Description: There is a need for automatic systems that can reliably detect, track and classify fish and other marine species in underwater videos without human intervention. Conventional computer vision techniques do not perform well in underwater conditions where the background is complex and the shape and textural features of fish are subtle. Data-driven classification models like neural networks require a huge amount of labelled data, otherwise they tend to over-fit to the training data and fail on unseen test data which is not involved in training. We present a state-of-the-art computer vision method for fine-grained fish species classification based on deep learning techniques. A cross-layer pooling algorithm using a pre-trained Convolutional Neural Network as a generalized feature detector is proposed, thus avoiding the need for a large amount of training data. Classification on test data is performed by a SVM on the features computed through the proposed method, resulting in classification accuracy of 94.3% for fish species from typical underwater video imagery captured off the coast of Western Australia. This research advocates that the development of automated classification systems which can identify fish from underwater video imagery is feasible and a cost-effective alternative to manual identification by humans.

Description: Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez oil spill (EVOS) for demersal fish. We delineate areas across a range of exposure to EVOS and use spatio-temporal models to quantify the abundance of 53 species-groups over 31 years. We compare multiple community metrics for demersal fish in EVOS and Control areas. We find that areas more exposed to EVOS have more negative trends in total groundfish biomass than non-EVOS areas, and that this change is driven primarily by reductions in the abundance of the apex predator guild. We show no signature of increased variability or increased levels of synchrony within EVOS areas. Our analysis supports mild consequences of EVOS for groundfish communities, but suggests that long time-series and assessments of changes at the community level may reveal sub-lethal effects in marine communities.

Description: We gratefully acknowledge the following reviewers for their contributions during 2017.

Description: Fatty acids (FAs) were analysed in Baltic herring ( Clupea harengus membras ) stored in the Swedish Environmental Specimen Bank for up to 40 years. The purpose was to evaluate the retrospective use of FA signatures to detect temporal and spatial changes in the Baltic ecosystem. Fish from northern and central Baltic captured in the 1970s, the 1980s, in 1990, 2000, and 2009 and stored at − 25 °C were analysed. From the 1980s and onward herring from the south Baltic were included. A total of 55 FA and 4 alkenyl chains (detected as dimethyl acetals) were identified, and 28 of these (present at 〉 0.5% by weight) were used in evaluation of the data. The amount of some 20–22 carbon polyunsaturated fatty acids (PUFA) was related to time with lower amounts in older samples while other PUFAs were not related to time. Principal component analysis with saturated FAs and monounsaturated FAs showed similar sample groupings as the one obtained by including the PUFAs. The differences found in herring FA in this longitudinal study could be attributed to location of sampling, year of collection and storage time. However, the clearly distinguishable pattern in the FA composition in herrings from different locations in the Baltic Sea seen at all decades indicate that this technique can be used retrospectively.

Description: Real-time spatial management in fisheries, a type of dynamic ocean management, uses nearly real-time data collection and dissemination to reduce susceptibility of certain species or age classes to being caught in mixed fisheries. However, as with many fisheries regulations, it is difficult to assess whether such a regulation can produce tangible results on population dynamics. In this study, we take advantage of a rare opportunity in which data regarding real-time closures (RTCs) are available for 1990–2014 alongside annual estimates of fishing mortality for three species (Atlantic cod, haddock, and herring) and catch for four species (all plus saithe) in Icelandic fisheries management. We use time series analyses to assess whether RTCs work as expected and yield a lower susceptibility of small fish to being caught, indicated by lower catch levels and selectivities (as estimated from fishing mortalities) in years with more closures. Results indicate that haddock and herring followed this pattern, but only under conditions of generally high fishing mortality. This study represents the first time evidence has been presented that real-time fishery closures can have a beneficial effect on population dynamics, but also suggests that results differ among species.

Description: Ecosystem structure and function in the eastern Bering Sea are impacted by seasonal, interannual, and spatial variation of the zooplankton community. Zooplankton abundance, community composition and individual responses of key taxa, in spring, summer, and fall were evaluated across ecoregions during three years with high sea-ice, 2008–2010 (cold years). Interannual variations were greatest in spring, but less pronounced compared with intra-annual variations. Intra-annual variations were greatest in the south middle domain in spring and the north middle domain in all seasons. Models using environmental variables were able to explain 69–77% of zooplankton community variation within each season. Among individual taxa, Calanus marshallae/glacialis had delayed stage progression in spring 2009 compared with 2008 and 2010 on the south middle shelf, likely due to late ice retreat and cold temperatures that increased development times. In contrast, stage progression was fastest in summer 2008 likely due to warmer temperatures. Our findings indicate that intra-annual variation of zooplankton community composition, life history stage, and abundance within a cold period may affect the amount of high–lipid zooplankton prey (e.g. Neocalanus and Calanus spp. copepods and euphausiids) available seasonally for forage fish (e.g. age-0 walleye pollock) to grow to a sufficient size (to avoid size-dependent predation) and have sufficient lipid stores (to avoid starvation) to survive the first winter at sea.

Description: This article presents a non-invasive fully automatic procedure for Bluefin Tuna sizing, based on a stereoscopic vision system and a deformable model of the fish ventral silhouette. An image processing procedure is performed on each video frame to extract individual fish, followed by a fitting procedure to adjust the fish model to the extracted targets, adapting it to the bending movements of the fish. The proposed system is able to give accurate measurements of tuna snout fork length (SFL) and widths at five predefined silhouette points without manual intervention. In this work, the system is used to study size evolution in adult Atlantic Bluefin Tuna ( Thunnus Thynnus ) over time in a growing farm. The dataset is composed of 12 pairs of videos, which were acquired once a month in 2015, between July and October, in three grow-out cages of tuna aquaculture facilities on the west Mediterranean coast. Each grow out cage contains between 300 and 650 fish on an approximate volume of 20 000 m 3 . Measurements were automatically obtained for the 4 consecutive months after caging and suggest a fattening process: SFL shows an increase of just a few centimetres (2%) while the maximum width ( A1 ) shows a relative increase of more than 20%, mostly in the first 2 months in farm. Moreover, a linear relation (with coefficient of determination R 2 〉 0.98) between SFL and widths for each month is deduced, and a fattening factor ( F ) is introduced. The validity of the measurements is proved by comparing 15 780 SFL measurements, obtained with our automatic system in the last month, versus ground truth data of a high percentage of the stock under study (1143 out of 1579), obtaining no statistically significant difference. This procedure could be extended to other species to assess the size distribution of stocks, as discussed in the article.

Description: Marine ecosystems have been heavily impacted by fishing pressure, which can cause major changes in the structure of communities. Fishing directly removes biomass and causes secondary effects such as changing predatory and competitive interactions and altering energy pathways, all of which affect the functional groups and size distributions of marine ecosystems. We conducted a meta-analysis of eighteen trawl surveys from around the world to identify if there have been consistent changes in size-structure and life history groups across ecosystems. Declining biomass trends for larger fish and invertebrates were present in nine systems, all in the North Atlantic, while seven ecosystems did not exhibit consistent declining trends in larger organisms. Two systems had alternative patterns. Smaller taxa, across all ecosystems, had biomass trends with time that were typically flat or slightly increasing. Changes in the ratio of pelagic taxa to demersal taxa were variable across the surveys. Pelagic species were not uniformly increasing, but did show periods of increase in certain regions. In the western Atlantic, the pelagic-to-demersal ratio increased across a number of surveys in the 1990s and declined in the mid 2000s. The trawl survey data suggest there have been considerable structural changes over time and region, but the patterns are not consistent across all ecosystems.

Description: As with many other regions in the world, more complete information on the distribution of marine habitats in the Gulf is required to inform environmental policy, and spatial management of fisheries resources will require better understanding of the relationships between habitat and fish communities. Towed cameras and sediment grabs were used to investigate benthic habitats and associated epifauna, infauna and fish communities in the central Gulf, offshore from the east coast of Qatar, in water depths of between 12 and 52 m. Six different habitats were identified: (i) soft sediment habitats of mud and (ii) sand, and structured habitats of (iii) macro-algal reef, (iv) coral reef, (v) mixed reef, and (vi) oyster bed. The epibenthic community assemblage of the mud habitat was significantly different to that of sand, which in turn differed from the structured habitats of coral reef, mixed reef and oyster bed, with the macroalgal assemblage having similarities to both sand and the other structured habitats. Fish assemblages derived from video data did not differ between habitats, although certain species were only associated with particular habitats. Epibenthic diversity indices were significantly lower in mud, sand and macro-algal habitats, with no differences recorded for fish diversity. Soft sediment grab samples indicated that mud habitats had the highest benthic diversity, with Shannon-Weiner values of 〉4, and were more diverse than sand with values of 3.3. The study demonstrates high biodiversity in benthic habitats in the central and southwestern Gulf, which may in part be due to the absence of trawling activity in Qatari waters. There is a strong influence of depth on benthic habitat type, so that depth can be used to predict habitat distribution with a high level of accuracy. The presence of outcrops of hard substrata creates a mosaic of patchy shallow structured benthic habitat across extensive areas of the offshore seabed. Such heterogeneity, and the association of commercially exploited fish species with specific habitats, indicates that this region is well suited to a spatial approach to fisheries management.

Description: States have acknowledged that the new internationally legally binding instrument (ILBI) for the conservation and sustainable use of marine biodiversity beyond national jurisdiction must take account of the interests of coastal states with continental shelves that extend beyond 200 nautical miles. This article argues that the ILBI should go beyond repeating the existing legal position as set out in international treaties and customary international law. In particular, the concept of sedentary species is unhelpful in the context of a legal regime governing the use of marine genetic resources. The article makes a number of suggestions for possible inclusions in the ILBI to clarify the relationship between the continental shelf regime and the regime for biodiversity beyond national jurisdiction.