ICES Journal of Marine Science: Journal du Conseil

Andrews, Adam J; Di Natale, Antonio; Bernal-Casasola, Darío; Aniceti, Veronica; Onar, Vedat; Oueslati, Tarek; Theodropoulou, Tatiana; Morales-Muñiz, Arturo; Cilli, Elisabetta; Tinti, Fausto

doi: 10.1093/icesjms/fsab261pmid: N/A

Overexploitation has directly, negatively affected marine fish populations in the past half-century, modifying not only their abundance but their behaviour and life-history traits. The recovery and resilience of such populations is dependent upon their exploitation history, which often extends back millennia. Hence, data on when exploitation intensified and how populations were composed in historical periods, have the potential to reveal long-term population dynamics and provide context on the baselines currently used in fisheries management and conservation. Here, we setup a framework for investigations on the exploitation history of Atlantic bluefin tuna (Thunnus thynnus; BFT) in the eastern Atlantic and Mediterranean by collating records of their zooarchaeological remains and critically reviewing these alongside the literature. Then, we outline how novel multidisciplinary applications on BFT remains may be used to document long-term population dynamics. Our review of literature provides clear evidence of BFT overexploitation during the mid-20th century ce. Furthermore, a strong case could be made that the intensification of BFT exploitation extends back further to at least the 19th century ce, if not the 13th–16th century ce, in the eastern Atlantic and Mediterranean. However, a host of archaeological evidence would suggest that BFT exploitation may have been intensive since antiquity. Altogether, this indicates that by the currently used management baselines of the 1970s,  population abundance and complexity was already likely to have declined from historical levels, and we identify how biomolecular and morphometric analyses of BFT remains have the potential to further investigate this.

Li, Daoliang; Wang, Qi; Li, Xin; Niu, Meilin; Wang, He; Liu, Chunhong

doi: 10.1093/icesjms/fsab264pmid: N/A

Automatic classification of different species of fish is important for the comprehension of marine ecology, fish behaviour analysis, aquaculture management, and fish health monitoring. In recent years, many automatic classification methods have been developed, among which machine vision-based classification methods are widely used with the advantages of being fast and non-destructive. In addition, the successful application of rapidly emerging deep learning techniques in machine vision has brought new opportunities for fish classification. This paper provides an overview of machine vision models applied in the field of fish classification, followed by a detailed discussion of specific applications of various classification methods. Furthermore, the challenges and future research directions in the field of fish classification are discussed. This paper would help researchers and practitioners to understand the applicability of machine vision in fish classification and encourage them to develop advanced algorithms and models to address the complex problems that exist in fish classification practice.

Fowler, Ashley M; Ochwada-Doyle, Faith A; Dowling, Natalie A; Folpp, Heath; Hughes, Julian M; Lowry, Michael B; Lyle, Jeremy M; Lynch, Tim P; Miles, Nathan G; Chick, Rowan C

doi: 10.1093/icesjms/fsab270pmid:

Hutchings, Jeffrey A

doi: 10.1093/icesjms/fsab271pmid: N/A

Providing science-based advice can be challenging. Personal in its reflections, the story that follows asks throughout: What constitutes an appropriate model for the communication of science-based advice that best serves society? The first “front line,” in 1992, involved tenuous hypotheses on the collapse and recovery of Newfoundland's Northern cod (Gadus morhua), raising troubling questions about political influence on science-based advice and on its integrity. These questions subsequently motivated a critique written with two colleagues on the communication of science to decision-makers, provoking a telling invective from a government department in defence of the status quo. The story transitions to my 2000–2012 tenure as a member and then as chair of Canada's national body advising which species should be on the legally binding national at-risk register, illustrating how politically sensitive science-based advice can be objectively, effectively, and independently communicated, unfiltered by vested interests. Since 2009, I have served as independent science advisor on the sourcing of sustainable seafood to Canada's largest food retailer, providing a meaningful, impactful opportunity to advise their decision-makers. Science-based advice, free from political and advocacy-driven vested interests, is a requisite return for tax-supported investments in science. If provision of such advice is a “moral imperative,” as argued more than 60 years ago by C.P. Snow, then scientists are obliged to be the best advisors that we can be.

Goodwin, Morten; Halvorsen, Kim Tallaksen; Jiao, Lei; Knausgård, Kristian Muri; Martin, Angela Helen; Moyano, Marta; Oomen, Rebekah A; Rasmussen, Jeppe Have; Sørdalen, Tonje Knutsen; Thorbjørnsen, Susanna Huneide

doi: 10.1093/icesjms/fsab255pmid: N/A

The deep learning (DL) revolution is touching all scientific disciplines and corners of our lives as a means of harnessing the power of big data. Marine ecology is no exception. New methods provide analysis of data from sensors, cameras, and acoustic recorders, even in real time, in ways that are reproducible and rapid. Off-the-shelf algorithms find, count, and classify species from digital images or video and detect cryptic patterns in noisy data. These endeavours require collaboration across ecological and data science disciplines, which can be challenging to initiate. To promote the use of DL towards ecosystem-based management of the sea, this paper aims to bridge the gap between marine ecologists and computer scientists. We provide insight into popular DL approaches for ecological data analysis, focusing on supervised learning techniques with deep neural networks, and illustrate challenges and opportunities through established and emerging applications of DL to marine ecology. We present case studies on plankton, fish, marine mammals, pollution, and nutrient cycling that involve object detection, classification, tracking, and segmentation of visualized data. We conclude with a broad outlook of the field’s opportunities and challenges, including potential technological advances and issues with managing complex data sets.

Dumas, Pascal; Peignon, Christophe; Dumas, Mahé; Bourgeois, Bertrand; Gossuin, Hugues; Fiat, Sylvie

doi: 10.1093/icesjms/fsab262pmid: N/A

Outbreaks of the corallivorous starfish Acanthaster cf. solaris (COTS) are not fully understood, especially in the shallowest areas behind the reef crests where limited COTS impacts are often reported. Here, we investigated the outbreak occurrence and compared post-outbreak habitat impacts in reef flats vs. upper fore reefs at 13 sites in New Caledonia. In this Pacific territory so far considered marginally affected by COTS, we documented wide occurrences of aggregations, combining massive population increases (maximum 605 COTS per swim, abundances >100 COTS recorded in 46% of the sites) with limited spatiotemporal boundaries. Abundance levels met the highest values in the literature, but were restricted to relatively small, isolated mid-shelf reefs. Typical residence time was short (< two years), with at least one site where COTS seemingly disappeared within seven months. The spread of COTS population and subsequent impacts appeared self-contained, and never affected the reef flats (0.5–1.5 m). The transition to severely affected fore reefs was abrupt, with live coral cover divided by nine and morphological diversity halved within a very few meters (3–5 m). We suggest that these differential impacts likely result from harsh environmental conditions making shallow, coral-rich areas less suitable for COTS, thereby pushing predation pressure further downwards.

Mazur, Mackenzie D; Tanaka, Kisei R; Shank, Burton; Chang, Jui-Han; Hodgdon, Cameron T; Reardon, Kathleen M; Friedland, Kevin D; Chen, Yong

doi: 10.1093/icesjms/fsab266pmid: N/A

ABSTRACTFunctional stock-recruitment relationships (SRRs) are often difficult to quantify and can differ over space. Additionally, climate change adds to the complexity of recruitment dynamics. This paper's aim was to incorporate spatial heterogeneity and environmental effects on productivity in SRRs with American lobster in the Gulf of Maine (GOM) as a case study. GOM lobster recruitment has substantially increased since the mid-2000s,  due to improved survival rates of pre-recruits and increased spawning stock biomass (SSB). GOM bottom water temperatures have increased at a rate of 0.2ºC per decade, which caused lobster settlement area to expand and improved survival rates. We first estimated local SSB using bottom trawl survey data and a geostatistical model. Using estimated SSB, recruitment data from a ventless trap survey, and an interpolated bottom water temperature field, we developed modified Ricker stock-recruitment models accounting for spatial heterogeneity and temperature impacts with varying coefficient generalized additive models. Results showed that temperature significantly impacted recruitment. Changes in temperature mediated productivity differed between the eastern and western GOM. Our study demonstrated that the incorporation of spatial heterogeneity and environmental effects impacts our understanding of SRRs. These methods can be applied to other species to understand recruitment dynamics influenced by climate change.

Savina, Esther; Herrmann, Bent; Frandsen, Rikke P; Krag, Ludvig A

doi: 10.1093/icesjms/fsab267pmid: N/A

Gillnets are used world-wide for harvesting groundfish and pelagic species at sea and in freshwater. Little consideration has been given to how fish are caught in gillnets, even though the capture mode provides valuable information for understanding gear catchability. This paper describes a new method of estimating the length-dependent fish capture modes in gillnets. Using this method, we investigated the length-dependent capture modes for cod (Gadus morhua) in commercial monofilament nylon gillnets. Cod is a target species for several fisheries in the Northern Atlantic. This is the first time the capture mode was formally related to fish size with a direct representation of the experimental observations. The results demonstrated that gillnets are clearly designed for gilling. However, capture modes were size dependent, with small fish being caught by the mouth and larger fish by the maxillary. The application of the method is relevant when used by gear technologists to evaluate different gear characteristics to improve size or species selectivity. Changing the hanging ratio, for instance, or replacing nylon twine by thicker biodegradable material may considerably change the capture modes and their effect on gear efficiency.

Martínez-Silva, Maria Angelica; Vagner, Marie; Senay, Caroline; Audet, Céline

doi: 10.1093/icesjms/fsab269pmid: N/A

Deepwater redfish Sebastes mentella will be among the most important resource-sustaining commercial bottom-fish fisheries in the years to come in the Estuary and Gulf of St. Lawrence (EGSL). In 2011, 2012, and 2013, three strong cohorts were recruited to the stock; their abundance in 2018 was 80 times higher than that of the 1993–2012 period. The main goal of this work was to deepen our knowledge of their growth regulation and metabolism in order to identify molecular indicators and determine how they are influenced by natural environmental conditions. Fish weight and water temperature explained 11% of the variation in relative mRNA levels of specific gene targets in liver and muscle among seven sites where deepwater redfish were captured in the EGSL. The relative expression of liver insulin-like growth factor-1 (igf-1) and white muscle A-chain lactate dehydrogenase (ldh-a) correlate positively with weight, whereas heavy chain muscle myosin (myo), heart citrate synthase (cs), and white muscle pyruvate kinase (pk) correlate negatively. The relative expression of heart cytochrome c oxidase subunit 1 (cox-1) and white muscle igf-1 receptor isoform a (igf-1ra) correlate negatively with temperature. Deepwater redfish from the estuary were smaller than those caught at other sites. Since the growth potential of deepwater redfish was strongly correlated with temperature (being enhanced by higher temperatures), this study suggests an ecological advantage for this species in a climate-warming context.

Dalpé, Andréanne; Lalonde-Larue, Ariane; Choquette, Thierry; Cimmino, Jade; Leroux, Émélie; Leung, Christelle; Stewart, Donald T; Angers, Bernard; Breton, Sophie

doi: 10.1093/icesjms/fsab272pmid: N/A

The factors affecting sex determination remain largely unknown for most bivalve species. Environmental factors, such as temperature, are known to influence sex determination in some species, and this has been hypothesized for the mussel Mytilus edulis, but not experimentally validated yet. Adult exposure to different environmental conditions during gametogenesis, which occurs seasonally, may also affect offspring phenotype, including sex determination. Intergenerational carryover effects have been reported in bivalves, but the impact of parental exposures on offspring sex determination has not been examined so far. To address these questions, artificial fertilizations were performed on individuals collected in three different years and their embryos were reared at three different temperatures to specifically test if the environment influences offspring sex ratio through effects on parental developing gametes and/or on developing embryos. The analysis of 1938 embryos from 25 crosses revealed a significant effect of both temperature treatments and sampling years on the proportion of females. However, the overall variation is mostly explained by the “temperature treatment × sampling years” interaction. Taken together, our results suggested that interannual environmental variations experienced by the parents (during gametogenesis) and embryo (during development) can influence the sex of the offspring in M. edulis.