ZooKeys, unlocking Earth’s incredible biodiversity and building a sustainable bridge into the public domain: From “print-based” to “web-based” taxonomy, systematics, and natural history. ZooKeys Editorial Opening Paper

Photographs as an essential biodiversity resource: drivers of gaps in the vascular plant photographic record

The photographic record is increasingly becoming an important biodiversity resource for primary research and conservation monitoring. However, globally, there are important gaps in this record even in relatively well-researched floras. To quantify the gaps in the Australian native vascular plant photographic record, we systematically surveyed 33 sources of well-curated species photographs, assembling a list of species with accessible and verifiable photographs, as well as the species for which this search failed. Of 21 077 Australian native species, 3715 lack a verifiable photograph across our 33 surveyed resources. There are three major geographic hotspots of unphotographed species in Australia, all far from current population centres. Many unphotographed species are small in stature or uncharismatic, and many are also recently described. The large number of recently described species without accessible photographs was surprising. There are longstanding efforts in Australia to organise the plant photographic record, but in the absence of a global consensus to treat photographs as an essential biodiversity resource, this has not become common practice. Many recently described species are small-range endemics and some have special conservation status. Completing the botanical photographic record across the globe will facilitate a virtuous feedback loop of more efficient identification, monitoring and conservation.

Terry Erwin’s legacy: from taxonomy and natural history to biodiversity research and conservation biology

No abstract

Terry L. Erwin and the race to document biodiversity (1940-2020)

Terry Erwin's race to document arthropod diversity inspired taxonomists, systematists, ecologists, evolutionary biologists, and the conservation community at large, as his curatorial work of more than 50 years at the Smithsonian's National Museum of Natural History and prolific publication record attests. The biography compiles public records, publications, as well as personal memoirs to describe the context in which Erwin's studies with carabid beetles evolved as formalization of concepts, such as biological diversity, megadiverse countries, biodiversity loss, and conservation biology, will become central for science in the upcoming years. Awareness to explore new frontiers such as the forest canopy and Erwin's studies in tropical forests, his easy-going personality, and dedicated mentoring attracted colleagues, students, and the general public, making him one of the leaders of tropical biology in the world.

DKey software for editing and browsing dichotomous keys

Despite advances in computer technology and the increasing availability of multiple-access taxonomic keys, traditional dichotomous keys remain the most often used taxonomic identification tools. On the other hand, there seems to be a lack of an editor of dichotomous keys, which is both freely available and easy to use. The DKey software was developed in order to alleviate this problem. A taxonomic key in text format can be imported to the software in order to edit it. Various editing options are possible, including: moving couplets, removing couplets, combining keys and renumbering keys. The software can output the key either in the traditional text format, ready for publication in a scientific journal, or in hypertext linked format, which makes identification faster and easier, due to the fact that pointers can be clicked in order to move to the next couplet. The DKey software should be useful for both taxonomic experts creating keys and those who use them for identification. The DKey software is freely available and open source.

A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank)

Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.

Symbiota - A virtual platform for creating voucher-based biodiversity information communities

We review the Symbiota software platform for creating voucher-based biodiversity information portals and communities. Symbiota was originally conceived to promote small- to medium-sized, regionally and/or taxonomically themed collaborations of natural history collections. Over the past eight years the taxonomically diverse portals have grown into an important resource in North America and beyond for mobilizing, integrating, and using specimen- and observation-based occurrence records and derivative biodiversity information products. Designed to mirror the conceptual structure of traditional floras and faunas, Symbiota is exclusively web-based and employs a novel data model, information linking, and algorithms to provide highly dynamic customization. The themed portals enable meaningful access to biodiversity data for anyone from specialist to high school student. Symbiota emulates functionality of modern Content Management Systems, providing highly sophisticated yet intuitive user interfaces for data entry, batch processes, and editing. Each kind of content provision may be selectively accessed by authenticated information providers. Occupying a fairly specific niche in the biodiversity informatics arena, Symbiota provides extensive data exchange facilities and collaborates with other development projects to incorporate and not duplicate functionality as appropriate.

A comprehensive DNA barcode library for the looper moths (Lepidoptera: Geometridae) of British Columbia, Canada

Background

The construction of comprehensive reference libraries is essential to foster the development of DNA barcoding as a tool for monitoring biodiversity and detecting invasive species. The looper moths of British Columbia (BC), Canada present a challenging case for species discrimination via DNA barcoding due to their considerable diversity and limited taxonomic maturity.

Methodology/Principal Findings

By analyzing specimens held in national and regional natural history collections, we assemble barcode records from representatives of 400 species from BC and surrounding provinces, territories and states. Sequence variation in the barcode region unambiguously discriminates over 93% of these 400 geometrid species. However, a final estimate of resolution success awaits detailed taxonomic analysis of 48 species where patterns of barcode variation suggest cases of cryptic species, unrecognized synonymy as well as young species.

Conclusions/Significance

A catalog of these taxa meriting further taxonomic investigation is presented as well as the supplemental information needed to facilitate these investigations.

Species as ranked taxa

Because species names play an important role in scientific communication, it is more important that species be understood to be taxa than that they be equated with functional ecological or evolutionary entities. Although most biologists would agree that taxa are composed of organisms that share a unique common history, 2 major challenges remain in developing a species-as-taxa concept. First, grouping: in the face of genealogical discordance at all levels in the taxonomic hierarchy, how can we understand the nature of taxa? Second, ranking: what criteria should be used to designate certain taxa in a nested series as being species? The grouping problem can be solved by viewing taxa as exclusive groups of organisms- sets of organisms that form a clade for a plurality of the genome (more than any conflicting set). However, no single objective criterion of species rank can be proposed. Instead, the species rank should be assigned by practitioners based on the semisubjective application of a set of species-ranking criteria. Although these criteria can be designed to yield species taxa that approximately match the ecological, evolutionary, and morphological entities that taxonomists have traditionally associated with the species rank, such a correspondence cannot be enforced without undermining the assumption that species are taxa. The challenge and art of monography is to use genealogical and other kinds of data to assign all organisms to one and only one species-ranked taxon. Various implications of the species-as-ranked-taxa view are discussed, including the synchronic nature of taxa, fossil species, the treatment of hybrids, and species nomenclature. I conclude that, although challenges remain, adopting the view that species are ranked taxa will facilitate a much-needed revolution in taxonomy that will allow it to better serve the biodiversity informatic needs of the 21st century.