Search publications of the members of the Royal Belgian institute of natural Sciences
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Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
- Ostracods are microscopic, bi-valved crustaceans with the best fossil record of all living arthropods. Their fossil record, starting 400 million years ago, together with a high prevalence of parthenogenetic reproduction and putative ancient asexuality, make non-marine ostracods fascinating evolutionary model organisms. In the absence of high quality ostracod reference genomes, we here compare transposon landscapes between two Illumina genome assemblies from the putative ancient asexual Darwinula stevensoni and the fully sexual ostracod Notodromas monacha. Both assemblies have around 60,000 contigs, sizes of 360-380 Mb, more than 100X coverage and BUSCO scores of 93 and 94%, respectively. Because homology-based programs are not sensitive enough to detect families of transposable elements (TEs) in species missing from Repbase or Dfam, we used three different pipelines for de novo analyses: REPET, RepeatMasker2 (RM2) and EarlGrey (RM2-based, with automated curation). TE diversity between the two genomes differs substantially regardless which pipeline was used. The Illumina assembly of N. monacha is dominated by LTR retrotransposons (6.5%) with some DNA transposons (3.7%), whereas DNA (15.5%), LINE-like (5.9%) and rolling circle Helitron elements (1.5%) were most abundant in the assembly of D. stevensoni. Our results on the dominance of DNA (Tc/mar, hAT) and LINE-like (CR1, RTE) TEs in D. stevensoni parallel earlier findings from a partial genomic library, and differ from those of other asexuals. TE copies with a low number of nucleotide substitutions are only observed with REPET (“L” shape landscape) in both genomes. Although the presented results may underestimate TE abundance, they indicate pronounced differences of the transposon landscapes and diversity between these two ostracod species. Analysis of related species should determine whether the differences are correlated with the reproductive mode or are lineage specific. We are currently curating TEs in an Oxford Nanopore draft assembly of D. stevensoni to further confirm our initial results.
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Ecology of ostracods inhabiting groundwater in Benin, West Africa, with potential use of stygobites as indicators for groundwater quality
- Ostracods are significant members of groundwater ecosystems, affected by both abiotic environmental factors and biotic interactions. This study investigates the factors influencing ostracod communities in groundwater from dug wells in several regions of Benin, West Africa, which experiences chronic anthropogenic disturbances such as nutrient enrichment from sewage and fertilizer infiltration. We evaluated the presence of ostracod species in 219 wells across seven catchment areas, examining 31 predictor variables, which include a variety of water quality parameters, hydrology as well as well closure, usage and type. The influence of these variables was analyzed using distance-based linear models and redundancy analysis. Our research identified 60 ostracod species, which we classified into two ecological groups: 1) 36 stygobitic species from the family Candonidae, which represent an endemic evolutionary radiation, and 2) 24 non-stygobitic species, mostly from the family Cyprididae. Through our analysis, we identified several key factors influencing ostracod community structure, with consistent patterns observed at both species and genus levels. The primary predictors, aside from well descriptors, included water chemical and physical properties, such as electrical conductivity, pH, temperature, and bicarbonate concentration, along with NO2- concentration, a factor not previously demonstrated to be crucial for ostracod assemblages. Elevated nitrite levels in groundwater were found to significantly affect the distribution of stygobites and non-stygobites. Stygobites were notably less frequent in environments with higher NO2- concentrations, likely due to their greater vulnerability to periodic or chronic anthropogenic disturbances compared to non-stygobites. Therefore, we suggest that stygobitic ostracod species, identifiable even at the genus level, have a potential as reliable indicators of groundwater quality in the tropical regions of western Africa.
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Accounting for interspecies and intraspecies variation in swimming performance for fish passage solutions
- Across the globe, there are millions of in-stream structures that fragment the world'’s river networks, acting as barriers that can impede the movements of fish. Designing effective solutions to accommodate fish communities requires information about the swimming abilities and behaviours of all species. This should account for different swimming modes, abilities, behaviours, and niches. We investigated the swimming speeds of nine migratory New Zealand species to assess both inter- and intraspecies variation. We then calculated maximum traversable speeds for culverts of a given length, based on the endurance abilities of our lowest performing species (Galaxias maculatus). Our findings reveal significant inter- and intraspecies variation in swimming speeds. Among the species studied, Galaxias brevipinnis, Galaxias argenteus, and Galaxias postvectis were the strongest swimmers. In contrast, Galaxias maculatus was one of the weakest swimmers. Body length positively correlated with Umax indicating that fish passage barriers select against the weakest swimming species, as well as smaller individuals within a species. Maximum water speeds in a culvert must be lower than 0.3 m s−-1, the previously assumed standard rule-of-thumb for New Zealand, to provide adequate passage for a high proportion of a weak-swimming indicator species (Galaxias maculatus). Synthesis and applications: . Previous maximum traversable water speeds for fish passage designs have been based on average swimming ability, but this approach only enables fish that are better than the average swimmers of their species to overcome barriers. This study highlights the importance of evidence-based designs for successful fish passage solutions to account for the ability of all fish. By considering differences between and within species, rather than assuming a “‘one-size-fits-all” ’ approach we can develop more effective passage solutions that better preserve fish communities.
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A New Species of Elpidium (Crustacea, Ostracoda) from Bromeliad and Non-bromeliad Phytotelmata in the Northeast of Argentina
- A new species of the ostracod genus Elpidium (Timiriaseviinae), a group almost exclusively known from Neotropical bromeliad phytotelmata, is here described and illustrated from the northeast of Argentina. Elpidium chacoense n. sp. represents the first record of the genus in this country and brings the total of described Elpidium species to 19. In view of the recently increased knowledge on the distribution of the species in this Neotropical genus, we discuss potential drivers of speciation that might have led to the high (endemic) diversity of the group: allopatry in bromeliad islands, sexual selection and putative co-evolution between ostracod and bromeliad species. We also point out the biogeographical relevance of the present records, which are amongst the most southern of the genus. Finally, also the fact that species of Elpidium can now also be found in non-bromeliad phytotelmata is of relevance.
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Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
- Ostracods are microscopic, bi-valved crustaceans with the best fossil record of all living arthropods. Their fossil record, starting 400 million years ago, together with a high prevalence of parthenogenetic reproduction and putative ancient asexuality, make non-marine ostracods fascinating evolutionary model organisms. In the absence of high quality ostracod reference genomes, we here compare transposon landscapes between two Illumina genome assemblies from the putative ancient asexual Darwinula stevensoni and the fully sexual ostracod Notodromas monacha. Both assemblies have around 60,000 contigs, sizes of 360-380 Mb, more than 100X coverage and BUSCO scores of 93 and 94%, respectively. Because homology-based programs are not sensitive enough to detect families of transposable elements (TEs) in species missing from Repbase or Dfam, we used three different pipelines for de novo analyses: REPET, RepeatMasker2 (RM2) and EarlGrey (RM2-based, with automated curation). TE diversity between the two genomes differs substantially regardless which pipeline was used. The Illumina assembly of N. monacha is dominated by LTR retrotransposons (6.5%) with some DNA transposons (3.7%), whereas DNA (15.5%), LINE-like (5.9%) and rolling circle Helitron elements (1.5%) were most abundant in the assembly of D. stevensoni. Our results on the dominance of DNA (Tc/mar, hAT) and LINE-like (CR1, RTE) TEs in D. stevensoni parallel earlier findings from a partial genomic library, and differ from those of other asexuals. TE copies with a low number of nucleotide substitutions are only observed with REPET (“L” shape landscape) in both genomes. Although the presented results may underestimate TE abundance, they indicate pronounced differences of the transposon landscapes and diversity between these two ostracod species. Analysis of related species should determine whether the differences are correlated with the reproductive mode or are lineage specific. We are currently curating TEs in an Oxford Nanopore draft assembly of D. stevensoni to further confirm our initial results.
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An updated subjective global checklist of the extant non-marine Ostracoda (Crustacea)
- We present an updated global checklist of extant non-marine Ostracoda, covering taxonomic changes in the published literature up to 31st December 2023. The checklist is subjective, as apart from published taxonomic changes, also some additional alterations are proposed, including ten candonid tribes which are upgraded to subfamilies, six new combinations, one new name, five synonymies and one new taxonomic placement. The checklist presently includes 2420 accepted species in 295 genera,as well as 84 uncertain species that are too poorly described to be recognisable. We also provide the totals of species numbers for each taxonomic rank, from genera up to order, and numbers of species and endemic species in each of the world’s major zoogeographical regions.
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Benthic Food Webs in Antarctica ~ Would you care for some more (micro)algae ?
- The West Antarctic Peninsula (WAP) is experiencing rapid warming, which will impact ecosystem processes, particularly sympagic algae dynamics. As these ice-associated microalgae are a vital food source for primary consumers, this disruption is likely to cascade through the communities via trophic interactions. To study these effects, we sampled benthic communities along the WAP in February 2023, focusing on macroalgae forests (n=2) and soft bottoms (n=3) at Dodman Island and Blaiklock Island. Basal resources and benthic invertebrates (n=410, 49 morphospecies) were collected for carbon and nitrogen stable isotope analysis to explore differences in food webs structure between macroalgae forests and soft bottoms, addressing three questions: 1) Are sympagic algae more crucial as basal resources in one of the two habitats? 2) Is there a difference in trophic diversity between macroalgae forests and soft bottoms? 3) How does the vertical food web structure differ between the two habitats? In soft bottoms communities, consumers’ stable isotopes ratios showed a switch toward higher δ¹³C values, typical of sympagic algae in Antarctica. This may suggest a higher vulnerability of WAP soft bottoms communities to alterations of sympagic algae dynamics. Trophic diversity was generally higher in communities with a wider range of basal resources. However, significant local-scale variations in trophic diversity surpassed habitat-related differences, limiting conclusions about habitat influence on trophic diversity. Finally, soft bottoms consumers tended to occupy a higher trophic position than those in macroalgae forests, resulting in a higher mean trophic position at the community scale. This could reflect a diet shift by generalist invertebrates—common in Antarctica—towards increased consumption of more degraded organic matter or necrophagy in habitats with fewer basal resources. Overall, these results underscore the complexity of trophic dynamics in Antarctica, where both local variability and large-scale environmental changes influence food web structure and community resilience to climate change.
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The late Holocene tsunami in the Shetland Islands (UK) identified in Loch Flugarth, north Mainland
- Tsunami deposits around the North Sea basin are needed to assess the long-term hazard of tsunamis. Here, we present sedimentary evidence of the youngest tsunami on the Shetland Islands from Loch Flugarth, a coastal lake on northern Mainland. Three gravity cores show organic-rich background sedimentation with many sub-centimetre-scale sand layers, reflecting recurring storm overwash and a sediment source limited to the active beach and uppermost subtidal zone. A basal 13-cm-thick sand layer, dated to 426–787 cal. a CE based on 14C, 137Cs and Bayesian age–depth modelling, was found in all cores. High-resolution grain-size analysis identified four normally graded or massive sublayers with inversely graded traction carpets at the base of two sublayers. A thin organic-rich ‘mud’ drape and a ‘mud’ cap cover the two uppermost sublayers, which also contain small rip-up clasts. Grain-size distributions show a difference between the basal sand layer and the coarser and better sorted storm layers above. Multivariate statistical analysis of X-ray fluorescence core scanning data also distinguishes both sand units: Zr, Fe and Ti dominate the thick basal sand, while the thin storm layers are high in K and Si. Enriched Zr and Ti in the basal sand layer, in combination with increased magnetic susceptibility, may be related to higher heavy mineral content reflecting an additional marine sediment source below the storm-wave base that is activated by a tsunami. Based on reinterpretation of chronological data from two different published sites and the chronostratigraphy of the present study, the tsunami seems to date to c. 1400 cal. a BP. Although the source of the tsunami remains unclear, the lack of evidence for this event outside of the Shetland Islands suggests that it had a local source and was smaller than the older Storegga tsunami (8.15 cal. ka BP), which affected most of the North Sea basin.
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A 1500-year record of North Atlantic storm flooding from lacustrine sediments, Shetland Islands (UK)
- Severe storm flooding poses a major hazard to the coasts of north-western Europe. However, the long-term recurrence patterns of extreme coastal flooding and their governing factors are poorly understood. Therefore, high-resolution sedimentary records of past North Atlantic storm flooding are required. This multi-proxy study reconstructs storm-induced overwash processes from coastal lake sediments on the Shetland Islands using grain-size and geochemical data, and the re-analysis of historical data. The chronostratigraphy is based on Bayesian age–depth modelling using accelerator mass spectrometry 14C and 137Cs data. A high XRF-based Si/Ti ratio and the unimodal grain-size distribution link the sand layers to the beach and thus storm-induced overwash events. Periods with more frequent storm flooding occurred 980–1050, 1150–1300, 1450–1550, 1820–1900 and 1950–2000 ce, which is largely consistent with a positive North Atlantic Oscillation mode. The Little Ice Age (1400–1850 ce) shows a gap of major sand layers suggesting a southward shift of storm tracks and a seasonal variance with more storm floods in spring and autumn. Warmer phases shifted winter storm tracks towards the north-east Atlantic, indicating a possible trend for future storm-track changes and increased storm flooding in the northern North Sea region.
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Environmental Impacts of Offshore Wind Farms in the Belgian Part of the North Sea: Progressive Insights in Changing Species Distribution Patterns Informing Marine Management. Memoirs on the M
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Coastal wetland adaptability to sea level rise: The neglected role of semi-diurnal vs. diurnal tides
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A dynamic 2DH flocculation model for coastal domains
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Sample basedwater quality monitoring of coastal seas: How significant is the information loss in patchy time series compared to continuous ones?
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Longitudinal survey identifies temporal shift in genetic structure among Dutch house sparrow populations.
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Potential of High Spatial and Temporal Ocean Color Satellite Data to Study the Dynamics of Suspended Particles in a Micro-Tidal River Plume
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Improved correction methods for field measurements of particulate light backscattering in turbid waters
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rocessing and exploitation of Sentinel-2 data for coastal water applications: The HIGHROC Project
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Towards an autonomous turbidimeter network for multi-mission ocean colour satellite data validation activities
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Ocean colour remote sensing of extreme Case-2 waters
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Particulate backscattering retrieval from remotely-sensed turbidity in various coastal and riverine turbid waters
