ICES Journal of Marine Science: Journal du Conseil

Aaron, Kyle D; Greer, Adam T; Duffy, Patrick I; Treible, Laura M; Frischer, Marc E

doi: 10.1093/icesjms/fsaf089pmid: N/A

Zooplankton composition and distribution influence prey quality and availability for higher trophic levels, yet ecological forces structuring communities are not often resolved on spatial scales relevant to predator–prey encounters (1–10 m). Because continental shelf water columns are often vertically stratified, fine-scale interactions may influence overall biological productivity. Using a towed imaging system, we measured meso- and macrozooplankton abundances (>2.2 mm equivalent spherical diameter) in the South Atlantic Bight between the 25 and 45 m isobaths in August 2021. Zooplankton were parsed into four key traits (size, carbon content, trophic strategy, and swimming speed), and buoyancy frequency was used to identify discrete vertical oceanographic zones. Trait diversity was less variable in mixed waters due to the dominance of low carbon content zooplankton or passive swimmers. Upwelling intrusions generated high chlorophyll-a and sharp stratification, which favoured high-carbon, fast swimming zooplankton. Trait group abundances were often higher in these deeper, sharply stratified waters, suggesting that intrusions generally favour secondary production, with gelatinous organisms gradually becoming more dominant as the pycnocline weakens. The distribution of size classes, however, did not change among water masses. Stratification and mixing generate distinct environments and consistent trait assemblages, potentially improving predictions of community responses to oceanographic structure.

Skaala, Øystein; Harvey, Alison; Borgstrøm, Reidar; Fjeldheim, Per Tommy; Andersen Fjeldheim, Kaja Christine; Winterthun, Synne; Knutar, Sofie; Wennevik, Vidar; Glover, Kevin Alan

doi: 10.1093/icesjms/fsaf101pmid: N/A

Sustainable management of anadromous salmonid populations rests on good data on population status and knowledge about how populations and environments are linked. We used a 10-year data set consisting of river water temperature and discharge and complete daily sampling of the spawning runs of Atlantic salmon and sea trout in the river Etneelva, western Norway, to model the association between environmental triggers and timing of river ascendance. Median day for ascendance varied significantly among years. Peak migration for both species occurred at water discharges between 20 and 30 m3/s and temperatures between 10°C and 20°C. Escaped farmed salmon arrived 4–59 days later than wild salmon. Modelled projections in river temperature and discharge, based on different climate scenarios, suggest unpredictable effects from climate changes on population phenology. Angling exploitation rate of salmon after 2013 was significantly reduced compared with exploitation rates between 2005 and 2009. We conclude that (a) water discharge and temperature are major triggers for river ascendance in both species, (b) more extreme fluctuations in river temperature and discharge will affect ascendance timing, and (c) the changes may confound catch statistics and other data sources that are used to infer population status in salmonid populations. We encourage development of long and detailed time series of spawning stocks in index rivers to model impact factors and to calibrate information from other rivers.

Jung, Hyungtaek; Jeon, Min-Seung; Choi, Hyeongwoo; Song, Chi-une; Doh, Huijeong; Kwak, Jung Hyun; Eyun, Seong-il

doi: 10.1093/icesjms/fsaf105pmid: N/A

Next-generation sequencing has significantly advanced omics and post-omics technologies, facilitating detailed analysis of whole-genome profiles through comparative genomics and reshaping our understanding of evolutionary and ecological dynamics for more precise biotechnological applications. Specifically, analyzing genomic similarities and differences through synteny and structural variations (SVs) has clarified the relationship between genetic variations and phenotypic changes. This study represents the first instance of employing chromosome-level comparative genomics and long-read SV detection in the Pacific oyster Crassostrea gigas, a species crucial for both ecology and economy, aiming to pinpoint genes and genomic regions linked to growth and disease. Utilizing the latest Pacific oyster genomes and their PacBio long reads, we uncovered significant genetic variability that explains differences between individuals. By integrating results from five state-of-the-art read mappers (LRA, Minimap2, NGMLR, Vulcan, and WinnowMap) and two SV callers (cuteSV and Sniffles2), we identified between 193 355 and 219 501 SVs, accounting for 183 Mb (31.2%) and 228 Mb (35.2%) of the total genome in two distinct reference genomes, respectively. This approach, leveraging PacBio long reads, surpassed short-read technologies in identifying candidate genes associated with SVs, such as bone morphogenetic proteins and superoxide dismutase, thereby highlighting their potential roles in growth and disease resistance. Our findings offer a comprehensive view of comparative genomics and long-read SVs, revealing their significance in oyster genome evolution and providing valuable insights for future marine biotechnological research, including the development of genome editing and surrogate broodstock technologies.

Peters, Janna; Albaina, Aitor; Blanco-Bercial, Leocadio; Bucklin, Ann; Di Capua, Iole; Dos Santos, Antonina; Falkenhaug, Tone; Fernandez de Puelles, Mariluz; Fileman, Elaine; Garić, Rade; Holst, Sabine; Hosia, Aino; Laakmann, Silke; Majaneva, Sanna; Mańko, Maciej K; Mazzocchi, Maria Grazia; O’Brien, Todd; Peijnenburg, Katja T C A; Renz, Jasmin; Rossel, Sven; Weydmann-Zwolicka, Agata; Winkler, Gesche; Yebra, Lidia; Cornils, Astrid

doi: 10.1093/icesjms/fsaf077pmid: N/A

Taxonomic discussions often permeate the broader scientific community slowly, yet they may hold more relevance than typically assumed. In many zooplankton groups, identification issues arise from cryptic species complexes, increasingly revealed by molecular approaches, and from groups with high morphological similarity. These challenges can lead to substantial uncertainties in species-level identification, questioning whether the expected species are truly covered and whether those sharing names across ecosystems are indeed distinct entities. This review provides a condensed overview on identification challenges of key species in the ICES zooplankton time series from the North Atlantic and adjacent seas. Examples are given across all relevant groups, including copepods, gelatinous plankton, and meroplanktonic larvae. The high prevalence of challenging species complexes underscores the need to further explore the implications of an accurate species assignment for understanding what defines a species’ role in an ecosystem. This review highlights the dynamic nature of taxonomy, with species being split and cryptic species eventually becoming morphologically distinguishable. It provides examples showing that relying solely on molecular methods without deep taxonomic expertise poses significant risks. It also aims to serve as a starting point for delving deeper into the taxonomy of the ICES zooplankton time series.

Westergerling, Taraneh; Tenningen, Maria; Enberg, Katja; Rosen, Shale Pettit

doi: 10.1093/icesjms/fsaf094pmid: N/A

In-trawl stereo cameras can provide fine-scale spatial and temporal information on species along the trawl path and record small-sized and fragile organisms typically absent from catches. Reliable estimates of abundance and length frequency from in-trawl cameras will improve ecosystem understanding and lessen the need for physical catches on scientific surveys. However, determining these estimates from camera footage is challenging since the same individual can appear in multiple frames and swim repeatedly in and out of the camera’s field of view. The manual image analysis performed in this study provides important information on how the swimming behaviour of three abundant pelagic taxa in the Norwegian Sea, along with a camera’s field of view and frame rate, affect the number of repeated appearances. Moreover, these manual annotations serve as a valuable dataset for validating automatic image analyses. Our results show that, depending on the taxa, swimming orientation, length, density of individuals, and distance to the camera affect the extent of time an individual is observed. If the repeated appearance of individuals is not accounted for, taxa or length classes with fewer appearances are under-represented in relative abundance and lead to skewed length frequency distributions. Compared to herring and blue whiting, a large fraction of mesopelagic fishes remains undetected during automatic analysis (RetinaNet). Assessing the factors driving repeated appearances improves our understanding of in-trawl camera data and highlights the importance of integrating tracking with automatic image analysis.

Rybicki, Sandra; Woods, Pamela J; Elvarsson, Bjarki Þór; Agnarsson, Sveinn; Ólafsdóttir, Anna H; Oostdijk, Maartje; Kristofersson, Dadi

doi: 10.1093/icesjms/fsaf090pmid: N/A

Understanding how fishers react to incentives created by fisheries policy, fish density, and market conditions is essential to understanding and predicting the impact of industrial fishing on the development of marine fish stocks. While most empirical studies focus on demersal species, this study explores the behavior of pelagic fisheries as a recent expansion of Northeast Atlantic mackerel (Scomber scombrus), due to its dynamic geographical nature, brought a new lucrative fishery to Iceland. We fit a spatial choice model for the time period 2011–2020 to understand the importance of environmental and socioeconomic predictors and their impact on individual fisheries behavior. Several models were tested, with the best model predicting 86% of the overall choices correctly. The inclusion of fish price, oil price, vessel size, processing type (frozen/fresh), expected catch, distance to ports, biological parameter of fish density, and environmental parameters such as surface temperature and net primary production played a significant role in improving the model’s accuracy. This highlights the importance of considering both cost-related factors and ecological conditions in understanding fishing location choices.

Calewaert, Jan-Bart; Sierra-Correa, Paula; McMeel, Oonagh; McConnell, Terry; Alvarez Fanjul, Enrique; Leadbetter, Adam

doi: 10.1093/icesjms/fsaf072pmid: N/A

Ocean Decade Challenge 8 of the Ocean Decade seeks to create and make available an adaptive and dynamic digital representation of the ocean to enhance decision-making and support sustainable ocean management. For Challenge 8, success depends on our ability to create the enabling environment that allows diverse stakeholders to access, contribute to, and benefit from an inclusive and interconnected global digital ocean ecosystem. The strategic ambition has thus focused on defining the concrete outcomes and fostering the transformational change needed to create the enabling environment and initial digital assets by 2030 that will allow us to generate a comprehensive digital representation of the Ocean. This requires access to the global collection of interlinked and interoperable digital assets, including FAIR data, information, models, software, applications, as well as the digital architectures and infrastructures which support and connect them. Only collectively, will these assets allow us to better understand the ocean’s past, present, and future state and support informed decision-making. Challenge 8 is a cross-cutting endeavour underpinning all other challenges and must therefore deliver resources that are relevant and useful for the widest possible range of users and stakeholders in ways adapted to their needs and capacities, leaving no one behind. This will require a continuous and iterative process, significant resources, multi-stakeholder collaborations, transparent processes, and clear focus on inclusivity and equity, to establish the digital foundations needed to support sustainable ocean management for the decades to come.

Niemisto, Maura; Contreras, Adrián; Wahle, Richard A; Fields, David M

doi: 10.1093/icesjms/fsaf088pmid: N/A

The geographic range of the American lobster, Homarus americanus, spans a steep thermal gradient along the coastal Northwest Atlantic. As CO2 emissions increase globally, this range is rapidly warming and acidifying. Larval H. americanus hatch with a finite amount of maternally sourced lipid stores in their yolk sac, which provide an energetic buffer during the intermediate period between hatch and first feed. This study examines the response of newly-hatched, unfed H. americanus larvae to the combined effects of elevated pCO2 and temperature. Using a space-for-time approach, we compared larvae of two distinct sub-populations from thermally contrasting regions: Rhode Island, at the warmer, southern limit of the species range, and Midcoast, Maine, a cooler northern region. Average larval initial post-hatch weight was similar across regions and variability therein could be explained by maternal effects. Under 6 days of starvation, larvae from the two regions lost ∼14% of their initial dry weight and 25% of their Carbon weight. Still, end-century elevated temperature or acidification did not substantially alter those rates for larvae from either region. However, under an identical range of conditions over the 6-day experiment, larvae from the warmer regime maintained relatively stable oxygen consumption rates, while those from the cooler regime started 50% higher, then dropped by 80% within 2 days. If depressed metabolic functioning translates to reduced feeding efficiency for cool regime larvae, our findings suggest that subpopulations in the southern edge of the species range have a relative advantage in food-scarce environments under these conditions, adding to previous evidence for countergradient variation in this species. Further analysis of total fatty acid losses conducted on Midcoast larvae suggested starved larvae exposed to elevated temperature (19°C) experienced considerably greater losses of key lipid groups than larvae under ambient conditions (16°C, 400 ppm), particularly within the first 2 days of exposure. Our results highlight the short time frames over which ocean warming can accelerate the depletion of energy stores and make larvae more vulnerable to starvation.

Carreño-Castilla, Alejandro; Palmer, Miquel; Cabanellas-Reboredo, Miguel; Alós, Josep; Macías, David; Álvarez-Berastegui, Diego; Saber, Sámar

doi: 10.1093/icesjms/fsaf091pmid: N/A

We propose that catch-per-unit-effort (CPUE) data from fishing tournaments can derive a sentinel time series, serving as an indicator of unusual changes in unobserved abundance trends when stock assessments are uncertain. This proposition relies on strict tournament regulations that enforce consistent fishing tactics and standardized monitoring of catch and effort over time. However, three key challenges must be addressed to ensure its reliability: (i) correcting for daily bag limit effects on catch underreporting, (ii) accounting for between-boat variability and environmental factors affecting catchability at the trip scale, and (iii) modelling environmental effects on CPUE at the year scale. As a case study, we analyse a 19-year sentinel time series for the Mediterranean albacore (Thunnus alalunga), whose stock status remains uncertain due to data limitations. On average, 2.2 albacore were unreported per boat upon reaching the bag limit. No unusual changes were detected, as the series exhibited an apparent stability, with an average growth rate of 1.06 (95% credible interval: 0.77–1.48). Despite uncertainty, catchability peaked at an optimal wave height, while a hyperstability scenario was rejected by accounting for the boat consistency in tournament participation. Overall, our framework holds promise for improving the understanding of data-limited fisheries dynamics.