TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research.

Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.

Floristic survey of vascular plants of the Parque Estadual da Pedra Selada, Rio de Janeiro, Brazil.

Background: The Atlantic Forest is one of the most diverse and threatened phytogeographical domains in the world. Despite that, it includes regions with poor floristic knowledge, even in protected areas. Although the importance of protected areas in conserving the Atlantic Forest hotspot is undisputed, it is necessary to recognise the floristic richness of these areas to propose effective conservation actions. In this sense, online databases have proved to be a promising tool for compiling species lists with relevant biodiversity information. This study is based on the list of vascular plants of the "Parque Estadual da Pedra Selada", published in the "Catálogo de Plantas das Unidades de Conservação do Brasil". It summarises the species richness, endemism and conservation status of this protected area. New information: The published list of vascular plants was based on data obtained from herbarium collections available in online databases. A total of 303 species have been recorded for the "Parque Estadual da Pedra Selada," of which 297 are native to Brazil, 78 are endemic to the Brazilian Atlantic Forest, and seven are endemic to the State of Rio de Janeiro. More than 60% of the species are woody, and more than 40% are trees. Eight threatened species (Endangered - EN and Vulnerable - VU), of which five are endemic to the State of Rio de Janeiro, are housed in this protected area. One species was classified as Data Deficient (DD). Our results increase the knowledge of the Atlantic Forest flora in the State of Rio de Janeiro and support effective conservation planning for this protected area.

Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification.

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Ceratonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.

A new generic circumscription of Hydrochorea (Leguminosae, Caesalpinioideae, mimosoid clade) with an amphi-Atlantic distribution.

Hydrochorea and Balizia were established to accommodate four and three species, respectively, that were previously included in different ingoid genera, based primarily on differences in fruit morphology. Both genera have Amazonia as their centre of diversity, extending to Central America and the Brazilian Atlantic Rainforest. Previous phylogenetic evidence showed Balizia to be paraphyletic with respect to Hydrochorea, and species of Hydrochorea and Balizia were placed in a large unresolved polytomy with species of Jupunba. Here we present a new phylogenomic analysis based on 560 exons, from which 686 orthologous alignments were derived for gene tree inference. This analysis confirms a paraphyletic Balizia in relation to Hydrochorea, together with two African species formerly placed in Albizia nested within the clade. Jupunbamacradenia was resolved as sister to the clade combining those taxa. However, quartet support is low for several of the branches at the base of the clade combining the genera Jupunba, Balizia and Hydrochorea, suggesting that rapid initial divergence in this group led to extensive incomplete lineage sorting and consequently poor phylogenetic resolution. Because of these phylogenomic complexities, we decided to use morphology as the main guide to consider Hydrochorea as a distinct genus from Jupunba, and Balizia as a new synonym for Hydrochorea. The taxonomic treatment includes the study of collections from various herbaria and fieldwork expeditions. We present a re-circumscribed Hydrochorea accommodating a total of 10 species, including six new combinations, five new synonyms, one new taxonomic status, two corrections of nomenclature category for lectotypes, and a second step lectotype and three new lectotypes. A new species from the Brazilian Amazon is described and illustrated. An identification key for all species of Hydrochorea is presented, together with comments and illustrations.