Photo-identification (photo-ID) is commonly used in wildlife ecology and management, but its effectiveness depends on reliable determination of whether an observed individual is already contained within the database. This is typically done by trained human operators but becomes an increasingly demanding task as photo-ID databases expand, potentially limiting the method's applicability. Artificial intelligence approaches have been suggested as potential solutions to this problem. We present a case study involving a photo-ID database of flapper skate (Dipturus intermedius) from Scotland, which was used to train a multistage, deep learning model using a method similar to high-performing facial recognition system, FaceNet, to enable automatic assessment of the similarity between flapper skate newly submitted to the database and those pre-existing in the database. Evaluation using a blind test set of 100 images taken from the database and also a second, smaller test set of tagged animals of known identity to confirm the model's photo-ID performance for end users. When assessed against the previously unseen test set, the model achieved a mean average precision (mAP) of 84.1% and a top-1 accuracy of 80%. The resulting photo-ID model was integrated into the photo-ID database, which was further tested with images of tagged individuals of known identity. This integration significantly reduced the time required to confirm whether new skates were already included in the database. With a top-1 accuracy of 80%, the matching skate, if contained in the database, will likely be returned as a match, removing the need to check by eye against 2500+ individuals already in the database. Solution. The integration of machine-assisted image analysis into a photo-ID database of skate improved our ability to track individuals and understand movement and residency at far larger scales, essential for the continued management of the species. This approach is suitable for a wide range of research projects reliant on photo-ID and should be considered for new and legacy data sets.

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.

Animal movements affect their exposure to threats and the efficacy of conservation measures, such as marine protected areas (MPAs). However, many species' movements are difficult to reconstruct from available datasets, hampering conservation efforts. This is especially the case for aquatic species that rarely surface, for which data are often limited to observations from acoustic telemetry (detections) and ancillary sensors. Here, we pioneer the use of state-of-the-art particle algorithms to model movements, integrate datasets, and assess MPA design, leveraging a case study of a Critically Endangered elasmobranch. Our algorithms led to 5-fold improvements in space-use maps and 30-fold improvements in residency estimates compared to prevailing methods. By integrating tracking datasets, we were uniquely able to examine movements beyond acoustic receivers, MPA-scale residency, and specific habitats beyond protected areas that warrant protection. This work reveals a modeling framework that enhances the conservation value of acoustic telemetry, supporting analyses of MPA efficacy worldwide.

Identifying critical habitats is important for the effective management of vulnerable species. Critical habitats, such as mating or nursery grounds, support populations during key life stages and help to maximise reproductive output and population growth. In elasmobranchs, mating often happens over a defined season, suggesting sites associated with this process may only require temporal protection. However, knowledge gaps on such sites exist for many elasmobranchs due to the challenges associated with identifying temporal mating periods, which hinders conservation efforts. Here, we investigated the application of photographs to estimate reproductive timing in an oviparous elasmobranch, the flapper skate (Dipturus intermedius), as a non-invasive and low-cost alternative to other approaches. Using a pre-existing citizen science photo-ID database of over 2000 images, we identified signs of reproductive behaviour: the presence or absence of pelvic swelling, bite wounds and scratch wounds. Statistical models were created for each feature to explore seasonal trends and other parameters explaining their presence. Seasonal trends were present for all features and feature occurrence differed with sex. The occurrence of bite wounds and pelvic swelling in flapper skate peaked over winter and spring months, suggesting a winter-spring mating and egg-laying period. These results are corroborated by previous reproductive research on the flapper skate, suggesting the applied method is a valid tool to estimate reproductive timing in an elusive elasmobranch. The approach could be applied to other flapper skate populations and other elasmobranch species, helping to close existing knowledge gaps on reproductive behaviours.

Catch-and-release angling is a popular recreational pastime and an essential component of many fish research programmes. Marked physiological disturbances have been documented in elasmobranchs in response to angling and handling, but skates and rays remain understudied. Here, we describe for the first time the physiological responses of the critically endangered flapper skate (Dipturus intermedius) to angling, handling and tagging in Scotland. Sixty-one skate were captured by angling as part of a tagging research programme. We assessed individual health, measured blood parameters at two time points (post-capture and prior to release) and recorded heart and respiratory rates during handling and the surgical insertion of acoustic tags. Injuries or infections were identified in 10% of individuals and attributed to prior angling in two cases. Skate generally experienced a mild metabolic acidosis characterized by decreases in blood pH and bicarbonate and increases in lactate and glucose. Respiratory acidosis characterized by limited increases in PCO2 was also observed. The degree of acidosis was greater with warmer sea temperatures and longer fight times, and worsened during the time that skate were handled on deck. Heart rates during handling were negatively associated with body size, positively associated with temperature and also linked to time on the line. Taken together, our results suggest that elevated fight times and temperatures increase the physiological stress experienced by rod and reel-caught flapper skate. Efforts to reduce fight times and minimize heat exposure (including shading, irrigation and reduced handling time) should be beneficial for skate.

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.

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.

Due to global population declines, there is a pressing need for data on the life history traits of many elasmobranch species to support the development of species-specific management plans. A lack of information on the reproductive cycle of the Critically Endangered flapper skate Dipturus intermedius was recently identified as a hindrance to its conservation. To address this data gap, we combined non-lethal ultrasound and hormone analysis to investigate the size at maturity and reproductive cycle of the flapper skate in the Loch Sunart to the Sound of Jura Marine Protected Area off the west coast of Scotland. In-field ultrasound imagery revealed encapsulated eggs in utero and was used to determine the presence and size of ovarian follicles. Combining these images with levels of plasma testosterone, progesterone and oestradiol provided valuable insights into the timing of the reproductive cycle and maturity state of the flapper skate. This preliminary study suggests that male skate start to mature at 165 cm and females at 203 cm total length. Oestradiol appears to be the primary hormone controlling the female reproductive cycle and, along with ultrasound images, indicates that females lay pairs of eggs throughout a winter egg-laying season. Our study further highlights how non-lethal methods can be used to investigate the life history of oviparous elasmobranchs in the field. This information will support the identification of important life history groups and their associated habitats and contribute to the development of management strategies for these species.

This study provides the first report of an egg nursery for the Critically Endangered flapper skate Dipturus intermedius and a description of the habitat, thus contributing towards our understanding of essential habitats for the species. In total, 1,395 flapper skate egg cases were recorded (accounting for overlapping surveys) in two egg case collection dives (n = 67 egg cases), one photogrammetry dive (n = 10 egg cases), 509 drop-down video (DDV) camera drifts (n = 510 egg cases) and 18 remote operated vehicle (ROV) flights (n = 1,031 egg cases), carried out in the Inner Sound on the west coast of Scotland from 2018 to 2021. All of the egg cases were found on a shallow bedrock plateau between the Isle of Scalpay and a deep (>100 m) water channel between the Isle of Longay and the Crowlin Islands. Egg cases were observed on a cobble/boulder reef between 25 and 58 m depth, with a modelled annual temperature range of 9-12 degrees C, modelled current speeds up to 0.2 m(-1), a rugosity index of 1.7 and low levels of sedimentation. Flapper skate egg cases are large and the incubation period is protracted (18 months), making them potentially vulnerable to anthropogenic disturbance. A description of the habitat where egg cases were observed in this study will help inform the search for egg nurseries for this Critically Endangered species elsewhere. Targeted DDV, ROV and scuba diving surveys will support this search in areas where suitable bathymetric and hydrodynamic conditions are identified. Safeguarding egg nurseries is essential for successful conservation. Protection should involve the designation of egg nurseries as Marine Protected Areas where activities that are likely to damage or alter seabed habitats are managed.

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.

Catch-and-release angling is widespread, but the impacts of this practice for captured individuals are understudied, especially among elasmobranchs. Studies on sub-lethal behavioural impacts are particularly sparse, despite their importance for the interpretation of biologging data and for assessments of species’ tolerance to capture. In this study, the behavioural responses of flapper skate ( Dipturus intermedius ) to catch-and-release angling were described for the first time, using archival observations (depth and temperature) for 21 tag deployment/retrieval events and five recreational angling events that occurred during tagged individuals’ time at liberty from charter vessels off the west coast of Scotland in 2016–17. During capture (8–50 minutes), the changes in depth and temperature experienced by individuals typically exceeded natural variability. Post-release, behavioural change was apparent from visual inspection, regression and functional data analysis of the time series. Immediately following release, movements into deeper water and short periods of low vertical activity (usually 1–2 hours in duration) were common. However, overall average vertical activity was typically around 38% higher in the 12 hours following release than in undisturbed activity. A small number of individuals (n = 3, 14%) exhibited irregular post-release behaviour in the form of rapid, transient re-ascents towards the surface following release. Collectively, the evidence for limited, short-term behavioural changes suggests that flapper skate behaviour is relatively resilient to catch-and-release angling from charter vessels, but irregular post-release behaviour in 14% of individuals is sufficiently notable to indicate that further research is required on the impacts of this practice. This study clearly demonstrates the value of biologging data and behavioural analyses for examining the impacts of disturbance and separating ‘disturbed’ and ‘undisturbed’ behaviours in studies of animal movement.

Developments in animal electronic tagging and tracking have transformed the field of movement ecology, but interest is also growing in the contributions of tagged animals to oceanography. Animal-borne sensors can address data gaps, improve ocean model skill and support model validation, but previous studies in this area have focused almost exclusively on satellite-telemetered seabirds and seals. Here, for the first time, we develop the use of benthic species as animal oceanographers by combining archival (depth and temperature) data from animal-borne tags, passive acoustic telemetry and citizen-science mark-recapture records from 2016–17 for the Critically Endangered flapper skate ( Dipturus intermedius ) in Scotland. By comparing temperature observations to predictions from the West Scotland Coastal Ocean Modelling System, we quantify model skill and empirically validate an independent model update. The results from bottom-temperature and temperature-depth profile validation (5,324 observations) fill a key data gap in Scotland. For predictions in 2016, we identified a consistent warm bias (mean = 0.53 °C) but a subsequent model update reduced bias by an estimated 109% and improved model skill. This study uniquely demonstrates the use of benthic animal-borne sensors and citizen-science data for ocean model validation, broadening the range of animal oceanographers in aquatic environments.

To fill the prevailing gap in methodology for whole spinal cord (SC) analysis, we have (1) designed scaffolds (SpineRacks) that facilitate efficient and ordered cryo-sectioning of the entire SC in a single block, (2) constructed a 3D reference atlas of adult mouse SC, and (3) developed software (SpinalJ) to register images of sections and for standardized analysis of cells and projections in atlas space. We have verified mapping accuracies for known neurons and demonstrated the usefulness of this platform to reveal unknown neuronal distributions. Together, these tools provide high-throughput analyses of whole mouse SC and enable direct comparison of 3D spatial information between animals and studies.

Trends in depth and vertical activity reflect the behaviour, habitat use and habitat preferences of marine organisms. However, among elasmobranchs, research has focused heavily on pelagic sharks, while the vertical movements of benthic elasmobranchs, such as skate (Rajidae), remain understudied. In this study, the vertical movements of the Critically Endangered flapper skate (Dipturus intermedius) were investigated using archival depth data collected at 2 min intervals from 21 individuals off the west coast of Scotland (56.5°N, −5.5°W) in 2016–17. Depth records comprised nearly four million observations and included eight time series longer than 1 year, forming one of the most comprehensive datasets collected on the movement of any skate to date. Additive modelling and functional data analysis were used to investigate vertical movements in relation to environmental cycles and individual characteristics. Vertical movements were dominated by individual variation but included prolonged periods of limited activity and more extensive movements that were associated with tidal, diel, lunar and seasonal cycles. Diel patterns were strongest, with irregular but frequent movements into shallower water at night, especially in autumn and winter. This research strengthens the evidence for vertical movements in relation to environmental cycles in benthic species and demonstrates a widely applicable flexible regression framework for movement research that recognises the importance of both individual-specific and group-level variation.

Knowledge of vital data such as growth and age at maturity is necessary to develop effective management strategies for endangered species. The Critically Endangered flapper skate (Dipturus intermedius) is the largest skate in the North Atlantic and growth information, necessary to assess key life-history traits, populations' growth rates and anticipate their response to management measures, is still lacking. While classical age estimation methods used in fish generally require the analysis of calcified structures, destructive methods are incompatible with conservation objectives for this species. Taking advantage of the high recreational value of the flapper skate, this study uses citizen-science data originating from photo-identification of trophy pictures and tag-recapture data supported by anglers to estimate growth in this Critically Endangered species. Using the growth increments measured between recapture events, an individual-based Von Bertalanffy growth model was fitted to the data using Bayesian inference. The results confirm that the flapper skate is a long-lived species with ages estimated as >40 years for the largest individuals captured. Despite this longevity, the model reveals a relatively fast initial growth but relatively late ages at maturity and significant sex-related differences in both growth rate and maximum size. These results suggest that population growth rate, and therefore recovery, might be much slower than previously reported. By using citizen science this study provides the necessary information to begin understanding population dynamics and monitor the recovery of an iconic Critically Endangered species.

Spatial analysis of spinal neurons is currently limited by a lack of tools for efficient preparation and imaging of the whole spinal cord (SC) and the absence of a 3D reference atlas. Here, we describe protocols for efficient sectioning of whole SC using SpineRacks and subsequent image registration, atlas mapping, and 3D analysis of cells and projections, using SpinalJ. Together, these tools enable high-throughput analyses of adult mouse SC and direct comparison of spatial information of neurons between animals and studies. For complete details on the use and execution of this protocol, please refer to Fiederling et al. (2021).

Seasonal and ontogenetic variations in depth use by benthic species are often concomitant with changes in their spatial distribution. This has implications for the efficacy of spatial conservation measures such as marine protected areas (MPAs). The critically endangered flapper skate (Dipturus intermedius) is the designation feature of an MPA in Scotland. This species is generally associated with deeper waters >100 m; however, little is known about its seasonal or ontogenetic variation in habitat use. This study used archival depth data from 25 immature and mature flapper skate tagged in the MPA over multiple years. Time series ranged from 3 to 772 (mean = 246) days. Generalised additive mixed models and highest density intervals were used to identify home (95%) and core (50%) highest density depth regions (HDDRs) to quantify depth use in relation to time of year and body size. Skate used a total depth range of 1–312 m, but home HDDRs typically occurred between 20 and 225 m. Core HDDRs displayed significant seasonal and ontogenetic variations. Summer core HDDRs (100–150 m) suggest high occupancy of the deep trenches in the region by skate of most size classes. There was an inverse relationship between body size and depth use and a seasonal trend of skate moving into shallow water over winter months. These results suggest that flapper skate are not solely associated with deep water, as skate, especially large females, are frequently found in shallow waters (25–75 m). The current management, which protects the entire depth range, is appropriate for the protection of flapper skate through much of its life history. This research demonstrates why collecting data across seasonal scales and multiple ontogenetic stages is needed to assess the effectiveness of spatial management.

The flapper skate, Dipturus intermedius (Parnell, 1837), is the largest of all European skate and rays (Superorder: Batoidea). It is found in coastal waters of the European continental shelf and slopes in the North-East (NE) Atlantic. With the 2006 IUCN Red List of Threatened Species classification of 'common skate' as Critically Endangered, and the recognition in 2010 that this name masked two species (flapper skate and blue skate D. batis (Linnaeus, 1758)), and to better support conservation on this regional scale, the Flapper Skate Working Group (SWG) was formed. The SWG is a consortium of government, NGOs, sport-fishing associates and academics, including participants from the UK, Ireland and the Netherlands. The purpose of the SWG is to consolidate relevant research, advocacy and policy expertize for the purpose of flapper skate conservation. The first SWG workshop took place in Belfast, November 2019, with discussions focussed on conservation in the NE Atlantic. Following two days of talks, workshops and discussions, we present the SWG's key recommendations for future collaborative conservation.

An egg of the critically endangered flapper skate Dipturus intermedius was successfully incubated to hatching in captivity in what is believed to be a first for the species. Water conditions (temperature, salinity, flow rate) were recorded, with mean water temperatures ranging from a monthly mean of 8.3 +/- 1.2 to 13.2 +/- 0.3 degrees C and salinity from a monthly mean of 30.5 +/- 1.2 to 36.6 +/- 2.3 ppt. Hatching occurred after 534 days, suggesting that flapper skate eggs take c. 5700 growing degree-days to incubate to hatching. The egg's prolonged embryonic development raises concerns about flapper skate eggs' vulnerability to anthropogenic disturbance.