The movements of aquatic animals affect their exposure to threats and the efficacy of conservation measures, such as Marine Protected Areas (MPAs). However, many species' movements remain poorly understood and difficult to reconstruct from available datasets, hampering conservation efforts. This is especially the case for species that rarely surface, for which data are often limited to observations from acoustic telemetry (detections) and ancillary sensors, such as archival tags. Here, we pioneer the use of state-of-the-art particle algorithms to model animal movement, integrate datasets and assess MPA design, using a case study of the Critically Endangered flapper skate ( Dipturus intermedius ) in Scotland. Our algorithms led to 5-fold improvements in maps of space use and 30-fold improvements in residency estimates (lower mean error) compared to prevailing heuristic methods. By formally integrating tracking datasets, we were uniquely able to examine movements beyond receivers into fished zones, MPA-scale residency and specific habitats beyond protected areas that may warrant protection. This work showcases a probabilistically sound modelling framework that is sufficiently fast, flexible and accessible to meet the demands of modern animal-tracking datasets in acoustic telemetry systems. This represents a marked advance for analyses of animal movements and MPA efficacy worldwide. ### Competing Interest Statement The authors have declared no competing interest.

To make the best-informed decisions on managing marine resources whilst also restoring biodiversity, the creation and analysis of benthic maps is highly valuable. This study focuses on benthic mapping to study patch - and landscape - level processes affecting epifauna and demersal species using Stereo Baited Remote Underwater Video (SBRUV) and Drop-Down Video (DDV) surveys. Surveys were conducted within the South Arran Marine Protected Area between 2013-2019 and yielded 554 SBRUV data points and 333 DDV data points. These data were processed to determine proportional coverage of substrata and kriged to produce benthic maps. From this it was possible to estimate the patch scale of substrata to gain a more detailed understanding of the marine landscape, composition structure, and epibenthic biodiversity. The resulting validated maps allowed the number of substrata patches and patch characteristics such as area and perimeter-to-area ratio to be calculated to support management and understanding of the value of this seascapes for benthic and demersal biodiversity. Our approach allowed for the identification of areas of higher biodiversity that may assist during mapping of Marine Protected Areas' (MPA) vulnerable features. These methods should provide better information about site condition and ecosystem service provision than existing methods.

Declining body sizes are prevalent in marine fish. While these declines have been suggested to be a response to increasing temperatures, the evidence is mixed and the underlying causes of observed declines often unknown. Here, we explore drivers of spatio-temporal patterns in size in lesser sandeel (Ammodytes marinus), an important prey for seabirds and marine mammals, focusing on ongoing size declines in the North Sea. We combine experimental and field data with ecological theory to develop a biologically realistic dynamic energy budget model that explicitly models feeding, metabolism and energy allocation to produce daily predictions of size during the juvenile growth season from 1979 to 2016. When forced with daily temperature estimates and zooplankton data from the Continuous Plankton Recorder, model predictions reproduce observed spatio-temporal patterns in size well. Our results suggest that the most plausible driver of observed size declines in the western North Sea is declining prey densities. In contrast, the direct effect of temperature on sandeel size is small, but interacts with local prey availability so that the effect varies in both size and direction over space. Our results thus suggest that to understand effects of climate change on fish size we need to account for both direct physiological effects and changes in resource availability. Finally, we use the model to show that early-life phenology and turbidity (via its impact on intake rates in the visually foraging sandeel) may also impact sandeel size, highlighting the importance of broadening our view of potential drivers of size declines. ### Competing Interest Statement The authors have declared no competing interest.

Understanding the responses of seabirds to climate-induced variations in phenology and abundance of their prey is key to developing ecosystem-based fisheries management measures that benefit higher trophic levels. The match/mismatch hypothesis (MMH) emphasizes the need to consider synchrony in the seasonal cycles of predators and prey, while the match/mismatch/abundance hypothesis (MMAH) proposes that prey abundance may reinforce/compensate mismatch effects. This study considers the effects of both variations in seasonal availability and abundance of lesser sandeel Ammodytes marinus on hatching, fledging and breeding success of 5 seabird species: black-legged kittiwake Rissa tridactyla , Atlantic puffin Fratercula arctica , razorbill Alca torda , common guillemot Uria aalge and European shag Gulosus aristotelis . Consistent with MMH, temporal asynchrony between sandeel availability and seabird breeding schedules affected productivity in 4 species. The effects of trophic asynchrony were either reinforced or compensated by sandeel abundance for some species, supporting MMAH. Breeding success in the late-breeding kittiwake was high when conditions favoured both high sandeel abundance and temporal synchrony while the cost of asynchrony could be compensated by high sandeel abundance in the earlier-breeding puffin. Differential effects of sandeel abundance and trophic synchrony at different stages of the seabird breeding season suggest that distinct mechanisms are involved. The effects were most evident in the most sandeel-reliant seabirds. As further disruption of sandeel phenology and abundance is anticipated under the current climate crisis, the present study is an important step towards understanding bottom-up effects of environmental change on higher trophic levels.

Stability and long-term persistence of a species rely heavily on its genetic diversity, which is closely allied to its capacity for adaptation. In threatened species, population connectivity can play a major role in maintaining that diversity, and genetic assessments of their populations can be crucial for the design of effective spatial conservation management. Not only is it worth evaluating the amount of diversity in a candidate population for protection, but the magnitude of outgoing gene flow can provide insight into its potential to replenish others via emigrants. The critically endangered flapper skate Dipturus intermedius receives protection in the Loch Sunart to the Sound of Jura Marine Protected Area (MPA) in Scotland. However, there is insufficient knowledge of genetic diversity and connectivity across its range. Recent tagging studies in the MPA suggest the presence of animals with high levels of site fidelity and residency, as well as transient individuals, raising concerns of limited connectivity to populations beyond the MPA. In this study, a newly developed mitochondrial haplotype marker allowed use of DNA sourced from fin clips, mucus and egg cases to investigate population structure and mitochondrial variability across several sites around the British Isles, including the MPA. Unfortunately, results characterized the MPA as having particularly low haplotype diversity and significant population differentiation from other sample sites. More than a quarter of its individuals carry a haplotype rarely observed elsewhere, leaving outgoing gene flow questionable. The MPA appears unlikely to sustain the species’ existing mtDNA genetic diversity or act as an effective source population.

Increasing ocean temperature will speed up physiological rates of ectotherms. In fish, this is suggested to cause earlier spawning due to faster oocyte growth rates. Over time, this could cause spawning time to become decoupled from the timing of offspring food resources, a phenomenon referred to as trophic asynchrony. We used biological data, including body length, age, and gonad developmental stages collected from >125,000 individual Northeast Arctic cod (Gadus morhua) sampled between 59 and 73° N in 1980-2019. Combined with experimental data on oocyte growth rates, our analyses show that cod spawned progressively earlier by about a week per decade, partly due to ocean warming. It also appears that spawning time varied by more than 40 days, depending on year and spawning location. The significant plasticity in spawning time seems to be fine-tuned to the local phytoplankton spring bloom phenology. This ability to partly overcome thermal drivers and thus modulate spawning time could allow individuals to maximize fitness by closely tracking local environmental conditions important for offspring survival. Our finding highlights a new dimension for trophic match-mismatch and should be an important consideration in models used to predict phenology dynamics in a warmer climate.

1. While elasmobranchs are often a designated feature in Marine Protected Areas, there are few studies that have evaluated the effectiveness of spatial fishery restrictions on their recovery. 2. Here we examine the effectiveness of fishery restrictions on the critically endangered flapper skate, Dipturus intermedius, based on changes in their abundance, demography and survival rate. 3. Trends in local abundance at two sites within the Loch Sunart to the Sound of Jura Marine Protected Area (LStSJ MPA), were contrasted with that in surrounding waters off the west of Scotland where fishing remains unrestricted. Survival rate was estimated using a multi-state model of capture mark recapture data, and spill-over from the LStSJ MPA was considered from tag-recapture rates between the two LStSJ MPA study areas and a further site south of the LStSJ MPA. 4. In contrast to the wider trend across adjacent waters, skate abundance increased, especially for young juveniles, following the introduction of fishing restrictions in the LStSJ MPA. This increase could be explained by a reduction in juvenile and adult mortality as population growth rates following fishing restrictions were markedly higher than estimated in a pre-restriction study of one site. 5. Limited exchange of skate between the two study areas within the LStSJ MPA and a southern site beyond the LStSJ MPA indicated a low rate of spill-over. 6. This study demonstrates that spatial fishery restrictions have the potential to benefit populations of elasmobranchs which have a high site-fidelity, but their wider conservation benefit may be partly confounded by a high level of residency.

This study examines the sediment preferences of small sandeel (Ammodytes tobianus), an elongated forage fish common in marine and brackish environments of northern Europe. Sandeel have a high fidelity for sandy habitats and spend much of their lives buried, as an important part of both their diel behavioural cycles and overwintering behaviour. A series of independent choice laboratory assays were conducted using wild-caught schools of small sandeel, to: (1) determine their preferred substrate composition for burial; (2) identify the upper limits of sediment grain-sizes that may be utilised for burial, and; (3) investigate the effects of light intensity on burial behaviour. Initial experiments found a clear preference for burial within sediments composed of coarse sand and fine gravel (0.5-4.0 mm) but showed at least some utilisation of both coarser and finer sediment compositions. In further trials, burial was found to be almost entirely eliminated in sediments that contained significant gravel components >4.0 mm. Light manipulation experiments also showed that light intensity was an important factor that influences their choice of burial area. This study is the first to experimentally investigate the sediment preferences and grain-size tolerance limits of small sandeel. These results specifically highlight how subtle differences in both sediment composition and light may influence the habitat usage of small sandeel, which may be valuable for understanding their distribution in the wild and to inform future management and conservation for the species.

While concepts of connectivity are increasingly used in determining locations for marine protected areas, they are much less applied in the management of fish stocks, which are assumed to be well-mixed populations. However, due to seascape structure and often asymmetrical dispersal, the stocks of many species are unlikely to be well mixed and there is potential to enhance management by utilising emerging ecological modelling approaches that incorporate functional connectivity. Here, we apply a new model, MerMADE, that couples biophysical modelling of dispersal with spatial population demography, to predict within-stock patterns of connectivity of sandeels in the North Sea. By deriving origin- and destination-centrality measures, we highlight a set of key origin sites within the area occupied by the stock that contribute immigrants to many other sites and also identify patches that are particularly isolated, unlikely to receive immigrants from elsewhere. We show that the connectivity characteristics of the stock have a strong impact on how rapidly it recovers following a major harvesting event that leads to a patch depletion. Furthermore, the recovery of a local population will depend on the demographic status of the sites from which it can obtain immigrants. Thus, sites that provide strong out-centrality (especially if they themselves have weak in-centrality) and sites that are especially isolated should be harvested less heavily. To reduce the potential for local or regional stock collapse, models incorporating both biophysical dispersal and local demography are needed to support spatially explicit management of commercial marine species.

Passive acoustic telemetry is widely used to study the movements of aquatic animals. However, a holistic, mechanistic modelling framework that permits the reconstruction of fine‐scale movements and emergent patterns of space use from detections at receivers remains lacking. Here, we introduce an integrative modelling framework that recapitulates the movement and detection processes that generate detections to reconstruct fine‐scale movements and patterns of space use. This framework is supported by a new family of algorithms designed for detection and depth observations and can be flexibly extended to incorporate other data types. Using simulation, we illustrate applications of our framework and evaluate algorithm utility and sensitivity in different settings. As a case study, we analyse movement data collected from the Critically Endangered flapper skate ( Dipturus intermedius ) in Scotland. We show that our methods can be used to reconstruct fine‐scale movement paths, patterns of space use and support habitat preference analyses. For reconstructing patterns of space use, simulations show that the methods are consistently more instructive than the most widely used alternative approach (the mean‐position algorithm), particularly in clustered receiver arrays. For flapper skate, the reconstruction of movements reveals responses to disturbance, fine‐scale spatial partitioning and patterns of space use with significant implications for marine management. We conclude that this framework represents a widely applicable methodological advance with applications to studies of pelagic, demersal and benthic species across multiple spatiotemporal scales.

Microgreens, the immature plants harvested after a few weeks of growth, are perceived as a heathy, nutritious food ingredient but may be susceptible to colonisation by human pathogens including Shiga-toxigenic Escherichia coli (STEC). Some microgreen cultivars accumulate anthocyanins or secrete essential oils which, when extracted or purified, have been reported to inhibit bacterial growth. Therefore, the impact of anthocyanins on bacterial colonisation by STEC (Sakai) was compared for three species that have pigmented cultivars: basil (Ocimum basilicum L.), cabbage (Brassica oleracea L.) and mustard greens (Brassica juncea L.). Inoculation with low concentrations of STEC (Sakai) (3 log10 colony forming units/ml (CFU/ml)) during seed germination resulted in extensive colonisation at the point of harvest, accumulating to ∼ 8 log10 CFU/g FW in all cultivars. Bacterial colonies frequently aligned with anticlinal walls on the surface of epidermal cells of the cotyledons and, in basil, associated with peltate and capitate gland cells. Crude lysates of pigmented and non-pigmented basil cultivars had no impact on STEC (Sakai) growth rates, viability status or biofilm formation. Anthocyanins are located within plant vacuoles of these microgreen cultivars and did not affect colonisation by STEC (Sakai) and pigmentation therefore cannot be considered as a controlling factor in bacterial interactions.

The reproductive success of marine ectotherms is especially vulnerable in warming oceans due to alterations in adult physiology, as well as embryonic and larval survival prospects. These vital responses may, however, differ considerably across the species' geographical distribution. Here we investigated the life history, focusing on reproductive ecology, of three spatially distant populations (stocks) of Atlantic cod (Gadus morhua, Gadidae) (50-80 degrees N), in the Irish/Celtic Seas-English Channel Complex, North and Barents Seas, under past and projected climate. First, experimental tracking of spawning behaviour evidenced that the ovulation cycle is highly distressed at >= 9.6 (+/- 0.25)degrees C (T-up). This knife-edge threshold resulted in erratic spawning frequencies, whereas vitellogenin sequestration remained unaffected, indicating endocrine rather than aerobic scope constraints. Cod in the Celtic Sea-English Channel are, therefore, expected to show critical stock depensation over the next decades as spawning grounds warm above T-up, with Irish Sea cod subsequently at risk. Second, in the relatively cooler North Sea, the northward retraction of Calanus finmarchicus (Calanidae) and Para-Pseudocalanus spp. (Clausocalanidae) (1958-2017) limit cod larvae feeding opportunities, particularly in the southernmost subarea. However, the contrasting increase in Calanus helgolandicus (Calanidae) does not counteract this negative effect, likely because cod larvae hatch ahead of its abundance peaks. Overfishing again comes as a twin effect. Third, in the still relatively cold Barents Sea, the sustainably harvested cod benefit from improved food conditions in the recent ice-free polar region but at the energetic cost of lengthier and faster spawning migrations. Consequently, under climate change local stocks are stressed by different mechanistic factors of varying management severity.

There is an urgent need to reduce global greenhouse gas emissions. One method of achieving this is through Carbon Capture and Storage (CCS). Geological structures that lie offshore under continental shelf seas offer huge CCS storage potential. An emerging marine industry is developing to exploit this potential and national marine monitoring agencies will soon need to consider the potential impacts of this emerging industry. This review of published literature is aimed at generalists responsible for the delivery of national marine monitoring, as well as those involved in the management of the marine environment. It briefly summarizes why the emerging offshore CCS industry is needed, how large it may be and what marine infrastructure may be involved. For the purposes of this paper, a hypothetical 20 Mtpa industry has been used to gauge the potential impact of a developing offshore CCS industry. The probability of CO2 leaks from such an industry is low. If they do occur, the spatial scale of impact will be small, and the potential environmental impacts will be low. Irrespective of how CO2 is transported or stored within shelf seas, leaked CO2 will enter the sea as a gas or as a solution dissolved in sediment pore water. CO2 as a gas will dissolve into seawater and/or directly vent to the atmosphere, depending on the initial conditions of the leak. The most probable source of leaks in a developed CCS industry is from pipelines (currently a 2-year event per 1000 km pipeline). The most probable source of leakage from geological storage is through abandoned wells (a 20- to 80-year event for a 20 Mtpa industry). The source of leaks from a CCS scheme with the potential to release the greatest mass of CO2 is through geological faults, as these may go undetected (if they occur) for long periods. The probability of leaks from geological storage, through faults or abandoned wells, is site dependent and minimized by the site selection process. The review concludes with recommended priorities for future marine science development.

We describe the complete mitochondrial genomes of the flapper skate Dipturus intermedius (Parnell 1837) and the longnose skate Dipturus oxyrinchus (Linnaeus 1758), which have been obtained by Sanger sequencing. We report the length of the sequences to be 16,906 and 16,911 bp, respectively. The length and structure of gene regions, containing 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and two non-coding areas, resemble those of related skate species. Despite D. intermedius being considered a cryptic species with D. batis, the full mitogenomes confirm that D. intermedius and D. oxyrinchus are more genetically similar. In comparison to other Dipturus species, D. intermedius is missing a whole codon in its cytochrome oxidase subunit 2 gene. These mitogenomes will be a useful resource furthering investigation of the population genetic differences and evolutionary history of skate species.

Marine Protected Areas (MPAs) are widely used in marine management, but for mobile species understanding the spatio-temporal scale of management measures that is required to deliver conservation benefits depends on a detailed knowledge of species' movements that is often lacking. This is especially the case for species of skate (Rajidae) for which relatively few movement studies have been conducted. In Scotland, the Loch Sunart to the Sound of Jura MPA covering 741 km(2) has been designated for the conservation of the Critically Endangered flapper skate (Dipturus intermedius), but fine-scale movements within this area remain poorly understood. A passive acoustic telemetry study which coupled acoustic tagging of 42 individuals and a static array of 58 receivers was conducted from March 2016 to June 2017. Using acoustic detection time series, angler capture-recapture data and depth time series from archival tags, fine-scale movements of individuals were investigated. Overall, 33 of the 42 tagged individuals were detected. Residency, site fidelity and transiency were documented. Residency around receivers, lasting from 3 to more than 12 months, was documented in 16 acoustically detected individuals (48%) and all life-history categories, but was most noticeable among females. Acoustic detections were associated with depth, salinity and season, but there was no evidence that individuals formed close-knit groups in the areas in which they were detected. Taken together with historical occurrence records of flapper skate, the prevalence and scale of residency documented here suggest that the MPA is sufficiently large to benefit a notable percentage (38 [24-52]%) of skate found in the study area over monthly and seasonal timescales. This result strengthens the case for the use of MPAs to support the conservation of flapper skate and other skate species that display similar movement patterns in areas of high local abundance.

ABSTRACTIn order to understand patterns in species’ distributions, we need to understand the underlying mechanisms of dispersal, demography and evolutionary capability of these species. In the marine environment, few models combine these three key components likely due both to the computational challenges involved and the inherent challenges in data collection for parameterisation. To fill this gap, we have developed MerMADE, an individual-based, spatially explicit, eco-evolutionary coupled biophysical model for predicting population dynamics, dispersal and movement evolution in the marine environment (or aquatic environments in general). MerMADE combines dispersal in a 3D, hydrodynamically informed environment with population dynamics, demography and evolutionary functionality in order to investigate questions of connectivity, population persistence and evolution under environmental change and anthropogenic pressure. We illustrate its range of behavioural and physiological functionality using the lesser sandeel,Ammodytes marinus, as a case-study species in an invasion scenario. MerMADE’s flexibility in species-specific parameterisation makes it a widely applicable, exciting tool in future sustainable management and conservation of aquatic species under environmental change.