ARPHA Preprints
Not a member yet
49208 research outputs found
Sort by
Exploring the drivers and effects of biodiversity change in the coast of Cantabria and Santander Bay (Southern Gulf of Biscay)
No full textThis preprint has been retracted, due to duplication. Please refer to: https://doi.org/10.3897/arphapreprints.e175173 for its content
A new cave-dwelling species of Trimma (Teleostei, Gobiidae) from the Red Sea, with notes on Red Sea endemism in Trimma spp.
No full textA new species of the gobiid genus Trimma is described from the Farasan Banks in the southeastern Red Sea. The new species is characterized by having a predorsal midline with 7–8 scales, the fifth pelvic-fin ray unbranched, cheek and opercle scaleless, all pectoral-fin rays unbranched, and a dorsal fin VI + I,7, without elongate spines. In life, the species is bright yellow throughout, with a distinctive yellow-green longitudinal band in the central third of the dorsal fins. The new species inhabits caves on exposed offshore reefs at depths between 15 and 30 m where it occurs in small groups of up to 10 individuals. The new species appears to be sister to T. winchi from the western Indian Ocean. We also present a multilocus phylogeny (COI, 16S, Ptr, S7I1), including all known Red Sea Trimma and 21 non-Red Sea species, and an expanded supermatrix tree with 93 species to place Red Sea endemism in broader context. This brings the total number of Trimma species known from the Red Sea to 10, with eight appearing to be endemic to the region. The high proportion of endemism in the genus is noteworthy, even for the Red Sea, which has one of the highest proportions of endemic reef fishes in the Indo-Pacific. Moreover, K2P distances in the two widespread species suggest they may also represent cryptic endemic species, but further analyses are needed. The new species is currently known only from the Farasan Banks region despite extensive sampling along the Saudi Arabian Red Sea coast
Emergence of an invasive ascidian in Canary Islands (Eastern Atlantic): Tracking the arrival and spread of Cnemidocarpa irene
No full textThis study documents the first occurrence and rapid expansion of the solitary ascidian Cnemidocarpa irene in natural marine habitats of Tenerife (Canary Islands). Native to the Indo-Pacific, C. irene had previously been introduced to the Caribbean, Brazil, and Cape Verde. It was first observed in Tenerife in 2020, though retrospective records through citizen science tools date its presence back to 2018. A total of 74 sightings along the island’s coasts were reported between 2018 and 2024, when it reached densities of ca. 2 individuals/aggregates per square metre in the initial introduction area. Thus, the species is undergoing a clear proliferation and a spatial expansion. Morphological and genetic analyses confirmed the identity of C. irene and its phylogenetic placement, closely related to other Cnemidocarpa and related genera such as Asterocarpa. This species shows concerning invasive characteristics, such as a fast expansion, abundance in natural habitats, and aggregative behaviour, suggesting potential threats to native biota. Due to its limited natural dispersal capacity, the introduction of C. irene to Tenerife is attributed to anthropogenic vectors, particularly oil platforms arriving at major Canary Island ports. The proximity of the initial records to port areas supports this hypothesis. Given the potential species’ ecological risks, the authors recommend close monitoring, manual removal where feasible, and strengthened involvement of citizen science. This case highlights the vulnerability of oceanic islands to marine biological invasions and the importance of ports and marinas as critical entry points, underscoring the need for proactive surveillance and early intervention strategies
First early-stage observations for Tenaga Clemens, 1862 with notes on biology and distribution of T. nigripunctella (Haworth, 1828) (Lepidoptera, Tineidae)
No full textEarly stages of the tineid genus Tenaga Clemens, 1862 are reported for the first time, for T. nigripunctella (Haworth, 1828). Its larvae were found within the shells of dead Garden Snails Cornu aspersum (Müller, 1774), feeding on the dried body tissues. Larvae of the moth have been found, but not reared, among a range of detritus substrates, with traces of likely feeding observed on dry mouse droppings, and in a dead Western Honeybee Apis mellifera Linnaeus, 1758. Adults of the species have been seen annually since 2013 in a small area of Dorset, England. Historical and modern occurrences in Great Britain (until 1934) and country records elsewhere are reviewed, with new records reported for Lebanon and Syria. Two live larvae have been found within dead snail shells, one reared to the adult stage, the other was identified from its DNA barcode. Only a single COI-5P haplotype is known worldwide and ours is the fourth known DNA sequence. The taxonomic placement of the genus Tenaga, containing only two closely related species, sometimes placed in the family Meessiidae, is also discussed
Taxonomy OWLizer: A Tool for Converting Taxonomic Data into OWL
No full textThe growing demand for high-quality, interoperable biodiversity data exposes the current challenges of standardizing taxonomic information across platforms. While the Global Biodiversity Information Facility Backbone Taxonomy (GBIF Secretariat 2023) offers a valuable reference for species names, translating this information into formal ontology structures for semantic integration remains a complex task. A key challenge lies in the dynamic nature of taxonomic knowledge: as GBIF-BT is continuously updated, ontologies built manually from its data risk becoming outdated or misaligned. Without automated mechanisms for synchronizing with these updates, such ontologies may fail to reflect current taxonomic consensus, limiting their interoperability and long-term usefulness in biodiversity informatics.To address this problem, we developed the Taxonomy OWLizer (TOWLizer), a lightweight web application that allows users to convert species names into Web Ontology Language (OWL) ontologies based on taxonomic data retrieved directly from the GBIF Species API, as detailed in Fig. 1. Users input one or multiple scientific names, and the application fetches, organizes, and outputs a structured OWL file, facilitating taxonomic integration into semantic web projects. OWLizer automates synonym handling (see Fig. 2) and taxonomic hierarchy generation, and reuses GBIF URIs in the code, following linked data principles (Berners-Lee 2006). It aims to lower the technical barriers for researchers working in biodiversity informatics who need machine-actionable taxonomies but may lack programming expertise.The application was implemented using HTML, JavaScript, Bootstrap, and a Flask backend, with ChatGPT-4 providing support for code drafting and debugging, which accelerated prototyping and streamlined development. The tool is freely available through a GitHub-hosted interface with the backend deployed on Render, and a backup archived in Zenodo (Soares 2025).TOWLizer has some limitations though. Its performance depends on free-tier hosting services: the backend may enter a sleep state after periods of inactivity, causing occasional delays, while caching is limited to local storage on a single device and browser. The algorithm is also sensitive to typographical errors in scientific names; a recommended workflow is to combine ChatGPT for spelling verification with TOWLizer for synonym management. Finally, GBIF URLs used in the application do not yet support content negotiation, which constrains their reusability in some semantic web contexts. We tested TOWLizer in the development of a real-world ontology, namely the Agricultural Product Types Ontology (APTO), which was designed to represent agricultural commodities in Brazil. In this context, we addressed the content negotiation issue by replacing the GBIF URLs with URIs from the APTO namespace. These URIs are served via AgroPortal (Jonquet et al. 2018), enabling proper content negotiation.Despite these constraints, the Taxonomy OWLizer has proven to be a practical and accessible way to generate OWL representations of taxonomic data. It provides an initial step toward automating taxonomic ontology construction, highlights the potential of AI-assisted development, and contributes to ongoing discussions in biodiversity informatics about sustainable, interoperable, and machine-actionable taxonomies. More details on the tool development are provided in Soares et al. 2025
Mobilising Legacy Georeferencing Efforts
No full textAs we progress towards a globally accessible natural history collection, the ways in which we digitally curate, share and use our data will inevitably change. Digital specimen records enable access by in-country experts, increase the opportunity for specimen enhancement by the scientific community, and improve the breadth of research to which the specimens contribute.Digitisation workflows capture an image often with minimal transcription; they do not include the further enhancement of specimen records, such as georeferencing - the addition of coordinates to text based locality information. Typically used to georeference herbarium specimens, the point radius method assigns a coordinate and a measurement of maximum uncertainty (Wieczorek and Chapman 2020). Some herbarium specimens that lack coordinates still cannot be georeferenced using this method due to poor label data or the unavailability of contextual information.Data derived from herbarium specimens form the basis of species distribution modelling, taxonomic research and IUCN extinction risk assessments. If a specimen record does not have coordinates, then it is often discarded early in the data mining process, highlighting the importance of data enhancement through georeferencing, which confirms the species occurrence in space and time.The Kunming-Montreal Global Biodiversity Framework targets help to guide the most important applications of collection data for biodiversity conservation; Target 4, for example, aims to halt species extinction and protect genetic diversity (Convention on Biological Diversity 2023). Extinction risk assessments of plant species are underpinned by distribution maps derived from preserved specimens and observation records with coordinate information either recorded at the time of collection or through subsequent georeferencing of the specimen. However, over half of all herbarium specimens on Global Biodiversity Information Facility (GBIF) do not have coordinates and so robust extinction risk assessments often require a georeferencing step before applying the IUCN’s criteria. Other data types contributing to extinction risk assessment, such as population size and trend are often lacking and, where available, subjective and restricted to an expert’s firsthand knowledge of the species, making the data untraceable for the wider community (Nic Lughadha et al. 2019, Willis et al. 2003).As highlighted in Bloom et al. (2018), the estimated distribution of a species differs depending on the origin of the coordinate data. For example, non-georeferenced records tend to inflate the estimated distribution of a species. Working with collaborators with regional geographical expertise, and using datasets following standardised protocols, will more likely result in accurate and precise georeferenced records.As herbarium specimen labels can contain qualitative context on collection localities, the process of georeferencing is subjective and so an indicator of confidence and the georeferencer's method is important for end user trust and usability of the record. As more herbarium specimens are digitised, there is a growing need to produce georeferenced locality data at scale.. Although there are robust tools that can be used to supplement manual georeferencing, georeferencing of all specimens in natural history collections currently lacking coordinates is not feasible to resource, as georeferencing is time and resource heavy.The Royal Botanic Gardens, Kew now contributes 5.8 million herbarium specimen records to GBIF, many of which will have between three and six duplicate specimens located in herbaria around the world. Enhancing these records with existing georeferencing efforts accumulated through the completion of several thousand extinction risk assessments will reduce duplicated effort and uncover georeferenced localities that would otherwise go undocumented. This dataset will also help in establishing protocols to apply when georeferencing plant collections in the future, particularly in data-poor tropical regions
WatchListR: a tool for developing watch-lists of invasive species to inform biosecurity decision-making
No full textThe Global Biodiversity Framework calls for member countries to reduce the rate of introduction of known or potential invasive alien species by at least 50 percent by 2030. An essential tool that will assist countries in achieving this ambitious target is a list of known or potential invasive alien species that are absent from their territories but might enter along a variety of pathways (‘watch-list’ hereafter). Generating watch-lists requires consideration of curated information on a large number of species. The growing volume of distribution data and the improved understanding of historical species introductions and invasions have created a significant data overload for countries compiling watch-lists. We have developed a computational workflow to automate part of this process, enabling countries to draw up these lists quickly and cost-effectively. The WatchListR tool requires reliable and accurate information on species present in the country (indigenous and introduced, as well as economically important). As information on which species are present is sometimes not readily available, local experts should ideally review and verify the watch-lists developed by WatchListR. As a case study, we used WatchListR to develop a list of species prohibited for importation into the Republic of Mauritius. We explore the development of WatchListR, describe the processes used, consider the efficacy of the tool, highlight planned future advancements, and suggest how countries can support the tool’s development through the use and creation of expert-validated watch-lists
Chironomus sp. J – an elusive species from the Chironomus plumosus (Linnaeus, 1758) sibling-species group (Diptera, Chironomidae)
No full textData on chromosomal polymorphism in two natural populations from the Inya River in Western Siberia (Novosibirsk province) of Chironomus sp. J (Kiknadze, 1991) —one of the sibling species from the Chironomus plumosus group — are presented for the first time. The species belongs to the “thummi” cytocomplex with 2n = 8 and the arm’s combination AB CD EF G and is closely related to Ch. nudiventris Ryser, Scholl et Wülker, 1983, which has 2n = 6 with the arm’s combination AB CD GEF (a modified “thummi” cytocomplex). The main difference between these two species is the number of chromosomes, apart from that they only differ by the frequencies of banding sequences in arm A, and the presence or absence of some polymorphic inversions. The banding sequence pool of Chironomus sp. J consists of 15 banding sequences. Inversions were found in five chromosomal arms – A, B, D, E, F. The most polymorphic arms were B and D. Two studied populations differed by the level of chromosomal polymorphism with one population being completely monomorphic and the other showing high level of polymorphism with 62–65% of heterozygotes and 0.83–0.88 heterozygotic inversion per larva (depending on the year of collection). Comparison of banding sequences to other species from the group showed that Chironomus sp. J is indeed closest to Ch. nudiventris, with the cytogenetic distance of 0.058 or 0.471 depending on the method of calculation, which indicates that these two species are very closely related. The relationship between Chironomus sp. J and other species from the Ch. plumosus group was discussed
Penicillium and Talaromyces diversity in cystic fibrosis patient sample and the description of a new species, Penicillium subluteum sp. nov. (Eurotiales, Aspergillaceae)
No full textPenicillium and Talaromyces species are frequently isolated from the respiratory tracts of cystic fibrosis (CF) patients, yet their diversity, ecological roles, and clinical significance remain poorly understood. In this study, we analyzed 521 fungal isolates (482 Penicillium and 39 Talaromyces) obtained from Dutch CF patients to investigate species diversity and prevalence. Using a combination of AFLP fingerprinting and DNA sequences analysis, we identified 57 Penicillium and 18 Talaromyces species, including a putatively new species named Penicillium subluteum sp. nov. The most commonly isolated Penicillium species included P. crustosum, P. frequentans, P. chrysogenum, P. rubens, and P. brevicompactum, while Talaromyces rugulosus was the most prevalent Talaromyces species. Our findings highlight the underestimated diversity of Penicillium and Talaromyces in CF patients and emphasize the importance of accurate species identification for understanding fungal colonization patterns and assessing pathogenic potential. This study provides the most comprehensive overview to date of Penicillium and Talaromyces diversity in the CF airway and contributes valuable taxonomic and ecological insights into the role of these fungi in patients with chronic airway disease
First record of leucism in spotted eagle ray, Aetobatus narinari (Elasmobranchii, Myliobatiformes, Aetobatidae)
No full textThis paper reports the first record of leucism in the spotted eagle ray, Aetobatus narinari (Euphrasen, 1790). The specimen was captured on the coast of Seybaplaya, Campeche, on 15 August 2025, using a 20 cm mesh-size gillnet. The disc length and disc width of the leucistic specimen were 376 mm and 656 mm, respectively, and the gutted weight was 3.895 kg. This report contributes to the current knowledge of chromatic abnormalities in elasmobranchs in the southern Gulf of Mexico, which now includes four species. The cause of leucism in this ray remains unknown. Further studies and monitoring are important to identify possible causes of this abnormality, taking into account the health of the specimens and their environmental interactions