Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to \'translate\' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.

We propose a new genus of plexippine jumping spiders from the Western Ghats of India based on the new species Ghatippuspaschimagen. et sp. nov. While it bears a superficial resemblance to Pancorius in body form and Hyllus in membrane-bearing embolus, our UCE phylogenomic data-the first to resolve broad relationships within the Plexippina-as well as morphological features justify its status as a new genus. In addition to the molecular data and morphological descriptions, we provide photographs of living specimens of Ghatippuspaschimagen. et sp. nov. and information on their natural history.

Metabarcoding of environmental samples is nowadays an established method in biodiversity research. When it comes to studying fungal populations in various ecotypes, fruit body inventories are the traditional method to assess the diversity of fungal communities. In this study, both methods-metabarcoding of soil samples and a traditional fruit body inventory-were conducted on 144 sample plots in an altitudinal gradient in the Bavarian Forest (Germany) and the results were compared. Metabarcoding detected significantly more species than the traditional fruit body inventory. The majority of taxa recorded in the fruit body inventory belonged to the Basidiomycota, whereas in the metabarcoding data, the distribution of species between Basidiomycota and Ascomycota was approximately balanced. Species of several orders forming inconspicuous or hypogeous fruit bodies were detected only by metabarcoding, while several wood decomposers were recorded only in the fruit body inventory. The proportion of detected wood-colonising species with melanized spores was considerably higher with metabarcoding than with the fruit body inventory, where more than 70% of recorded wood-colonisers had hyaline spores. Based on the metabarcoding data, a decline of species richness with increasing altitude was evident, but this was not visible in the fruit body inventory data. Detrended correspondence analyses yielded similar results for relative species community similarities with both survey methods.

The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.

UNASSIGNED: Biodiversity is the assortment of life on earth covering evolutionary, ecological, biological, and social forms. To preserve life in all its variety and richness, it is imperative to monitor the current state of biodiversity and its change over time and to understand the forces driving it. This need has resulted in numerous works being published in this field. With this, a large amount of textual data (publications) and metadata (e.g. dataset description) has been generated. To support the management and analysis of these data, two techniques from computer science are of interest, namely Named Entity Recognition (NER) and Relation Extraction (RE). While the former enables better content discovery and understanding, the latter fosters the analysis by detecting connections between entities and, thus, allows us to draw conclusions and answer relevant domain-specific questions. To automatically predict entities and their relations, machine/deep learning techniques could be used. The training and evaluation of those techniques require labelled corpora.
UNASSIGNED: In this paper, we present two gold-standard corpora for Named Entity Recognition (NER) and Relation Extraction (RE) generated from biodiversity datasets metadata and abstracts that can be used as evaluation benchmarks for the development of new computer-supported tools that require machine learning or deep learning techniques. These corpora are manually labelled and verified by biodiversity experts. In addition, we explain the detailed steps of constructing these datasets. Moreover, we demonstrate the underlying ontology for the classes and relations used to annotate such corpora.

Decades of research and policy interventions on biodiversity have insufficiently addressed the dual issues of biodiversity degradation and social justice. New approaches are therefore needed. We devised a research and action agenda that calls for a collective task of revisiting biodiversity toward the goal of sustaining diverse and just futures for life on Earth. Revisiting biodiversity involves critically reflecting on past and present research, policy, and practice concerning biodiversity to inspire creative thinking about the future. The agenda was developed through a 2-year dialogue process that involved close to 300 experts from diverse disciplines and locations. This process was informed by social science insights that show biodiversity research and action is underpinned by choices about how problems are conceptualized. Recognizing knowledge, action, and ethics as inseparable, we synthesized a set of principles that help navigate the task of revisiting biodiversity. The agenda articulates 4 thematic areas for future research. First, researchers need to revisit biodiversity narratives by challenging conceptualizations that exclude diversity and entrench the separation of humans, cultures, economies, and societies from nature. Second, researchers should focus on the relationships between the Anthropocene, biodiversity, and culture by considering humanity and biodiversity as tied together in specific contexts. Third, researchers should focus on nature and economies by better accounting for the interacting structures of economic and financial systems as core drivers of biodiversity loss. Finally, researchers should enable transformative biodiversity research and action by reconfiguring relationships between human and nonhuman communities in and through science, policy, and practice. Revisiting biodiversity necessitates a renewed focus on dialogue among biodiversity communities and beyond that critically reflects on the past to channel research and action toward fostering just and diverse futures for human and nonhuman life on Earth.
Una Agenda para la Investigación y la Acción hacia un Futuro Diverso y Justo para la Vida sobre la Tierra Resumen Las décadas de investigación e intervenciones políticas sobre la biodiversidad han tratado significativamente los temas de la degradación de la biodiversidad y la justicia social. Debido a esto, se requieren nuevas estrategias. Diseñamos una agenda de investigación y acción que llama a la labor colectiva de revisar la biodiversidad hacia el objetivo de sustentar un futuro diverso y justo para la vida sobre la Tierra. Cuando se revisa la biodiversidad, se requiere de una reflexión crítica sobre las investigaciones, políticas y prácticas presentes y pasadas sobre la biodiversidad para inspirar un pensamiento creativo acerca del futuro. Desarrollamos la agenda por medio de un proceso de diálogo de dos años que involucró a casi 300 expertos de diversas disciplinas y localidades. Este proceso estuvo orientado por el conocimiento de las ciencias sociales que muestra cómo la investigación y la acción para la biodiversidad están sostenidas por las opciones de cómo están conceptualizados los problemas. Reconocimos al conocimiento, la acción y la ética como inseparables y sintetizamos un conjunto de principios que ayuda a navegar la labor de revisar la biodiversidad. La agenda articula cuatro áreas temáticas para la investigación en el futuro. Primero, los investigadores necesitan revisar las narrativas de la biodiversidad mediante el cuestionamiento de las conceptualizaciones que excluyen a la diversidad y consolidan la separación entre humanos, culturas, economías y sociedades y la naturaleza. Segundo, los investigadores deberían enfocarse en las relaciones entre el antropoceno, la biodiversidad y la cultura al considerar a la humanidad y la biodiversidad como interconectadas en contextos específicos. Tercero, los investigadores deberían enfocarse en la naturaleza y las economías al tener en mejor cuenta la interacción de las estructuras de los sistemas económico y financiero como conductores nucleares de la pérdida de la biodiversidad. Finalmente, los investigadores deberían permitir la investigación y acción transformadoras de la biodiversidad al reconfigurar las relaciones entre las comunidades humanas y no humanas dentro y a través de la ciencia, la política y la práctica. La revisión de la biodiversidad necesita de un enfoque renovado sobre el diálogo entre las comunidades de la biodiversidad y más allá, que reflexione críticamente sobre el pasado para canalizar a la investigación y acción hacia el fomento del futuro justo y diverso para la vida humana y no humana sobre la Tierra.

Parcels, Sales and Gifts: Hans Sauter\'s Entomological Practices between Formosa and Europe, 1902-1914. The exploration of global biodiversity is a form of knowledge production that is necessarily specimen-based. In the endeavor to chart the natural world, not only ideas and writings travelled across the oceans, but also a flood of scientific objects. The German entomologist Hans Sauter (1871-1943) spent most of his life in Formosa, then a Japanese colony. His pronounced aim was to complete an inventory of the entire fauna of Formosa. He aimed for the mass production of knowledge, becoming a collecting-entrepreneur who employed scores of local collectors. Between 1902 and 1914, they amassed large quantities of insects, which required specialized practices in collecting, preserving, documenting, and packaging. Sauter sent these insects, but also hundreds of reptiles, mammals, birds, fish etc., to zoologists all over Europe who identified and published hitherto undescribed species. At first, Sauter sold his finds. Later, he stopped asking for money - pushing instead for speed in publication and making demands about the content and naming of these articles. His demands were met, especially by the Deutsches Entomologisches Museum in Dahlem. Despite almost no publications to his name, Sauter quickly gained considerable influence in the world of entomological research. In this paper, the circulation of these scientific objects serves as a focal point in order to embed local circumstances in the process of knowledge production in a global context. The practices associated with the specimens illustrate the economic, political and social dimensions of the formation of knowledge. Hans Sauter\'s case defies traditional dichotomies as it illustrates the interdependence of practical and theoretical knowledge, of science and trade and of center and periphery. Practical knowledge gained in a local setting in Formosa allowed Sauter to amass large amounts of insect specimens, a resource he used to steer the course of scientific practice in Europe.

This paper aims to get a better understanding of the motivational and transaction cost features of building global scientific research commons, with a view to contributing to the debate on the design of appropriate policy measures under the recently adopted Nagoya Protocol. For this purpose, the paper analyses the results of a world-wide survey of managers and users of microbial culture collections, which focused on the role of social and internalized motivations, organizational networks and external incentives in promoting the public availability of upstream research assets. Overall, the study confirms the hypotheses of the social production model of information and shareable goods, but it also shows the need to complete this model. For the sharing of materials, the underlying collaborative economy in excess capacity plays a key role in addition to the social production, while for data, competitive pressures amongst scientists tend to play a bigger role.