(Re)Discovering Known Biodiversity: Introduction

Biodiversity sciences, including taxonomy, are empirical sciences where all results are published in scholarly publications as part of the research life cycle. This creates a corpus of an estimated 500 million printed pages (Kalfatovic 2010) including billions of facts such as traits, biotic interactions, observations characterizing all the estimated 1.9 million known species (Costello et al. 2013). This library is continually reused, cited and extended, for example with more than an estimated 15,000–20,000 new species annually (Polaszek 2005). All of these figures are estimates because we neither know how many species have been discovered, nor how many are being discovered every day, let alone what we know about them. Following standard scientific practice, previous publications, specimens, gene sequences, or taxonomic treatments (Catapano 2019) are cited more or less explicitly. In the pre-digital age, these links were meant for the human reader to be understood. For example, "L. 1758" is an established reference and links to both, Carolus Linnaeus and Linnaeus 1758, understandable at least by an expert human, and in the digital age, provides access to the respective digital representation. These data within the hundreds of millions of printed and now increasingly digitally published pages form a seamless, albeit implicit knowledge graph. Unfortunately, most of these publications are in print—the Biodiversity Heritage Library digitized about 50 million pages (Kalfatovic 2010)—or in many cases, closed access publications, and thus this knowledge is not readily accessible in the digital age. However, in today's digital age, each of these kinds of implicit links is an expensive stumbling block to access and reuse of the referenced data, its parent publications and the cited referenced data therein. Inadequate formats, language and access to taxonomic information were already recognized in 1992 at the Rio Summit (Taxonomic Impediment). The consequences of these impediments are only now obvious with the realization of the daunting amount of human resources needed to digitally catalogue and index this unknown (not discoverable and inaccessible) known knowledge, let alone making the data itself findable, accessible, interoperable and reusable (FAIR). This is a formidable and complex scientific challenge. Plazi is taking on this challenge. Its vision is to promote and enable the discovery and liberation of data to transform the unknown known data into digitally accessible knowledge, i.e., to build a digital knowledge base aimed at discovering all the species (and other taxa) we know, and what we know about them. Taxonomic publications with their highly standardized taxonomic names, taxonomic treatments, treatment citations, material citations and illustrations are well suited to machine extraction. Together they include the entire catalogue of life with all the discovered species and their synonyms, often tens to hundreds of treatments, and figures that depict the myriad forms that comprise the world’s biodiversity. Once these data are FAIR, it allows bidirectional linking, for example of taxonomic names to the referenced taxonomic treatment, other digital resources such as gene sequences or digital specimens. At the same time, each datum is an entry point to the wealth of information that can be followed by the human user by clicking the links, but more importantly, analysed by machines. Here, digitally accessible knowledge will be defined in the context of discovering known biodiversity, including strategies of how to approach the challenge, which then will be detailed in subsequent talks in this symposium. This symposium is based on Plazi’s ongoing data liberation and discovery supported by the European Union (e.g. Biodiversity Community Integrated Knowledge Library BiCIKL), United States (e.g. NIH) and Swiss research funding (e.g. e-BioDiv and the Arcadia Fund), collaboration with publishers (e.g. Pensoft, Muséum national d'Histoire naturelle, Consortium of European Taxonomic Facilities Publications, the Zenodo repository, Biodiversity Heritage Library), and data reusers like the Global Biodiversity Information Facility, Ocellus, Synospecies and openBiodiv. Currently, over 500,000 taxonomic treatments and 300,000 illustrations have been liberated and are accessible through TreatmentBank and the Biodiversity Literature Repository.

International Palaeoentomological Society Statement on unethical practices in describing new taxa

Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. Taxonomy as the scientific discipline that explores, discovers, interprets, represents, names, and organizes organic beings (Ebach et al., 2011), is one of the oldest biological disciplines. Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge (Thomson et al., 2018). However, taxonomic impediment, decrease in the number of taxonomists, lack of appreciation for this area of research is not only the problem for studies on Recent organisms and their diversity (Wägele et al., 2011; Britz et al., 2020; Vinarski, 2020; Raposo et al., 2021), but it is affecting seriously also research and studies on fossils, their taxonomy and their palaeodiversity.

Response to Zamani et al. (2020): The omission of critical data in the pursuit of “revolutionary” methods to accelerate the description of species

Here we respond to the criticisms leveled against a proposal that suggested an efficient solution to the taxonomic impediment. We clarify some of our objectives and demonstrate that many of the criticisms apply more to traditional approaches to taxonomy rather than to our minimalist approach.

From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae)

Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.

Electronic identification keys for species with cryptic morphological characters: a feasibility study using some Thesium species

The popularity of electronic identification keys for species identification has increased with the rapid technological advancements of the 21st century. Although electronic identification keys have several advantages over conventional textual identification keys and work well for charismatic species with large and clear morphological characters, they appear to be less feasible and less effective for species with cryptic morphology (i.e. small, obscure, variable characters and/or complicated structures associated with terminology that is difficult to interpret). This is largely due to the difficulty in presenting and illustrating cryptic morphological characters unambiguously. When taking into account that enigmatic species with cryptic morphology are often taxonomically problematic and therefore likely exacerbate the taxonomic impediment, it is clear that species groups with cryptic morphology (and all the disciplines dependent on their correct identification) could greatly benefit from a user-friendly identification tool, which clearly illustrates cryptic characters. To this end, the aim of this study was to investigate and develop best practices for the unambiguous presentation of cryptic morphological characters using a pilot interactive photographic identification key for the taxonomically difficult plant genus Thesium (Santalaceae), as well as to determine its feasibility. The project consisted of three stages: (1) software platform selection, (2) key construction and (3) key evaluation. The proposed identification key was produced with Xper3 software and can be accessed at http://www.xper3.fr/xper3GeneratedFiles/publish/identification/1330098581747548637/mkey.html. Methodologies relating to amongst others, character selection and delineation, visual and textual descriptions, key construction, character coding and key evaluation are discussed in detail. Seventeen best practices identified during this study are subsequently suggested for future electronic key compilation of species with cryptic morphology. This study indicates that electronic identification keys can be feasible and effective aids for the identification of species with cryptic morphological characters when the suggested best practices are followed.