Nomenclatural benchmarking: the roles of digital typification and telemicroscopy

Genera of Tischeriidae (Lepidoptera): a review of the global fauna, with descriptions of new taxa

For the first time, genera of leaf mining Tischeriidae of the global fauna are reviewed and four new genera are described: Coptotrichoides Dikus & Stonis, gen. nov., trophically associated with Sapindaceae from Central and South America; Rytietia Dikus, Xu & Dai, gen. nov., trophically associated with Annonaceae from East and South East Asia; Pafazaria Dikus & Stonis, gen. nov., trophically associated with Fabaceae and Malvaceae from East and South East Asia; and Gnathitischeria Dikus, gen. nov., trophically associated with Malvaceae and Asteraceae from Central America. In addition to the descriptions of new genera, all previously described genera (Coptotriche Walsingham, 1890; Dishkeya Stonis, 2020; Tischeria Zeller, 1839; Manitischeria Dikus & Stonis, 2021; Neotischeria Dikus & Stonis, 2021; Paratischeria Dikus & Stonis, 2017; and Astrotischeria Puplesis & Dikus, 2003) are characterized and a pictorial identification key for all 11 genera is provided. Morphological and biological characteristics of all genera are supplemented with some molecular data. We described 12 new species: South East Asian Coptotriche sapaensis Dikus & Stonis, sp. nov.; Central American Coptotrichoides sapindoidum Dikus & Stonis, sp. nov. and Tischeria neokristenseni Dikus & Stonis, sp. nov.; South East Asian Rytietia uncinata Dikus, Xu & Dai, sp. nov., East Asian R. chongyiensis Xu & Dai, sp. nov.; South East Asian Pafazaria capitata Dikus & Stonis, sp. nov. and P. faboidica Dikus & Stonis, sp. nov.; Central American Neotischeria antigua Dikus & Remeikis, sp. nov. and N. subantigua Dikus & Remeikis, sp. nov.; South American Astrotischeria incae Dikus & Stonis, sp. nov.; and Central American Gnathitischeria atitlani Dikus & Stonis, sp. nov. and G. arcana Dikus & Stonis, sp. nov. The taxonomic rank of the East Asian subspecies Tischeria decidua siorkionla Kozlov, 1986 is elevated to species rank: T. siorkionla Kozlov (stat. nov.). The male genitalia of holotypes, paratypes, lectotypes or paralectotypes, or non-type specimens of some little-known species are examined for the first time. We provide the first morphological documentation for the following: Tischeria ceanothi lectotype and paralectotype; T. immaculata (stat. restored) paratype; Coptotrichoides deliquescens (Meyrick) lectotype and paralectotype; lectotypes of Coptotriche aenea (Frey & Boll), Astrotischeria plagifera (Meyrick), A. helianthi (Frey & Boll), and A. ephaptis (Meyrick); Coptotriche berberella (De Prins) paratype; and the first photographic documentation of Tischeria lvoskyi Kozlov holotype. Some non-type specimens deposited at NHMUK, including a few previously neglected species, are also examined and documented, including the American Astrotischeria solidagonifoliella (Clemens) and A. omissa (Braun). Nine new combinations are provided: Coptotrichoides deliquescens (Meyrick, 1915), comb. nov.; C. singularis (Stonis & Dikus) comb. nov.; C. suprafasciata (Dikus & Stonis) comb. nov., C. serjaniphaga (Remeikis & Stonis) comb. nov.; C. braziliensis (Dikus & Stonis) comb. nov.; Pafazaria jingdongensis (Xu & Dai), comb. nov.; Neotischeria explosa (Braun) comb. nov.; N. pallidipennella (Braun) comb. nov.; and Astrotischeria heteroterae (Frey & Boll) comb. nov. The synonymization of Tischeria longeciliata Frey & Boll, 1878 with Astrotischeria helianthi (Frey & Boll, 1878) is confirmed. One new species group, the Tischeria ceanothi group, is established. We also report a new distribution record of T. dodonaea Stainton from the Caucasus, Armenia. Three tables and 569 figures of adult external morphology, male and female genitalia, leaf mines, and cladograms based on molecular characters are provided.

scAnt-an open-source platform for the creation of 3D models of arthropods (and other small objects)

We present scAnt, an open-source platform for the creation of digital 3D models of arthropods and small objects. scAnt consists of a scanner and a Graphical User Interface, and enables the automated generation of Extended Depth Of Field images from multiple perspectives. These images are then masked with a novel automatic routine which combines random forest-based edge-detection, adaptive thresholding and connected component labelling. The masked images can then be processed further with a photogrammetry software package of choice, including open-source options such as Meshroom, to create high-quality, textured 3D models. We demonstrate how these 3D models can be rigged to enable realistic digital specimen posing, and introduce a novel simple yet effective method to include semi-realistic representations of approximately planar and transparent structures such as wings. As a result of the exclusive reliance on generic hardware components, rapid prototyping and open-source software, scAnt costs only a fraction of available comparable systems. The resulting accessibility of scAnt will (i) drive the development of novel and powerful methods for machine learning-driven behavioural studies, leveraging synthetic data; (ii) increase accuracy in comparative morphometric studies as well as extend the available parameter space with area and volume measurements; (iii) inspire novel forms of outreach; and (iv) aid in the digitisation efforts currently underway in several major natural history collections.

Research and development in robotics with potential to automate handling of biological collections

This report investigates the current state of physical (mechanical) robotics, automated warehousing approaches and assistive technologies in relation to the storage, handling and processing (particularly digitisation) of natural history collections.

Robotics can sound futuristic, however we provide case studies that show many and growing examples of physical automation in the natural history and cultural heritage sectors, including barcodes and conveyor belts for digitisation; robots that handle multiple vials for molecular and genetic work; robots for use in in display or exhibition contexts; and automated warehousing of library collections. We provide a non-exhaustive example of an end to end workflow of storage, retrieval and processing and discuss aspects of the tools and challenges relevant to these stages. The Distributed System of Scientific Collections (DiSSCo), a new Research Infrastructure for natural science collections, should build on this, leading a future programme of pilots that develop understanding of independent stages, and can be connected to make progress towards end-to-end solutions.

Robots, or automated systems, excel at repetitive tasks, and are developing rapidly to be able to handle more complex object types, at lower cost. High volume, high variety of objects, and considerations such as fragility are not unique to the natural history sector - they apply for example to major retail operations - however natural history collections do offer some of the more extreme examples of these challenges, and in particular are not replaceable. Increased consistency of storage units is likely to be a critical factor in enabling automated handling in future, as well as looking at automation possibilities when new collections storage spaces are developed and built. Engagement with industry and subject matter experts has been patchy and again we recommend that DiSSCo help to ensure a joined up engagement with the right incentives in place, and with clear communication of requirements and challenges for shared R&D.

When examining return on investment for particular automation, collections-holding institutions need to consider not only time and cost of automation compared to human labour, but wider factors including: health and safety such as physical environment and repetitve strain injury; security; quality and consistency of outputs; degree of criticality in response times (e.g. if digitising on demand); effective use of spaces; and freeing up staff to conduct other tasks.

Purely software-based automation is outside the scope of this report, but is also in increasing use and has enormous potential, for example to transform the extraction of label and specimen data at scale from images. The challenges of managing and digitising collections at scale under DiSSCo are likely to require a combination of hardware and software automation approaches.

Repositories for Taxonomic Data: Where We Are and What is Missing

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].

Next-generation morphological character discovery and evaluation: an X-ray micro-CT enhanced revision of the ant genus Zasphinctus Wheeler (Hymenoptera, Formicidae, Dorylinae) in the Afrotropics

New technologies for imaging and analysis of morphological characters offer opportunities to enhance revisionary taxonomy and better integrate it with the rest of biology. In this study, we revise the Afrotropical fauna of the ant genus Zasphinctus Wheeler, and use high-resolution X-ray microtomography (micro-CT) to analyse a number of morphological characters of taxonomic and biological interest. We recognise and describe three new species: Z. obamaisp. n., Z. sarowiwaisp. n., and Z. wilsonisp. n. The species delimitations are based on the morphological examination of all physical specimens in combination with 3D scans and volume reconstructions. Based on this approach, we present a new taxonomic discrimination system for the regional fauna that consists of a combination of easily observable morphological characters visible at magnifications of around 80-100 ×, less observable characters that require higher magnifications, as well as characters made visible through virtual dissections that would otherwise require destructive treatment. Zasphinctus are rarely collected ants and the material available to us is comparatively scarce. Consequently, we explore the use of micro-CT as a non-invasive tool for the virtual examination, manipulation, and dissection of such rare material. Furthermore, we delineate the treated species by providing a diagnostic character matrix illustrated by numerous images and supplement that with additional evidence in the form of stacked montage images, 3D PDFs and 3D rotation videos of scans of major body parts and full body (in total we provide 16 stacked montage photographs, 116 images of 3D reconstructions, 15 3D rotation videos, and 13 3D PDFs). In addition to the comparative morphology analyses used for species delimitations, we also apply micro-CT data to examine certain traits, such as mouthparts, cuticle thickness, and thoracic and abdominal muscles in order to assess their taxonomic usefulness or gain insights into the natural history of the genus. The complete datasets comprising the raw micro-CT data, 3D PDFs, 3D rotation videos, still images of 3D models, and coloured montage photos have been made available online as cybertypes (Dryad, http://dx.doi.org/10.5061/dryad.4s3v1).

X-Ray microtomography for ant taxonomy: An exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar

We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrogsp. n. and T. nymeriasp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution maps for both new species. In addition to conventional morphological examination, we have used virtual reconstructions based on volumetric μCT scanning data for the species descriptions. We also include 3D PDFs, still images of virtual reconstructions, and 3D rotation videos for both holotype workers and one paratype queen. The complete μCT datasets have been made available online (Dryad, https://datadryad.org) and represent the first cybertypes in ants (and insects). We discuss the potential of μCT scanning and critically assess the usefulness of cybertypes for ant taxonomy.

Evaluation of a protocol for remote identification of mosquito vector species reveals BG-Sentinel trap as an efficient tool for Anopheles gambiae outdoor collection in Burkina Faso

Background

Feasibility and costs of monitoring efforts aimed to monitor mosquito species are strictly dependent on the presence of skilled entomologists directly in the field. However, in several contexts this is not possible or easy to organize, thus limiting the possibility to obtain crucial information on presence/abundance of potential disease vectors and of new invasive species. Digital imaging approaches could be extremely useful in the frame of medical entomology to overcome this limit. This work describes a surveillance approach to collect and morphologically identify host-seeking malaria vectors based on remote transmission of digital images of specimens collected with ad hoc modified traps.

Methods

CDC light trap (CDC) and the BG-Sentinel trap (BG), both baited with BG-lure and CO₂, were modified in order to have collected mosquitoes immobilized on a bi-dimensional surface. The performance of the two traps in the field was comparatively tested by Latin-square experiments in two villages of Burkina Faso under low and high mosquito densities. The efficiency of identifications based the inspection of digital images versus microscopic identifications of collected specimens was compared.

Results

A total of 1,519 mosquitoes belonging to 16 species were collected, of which 88.5% were microscopically identified as Anopheles gambiae s.l. (mainly Anopheles coluzzii, 85.7%). During dry season BG collected 15 times more females than CDC outdoors, whereas indoors the BG collected 0.4 times less than CDC. During rainy season the ratio BG/CDC was 6.4 and 0.7 outdoors and indoors, respectively. The efficiency of digital images versus microscopic identifications of collected specimens was 97.9%, 95.6% and 81.5% for Culicidae, Anophelinae and An. gambiae s.l., respectively.

Conclusions

Results strongly encourage the use of BG-trap for collecting host-seeking An. gambiae particularly in the outdoor environment, providing new perspectives to the challenge of collecting this fraction of the biting population, whose epidemiological relevance is increasing due to the success of large-scale implementation of indoor malaria vector control strategies. Moreover, results show that the transmission of digital images of specimens collected by the ad hoc modified host-seeking traps efficiently allows identification of malaria vectors, thus opening the perspective to easily carry out mosquito monitoring also in the absence of entomologists directly in the field.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-015-0674-7) contains supplementary material, which is available to authorized users.

Capturing natural-colour 3D models of insects for species discovery and diagnostics

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity—past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens “from all angles” and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. (“Natural-colour” is used to contrast with “false-colour”, i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.

Micro-computed tomography: Introducing new dimensions to taxonomy

Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called “cybertypes”, and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information.