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Article Reference Horizontal Transfer of Vingi Retrotransposons in a Putative Ancient Asexual
Ostracods are microscopic, bi-valved crustaceans with the best fossil record of living arthropods. The non-marine ostracod Darwinula stevensoni is furthermore one of the last remaining examples of an ancient asexual, and likely abandoned sexual reproduction >20 million years ago. Despite the limited genetic diversity of D. stevensoni, its cosmopolitan distribution in different aquatic habitats indicates this species can survive asexually in the long-term. To unravel the novel adaptations that made this possible, the UNTANGLE project is deeply investigating the D. stevensoni genome. Now, four families of the Vingi non-LTR retrotransposons within the D. stevensoni genome were found to be highly identical to those from other species. This suggests Vingi was horizontally transferred between these species, which include turtles, lamprey, and deep-sea tube worms. Vingi consensus sequences were generated for D. stevensoni using Oxford Nanopore and Illumina assemblies, and mapped to >10,000 Metazoan genomes. High-quality mappings will be used to generate species-specific consensus sequences, upon which phylogenetic trees can be based and compared to those of other transposons, as well as with the host phylogenies. HTT will be visible as discorrespondence across phylogenetic trees. In a deeper exploration, the divergence between Vingi copies from each host and their consensus will also be used for the relative aging of their HTT events.
Located in Library / RBINS Staff Publications 2025
Article Reference infraFADA: Upgrading the taxonomic backbone of global freshwater animal biodiversity research infrastructures
The Freshwater Animal Diversity Assessment (FADA) comprises an extensive set of global taxa lists for freshwater animal groups. At present, more than 125,000 described freshwater animal species in more than 11,000 genera have been documented. However, taxonomy is a living scientific discipline, where new taxa are continuously being described, and existing taxa are being placed in new taxonomic positions. Therefore, after a period of relative inactivity, the BELSPO (Belgian Science Policy) project “infraFADA” (2023-2026) re-establishes the global FADA consortium of taxonomic experts, so that all taxa lists will be brought up to date, both technically and in terms of content. infraFADA is developing a living, updated, and global FADA database, fully in open access and according to the FAIR principles. On the one hand, the infraFADA database helps the experts to curate their data (using FADAtims; see separate poster), on the other hand it is intended for use and consultation by the scientific freshwater community or interested stakeholders, for example, freshwater ecosystem managers, biodiversity conservationists, and others. Most importantly, FADA will also serve as a taxonomic backbone for other global biodiversity data infrastructures, such as the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF), the Freshwater Information Platform (FIP), and others. As such, FADA will provide a digital and living heritage of freshwater data, building bridges between science and society and helping to sustainably maintain freshwater resources.
Located in Library / RBINS Staff Publications 2025
Article Reference infraFADA: Upgrading the taxonomic backbone of global freshwater animal biodiversity research infrastructures
The Freshwater Animal Diversity Assessment (FADA) comprises an extensive set of global taxa lists for freshwater animal groups. At present, more than 125,000 described freshwater animal species in more than 11,000 genera have been documented. However, taxonomy is a living scientific discipline, where new taxa are continuously being described, and existing taxa are being placed in new taxonomic positions. Therefore, after a period of relative inactivity, the BELSPO (Belgian Science Policy) project “infraFADA” (2023-2026) re-establishes the global FADA consortium of taxonomic experts, so that all taxa lists will be brought up to date, both technically and in terms of content. infraFADA is developing a living, updated, and global FADA database, fully in open access and according to the FAIR principles. Part of FADA’s data originates from existing global resources such as FishBase. In particular, the freshwater fish component of FADA was established in close collaboration with FishBase as a primary reference to ensure taxonomic consistency and completeness of species lists. While FishBase offers authoritative coverage of fish species worldwide—including freshwater fishes—FADA goes further by encompassing all freshwater animal groups, from invertebrates to other vertebrates. SeaLifeBase is likewise relevant, as it includes many non-fish marine taxa with freshwater representatives or life stages, highlighting important connections between these systems. The FADA database is intended for use and consultation by the freshwater scientific community or interested stakeholders, for example, ecosystem managers, biodiversity conservationists, and others. On the other hand it helps the experts to curate their data using FADAtims. Most importantly, FADA will also serve as a taxonomic backbone for other global biodiversity data infrastructures, such as the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF), the Freshwater Information Platform (FIP), and others. As such, FADA will provide a digital and living heritage of freshwater data, building bridges between science and society and helping to sustainably maintain freshwater resources.
Located in Library / RBINS Staff Publications 2025
Article Reference Horizontal transfer of Vingi non-LTR retrotransposons in Darwinula stevensoni
Ostracods are microscopic, bi-valved crustaceans with the best fossil record of living arthropods. The non-marine ostracod Darwinula stevensoni is furthermore one of the last remaining examples of an ancient asexual, and likely abandoned sexual reproduction >20 million years ago. Despite the limited genetic diversity of D. stevensoni, its cosmopolitan distribution in different aquatic habitats indicates this species can survive asexually in the long-term. To unravel the novel adaptations that made this possible, the UNTANGLE project is deeply investigating the D. stevensoni genome. Now, four families of the Vingi non-LTR retrotransposons within the D. stevensoni genome were found to be highly identical to those from other species. This suggests Vingi was horizontally transferred between these species, which include turtles, lamprey, and deep-sea tube worms. Vingi consensus sequences were generated for D. stevensoni using Oxford Nanopore and Illumina assemblies, and mapped to >10,000 Metazoan genomes. High-quality mappings will be used to generate species-specific consensus sequences, upon which phylogenetic trees can be based and compared to those of other transposons, as well as with the host phylogenies. HTT will be visible as discorrespondence across phylogenetic trees. In a deeper exploration, the divergence between Vingi copies from each host and their consensus will also be used for the relative aging of their HTT events.
Located in Library / RBINS Staff Publications 2025
Article Reference Antarctica as an evolutionary incubator? Phylogenetic comparative study of the amphipod family Iphimediidae on the Antarctic shelf
From about 40 Mya, while Antarctica geographically isolated from the rest of the world, the marine shelf fauna faced a dramatic decrease in water temperatures. Many lineages went extinct, while others adapted and flourished. The Antarctic clade of the amphipod family Iphimediidae was among the successful ones. Here, a range of cutting-edge phylogenetic comparative and morphometric methods are used to investigate the evolutionary processes which generated the exceptional diversity of this clade. To this purpose, three types of data were collected: (1) a novel phylogeny of the family was first reconstructed using a multigene molecular dataset, (2) 3D shape data were obtained by applying 3D-geometric morphometric methods on micro-CT scans of the specimens and (3) stable isotope d13C and d15N were measured and used as variables describing the trophic ecology of the species. First, possible evolutionary correlations between 3D-morphometric dataset of mouthparts (mandible, maxilliped) and stable isotope ratios were assessed. Significant correlations suggest an adaptation of the mandible shape to the food source. Secondly, as a prerequisite to the study of species diversification, species boundaries were investigated using a combination of DNA-based delimitation methods and detailed morphological/morphometric analyses. The latter showed that species diversity in Antarctic iphimediids is greatly underestimated, as most of the described species appear to be complexes of multiple morphologically similar species. Finally, potential changes in the rate of lineage diversification were explored in parallel to the evolution of morphological traits (mouthparts 3D shape data) along the phylogeny. On one hand, we found no evidence of an early burst of lineage diversification. On the other hand, late bursts (appr. 7-3 Mya) were detected in two subclades. Such late radiations could result from the invasion of novel ecological niches, as a late partitioning of mouthparts’ shape diversity along the phylogeny is also observed. Plio-Pleistocene glacial cycles, which have been hypothesized to act as a diversity pump, might also have promoted late diversification events in Antarctic iphimediids. By applying such an integrative approach for the first time on Antarctic invertebrates, this study improves our general understanding of the evolutionary dynamics shaping the standing Antarctic shelf biodiversity.
Located in Library / RBINS Staff Publications 2025
Article Reference Exploring species diversity within the amphipod family Iphimediidae using DNA-based delimitation, traditional and 3D-Geometric Morphometrics
As an isolated ocean at the end of the thermal continuum, the Southern Ocean hosts a highly endemic cold-adapted marine fauna. However, this unique biota is now challenged by climate-related changes, as some parts of Antarctica are the fastest warming areas on Earth. In order to monitor and mitigate climate-induced changes, a baseline knowledge of species biodiversity and distributions is mandatory. However, this knowledge is currently insufficient for most Southern Ocean taxa, as the actual number of species is still likely to be greatly underestimated. For instance, most of the geographically widespread to circum-Antarctic amphipod species that have been subjected to molecular scrutiny were revealed to be complexes of similar species with a more restricted distribution range. In this study, we reconstructed a novel molecular phylogeny of Antarctic Iphimediidae and used a range of DNA-based species delimitation methods (bPTP, GMYC, ABGD) to explore species diversity. Furthermore, traditional and 3D-geometric morphometric methods were applied on micro-CT scans to characterize patterns of morphological variation within and among clades and DNA-based putative species. For two of the species complexes, namely Gnathiphimedia sexdentata and Echiniphimedia hodgsoni, the shapes of selected anatomical traits of potential taxonomic value at the species level were quantified: (i) a spine-like tooth, (ii) the head, (iii) the coxa 4 and (iv) the first article of Antenna I peduncle. Our results revealed that ten nominal iphimediid species are complexes of multiple species, most of which can be distinguished by small but consistent morphological differences. Ten of these new species were formally described: Stegopanoploea brevidentata sp. nov., Maxilliphimedia acutilobata sp. nov., Maxilliphimedia oliveri sp. nov., Echiniphimedia spinosior sp. nov., Echiniphimedia maxima sp. nov., Iphimediella longidentata sp. nov., Iphimediella brachyodonta sp. nov., Iphimediella longilobata sp. nov., Labriphimedia adeliae sp. nov., and Labriphimedia anneninae sp. nov. Altogether, molecular and morphometric methods were combined to revise species diversity within the iconic Antarctic Iphimediidae, increasing the number of species from 39 to 49, with 14 additional putative species requiring further study for formal description.
Located in Library / RBINS Staff Publications 2025
Article Reference Is Antarctica an evolutionary incubator? Phylogenetic comparative study of the amphipod family Iphimediidae on the Antarctic shelf
Around 40 million years ago, Antarctica’s geographic isolation led to a dramatic cooling of its marine shelf, causing many lineages to go extinct while others adapted and diversified. Among the successful ones is the amphipod family Iphimediidae. Here, we apply advanced phylogenetic comparative methods to explore the evolutionary processes underlying their exceptional diversity. To this end, we combined three datasets: (1) a novel molecular phylogeny, (2) 3D shape data from micro-CT-based geometric morphometrics, and (3) stable isotope ratios (δ13C and δ15N) as proxies for trophic ecology. We tested for evolutionary correlations between mouthpart shape and isotope values, and investigated changes in diversification rates in relation to morphological evolution. Late bursts of lineage diversification (ca. 7–3 Mya), along with late partitioning of mouthpart shape diversity, may reflect the invasion of novel ecological niches. Plio-Pleistocene glacial cycles may also have acted as a diversity pump promoting this late diversification.
Located in Library / RBINS Staff Publications 2025
Inproceedings Reference Understanding late medieval farming practices: an interdisciplinary study on byre remains from the historical centre of Brussels (Belgium)
During a preventive archaeological excavation in the historical centre of Brussels (Belgium), the waterlogged remains of a 13th century AD sunken byre (potstal) were discovered. The exceptional preservation instigated a multiproxy approach, including micro-archaeology, micromorphology, phytolith and parasite analysis on thin sections, palynology and the study of plant macroremains on the fill of the structure. Beyond detailing the content and multiple origins of the fill (including excremental waste and urines, fodder and bedding material, plaggen and/or soil sods, household and construction waste), this study also provides detailed insights into foddering customs, hygienic conditions within the stable, and the health status of the animals kept. Moreover, historians claim the importance of an agro-pastoral system where animals were kept in stables over winter as part of the explanation for cultivating new and less rich soils in high medieval times. The intensive study of high medieval cultivated fields in the historical centre of Brussels indeed shows that they have intensively been amended. So aside from documenting husbandry practices, this study also informs about late medieval farming practices in Brussels, more specifically the need to collect substantial amounts of manure to add as fertiliser onto cultivated poor sandy soils.
Located in Library / RBINS Staff Publications 2025
Inproceedings Reference Macrobotanical mixtures from river deposits in Brussels: from a rural Gallo-Roman site to the urbanisation of a medieval city
In the last decade, macrobotanical remains from meters-thick infills of riverbeds excavated at two archaeological sites in Brussels were extensively studied. To the north of the city centre, at the site of Tour & Taxis, the remains of a meandering river arm was brought to light. Archaeological finds indicate human occupation during the Gallo-Roman period, while in the early medieval period anthropogenic activities declined and the river arm gradually disappeared from the landscape. The second site is situated within the ancient city centre of Brussels, in the area of the medieval harbour on the Senne, where several phases of the medieval river were uncovered. The oldest layers document on the towns’ earliest developments while the most recent deposits shed light on the late medieval city and its urbanisation. The results of the macrobotanical analyses of these two similar contexts from a rural and an urban site illustrate the potential and challenges of archaeobotanical studies of fluvial deposits and highlight the importance of an integrated taphonomical approach. The exceptional diversity of the plant material and its excellent waterlogged preservation offer unique insights into various aspects of daily life through time. Plant remains from both sites consist of a mixture of naturally accumulated material and remains from anthropogenic deposits, including animal dung, human excrements, fuel, domestic and artisanal waste. Due to the diverse origins of the botanical material that ended up in the water, the assemblages not only provide information on the local vegetation history but also on agriculture, food economy, trade, ornamental plants and waste management. In addition, numerous remains from the urban Senne deposits give material evidence for textile working and dyeing with plants along the riverbanks for more than three centuries. Keywords: Archaeobotany; Vegetation; Food Economy; Textile Working; Urbanisation; Taphonomy; River Deposits Presentation in session E2: River and Inland Water Archaeology - Exploring submerged and Watercourse-Linked Cultural Heritage
Located in Library / RBINS Staff Publications 2025
Article Reference Parasite BioBlitz in a protected area: diversity across a forested wetland to tidal creek continuum in South Carolina, USA
The BioBlitz concept has become popular across taxonomic fields, attracting interest globally to increase knowledge of local biodiversity. However, large-scale application of BioBlitz events for parasites has not occurred due to the need for wide taxonomic expertise and in-field sample processing and microscopy. As a team of parasitologists with individual, complementary and methodologically aligned expertise, we adopted the concept of a BioBlitz as a ‘moonshot’-like endeavor and a proof-of-concept in our research field. Over ca. two weeks, we intensively screened fishes and various invertebrate taxa (annelids, crustaceans, snails, bivalves) for parasites, and sampled sediment and water for eDNA from four aquatic habitats: wetland, freshwater pond, brackish impoundment, and tidal creek at Stono Preserve (College of Charleston’s Foundation, South Carolina, USA) to cover ecosystem-level parasite diversity. Morphological and molecular identification of parasites collected revealed the presence of eight major parasite taxa (monogeneans, cestodes, digeneans, nematodes, copepods, myxozoans, flagellates, and leeches), several of which were new host and/or locality records with numerous host-parasite combinations. The finding of species new to science and numerous host-parasite combinations further supports that such short term and intensive surveys improve knowledge of parasite diversity, which is under-studied yet essential for deeper understanding of ecosystems at local and global scales.
Located in Library / RBINS Staff Publications 2025