Xper²: managing descriptive data from their collection to e-monographs

Computer Aided Identification (CAI) systems provide users with the resources to relate morpho-anatomic observations with names of taxa, and to subsequently access other knowledge about the organisms. Xper² version 2.1 is one of the most user-friendly software in its category. It provides a complete environment dedicated to taxonomic descriptions management. While assisting taxonomists with knowledge acquisition for identification keys, it also helps with the publication of descriptive data by providing a large panel of tools, including analysis facilities (comparison of taxa or descriptors used), full traceability of information and knowledge (by adding references or external links). Xper² provides excellent support for automatic online publication of descriptive data and free access keys, as well as for exporting of datasets for phylogenetic and systematic research. It focuses on interoperability between systems and can import and export into structured descriptive data format (TDWG-SDD), and export to HTML and Nexus formats. Written in Java, it is available on Windows™ Mac™ or Linux in French, English, and Spanish, and a new Chinese version can also be downloaded. With its intuitive interface, Xper² is aimed at professional taxonomists as well as naturalists who merely want to identify specimens using a readymade application. Xper² is free of charge. It can be downloaded at: http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2

IIKC: An Interactive Identification Key for female Culicoides (Diptera: Ceratopogonidae) from the West Palearctic region

In 2006, bluetongue virus (BTV) outbreaks appeared surprisingly in northern Europe and widely affected most of the European countries. Correct identification of Culicoides species (Diptera: Ceratopogonidae), known as BTV vectors, is a key component of all studies intending to understand vector dynamics and to develop vector control strategies. A computer-based system, Xper2, was used to develop an Interactive Identification Key (IIKC) for female Culicoides from the West Palearctic region. The current version of IIKC includes 108 taxa, 61 descriptors and 837 pictures and schemes. IIKC is a powerful tool for routinely identifying Culicoides species and for training young specialized taxonomists

Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability

The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration.In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications.To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities.Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement

Comparative biogeography of Southeast Asia and the West Pacific region

The file attached is the accepted/final draft post-refereeing version of the articl

Nouvelles inférences cladistiques sur la biogéographie historique du Sud-Est asiatique et de le région de l'Ouest du Pacifique. Réflexion sur une approche intégrative de la dimension temporelle en biogéographie historique

Historical biogeography is the science that deals with relationships between biogeographic areas, understood as set of taxa distributions. The complex geological history of South East Asia and the Indo‐West Pacific region makes it a very interesting area for biogeography studies. We propose a new approach, cladistic, for the study of this area around the famous “Wallace’s line”, placing our study in the paradigm of vicariance where speciation appears following the implementation of a geographic barrier (as opposed to the dispersal model from a center of origin, classically admitted). Indeed, here we use the existing analogy between Systematics and Biogeography to apply cladistics methods for Systematics to Biogeography. This is to answer the question : "Why is there such distributions of taxa in this region of the world ?” The expected results are a better understanding of the evolutionary history of the region and the life history traits of taxa that inhabit it. Provided that the joint distribution of several unrelated taxa cannot be obtained by "chance", thus it is necessarily due to a common event (ie a vicariant event) which affected equally these taxa. The cladistics approach we propose has been made possible by the completion of a software that implements the so‐called 3‐element analysis (3ia) method : LisBeth is now freely available for download from our website and offers new perspectives of analysis to its users, whether systematicians and biogeographers. We show that the representation of characters offered by LisBeth allows new inferences about the existing relationship between areas of endemism studied. We have highlighted the emergence of a general "pattern" from a joint analysis of 35 unrelated taxa (plants and animals). In a second step we are interested in a major theoretical problem of contemporary biogeography : "What about the time dimension in historical biogeography?". How to account unambiguously different time scales during diachronic analyzes ? We propose a model based on the 3ia which allows us to consider the temporal dimension and realize, therefore, true analysis of integrative biogeography.La biogéographie historique est la discipline qui s'occupe d'établir les relations de parenté entre aires biogéographiques, comprises comme des ensembles d'aires de distribution de taxons. L’histoire géologique complexe du Sud Est asiatique et de la région de l’Ouest du Pacifique en fait une région de choix pour les biogéographes. Nous proposons une nouvelle approche, cladistique, pour l’étude de cette région située autour de la célèbre “Ligne de Wallace”, en nous plaçant dans le paradigme de la vicariance où la spéciation apparaît suite à la mise en place d’une barrière géographique (par opposition au modèle dispersaliste à partir d’un centre d’origine). En effet, nous utilisons ici l’analogie existant entre Systématique et Biogéographie pour appliquer des méthodes cladistiques de la systématique à la Biogéographie. Il s’agit ici de répondre à la question : « pourquoi existe -t-il une telle distribution des taxons dans cette région du globe ? » Les résultats attendus sont une meilleure connaissance de l’histoire évolutive de la région ainsi que des traits d’histoire de vie des taxons qui la peuplent. Etant entendu que la distribution conjointe de plusieurs taxons non apparentés ne peut être obtenue par « chance », elle doit forcément rendre compte d’un événement commun (i. E. Un événement de vicariance) qui aurait affecté de manière égale ces taxons. L’approche cladistique, que nous proposons n’a été rendue possible que grâce à la finalisation d’un logiciel implémentant la méthode dite d’analyse à 3 éléments (3ia): LisBeth est aujourd’hui disponible en téléchargement librement depuis notre site web et offre de nouvelles perspectives d’analyses à ses utilisateurs, qu’ils soient systématiciens ou biogéographes. Nous montrons que la représentation des caractères offerte par LisBeth autorise de nouvelles inférences quant aux relations de parenté existant entre les aires d’endémismes étudiées. Nous avons ainsi mis en évidence l’émergence d’un «pattern » général de l’analyse conjointe de 35 taxons non apparentés (plantes et animaux). Dans un deuxième temps nous nous sommes intéressés à une problématique théorique majeure de la biogéographie contemporaine: « Quid de la dimension temporelle en biogéographie historique ?». Comment prendre en compte, sans ambiguïté, des échelles temporelles différentes lors d’analyses diachroniques ? Nous proposons ici un modèle, basé sur la 3ia qui permet de considérer la dimension temporelle et de réaliser, de ce fait, de véritables analyses de biogéographie intégrative

Do our Project Delimitations Display a Continued Legacy of Colonialism? Towards an independant Flora of Cambodia.តេីការកម្រិតព្រុំដែននៃគំរេាងក្នុងការស្រាវជ្រាវរបស់យេីង បញ្ជាក់ពីមត៌ក នៃសម័យអាណានិគមឬទេ ? ឆ្ពោះទៅរកការរុករកដោយឯករាជនៃរុក្ខជាតិនានារបស់ប្រទេសកម្ពុជា

Cambodia, located in continental Southeast Asia, is renowned for its rich and ancient architectural art. One of its most notable treasures is the archaeological site Angkor Wat, which holds the distinction of being a United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Site. However, Cambodia is also a developing country and a biodiversity hotspot (Myers et al. 2000, Sodhi et al. 2010).Regrettably, Cambodia's tragic and violent history has severely impacted the understanding of its biodiversity, particularly its plant life. This was depicted by Zizka et al. (2021), in one of their figures illustrating the significant decline in the number of recorded species occurrences in Cambodia between 1970 and 1992. This period includes the civil war from 1975 to 1979, which marked one of the most devastating genocides in human history.France and Cambodia share a long history of relations and collaboration. The French presence in Cambodia dates back to 1863 when Cambodia became a French protectorate. It later became part of French Indochina in 1887, alongside other French colonies and protectorates, such as Laos, Tonkin, Annam, Cochinchina, and Guangzhouwan in China. This French presence not only facilitated the "rediscovery" of Angkor Wat and Angkor Thom by Henri Mouhot, a French naturalist, botanist, and entomologist, but also contributed to the collection of Cambodia's biodiversity. The protectorate status for Cambodia ended in 1949, and it declared its independence in 1953.During the same period, the "General Flora of Indo-China" (Gagnepain et al. 1907) began its publication in 1907 and continued until 1951 by French editors. In 1960, this flora was reinitiated as the "Flora of Cambodia, Laos, and Viêt-Nam". Since 2013, it is jointly edited by the Museum National d'Histoire Naturelle in Paris and the Royal Botanic Garden of Edinburgh.The Flora of Cambodia project arose from a simple question: why is the flora still managed jointly with Laos and Viêt-Nam? Since the three countries have been independent since 1954, their respective floras should be separate and published independently. The project's initial phase involves compiling an up-to-date understanding of Cambodia's plant life, including an inventory of collections housed at the Museum National d'Histoire Naturelle in Paris and accessible Cambodian floristic data online through the Global Biodiversity Information Facility (GBIF) and other sources (Joyce et al. 2020). The ultimate goal is to produce a comprehensive flora of Cambodia. In the short term, the project aims to provide an open and curated checklist of vascular plants of Cambodia, in multiple languages, including Khmer and freely available following Findable, Accessible, Interoperable, Re-usable (FAIR) principles (Wilkinson et al. 2016). This endeavor seeks to empower both Khmer botanists and the broader local community, allowing them to reclaim and cherish their intrinsic knowledge of native plants.Although still in its early stages, this project aims to further enhance the strong collaboration between France and Cambodia while being FAIR and Collective benefit, Authority to control, Responsability, Ethics (CARE) (Carroll et al. 2020)

The Sociological History of Transforming TDWG to Biodiversity Information Standards (TDWG)

Thirty-seven years—why celebrate this prime number anniversary of the founding of the Taxonomic Databases Working Group (TDWG) in 1985? Because we wanted to look at the history of TDWG through its people (and coincidentally, 37˚C is considered "normal" human temperature, so why not?). Records from 1985's inaugural meeting at the Conservatoire et Jardin botaniques in Geneva, Switzerland, 28–30 September show that it was attended by 12 representatives of the botanical community. Although the attendees were listed by salutation (i.e., Dr., Prof., Mr.) and by first initials along with surnames, the group was all male, composed mainly of European and American botanists with doctorates.How has TDWG morphed over these 37 years from a group of geeky botanists in the early days of museum computerization and six years before the World Wide Web was introduced to the public, to the organization known today as Biodiversity Information Standards (TDWG)? TDWG has always been an open and community-driven organization with decisions made by consensus. Anyone can become a member, individuals as well as institutions (including government agencies, non-governmental organizations, programs, and projects). Everything TDWG produces comes from the expertise, collaboration, and support of its members—people and organizations who create, manage, integrate, and analyze biodiversity information. Today's TDWG looks very different from the one in 1985, but the seeds of the organization were there, even then.While this presentation is about TDWG's history as an organization, its focus will be on the heart of TDWG: its people. We would like to show how the organization has evolved in terms of gender balance, inclusivity actions, and our engagement to promote and enhance diversity at all levels. But more importantly, where do we—as a community—want to go in the future

BiGAEOn: an ontology for Biogeographic areas

In the current context of Biodiversity loss and climate change, it is more than ever necessary to adapt and develop our scientific practices to face these present-day global issues. Scientists, particularly biologists, have to define new protocols to optimize the tremendous amount of new data being generated and to analyse them. Monitoring Biodiversity is a complex problem because of its multiple facets and cross-domains links. The creation and use of ontologies to conceptualize those different aspects of Biodiversity is an efficient means for key stakeholders and policies makers to promote consistency and reliability of systems. For this purpose, the Environment Ontology (ENVO; http://www.environmentontology.org) is a community ontology for the concise and controlled description of environments. It is interoperating with other domain ontologies closely linked to the representation of biodiversity in order to better interface with efforts such as Darwin Core and initiatives to promote the achievement of the United Nations’ Sustainable Development Goals (SDGs). As part of the ENVO consortium, BiGAEOn is an ontology for biogeographic areas specifically. Biogeographic areas are the basic units used in Comparative Biogeography to produce classifications of biogeographic areas, here, bioregionalisation. BiGAEOn model describe and harmonize biogeographic entities (e.g. areas of endemism, endemic areas…) as well as their relationships. Hence, it provides a rigorous and simple framework that improves biogeographic analyses and interoperability between systems. In particular, BiGAEOn integrates formal descriptions of WWF ecoregions (http://www.worldwildlife.org). In this presentation, we will illustrate how our ontology fits current debates with a case study on Australia, since it’s the actual scene of the bioregionalisation revival

BIOREALM — An ontology of comparative biogeography: New insights into the semantics of biodiversity conservation

Aim: We aimed to apply ontological techniques to address semantic ambiguities in protected area and conservation informatics. By doing so, we aimed to create a coherent, machine-actionable semantic representation of the biogeographic areas (which often overlap protected areas) to support more efficient and standardized informatics, supporting research and decision-making. We present BIOREALM, the first informatic ontology for comparative biogeography. Location: Global. Taxon: Any taxon can be integrated in BIOREALM. Methods: We convert a cladogram of biogeographic areas—generated by a process known as bioregionalization—into a series of ontological classes. Areas of endemism are treated as formal objects related by hierarchical relationships and constrained by a condition of monophyly. We use semantic web approaches to extend the Environment Ontology (ENVO) with classes for (often semantically confounded) biogeographic entities, including biogeographic areas, areas of endemism and endemic areas. We applied this approach to a bioregionalization of Australia as a case study. In all, 20 subregions which are part of the Austral Bioregionalisation Atlas have been selected for the study and integrated in BIOREALM. Results: We have created an ontology—formatted in the Web Ontology Language and adhering to the practices of the Open Biomedical and Biological Ontology Foundry—which provides a rigorous, extensible and machine-actionable framework that can improve biogeographic analyses and interoperability between systems. One main class and 20 individuals per class were implemented. Main Conclusions: BIOREALM encodes a model-theoretic view of endemism using semantic web approaches, offering new avenues to express and analyse biogeographic units. This approach offers a means to identify monophyletic biogeographic areas for conservation, based on specific combinations of monophyletic endemic taxa. Such an ontology provides knowledge representation solutions which supports interoperability along the FAIR (Findable, Accessible, Interoperable, Reusable) principles, thus fostering more consistent ecological informatics