RESUMO
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.
RESUMO
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.
