ICES Journal of Marine Science
◐ Oxford University Press (OUP)
Preprints posted in the last 30 days, ranked by how well they match ICES Journal of Marine Science's content profile, based on 11 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.
Tytar, V.; Fedorenko, L.
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Habitat degradation and biodiversity loss in the Black and Azov Seas necessitate improved tools for spatially explicit conservation planning. We employed stacked species distribution modelling (SSDM) to assess habitat quality for the three resident cetacean species, the common dolphin (Delphinus delphis ponticus), the bottlenose dolphin (Tursiops truncatus ponticus), and the harbour porpoise (Phocoena phocoena relicta), which serve as apex predators and indicators of ecosystem health. Occurrence data were compiled from the Global Biodiversity Information Facility (GBIF), and ensemble species distribution models (ESDMs) were constructed using nine algorithms within the SSDM framework, with eight environmental predictors extracted from Bio-ORACLE v3.0. Individual ESDMs demonstrated excellent predictive performance (AUC: from 0.82 to 0.83; TSS: from 0.65 to 0.67; prop.correct: from 0.82 to 0.83). However, the initial continuous stacking method (pSSDM) yielded low community-level prediction success (0.36), prompting evaluation of three correction approaches. The Probability Ranking Rule (PRR) substantially improved performance (prediction.success = 0.459, sensitivity = 0.704, Jaccard = 0.465), effectively mitigating the overprediction bias inherent in stacked models. Species richness mapping identified multi-species hotspots along the southwestern Black Sea shelf, the Crimean coast, the Kerch Strait, and parts of the eastern coast, while the deep central basin exhibited the lowest richness. Variable importance ranking revealed bathymetry as the primary community-level driver (41.2%), followed by dissolved oxygen (13.8%), sea surface temperature (11.9%), and salinity (10.4%). Species-specific importance patterns confirmed ecological niche segregation, with common dolphins favouring deeper offshore waters and bottlenose dolphins and harbour porpoises associated with shallower shelf environments. The moderate richness observed in the highly productive northwestern shelf, despite high nutrient inputs, may reflect a combination of natural factors (elevated turbidity, reduced salinity) and anthropogenic pressures (fisheries bycatch, shipping, coastal development, and military activity) that limit species co-occurrence. Our findings demonstrate that PRR-corrected SSDM provides a robust framework for mapping cetacean habitat quality and identifying conservation priorities in the Black and Azov Seas, offering an evidence-based tool to inform ecosystem-based management in this ecologically unique and increasingly pressured marine region.
Kruger, L.; Santa Cruz, F.; Marquez, M.; Vianna, J. A.; Santos, M.; Pinones, A.; Cardenas, C.
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Fledging is a critical period of a seabird life cycle. Using satellite telemetry, we compared movements and survival proxies (transmission duration) of chinstrap penguin fledglings tracked in 2017 (n=8) and 2025 (n=17) relative to krill fishing vessel activity. In 2017, fishing vessels operated intensively near colonies during summer, resulting in early, frequent encounters (median 1.3 days post-fledging) and short transmission durations (median 9.2 days). In 2025, reduced fishing delayed encounters (median 10.0 days) and tripled tracking duration (median 24.0 days). Hidden Markov Models revealed that vessel encounters reduced the probability of transitioning from foraging to transit behavior ({beta} = -0.76), an effect stronger than the productivity ({beta} = -0.11). While 87.5% of 2017 fledglings ceased transmission prematurely within weeks (half of those right after entering areas intensively used by fishing vessels), 65% of 2025 fledglings survived beyond March, with half of those five transmitting until May after dispersing eastward to the South Orkney Islands. These findings suggest that spatiotemporal overlap with krill fisheries during the critical post-fledging window affected foraging behavior and was associated with shorter transmission durations. Our results support further research of post-fledging penguin ecology to better understand the potential impact of fishery, and, following the precautionary principle, support fishing seasonal protection of important areas during critical periods of krill predators life cycle.
Weber, S. B.; Afonso, A. S.; Clarke, L.; Curnick, D. J.; Cranfield, M.; Jones, K.; Letori, J.; Oliveira, P.; Simpson, D.; Simpson, T.; Viana, D.; Hussey, N. E.
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BACKGROUNDOceanic islands and seamounts are recognised as hotspots of abundance and diversity for marine top predators, such as sharks and large teleosts, and are hypothesised to function as migratory stepping stones for mobile, pelagic species. However, while movements of pelagic predators between such features have been documented in some oceans, evidence from the tropical Atlantic remains limited. RESULTSHere, we report on long-distance migrations of three species of pelagic predator between oceanic islands and seamounts in the tropical south Atlantic recorded via independent passive acoustic telemetry arrays. These include the first recorded trans-Atlantic migration of a Galapagos shark (Carcharhinus galapagensis) from Ascension Island (UK) to the Sao Pedro and Sao Paul Archipelago (Brazil) (minimum distance 1,930 km); the longest documented oceanic migration of an Almaco jack (Seriola rivoliana) from St Helena (UK) to Ascension Island (minimum 1,300 km); and multiple movements of Galapagos and silky sharks (C. falciformis) between two Mid-Atlantic Ridge seamounts and Ascension Island (minimum 265-325 km). These detections are notable given the limited duration, sample sizes, and temporal overlap of acoustic tracking studies in the region, suggesting substantial connectivity across large spatial scales. CONCLUSIONSOur findings provide empirical support for the role of oceanic islands and seamounts as connectivity hubs for pelagic predators in the tropical Atlantic, underscoring their importance as key nodes in marine protected area networks. More broadly, this study demonstrates the value of collaborative regional tracking networks in resolving large-scale movement patterns and informing marine management at ecologically relevant scales.
Potter, S.; Jansen, J.; Hill, N.; Lucieer, V.
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Antarctic benthic organisms are highly diverse and play a critical role in the Southern Ocean ecosystem. Despite decades of sampling, vast areas of the Antarctic continental shelf remain biologically unsurveyed due to logistical and financial constraints, limiting baseline knowledge essential for effective conservation planning. Species distribution models (SDMs) allow biodiversity to be inferred in the absence of biological data by linking benthic community patterns to environmental predictors. However, the resolution of the environmental predictors, particularly bathymetry, varies significantly between regions, casting doubt about how reliably SDMs can be used to predict into regions where only coarse-resolution data are available. Here, we show that SDMs trained on high-resolution data underestimate Antarctic benthic morphospecies richness by up to 18% when applied to aggregated coarse-resolution environmental data (and up to 50% when using satellite-derived ETOPO bathymetry). Using six systematically degraded versions of high-resolution multibeam bathymetry and annotated seafloor imagery across three Antarctic regions, we evaluate SDM performance both with and without additional environmental variables. High-resolution bathymetry captures terrain complexity most effectively, but we find that the spatial distribution of richness hotspots and the median richness per cell remain consistent, provided models are applied at the same resolution at which they were trained. Our results suggest that while high-resolution bathymetry may enhance local predictions, coarse-resolution data may be more robust for regional-scale predictions, such as those used for Antarctic shelf-wide spatial planning.
Ogonowski, M.
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Littoral mysids facilitate benthic-pelagic coupling through horizontal migration, yet quantitative monitoring in structurally complex habitats remains methodologically challenged where traditional active gears fail. We evaluated the efficacy of standardized light traps for monitoring littoral mysids (Neomysis integer, Praunus flexuosus) and mesopredatory three-spined sticklebacks (Gasterosteus aculeatus) in the northern Baltic proper, Baltic Sea. Using a paired experimental design with predator-exclusion and unmodified traps, alongside concurrent passive benthic trapping, we assessed abiotic drivers affecting catchability, biotic interactions, and statistical power to monitor changes in population size over time. Results indicated significant biotic interference: unmodified traps attracted high densities of sticklebacks, which reduced mysid catches by approximately 85% through predation or behavioural avoidance. Consequently, physical predator exclusion is mandatory for accurate mysid sampling. Generalized Linear Mixed Models (GLMMs) confirmed that catch rates for all taxa were primarily driven by night duration rather than water temperature. While passive benthic trap catches tracked metabolic activity (peaking in warm summer months), light trap efficiency peaked in spring and collapsed during summer, confirming that sampling efficiency was strictly limited by the short duration of the night. Simulation-based power analysis revealed a stark contrast in monitoring utility based on spatial aggregation. For highly aggregated mysids, the method demonstrated low precision (Power < 0.25 to detect a 50% decline), rendering it suitable primarily for detecting substantial population collapses (>90%). In contrast, for less aggregated sticklebacks, the method achieved a more robust statistical power (>0.80 for a 60% decline), validating light traps as a precise tool for monitoring these abundant mesopredators. We conclude that light traps fill a critical methodological gap for winter and early spring monitoring when traditional passive gears underperform. Appropriate abundance indices should be based on statistical models accounting for night duration and strictly employ physical exclusion barriers when targeting mysids.
Jacobson, P.; Spotowitz, L.; Heimbrand, Y.; Myrenas, E.; Gemert, R. v.; Sundin, J.
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Knowledge regarding variation in habitat use among individuals is crucial for understanding population dynamics and for management and conservation measures. This is especially important for diadromous fishes that shift between habitats, being affected by external pressures and environmental change in different habitats over ontogeny. Herer, we assessed individual variation in habitat use of European eel along a salinity gradient, ranging from fully marine to freshwater in northern Europe, using otolith microchemistry data from >3600 eel together with established time-series segmentation and clustering methods. We show that eel display high degree of individual variation in habitat use. Assigned life-histories included coastal resident, freshwater resident, and coastal and freshwater habitat shifting individuals. Coastal resident eels were observed in a large range of salinities. Given the widespread occurrence of migration barriers in freshwater, it is unknown whether the coastal resident eel preferred that habitat, or if it was the only available habitat for them. Our findings nonetheless highlight the need to include coastal habitats when assessing population development and silver eel production of the critically endangered European eel.
McInnes, J. C.; Burgess, T.; Mergard, G.; Wells, M. R.; McMahon, C. R.; Neave, M. J.; Polanowski, A.; Terauds, A.; Tornos, J.; Lejeune, M.; Briand, F.-X.; Baele, G.; Boulinier, T.; Achurch, H.; Alderman, R.; Lashko, A.; Wienecke, B.; Wynen, L. P.; Viola, B.; Virtue, P.; Hodgson, J. C.
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High pathogenicity avian influenza (HPAI) has spread across the sub-Antarctic, causing significant wildlife impacts. We report its first detection in an Australian external territory, Heard Island and McDonald Islands, which supports over one million breeding seabirds and seals. Drone and ground surveys (October 2025, January 2026), combined with viral genome analysis, confirmed infection with Influenza A H5N1 clade 2.3.4.4b at Heard Island. Drone surveys revealed mass mortality in southern elephant seals, with 8,573 pups (62%) recorded dead across Heard Island by the final surveys. Mortality increased at an average rate of 5.6% per day in a subset of harems, and the highest observed mortality in a harem was 97%. Based on the average (76%) mortality in the final surveys, total estimated pup mortality at Heard Island was 13,359 (from a total population of 17,364 pups), though this may be an underestimate as mortality was ongoing at this time. HPAI was detected in six of nine species tested and, we suspect, led to elevated mortality in king and gentoo penguins. Phylogenetic analysis indicates the virus was introduced from Crozet Islands, with an estimated arrival around August 2025. These data show the continued easterly spread of HPAI around the sub-Antarctic, with severe but heterogeneous impacts across taxa. Our results demonstrate the value of drones for large-scale monitoring, underscoring the need for continued and enhanced HPAI surveillance across the Southern Ocean.
Reichert, J.; Asbury, M.; Argall, R.; Chen, G. K.; Ehrenberg, J.; Huang, Z.; Jones, B.; Jorissen, H.; Levy, J.; Nims, A. D.; Rottmueller, M. E.; Rova, L. H.; Thode, A.; Wangpraseurt, D.; The R3D Consortium, ; Madin, J. S.
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The global coral reef crisis has prompted restoration initiatives worldwide. Targeting the coral larval stage is among the most scalable approaches as recruitment operates over large spatial scales. It thus represents one of the best levers for coral population recovery. Active coral larval seeding has shown considerable success, and passive substrate engineering has emerged as a promising complementary strategy. Coral settlement modules featuring helix recesses have increased settlement and survival by up to 80-fold on small experimental units, but whether these results translate to tools deployable at the scale of thousands of units, remains yet an open question. Here, we transferred structural features from successful experimental coral settlement designs into production-ready concrete modules to (i) evaluate coral recruitment on five designs at four reef sites differing in flow regime and coral cover over one year; (ii) compare production-scale performance against experimental clay modules and natural reef substrate; and (iii) identify key parameters for large-scale production. The helix recess geometry of coral settlement modules outperformed the featureless control design approximately 20-fold and exceeded natural reef recruitment at least 3- to 32-fold. The helix features were successfully transferred from experimental clay to production-scale concrete modules, yielding comparable settlement densities when standardized to crevice length, which proved to be the biologically relevant unit of available habitat. Production feasibility was demonstrated by producing 690 modules for deployment on a hybrid reef on the west side of Oahu, Hawaii. The passive coral larval recruitment approach presented here could substantially improve the logistical and economic feasibility of large-scale coral reef restoration. This approach requires neither coral larval rearing, handling, nor coral fragmenting, and is compatible with active larval seeding where genetic diversity or larvae supply are limiting factors. The coral settlement modules can be cast in standardized concrete molds at precast facilities. Modules have demonstrated consistent coral recruitment enhancement across reef environments with contrasting flow and coral cover. Deploying mixed arrays of helix-recess structures with designs offering multi-level complexity and three-dimensional rugosity maximizes outcomes for coral, fish, and invertebrate communities simultaneously. Site selection is the most critical deployment decision and should consider larval supply, hydrodynamics, and substrate stability which drive recruitment outcomes more than design choice alone. The modules offer a range of application potential, ranging from integration into existing coastal infrastructure over stand-alone reef restoration approaches, to substrate-consolidating interconnected arrangements.
Jac, R.; Van Beveren, E.; Le Pape, O.; Boudreau, M.; Coussau, L.; Sirois, P.; Robert, D.; Brosset, P.
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Capelin (Mallotus villosus), a key forage fish in the Northwest Atlantic, links zooplankton to predators including commercial fishes, seabirds, and marine mammals, yet its life-cycle movements in the Gulf of St. Lawrence (GSL) remain poorly understood. Between 2022 and 2024, otoliths from 927 individuals collected during and after spawning were analysed by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). Building on previous work on regional structuring, seven trace elements (Li, B, Mg, K, Zn, Sr, Ba) were used to discriminate three regions. Early-life regional signatures were inferred through an edge-to-core approach, assigning otolith core chemistry to one of these regions using quadratic discriminant analysis. The core was treated as an integrated early-life signal (late-larval to early juvenile period) rather than a strictly natal signature. Spatial variation in core chemistry was consistent across cohorts, mirroring the stability documented on the otolith edge. Results revealed widespread dispersal alongside partial regional residency: individuals with northeastern early-life signatures showed the strongest correspondence between early-life and capture regions, whereas other regions were more connected. Fish sampled during spawning were more often reassigned to their inferred early-life region than post-spawning fish, a regional-scale homing-like pattern consistent with regional spawning fidelity. This coexistence of dispersive and resident strategies likely generates a portfolio effect buffering the population against environmental variability and localised reproductive failures.
Berry, M.; Austad, B.; Aarestrup, K.; Davidsen, J. G.; Nevoux, M.; Alexandre, C. M.; Silva, S. S.; Stevens, J. R.; King, R. A.; Thorstad, E. B.; Höjesjö, J.
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Downstream migration and sea entry are periods of high mortality for sea trout smolts and migration timing is a critical aspect of survival. We aimed to investigate migration timing of PIT-tagged sea trout smolts across a latitudinal gradient in five freshwater systems across Europe: Norway, Sweden, Denmark, France and Portugal. In two systems, smolt migration was further examined to assess a) differences in sex, body size and condition between autumn and spring migrants; b) the influence of spatial origin within the stream; and c) relationships between individual body size and migration date. Tagged smolts were not detected migrating in the Portuguese watershed. Spring migration timing differed significantly between watersheds in Norway, Sweden, Denmark and France. Generally, there was a trend of earlier migration at lower latitudes. Autumn vs spring migration was examined in Gudso-Denmark. Autumn migrants were larger in both length and mass, with no differences in sex ratios or body condition. Fish originating from an upstream site were more likely to migrate in the autumn compared to the spring and vice versa. Size dependent migration was found in the Swedish system, Haga [a]-Sweden, with larger individuals migrating earlier in the spring than smaller individuals. Outward-migrating smolts were also more likely to originate from a downstream site than an upstream site. Overall, these results show both large-scale geographic and fine-scale individual influences on migration timing. Given that climate change may have large impacts on migration patterns in sea trout, understanding variability in migratory patterns across a latitudinal gradient is an important tool for predicting responses to environmental changes.
Shibata, Y.; Iwahara, Y.; Hino, H.; Tsukada, A.; Kisara, Y.; Nishino, T.; Endo, H.
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Artificial intelligence (AI)-based image analysis can efficiently estimate fish length, but differences in devices, imaging conditions, operators, and AI models limit comparability among surveys. We propose a standardization framework that estimates a bin-specific error matrix from paired reference measurements and AI-derived lengths and applies it to standardize (correct) AI-derived length-frequency distributions. The Richardson-Lucy expectation-maximization algorithm was used, with the number of iterations selected via cross-validation. Simulations based on empirical length-frequency data from 110 species showed that standardization reduced relative bias and distributional discrepancy; median relative-bias and root mean square error ratios were below 1, and the performance was more affected by the amount of paired data than by the number of cross-validation folds. In real data from 957 Japanese jack mackerel, standardized AI-derived distributions approached human-observer histograms, although discrepancies remained in the range of 160-230 mm. The proposed framework provides a practical approach for improving the comparability of image-derived length-frequency data using paired calibration data, without retraining the underlying AI model.
Tran Nguyen, A. H.; Ha, G.-H.; Tran, D.-P.; Le, N. T.; Glendining, S.; Fitzgibbon, Q.; Herzig, V.; Luu, P.-L.; Ventura, T.
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The slipper lobster (Thenus australiensis) is rapidly emerging as a high-potential species for commercial aquaculture. Because females exhibit superior growth characteristics due to less frequent moulting after sexual maturity, developing monosex breeding strategies is highly desirable for industry profitability. However, the lack of genomic resources and early sex-identification tools has hindered this development. Here, we report the first draft male genome assembly for T. australiensis, generated using a combination of whole-genome shotgun sequencing, DArT-seq, and multi-tissue transcriptomics. The curated assembly spans 0.913 Gbp with high functional completeness (93.0% BUSCO), providing a robust repertoire of 30,100 protein-coding genes. Through k-mer subtraction and population-level DArT-seq genotyping, we provide definitive evidence that T. australiensis utilizes an XX/XY sex-determination system. Crucially, by identifying male-specific structural variations within a neo-Y locus, we developed a diagnostic PCR assay targeting a male-exclusive sequence. This 171 bp marker achieved 100% accuracy in phenotypic sex identification across wild-caught populations. Ultimately, these foundational genomic resources, combined with a highly reliable molecular sexing tool, provide the critical framework necessary for early sex sorting, broodstock management, and the commercial advancement of monosex slipper lobster farming.
Mildenberger, T. K.; Maioli, F.; Berg, C. W.
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Scientific bottom-trawl surveys provide essential fisheries-independent data for fisheries and ecosystem research. In the Northeast Atlantic, the ICES Database of Trawl Surveys (DATRAS) compiles haul-level information, species- and length-specific catch data, and individual biological observations across multiple long-term surveys. However, reproducible workflows for processing and integrating these relational datasets remain challenging. We present DATRASextra, an open-source R package that provides modular end-to-end workflows for accessing, cleaning, harmonising, quality-controlling, and analysing DATRAS survey data. The package supports derivation of standardised haul-level survey variables, integration of multiple surveys, and generation of analysis-ready datasets for downstream applications including stock assessment, biodiversity analyses, and large-scale synthesis efforts such as FishGlob.
Cattano, C.; Mininni, C.; Remmers, D.; Santoro, M.; Milazzo, M.
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The white shark Carcharodon carcharias (Linnaeus, 1758) is one of the most iconic and threatened marine predators globally and is listed as critically endangered by the IUCN in the Mediterranean Sea, where populations are primarily affected by fishing pressure and the degradation of critical habitats. Available information on Mediterranean white sharks mostly relies on fishing interactions and opportunistic surface records, thereby limiting evaluations on the species ecology. Here, we report an exceptionally rare underwater encounter with this species, documented by divers involved in an expedition aimed at removing ghost fishing gear from a World War II shipwreck in the Strait of Sicily (SoS), central Mediterranean. Given the exceptional nature of this observation, we analysed the video footage in detail with the aim of providing morphological information and novel insights into the species ecology. The footage analysis also allowed close observations on behavioural aspects and on interspecific and parasitic associations, thus providing information that is rarely achievable through surface sightings or from captured individuals, which historically represent the majority of records for this species in the region. To contextualize this observation within the SoS--an area suggested to function as a nursery and reproductive ground for the species--we also provide an updated compilation of records reported in the scientific literature over the last decade, adding 18 new records to existing datasets. This study highlights the value of shipwrecks as observation sites for rare and elusive species, and underscores the importance of non-invasive, video-based approaches in advancing knowledge of a species whose ecology in the Mediterranean remains poorly understood.
Boles, S. E.; Swezey, D. S.; Aquilino, K. M.; Stott, H. K.; Rogers-Bennett, L.; Bush, D.; Sanford, E.; Whitehead, A.
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Absorption of CO2 by global oceans is decreasing pH resulting in ocean acidification (OA). Impacts on shellfish have been documented in ecologically and commercially important species. We examined the influence of diet and OA between two populations of red abalone (Haliotis rufescens) a species of aquaculture importance and declining wild populations. Populations experience different exposure histories: strong upwelling (Van Damme, California [VD]) historically exposed to low-pH conditions and weak-intermittent upwelling (Santa Barbara, California [SB]). Abalone were cultured under control-pH or OA-conditions and fed crustose coralline algae (CCA) or diatoms used in aquaculture. We tested treatment effects of population, settlement diet, and OA-exposure on survival as influenced by larval-energy stores. Survival in both populations was enhanced by CCA when cultured under both treatment conditions; however, by later stages, this effect remained only for SB. SB had reduced post-settlement survival when cultured under OA-conditions, whereas post-settlement survival of VD was not. Diet affected the relationship between larval-energy and post-settlement survival; a positive relationship when fed diatoms and a negative relationship with CCA. The relationship between larval energy and post-settlement survival was stronger in VD. CCA enhanced juvenile growth in SB cultured abalone at both three-months and one-year post-settlement. Settlement diets can reduce the impacts of OA on early-life stages of abalone, but population differences driven by underlying energetics affect the consistency of this outcome. These findings illuminate the impacts from OA, suggesting populations may be at risk, and inform strategies for developing and sustaining shellfish aquaculture in the face of changing ocean conditions.
Ogonowski, M.; Gerdes, Z.
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Environmental DNA (eDNA) has emerged as a promising tool for estimating fish abundance, yet linking eDNA concentration to true density remains a significant challenge in seasonal systems, where the signal is strongly influenced by temperature. We investigated whether eDNA can serve as an abundance index for three-spined stickleback (Gasterosteus aculeatus) in four coastal bays of the Baltic Sea (5.7-20.5{degrees}C, April-July 2023), by pairing eDNA sampling with two trap types of contrasting catchability. Light traps capture fish by phototactic attraction during darkness, so their catchability is driven primarily by night duration rather than temperature, while benthic traps respond to temperature through the same activity-driven mechanism as eDNA production. The temperature sensitivity of eDNA estimated from field data was far higher than physiological expectation (Q10 = 12.4, against a maximum metabolic rate benchmark of Q10 = 3.5), indicating that the field temperature signal reflects ecological change in addition to metabolism. We then compared how well three eDNA predictors tracked a combined trap-based abundance index: uncorrected eDNA, eDNA corrected with the temperature response constrained to the laboratory metabolic rate (a first-principles correction), and eDNA corrected with the response estimated from the field data. Uncorrected and first-principles-corrected eDNA were both strong predictors of abundance (standardised slopes of 0.45 and 0.43), whereas the field-corrected predictor was not (0.08). Uncorrected and first-principles-corrected eDNA performed comparably because temperature and abundance increased together over the season; the first-principles correction is nonetheless preferable, as it remains reliable when this covariation is unknown a priori. We conclude that estimating a temperature correction from field data should be avoided in seasonal eDNA monitoring, because it removes the abundance signal together with the temperature effect and assumes a stability in abundance that cannot be verified without independent reference data.
Tseitlin, M.; Garcia-Giron, J.; Crabot, J.; Jiang, X.; Larkin, D. J.
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Freshwater monitoring programmes like the European Unions Water Framework Directive (WFD) provide a wealth of data on European lake status, including water quality and macrophytes (aquatic plants) as critical habitat features that support health of humans and wildlife. Easier WFD data access can enable external management and research to better safeguard human and natural freshwater use. We demonstrate a replicable workflow to easily download and process multi-year (2007-2024) observations of lake macrophytes (425 sites) and complementary water quality variables (202 sites) from Swedish WFD data. Then, we illustrate the value of improved data access to address ecological questions that drive conservation, investigating how spatial scales influence macrophyte richness and associated water quality relationships using a spatial random intercept model. Decomposing the spatial intercept links small scales (<10 km) to site-level gradients and large scales (>100 km) to biogeographical drivers. Stochastic and environmentally-structured processes coexisted at intermediate scales (10-100 km). Adding water quality rarely improved overall predictive performance of macrophyte diversity models but consistently influences the role of different spatial scales. Water quality variables showed consistent spatially structured variation at intermediate scales and unique spatial patterns in tandem, overlapping with large-scale biogeographical influences. Altogether, we show context-dependencies for spatial model interpretation and provide guidance in accounting for spatial confounding to improve inferential and predictive performance. Our workflow and results show a clear way forward for accessing high-quality macrophyte and water quality data sets and their utility for addressing ecological questions that guide macrophyte protection under the WFD. HighlightsO_LIyears Swedish of macrophyte and water quality monitoring data were extracted. C_LIO_LIrichness showed scale-specific patterns linked to geographic gradients. C_LIO_LIbest predictive models for richness had no water quality at all. C_LIO_LIoverlap in their spatial scales and must be carefully separated. C_LIO_LIpen access data and multiscale analysis can apply to many ecological questions. C_LI
Kjaerner-Semb, E.; Fraser, T. W. K.; Vogelsang, P.; Skaftnesmo, K.; Ayllon, F.; Edvardsen, R. B.; Braathen, S.; Norberg, B.; Fjelldal, P. G.; Andersson, E.; Schulz, R. W.; Wargelius, A.
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The age at which Atlantic salmon reaches sexual maturity shows a strong hereditary component associated with the vgll3a locus. The role of Vgll3 in maturation has remained unknown in vertebrates until recently, when it has been linked to pleiotropic roles in killifish, both delaying male maturation and affecting lifespan by protecting against cancer. As Atlantic salmon has two vgll3 paralogs, where only vgll3a has been associated with sexual maturation, it may provide a suitable model for studying the maturation-specific function of vgll3, as the other paralog may buffer for pleiotropic roles of vgll3. To address this, we used CRISPR/Cas9 to generate fish highly mutated in the vgll3a gene. We monitored their maturation and crossed highly mutated crispants to generate two year-classes of complete loss-of-function. All groups were reared under environmental conditions triggering early maturation in one-year-old males. We found a clear difference in the proportion of sexually maturing or mature fish between the different genotypes: in all experiments significantly fewer vgll3a-/- males entered puberty and reached final maturation compared to vgll3a+/- and vgll3a+/+ males. Furthermore, loss of vgll3a resulted in lower frequencies of maturation also in females. We conclude that Vgll3a stimulates maturation and that its complete removal significantly reduced maturation rates in both sexes in Atlantic salmon. Our findings also identify vgll3a as the causative gene in the locus associated with age at sexual maturity. Together, our findings support a new role for Vgll3 in initiating puberty in vertebrates and identifying salmon as a promising model for functional studies regarding the timing of sexual maturation.
Gibbons, A.; Parnell, A.; Donohue, I.; Ogasawara, M.; Ross, S. R. P.-J.
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O_LIMonitoring and limiting the spread of invasive species on islands requires efficient detection and population estimation methods. However, elusive species can be difficult to monitor using traditional methods, making autonomous approaches such as camera trapping and acoustic monitoring increasingly valuable. C_LIO_LIOn the island of Okinawa, Japan, the small Indian mongoose ( Urva auropunctata) threatens many native species since its introduction in 1910. Listed among the worlds worst invasive species, effective monitoring of U. auropunctata in Okinawa is critical. The Okinawa Environmental Observation Network (OKEON) uses camera traps to detect U. auropunctata, but success depends on precise placement. Though OKEON also includes a high-resolution acoustic monitoring programme, no audio classification model currently exists for U. auropunctata. Developing such a model could improve substantially our capacity to detect and manage the species. C_LIO_LIUsing sparse U. auropunctata vocalisations collected from camera trap videos, we built a lightweight Convolutional Neural Network distilled from a more complex model for classifying contact calls and alarm calls of U. auropunctata. Our distilled model performed similarly to the full model at detecting vocalisations from training data, but was considerably faster. C_LIO_LIWe applied the distilled classifier to [~]486 hrs of audio collected over eight years from southern Okinawa, where we successfully detected U. auropunctata a handful of times in each year of recording. In spite of strong model performance on test data, our model did not transfer well to unseen data, perhaps owing to the rarity of U. auropunctata calls and consequent small training dataset size, limiting its utility for ecological monitoring. C_LIO_LIPractical implication. The use of sparse audio data from camera trap videos to train an acoustic classifier had limited utility to detect the rarely vocalising U. auropunctata from passive acoustic monitoring data. We provide several recommendations for enhancing classifier performance to provide robust actionable insights into the distribution and spread of U. auropunctata, and aid targeted conservation efforts for Okinawas threatened biodiversity. C_LI
Hofstetter, L.; Mueller, T. M.; Bourqui, M.; Burlakova, L. E.; Cristante, Z. C.; Karatayev, A. Y.; Kessler, S.; Narwani, A.; Santos, J. L.; Sturm, L.; Wellauer, N.; Spaak, P.; Weber, A. A.-T.
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Quagga mussels (Dreissena rostriformis bugensis) are ecosystem engineers that can alter nutrient cycling, benthic-pelagic coupling, and food-web structure in deep lakes. Although their invasion trajectories are well documented in the Laurentian Great Lakes in North America, depth-specific population dynamics remain poorly resolved in recently invaded European perialpine lakes. We analyzed five annual lake-wide surveys (2021-2025) from 54 stations spanning 2.4-253 m depth in Lake Constance to quantify changes in quagga mussel density, biomass, and shell-length distribution. Contrary to expectations of lake-wide exponential growth, shallow-water populations (< 20 m) showed no significant increase during the study period and appear to have reached carrying capacity before monitoring began. In contrast, densities increased monotonically at intermediate depths (40-125 m), indicating ongoing expansion into deeper strata. Mean shell length declined with depth, and size distributions in shallow waters shifted toward larger individuals, consistent with a transition from active recruitment to somatic growth of established mussels. Compared with the Laurentian Great Lakes, Lake Constance already has substantially higher shallow-water biomass, whereas deeper invasion trajectories are broadly similar. These results show that quagga mussel invasion in deep European lakes can combine rapid littoral saturation with slower profundal expansion, complicating direct transfer of predictions from the Great Lakes. Continued depth-stratified monitoring will be essential for anticipating future ecosystem effects in perialpine lakes.