriles. Les arbres genetiques du clade tempere des Nymphaea convergent sur un clade de nenuphars a petites fleurs (sect. Chamaenymphaea), incluant N. leibergii, N. tetragona et Nymphaea pygmaea. L'ETI nucleaire resout davantage un clade Americain (Nymphaea mexicana Zucc.--N. odorata), sreur de toutes les especes restantes. Ce detachement en deux sous-clades majeurs apparait aussi dans l'arbre rps4-trnT-trnF par ailleurs moins resolu. L'origine de N. loriana constitue alors une reticulation entre des lignages parentaux eloignes. [Traduit par la Redaction] Mots-cles : Nymphaea subg. Nymphaea, phylogenie, copies d'ETI divergents, hybridation, migration post-glaciaire, monophylie d'une espece., Introduction The water-lily genus Nymphaea is the most speciose, phenotypically diverse, and geographically widespread member of the Nymphaeales (Schneider and Williamson 1993; Borsch et al. 2007), with 45-50 species recognized [...]