Kristina M. Cammen

RNA viruses are infamous for their ability to cross species barriers, posing threats to global health and security. Influenza A virus (IAV) is naturally found in avian hosts but periodically spills over into marine wildlife. IAV outbreaks occur in the Northwest Atlantic, but grey seals (Halichoerus grypus) appear to be less susceptible to IAV compared to other species. The subclinical nature of IAV infection in addition to life history factors suggest grey seals are a potential wild reservoir host for IAV. We investigated differential gene expression among grey seals naturally exposed to IAV to elucidate genetic mechanisms involved in grey seal disease resistance. RNA sequencing was conducted on blood samples (N = 31) collected from grey seal pups in Massachusetts, US between 2014 and 2019. Samples were grouped for analysis based on presence/absence of viral RNA and antibodies. In the presence of IAV RNA, we observed widespread down‐regulation of genes, including immune genes, potentially as a result of IAV‐induced host shutoff. Immune down‐regulation occurred in acute stage of IAV infection (+ viral RNA, − antibodies), followed by up‐regulation of protein production in peak stage (+ viral RNA, + antibodies), possibly as a result of increased viral replication. Evidence of an activated immune response was observed in late stage of infection (− viral RNA, + antibodies) with up‐regulated adaptive immunity genes. We hypothesize that the combination of down‐ and up‐regulated immune gene expression may prevent overstimulation of the immune response, acting as an adaptation in grey seals to resist IAV‐associated mortality.

Wildlife populations globally have experienced widespread historical declines due to anthropogenic and environmental impacts, yet for some species, contemporary management and conservation programmes have enabled recent recovery. The impacts of decline and recovery on genomic diversity and, vice versa, the genetic factors that contribute to conservation success or failure are rich areas for inquiry, with implications for shaping how we manage species into the future. To comprehensively characterise these processes in natural systems requires range‐wide sampling and international collaboration, particularly for species with wide dispersal capabilities, broad geographic distributions, and complex regional metapopulation dynamics. Here, we present the first range‐ and genome‐wide population genomic analysis of grey seals based on 3812 nuclear SNPs genotyped in 188 samples from 17 localities. Our analyses support the existence of three main grey seal populations centred in the NW Atlantic, NE Atlantic and Baltic Sea, and point to the existence of previously unrecognised substructure within the NE Atlantic. We detected remarkably low levels of genetic diversity in the NW Atlantic population, and demographic analyses revealed a turbulent history of NE Atlantic and Baltic Sea grey seals, with bottlenecks in the Middle Ages and the 20th century due to hunting and habitat alterations. We found some localities deviated from isolation by distance patterns, likely reflecting wide‐scale metapopulation dynamics associated with recolonisation and recovery in regions where they were historically extirpated. We identify at least six grey seal genetic populations and reveal marked genetic effects of past declines and recent recovery across the species' range.

Wildlife management and conservation requires knowledge about a species’ population structure, diversity, demographic history and adaptive potential. However, often such information is lacking, or based on insufficient and sometimes contrasting data. This is the case for the grey seal (Halichoerus grypus), for which there remain uncertainties regarding subspecies and population delineations, diversity and recent evolutionary history, despite numerous genetic and non-genetic studies. Here, we present the first range- and genome-wide population genomic analysis of grey seals based on 3,812 nuclear SNP markers genotyped in 188 samples from 17 distinct localities. Our analyses support the existence of three main grey seal populations centred in the NW Atlantic, NE Atlantic and Baltic Sea, but also point to the existence of previously unrecognised substructure within the NE Atlantic, in particular separating grey seals sampled in Iceland, Norway and Russia from the core NE Atlantic population inhabiting the wider North Sea region. We detected remarkably low levels of genetic diversity in NW Atlantic grey seals, which may be the result of evolutionary founder effects, as well as more recent historic hunting and culling. We also found some localities that deviate from the general isolation by distance pattern, likely reflecting wide-scale metapopulation dynamics associated with recolonisation and recovery of grey seals in regions where they were historically extirpated. Our genetic results allow us to identify at least six grey seal management units across the species’ Atlantic range, but also highlights knowledge gaps that should be addressed in future research into this species.

Cooperative Fisheries Research (CFR) aims to incorporate different types of knowledge into fisheries science through the convergence of diverse perspectives, skills, and expertise. CFR can facilitate knowledge co-production and the salience, credibility, and legitimacy of science, yet it can be difficult to operationalize. In Maine’s American lobster fishery, where CFR is a hallmark of the fishery, pressure to implement conservation measures to protect North Atlantic right whales, one of the world’s most endangered large whale species, poses a major challenge for harvesters. Endeavoring to follow best practices associated with CFR, our research team set out to work with state management and fishing industry partners to evaluate the socioeconomic impacts of new whale conservation regulations on the fishery. We co-defined relevant and actionable research questions and designed a sampling approach that included multiple efforts to contact industry participants. Although the process we engaged in had some of the key ingredients for success, ultimately participation was too low to achieve our research aims. We use this paper to discuss our failure and draw on the theory of scalar politics from critical geography to reflect on challenges we encountered, including how the contentious socio-political backdrop within which the initiative transpired impacted our research.

Marine mammals in the North Atlantic have experienced severe depletions due to overexploitation. While some species and populations have now recovered, there are numerous other anthropogenic activities impacting their North Atlantic ecosystem. Studying marine mammals is often associated with logistical challenges, and many species have an elusive nature, resulting in substantial knowledge gaps on the distribution, abundance and diversity of marine mammals in the North Atlantic. Environmental DNA (eDNA) is an emerging tool in biodiversity monitoring and has successfully been demonstrated to complement traditional monitoring methods for a wide range of marine taxonomic groups. The promising potential of seawater eDNA is owe to advances within an array of molecular methods used to extract, detect and/or sequence the genetic material of marine organisms from a single seawater sample. We present a literature review of eDNA studies of marine mammals and discuss the potential applications and practical challenges of eDNA in marine mammal research, management and conservation. Environmental DNA has already been introduced to a wide range of applications within marine mammal science, from detection of endangered species to population genetic assessments. Furthermore, eDNA has the power to capture other biologically important species in the marine ecosystem and food web, which could facilitate insight into the spatiotemporal variation of different marine communities in a changing environment. With methodological and technological standardization, eDNA based approaches have a promising potential to be integrated into regular monitoring practices and management strategies.

Over the past several decades, the Gulf of Maine has experienced significant socio‐ecological change. Coastlines have become more densely populated and developed, rapid and dramatic climate change has affected coastal ocean environments, and seal populations have grown as a result of federal protections. Long‐term data sets from marine mammal stranding networks represent a valuable resource for investigating indicator species for coastal ocean health during this period of change. Using data collected from stranded harbor (Phoca vitulina), harp (Pagophilus groenlandicus), and gray (Halichoerus grypus) seals from 2002 to 2017 in Massachusetts, New Hampshire, and Maine, we tested for spatiotemporal correlations between stranding density and human population density, size of and proximity to seal haul‐outs, sea surface temperature, North Atlantic Oscillation, snowfall, and sea ice extent. We found that in the Gulf of Maine proximity to coastal human population centers and large seal haul‐outs are the greatest drivers of reported seal stranding density. Environmental factors played an important role only for harp seals, which do not breed in the study area, although recent shifts in the environmental seascape have the potential to affect all seal species in the Gulf of Maine.

Differences in disease susceptibility among species can result from rapid host–pathogen coevolution and differences in host species ecology that affect the strength and direction of natural selection. Among 2 sympatric pinniped species that differ in sociality and putative disease exposure, we investigate observed differences in susceptibility through an analysis of a highly variable, duplicated gene family involved in the vertebrate immune response. Using high-throughput amplicon sequencing, we characterize diversity at the 2 exons that encode the peptide binding region of the major histocompatibility complex class I (MHC-I) gene in harbor (N = 60) and gray (N = 90) seal populations from the Northwest Atlantic. Across species, we identified 106 full-length exon 2 and 103 exon 3 sequence variants and a minimum of 11 duplicated MHC-I loci. The sequence variants clustered in 15 supertypes defined by the physiochemical properties of the peptide binding region, including a putatively novel Northwest Atlantic MHC-I diversity sublineage. Trans-species polymorphisms, dN/dS ratios, and evidence of gene conversion among supertypes are consistent with balancing selection acting on this gene. High functional redundancy suggests particularly strong selection among gray seals at the novel Northwest Atlantic MHC-I diversity sublineage. At exon 2, harbor seals had a significantly greater number of variants per individual than gray seals, but fewer supertypes. Supertype richness and private supertypes are hypothesized to contribute to observed differences in disease resistance between species, as consistently, across the North Atlantic and many disease outbreaks, gray seals appear to be more resistant to respiratory viruses than harbor seals.

Seal populations in the Gulf of Maine have been recovering from historical bounty‐driven declines since they received federal protection in 1972. In the past few decades, their population growth has sparked renewed concerns over conflict between pinniped and fish conservation. In the Penobscot River in Maine, USA, where restoration efforts over the past decade have aimed at restoring diadromous fish runs, seal predation on the endangered Atlantic salmon (Salmo salar) has become a growing concern. Quantitative and qualitative data for individual salmon, as well as the presence of putative seal‐induced injury, have been collected from salmon passing upriver at dams in the Penobscot River since 2012. An analysis of seal‐induced injury rate with demographic data, river herring returns, estuary fish biomass estimates, and timing of peak estuary fish biomass revealed that the seal‐induced injury rate declined in the Penobscot River from 2012 to 2019, coincident with increasing river herring returns and estuary fish biomass. Despite a potentially increasing seal population, these results suggest that predator swamping from increasing forage fish may provide protection to salmon against seal predation. The presence of multiple injuries on an individual salmon was also significantly associated with the probability of a salmon having a seal‐induced injury. Lamprey wounds and lacerations on salmon were commonly associated with seal‐induced injury, suggesting a confounding effect of multiple stressors. This assessment illustrates how multi‐species diadromous restoration activities may alter predator–prey interactions in ways that support salmon conservation efforts. As demonstrated in the Penobscot River, a focus on overall ecosystem health and restoration can benefit multiple species that use the river. Insights from this study may help inform future management decisions in other human‐impacted systems where protected predators come into conflict with endangered prey.

The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonized its current range. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping‐by‐sequencing to analyse ~13,500 biallelic single nucleotide polymorphisms from 286 individuals sampled from 22 localities across the species’ range. Our results point to a Northeast Pacific origin of the harbour seal, colonization of the North Atlantic via the Canadian Arctic, and subsequent stepping‐stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer‐scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonize and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.

Recent marine mammal recovery and growth of human populations in coastal areas has led to increased human harassment of protected pinniped populations. Yet, current monitoring approaches lack the necessary resolution to describe this emerging issue. We therefore propose a new classification scheme for monitoring of marine mammal–human interaction (HI), which defines categories based on the type of human behavior and associated risks to the animal. Among harbor, harp, and gray seal strandings ( N = 3,525) from 2007 to 2019 in Maine, United States, evidence of HI was reported in 14.72% of strandings, with the majority (75.34%) of these cases involving harassment. The number of HI reports increased over time, particularly in the southern region of the state, and an analysis of geographic hotspots further identifies emerging areas of concern. Variation in the rate and type of HI among species, age classes, and seasons reflect differences in pinniped life history. The most commonly observed types of harassment included human approach, physical contact, and displacement. By breaking down harassment, we aim to inform ongoing mitigation efforts and contribute to our understanding of the impact of HI on marine mammal health, as well as offer a transferable methodological approach to monitoring human–wildlife interaction.