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Growing anthropogenic pressures increasingly impact marine wildlife, with cetaceans being particularly vulnerable to cumulative effects of stressors due to their position as top predators. As sensors and sentinels of ocean health, cetaceans offer critical insight into known and emerging threats to marine ecosystems. Stranding schemes provide a cost-effective means to assess mortality rates and population demographics, offering insights that are often challenging to obtain through live monitoring. Using a 30-year dataset from the Scottish Marine Animal Stranding Scheme (SMASS) we demonstrate how opportunistically obtained stranding data can be used to monitor populations and guide conservation strategies. Species were clustered into broad ecological groups - baleen whales, short-beaked common dolphins, deep divers, harbour porpoises and pelagic dolphins - for spatiotemporal analysis of stranding patterns. All groups showed increases in annual stranding rates over the study period, with common dolphins and baleen whales exhibiting exponential increases, suggesting these species may be facing heightened pressures. Distinct seasonal and spatial trends were detected, with harbour porpoises predominantly stranding on the east coast and other groups clustering to Scotland’s west coast. Identifying these trends helps focus surveillance and mitigation efforts, underscoring the importance of this approach for monitoring vulnerable species.

Assessing long‐term population health is an important feature of wildlife monitoring and is essential for understanding population resilience. Quantitative assessments of health indices are essential for effective monitoring yet they remain a challenge for cetaceans due to their highly mobile and largely cryptic nature. Quantified assessments of cetacean health typically rely on evaluating body condition, which reflects energetic reserves and nutritional status. However, this method may not capture sub‐lethal impacts or comorbidities resulting from chronic or cumulative stressors. Necropsies of stranded individuals provide unique insight into the morbidity of an individual and offer clues about the pressures an individual has faced over its lifetime, making necropsy reports a valuable source for understanding health. However, the predominantly qualitative and narrative format of necropsy reports limits their utility for systematic statistical analysis, thereby constraining their application in generating robust, population‐level inferences. Using 349 necropsy records of harbour porpoises (Phocoena phocoena ) stranded on the Scottish coastline as a case study, we developed a structured pathology database suitable for statistical analysis. The application of unsupervised and supervised machine learning techniques has revealed underlying patterns in harbour porpoise pathology. This has shown that necropsy data may provide a more comprehensive insight into health than traditional methods. We identified the respiratory and hepatic systems as explaining a high degree of variation in the data. This highlights these organ systems as priority areas for data collection and subsequent analysis. Patterns in the data revealed underlying compromised health, particularly in adult harbour porpoises, suggesting a vulnerability to additional stressors in this group. Our approach demonstrates how pathology data from necropsy reports can be used to derive population‐level health insights, offering a tool for monitoring the impacts of environmental and anthropogenic pressures on wildlife populations. Assessing long‐term health in wildlife populations remains challenging, especially for cetaceans, whose mobility and cryptic behaviour limit traditional assessments based solely on body condition. By analysing 349 necropsy records of harbour porpoises stranded along the Scottish coastline, we created a structured pathology database and applied machine learning techniques to identify patterns in organ‐specific morbidity, highlighting the respiratory and hepatic systems as key indicators of health. Our findings reveal underlying compromised health in adult harbour porpoises, suggesting reduced resilience to additional stressors. They demonstrate that necropsy data can provide robust, population‐level insights into the impacts of environmental and anthropogenic pressures on wildlife.

Dolphins are mobile apex marine predators. Over the past three decades, warm-water adapted dolphin species (short-beaked common and striped) have expanded their ranges northward and become increasingly abundant in British waters. Meanwhile, cold-water adapted dolphins (white-beaked and Atlantic white-sided) abundance trends are decreasing, with evidence of the distribution of white-beaked dolphins shifting from southern to northern British waters. These trends are particularly evident in Scottish waters and ocean warming may be a contributing factor. This mobility increases the likelihood of interspecific dietary overlap for prey among dolphin species previously separated by latitude and thermal gradients. Foraging success is critical to both individual animal health and overall population resilience. However, the degree of dietary overlap and plasticity among these species in the Northeast Atlantic is unknown. Here, we characterise recent (2015-2021) interspecific isotopic niche and niche overlap among six small and medium-sized delphinid species co-occurring in Scottish waters, using skin stable isotope composition ( δ 13 C and δ 15 N), combined with stomach content records and prey δ 13 C and δ 15 N compiled from the literature. Cold-water adapted white-beaked dolphin have a smaller core isotopic niche and lower dietary plasticity than the generalist short-beaked common dolphin. Striped dolphin isotopic niche displayed no interspecific overlap, however short-beaked common dolphin isotopic niche overlapped with white-beaked dolphin by 30% and Atlantic white-sided dolphin by 7%. Increasing abundance of short-beaked common dolphin in British waters could create competition for cold-water adapted dolphin species as a significant portion of their diets comprise the same size Gadiformes and high energy density pelagic schooling fish. These priority prey species are also a valuable component of the local and global fishing industry. Competition for prey from both ecological and anthropogenic sources should be considered when assessing cumulative stressors acting on cold-water adapted dolphin populations with projected decline in available habitat as ocean temperatures continue to rise.

Multiple stressors caused by human-induced disturbances can affect the foraging opportunities of cetaceans, potentially depleting their energy stores, and ultimately impact survival and reproductive success. Currently, blubber thickness and lipid composition is used as measure of health and nutritional status in cetaceans. This assumes that blubber functions in the same manner as adipose tissue in terrestrial mammals. However, cetaceans have evolved to have thickened blubber which serves as thermoregulation, buoyancy and energy store. In addition, blubber is composed of several layers and regions that have different physiological functions. We currently lack a clear understanding of how blubber biology contributes to maintaining energy status in cetaceans and several studies show blubber thickness, and composition in some body regions, is an inappropriate measure of health. Before new markers of health can be identified, we need to understand how environmental stressors influence blubber biology and particularly unravel its complex signalling roles with other organs. Currently, we do not understand how changes in energy status drive changes in health in cetaceans and eventually population dynamics. This review synthesises recent developments in cetacean blubber biology to propose potential directions to develop novel cetacean health markers.

Neisseria animaloris is considered to be a commensal of the canine and feline oral cavities. It is able to cause systemic infections in animals as well as humans, usually after a biting trauma has occurred. We recovered N . animaloris from chronically inflamed bite wounds on pectoral fins and tailstocks, from lungs and other internal organs of eight harbour porpoises. Gross and histopathological evidence suggest that fatal disseminated N . animaloris infections had occurred due to traumatic injury from grey seals. We therefore conclude that these porpoises survived a grey seal predatory attack, with the bite lesions representing the subsequent portal of entry for bacteria to infect the animals causing abscesses in multiple tissues, and eventually death. We demonstrate that forensic microbiology provides a useful tool for linking a perpetrator to its victim. Moreover, N . animaloris should be added to the list of potential zoonotic bacteria following interactions with seals, as the finding of systemic transfer to the lungs and other tissues of the harbour porpoises may suggest a potential to do likewise in humans.

The ecological value of the stranding record is often challenged due to the complexity in quantifying the biases associated with multiple components of the stranding process. There are biological, physical and social aspects that complicate the interpretation of stranding data particularly at a population level. We show how examination of baseline variability in the historical stranding record can provide useful insights into temporal trends and facilitate the detection of unusual variability in stranding rates. Seasonal variability was examined using harbour porpoise strandings between 1992 and 2014 on the east coast of Scotland. Generalized Additive Mixed modelling revealed a strong seasonal pattern, with numbers increasing from February towards a peak in April. Profiling seasonality this way facilitates detection of unusual variations in stranding frequencies and permits for any change in the incidence of strandings to be quantified by evaluation of the normalized model residuals. Consequently, this model can be used to identify unusual mortality events, and quantify the degree to which they deviate from baseline. With this study we demonstrate that a described baseline in strandings allows the detection of abnormalities at an early stage and can be used as a regional framework of reference for monitoring. This methodology provides means to quantify and partition the variability associated with strandings data and is a useful first step towards improving the stranding record as a management resource.

Elusive wildlife are challenging to study, manage, or conserve, as the difficulty of obtaining specimens or conducting direct observations leads to major data deficiencies. Specimens of opportunity, such as salvaged carcasses or museum specimens, are a valuable source of fundamental biological and ecological information on data-deficient, elusive species, increasing knowledge of biodiversity, habitat and range, and population structure. Stable isotope analysis is a powerful indirect tool that can be used to infer foraging behavior and habitat use retrospectively from archived specimens. Beaked whales are a speciose group of cetaceans that are challenging to study in situ , and although Sowerby's beaked whale ( Mesoplodon bidens ) was discovered >200 years ago, little is known about its biology. We measured δ 13 C and δ 15 N stable isotope composition in bone, muscle, and skin tissue from 102 Sowerby's beaked whale specimens of opportunity collected throughout the North Atlantic Ocean to infer movement ecology and spatial population structure. Median δ 13 C and δ 15 N values in Sowerby's beaked whale bone, muscle, and skin tissues significantly differed between whales sampled from the east and west North Atlantic Ocean. Quadratic discriminant analysis that simultaneously considered δ 13 C and δ 15 N values correctly assigned >85% of the specimens to their collection region for all tissue types. These findings demonstrate Sowerby's beaked whale exhibits both short- and long-term site fidelity to the region from which the specimens were collected, suggest that this species is composed of two or more populations or exhibits a metapopulation structure, and have implications for conservation and management policy. Stable isotope analysis of specimens of opportunity proved a highly successful means of generating new spatial ecology data for this elusive species and is a method that can be effectively applied to other elusive species.

Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromosome-resolved reference genomes for all cetacean species. Towards that goal, and using the methods, goals and genome assembly quality standards of the Vertebrate Genomes Project (VGP), we generated 13 new reference genomes across eight of the 14 cetacean families. Additionally, we summarize the genome assembly characteristics for 18 species, including these newly-generated and five published genome assemblies that meet the completeness and quality standards. We infer ancestral linkage groups (ALG) for cetaceans, showing that the ancestral karyotype of 22 ALGs is largely conserved in extant species, except for Ziphiidae, and for Balaenidae and Kogiidae, which exhibit similar independent fusions. Gene annotation, characterization of historical demography, heterozygosity and runs of homozygosity (ROH) reveal important information for conservation applications. By comparing the new reference genomes to previous draft assemblies, we show that the reference genomes have enhanced characteristics that will support and promote scientific research. Specifically, the genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of gene regions such as the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.

Reference genomes from representative species across families provide the critical infrastructure for research and conservation. The Cetacean Genomes Project (CGP) began in early 2020 to facilitate the generation of near error-free, chromosome-resolved reference genomes for all cetacean species. Towards that goal, and using the methods, goals and genome assembly quality standards of the Vertebrate Genomes Project (VGP), we generated 13 new reference genomes across eight of the 14 cetacean families. Additionally, we summarize the genome assembly characteristics for 18 species, including these newly-generated and five published genome assemblies that meet the completeness and quality standards. We infer ancestral linkage groups (ALG) for cetaceans, showing that the ancestral karyotype of 22 ALGs is largely conserved in extant species, except for Ziphiidae, and for Balaenidae and Kogiidae, which exhibit similar independent fusions. Gene annotation, characterization of historical demography, heterozygosity and runs of homozygosity (ROH) reveal important information for conservation applications. By comparing the new reference genomes to previous draft assemblies, we show that the reference genomes have enhanced characteristics that will support and promote scientific research. Specifically, the genomes improve resolution and characterization of repetitive elements, provide validation (or exclusion) of genes linked to complex traits, and allow more complete characterization of gene regions such as the highly complex Major Histocompatibility Complex (MHC) Class I and II gene clusters that are important for population health.

The problem of controlling tsetse flies in Africa is an old one. The tsetse fly transmits the trypanosome parasites which cause sleeping sickness in humans and disease in cattle. Because cattle are a favoured food source for tsetse much work has been done looking at the use of insecticide treated cattle as a control strategy for the tsetse fly. Such treatment methods possess many advantages; they are safe and relatively environmentally benign, they can be applied by individual farmers without the need for logistically demanding and costly traditional control programmes and, in addition to tsetse flies the insecticides are effective against a wide range of other harmful cattle parasites. The cost of the insecticide is however a significant constraint to the number of livestock keepers who can afford to employ the technique and as a result many cattle remain untreated. Following the discovery that tsetse had a significant predilection for feeding on the legs and belly of cattle, it was hypothesised that restricting the insecticide to only those areas could offer comparable protection to treating the whole animal. Such an approach would use up to 80% less drug and thus make the treatment per animal much cheaper. In addition, preferentially targeting areas favoured by tsetse, and leaving the rest of the animal untreated, preserves some important ecological balances between cattle and their parasites which traditional treatment methods destabilise. This thesis describes the design, implementation and analysis of a longitudinal study run over 8 months in south east Uganda that sought to compare the effect of applying insecticide to cattle only on the regions favoured by tsetse flies. Cattle were recruited to the study and assigned one of four treatment groups; a whole body application of deltamethrin insecticide pour-on; a restricted application of deltamethrin spray, applied to the front legs, ears and belly; a prophylactic trypanocide injection of isometamidium chloride, and a control group, that received no further treatments. All animals in the study were however cleared using twin doses of a trypanocide diminazene aceturate at the start of the study.