A multi-taxon analysis of European Red Lists reveals major threats to biodiversity

Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species' distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.

Type catalogue of Oedipodinae (Orthoptera: Acrididae) present in Naturalis Biodiversity Center Leiden (Netherlands)

A type catalogue of Oedipodinae in the collection of Naturalis Biodiversity Center is presented altogether 82 type specimens including 13 primary types and 5 junior synonyms: holotypes (4 species), neotype (1 species), lectotypes (2 species, 1 subspecies), and syntypes (5 species). Furthermore 50 additional secondary type specimens were recorded. Here, we present the full type material catalogue including a locality map of all species and pictures of the 15 primary type species.

A review of Eupholidoptera (Orthoptera, Tettigoniidae) from Crete, Gavdos, Gavdopoula, and Andikithira

Being nocturnal, hiding in prickly bushes and shrubs during the day, Eupholidoptera species in Crete and its neighbouring islands are easily overlooked, and until now our knowledge about their distribution was based on some thirty sightings across 11 species. In this paper results are presented of a study of Eupholidoptera specimens collected between 1987 and 2020 by hand-catches and pitfall and fermenting traps on the Greek islands of Crete, Gavdos, Gavdopoula, and Andikithira. Diagnostic features of all known species are presented and illustrated with stacked images. An updated key to all species is provided. Eupholidoptera francisae Tilmans & Odé, sp. nov. from Andikithira and southwestern Crete and Eupholidoptera marietheresae Willemse & Kotitsa, sp. nov. from Mt. Dikti are described. Female E. cretica, E. gemellata, and E. mariannae are described, and the female of E. astyla is redescribed. Bioacoustics for E. francisae Tilmans & Odé, sp. nov., E. giuliae, and E. jacquelinae are presented for the first time. Eupholidoptera smyrnensis is reported for the first time from Crete. A substantial amount of new distribution data for Eupholidoptera species on Crete is presented. The current distribution pattern and first analyses of phylogeny based on molecular data of Eupholidoptera species on Crete are discussed in relation to paleogeographical events.

Sharing taxonomic expertise between natural history collections using image recognition

Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.

Lost lovers linked at long last: elusive female Nanophyllium mystery solved after a century of being placed in a different genus (Phasmatodea, Phylliidae)

After successful laboratory rearing of both males and females from a single clutch of eggs, the genus Nanophyllium Redtenbacher, 1906 (described only from males) and the frondosum species group within Phyllium (Pulchriphyllium) Griffini, 1898 (described only from females) are found to be the opposite sexes of the same genus. This rearing observation finally elucidates the relationship of these two small body sized leaf insect groups which, for more than a century, have never been linked before. This paper synonymizes the frondosum species group with Nanophyllium Redtenbacher, 1906 in order to create a singular and clearly defined taxonomic group. Five species are transferred from the Phyllium (Pulchriphyllium) frondosum species group and create the following new combinations: Nanophylliumasekiense (Größer, 2002), comb. nov.; Nanophylliumchitoniscoides (Größer, 1992), comb. nov.; Nanophylliumfrondosum (Redtenbacher, 1906), comb. nov.; Nanophylliumkeyicum (Karny, 1914), comb. nov.; Nanophylliumsuzukii (Größer, 2008), comb. nov. The only taxon from this species group not transferred from the frondosum species group to Nanophyllium is Phyllium (Pulchriphyllium) groesseri Zompro, 1998. Based on protibial exterior lobes, this species belongs in the schultzei species group as described in Hennemann et al. 2009 and is therefore excluded from further discussion here. The rearing of Nanophyllium also yielded the male Nanophylliumasekiense (Größer, 2002), comb. nov. thus, enabling comparison of this male to the other previously known Nanophyllium species. Two new species of nano-leaf insects are described within, Nanophylliummiyashitaisp. nov., from Morobe Province, Papua New Guinea, and Nanophylliumdaphnesp. nov., from Biak Island, Papua Province, Indonesia. With such distinct sexual dimorphism in Nanophyllium between sexes, which have only now been matched up via captive rearing, illustrated within are numerous specimens which might represent the unknown opposite sexes of the many currently known species of Nanophyllium. Due to pronounced sexual dimorphism in Nanophyllium, only future captive rearing or molecular analysis will match up the many unknown sexes. To conclude, with the description of two new Nanophyllium species, dichotomous keys to species for known males and females are presented.

Digitisation of private collections

Results are presented of a study investigating solutions and procedures to incorporate private natural history collections into the international collections data infrastructure. Results are based on pilot projects carried out in three European countries aimed at approaches on how to best motivate and equip citizen collectors for digitisation:

1) In Estonia, the approach was to outline tools for registering, digitising and publishing private collection data in the biodiversity data management system PlutoF.

2) In Finland, the functionality of FinBIF, a portal offering a popular Notebook Service for citizens to store observations has been expanded to include collection specimens related to a field gathering event.

3) In the Netherlands private collection owners were approached directly and asked to start digitising their collection using dedicated software, either by themselves or with the help of volunteers who were recruited specifically for this task.

In addition to management tools, pilots also looked at motivation, persons undertaking the work, scope, planning, specific knowledge or skills required and the platform for online publication. Future ownership, legality of specimens residing in private collections and the use of unique identifiers are underexposed aspects effecting digitisation. Besides streamlining the overall process of digitising private collections and dealing with local, national or international challenges, developing a communication strategy is crucial in order to effectively distribute information and keep private collection owners aware of ongoing developments.

Besides collection owners other stakeholders were identified and for each of them a roadmap is outlined aimed at further streamlining the data from private collections into the international infrastructure.

In conclusion recommendations are presented based on challenges encountered during this task that are considered important to really make significant progress towards the overall accessibility of data stored in privately held natural history collections.

Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1

DiSSCo, the Distributed System of Scientific Collections, is a pan-European Research Infrastructure (RI) mobilising, unifying bio- and geo-diversity information connected to the specimens held in natural science collections and delivering it to scientific communities and beyond. Bringing together 120 institutions across 21 countries and combining earlier investments in data interoperability practices with technological advancements in digitisation, cloud services and semantic linking, DiSSCo makes the data from natural science collections available as one virtual data cloud, connected with data emerging from new techniques and not already linked to specimens. These new data include DNA barcodes, whole genome sequences, proteomics and metabolomics data, chemical data, trait data, and imaging data (Computer-assisted Tomography (CT), Synchrotron, etc.), to name but a few; and will lead to a wide range of end-user services that begins with finding, accessing, using and improving data. DiSSCo will deliver the diagnostic information required for novel approaches and new services that will transform the landscape of what is possible in ways that are hard to imagine today.

With approximately 1.5 billion objects to be digitised, bringing natural science collections to the information age is expected to result in many tens of petabytes of new data over the next decades, used on average by 5,000 – 15,000 unique users every day. This requires new skills, clear policies and robust procedures and new technologies to create, work with and manage large digital datasets over their entire research data lifecycle, including their long-term storage and preservation and open access. Such processes and procedures must match and be derived from the latest thinking in open science and data management, realising the core principles of 'findable, accessible, interoperable and reusable' (FAIR).

Synthesised from results of the ICEDIG project ("Innovation and Consolidation for Large Scale Digitisation of Natural Heritage", EU Horizon 2020 grant agreement No. 777483) the DiSSCo Conceptual Design Blueprint covers the organisational arrangements, processes and practices, the architecture, tools and technologies, culture, skills and capacity building and governance and business model proposals for constructing the digitisation infrastructure of DiSSCo. In this context, the digitisation infrastructure of DiSSCo must be interpreted as that infrastructure (machinery, processing, procedures, personnel, organisation) offering Europe-wide capabilities for mass digitisation and digitisation-on-demand, and for the subsequent management (i.e., curation, publication, processing) and use of the resulting data. The blueprint constitutes the essential background needed to continue work to raise the overall maturity of the DiSSCo Programme across multiple dimensions (organisational, technical, scientific, data, financial) to achieve readiness to begin construction.

Today, collection digitisation efforts have reached most collection-holding institutions across Europe. Much of the leadership and many of the people involved in digitisation and working with digital collections wish to take steps forward and expand the efforts to benefit further from the already noticeable positive effects. The collective results of examining technical, financial, policy and governance aspects show the way forward to operating a large distributed initiative i.e., the Distributed System of Scientific Collections (DiSSCo) for natural science collections across Europe. Ample examples, opportunities and need for innovation and consolidation for large scale digitisation of natural heritage have been described. The blueprint makes one hundred and four (104) recommendations to be considered by other elements of the DiSSCo Programme of linked projects (i.e., SYNTHESYS+, COST MOBILISE, DiSSCo Prepare, and others to follow) and the DiSSCo Programme leadership as the journey towards organisational, technical, scientific, data and financial readiness continues.

Nevertheless, significant obstacles must be overcome as a matter of priority if DiSSCo is to move beyond its Design and Preparatory Phases during 2024. Specifically, these include:

Organisational:

Strengthen common purpose by adopting a common framework for policy harmonisation and capacity enhancement across broad areas, especially in respect of digitisation strategy and prioritisation, digitisation processes and techniques, data and digital media publication and open access, protection of and access to sensitive data, and administration of access and benefit sharing.

Pursue the joint ventures and other relationships necessary to the successful delivery of the DiSSCo mission, especially ventures with GBIF and other international and regional digitisation and data aggregation organisations, in the context of infrastructure policy frameworks, such as EOSC. Proceed with the explicit aim of avoiding divergences of approach in global natural science collections data management and research.

Technical:

Adopt and enhance the DiSSCo Digital Specimen Architecture and, specifically as a matter of urgency, establish the persistent identifier scheme to be used by DiSSCo and (ideally) other comparable regional initiatives.

Establish (software) engineering development and (infrastructure) operations team and direction essential to the delivery of services and functionalities expected from DiSSCo such that earnest engineering can lead to an early start of DiSSCo operations.

Scientific:

Establish a common digital research agenda leveraging Digital (extended) Specimens as anchoring points for all specimen-associated and -derived information, demonstrating to research institutions and policy/decision-makers the new possibilities, opportunities and value of participating in the DiSSCo research infrastructure.

Data:

Adopt the FAIR Digital Object Framework and the International Image Interoperability Framework as the low entropy means to achieving uniform access to rich data (image and non-image) that is findable, accessible, interoperable and reusable (FAIR).

Develop and promote best practice approaches towards achieving the best digitisation results in terms of quality (best, according to agreed minimum information and other specifications), time (highest throughput, fast), and cost (lowest, minimal per specimen).

Financial

Broaden attractiveness (i.e., improve bankability) of DiSSCo as an infrastructure to invest in.

Plan for finding ways to bridge the funding gap to avoid disruptions in the critical funding path that risks interrupting core operations; especially when the gap opens between the end of preparations and beginning of implementation due to unsolved political difficulties.

Strategically, it is vital to balance the multiple factors addressed by the blueprint against one another to achieve the desired goals of the DiSSCo programme. Decisions cannot be taken on one aspect alone without considering other aspects, and here the various governance structures of DiSSCo (General Assembly, advisory boards, and stakeholder forums) play a critical role over the coming years.

A benchmark dataset of herbarium specimen images with label data

BACKGROUND

More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Different methods, such as crowdsourcing and artificial intelligence, are being developed to optimise transcription, but herbarium specimens pose difficulties in data extraction for many reasons.

NEW INFORMATION

To provide developers of transcription methods with a means of optimisation, we have compiled a benchmark dataset of 1,800 herbarium specimen images with corresponding transcribed data. These images originate from nine different collections and include specimens that reflect the multiple potential obstacles that transcription methods may encounter, such as differences in language, text format (printed or handwritten), specimen age and nomenclatural type status. We are making these specimens available with a Creative Commons Zero licence waiver and with permanent online storage of the data. By doing this, we are minimising the obstacles to the use of these images for transcription training. This benchmark dataset of images may also be used where a defined and documented set of herbarium specimens is needed, such as for the extraction of morphological traits, handwriting recognition and colour analysis of specimens.

Improved standardization of transcribed digital specimen data

There are more than 1.2 billion biological specimens in the world's museums and herbaria. These objects are particularly important forms of biological sample and observation. They underpin biological taxonomy but the data they contain have many other uses in the biological and environmental sciences. Nevertheless, from their conception they are almost entirely documented on paper, either as labels attached to the specimens or in catalogues linked with catalogue numbers. In order to make the best use of these data and to improve the findability of these specimens, these data must be transcribed digitally and made to conform to standards, so that these data are also interoperable and reusable. Through various digitization projects, the authors have experimented with transcription by volunteers, expert technicians, scientists, commercial transcription services and automated systems. We have also been consumers of specimen data for taxonomical, biogeographical and ecological research. In this paper, we draw from our experiences to make specific recommendations to improve transcription data. The paper is split into two sections. We first address issues related to database implementation with relevance to data transcription, namely versioning, annotation, unknown and incomplete data and issues related to language. We then focus on particular data types that are relevant to biological collection specimens, namely nomenclature, dates, geography, collector numbers and uniquely identifying people. We make recommendations to standards organizations, software developers, data scientists and transcribers to improve these data with the specific aim of improving interoperability between collection datasets.

Lung function in African infants: a pilot study

BACKGROUND

The burden of childhood respiratory illness is large in low and middle income countries (LMICs). Infant lung function (ILF) testing may provide useful information about lung growth and susceptibility to respiratory disease. However, ILF has not been widely available in LMICs settings where the greatest burden of childhood respiratory disease occurs.

AIM

To implement and evaluate a pilot study of ILF testing in a semi-rural setting in South Africa.

METHOD

Infant lung function testing was established at a community hospital in South Africa. All measures were done in unsedated infants during sleep. Measurements, made with the infant quietly breathing through a face mask and bacterial filter, included tidal breathing (TBFVL), exhaled nitric oxide (eNO), and sulphur hexafluoride multiple breath washout (MBW) measures using an ultrasonic flow meter and chemoluminescent NO analyzer.

RESULTS

Twenty infants, mean age of 7.7 (SD 2.9) weeks were tested; 8 (40%) were Black African and 12 (60%) were mixed race. Five (25%) infants were preterm. There were 19 (95%) successful TBFVL and NO tests and 18 (90%) successful MBW tests. The mean tidal volume was 30.5 ml (SD 5.9), respiratory rate 50.2 breaths per minute (SD 8.7), and eNO 10.4 ppb (SD 7.3). The mean MBW measures were: functional residual capacity 71 ml (SD 13) and the lung clearance index 7.6 (SD 0.5). The intra-subject coefficient of variations (CV) of lung function measures were similar to published normative data for Caucasian European infants.

CONCLUSION

In this study we demonstrate that unsedated infant lung function measures of tidal breathing, MBW, and eNO are feasible in a semi-rural African setting with rates comparable to those reported from high income countries.

A trial to control the tsetse fly, Glossina morsitans centralis, with low densities of odour-baited targets in west Zambia

A large-scale trial investigated the possibility of eradicating G.m.centralis from a traditional cattle rearing area using odour-baited targets at a reduced overall target density from 4 to 0.5-2.3 per km2, thus cutting down initial material costs by about 50%. Only the periphery of what was thought to be prime tsetse habitat (dense woodland) was treated with targets. These were all black or blue/black cloth (1.8 x 1 m), sprayed with deltamethrin suspension concentrate and baited with butanone and/or acetone (40-130 mg/h) and 1-octen-3-ol (0.5 mg/h). Although fly catches from traps and flyrounds initially dropped by approximately 3% per day and trypanosomiasis cases declined by 99% within a year, eradication was not achieved, so that more targets were deployed at a later stage. Although initially cheaper, the option of using reduced target densities proved financially unattractive because of prolonged periods of target maintenance prior to eradication. Revised strategies for tsetse control with odour-baited, insecticide-impregnated targets in west Zambia are presented.