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Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th–20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.

Sea otters are a keystone species with cultural significance to Indigenous populations. The increased mortality of Northern sea otters ( E. lutris kenyoni ) near Kachemak Bay, Alaska, led to a surveillance study to determine the cause of the increased deaths. Samples EL1562 and EL1411 were obtained from two dead-stranded sea otters. Whole genomes of two different orthoreoviruses with all ten segments were obtained. All EL1562 genome segments show the highest similarity to Phocid orthoreovirus 1 , a new species isolated from harbor seals. However, the σ1 protein exhibits high divergence (34% amino acid identity) that warrants re-evaluation of the species demarcation criteria. Cell culture and microscopy are consistent with EL1562 being similar to Phocid orthoreovirus 1 . Based on binomial naming conventions, we suggest the species name Orthoreovirus marinarum , which encompasses both EL1562 and PhRV1. Characterization of EL1411 sequences shows that it belongs to the species Orthoreovirus mammalis , which includes members from terrestrial mammals. This study represents the first orthoreovirus cultured and genome sequenced from sea otters, and is only the second report of a mammalian orthoreovirus in marine mammals. This study provides new insights into the genetic diversity of orthoreovirus in marine mammals and the evolutionary linkage between terrestrial and marine orthoreoviruses.

Fatal infections with the rare COUG strain of the zoonotic parasite Toxoplasma gondii were recently detected for the first time in four southern sea otters ( Enhydra lutris nereis ) exhibiting severe protozoal steatitis. The objectives of this study were to describe new COUG strain infections in sea otters, investigate the potential contributory role of a recently discovered parasite-infecting narnavirus ( Apocryptovirus odysseus ) in these infections, assess the potential contribution of vitamin E deficiency in the development of systemic steatitis, and explore the utility of serotyping for strain-specific diagnosis of T. gondii infections in sea otters. Since initial reporting, six additional sea otters died due to fatal COUG strain T. gondii infections. Five animals exhibited lesion patterns resembling the prior case definition including severe, widespread steatitis. The final case died due to severe T. gondii -associated meningoencephalitis with no grossly or microscopically apparent steatitis. In contrast with a recent report utilizing a cougar-derived parasite isolate, A. odysseus RNA was not detected in sea otter-derived COUG strain isolates, suggesting that this narnavirus is not associated with fatal COUG strain infections in sea otters. Serotyping using dense granule (GRA) peptides to distinguish between T. gondii strains infecting sea otters suggests that Type X, Type II, and COUG strains exhibit different peptide-reactivity profiles that may allow them to be distinguished serologically. COUG strain T. gondii infections are an emerging threat to southern sea otter population health, and this strain has the potential to infect other animal and human hosts that share their environment and food sources with sea otters. Additional studies are needed to clarify the environmental sources, epidemiology, pathophysiology, and premortem serodiagnosis of COUG strain T. gondii infections in southern sea otters and other susceptible hosts.

Understanding the role of apex predators on ecosystems is essential for designing effective conservation strategies. Supporting recovery of apex predators can have many benefits; one that has been rarely examined is control of invasive prey. We investigated whether a recovering apex predator, the southern sea otter ( Enhydra lutris nereis ), can exert local control over a global marine invader, the green crab ( Carcinus maenas ). We determined that southern sea otters in Elkhorn Slough estuary in California can consume large numbers of invasive green crabs and found strong negative relationships in space and time between otter and green crab abundance. Green crabs persisted at highest abundance in this estuary at sites with artificial tidal restriction that were not accessible to otters. Green crab abundance remained lower in this estuary than in all other estuaries in the region, which lack resident sea otters. Conservation organizations and agencies have invested heavily in recovery of southern sea otters, increasing their numbers in this estuary. Restoration of natural tidal exchange, lost marshes, and seagrass beds further support sea otter populations. We have demonstrated that these investments in top predator recovery and habitat restoration have reduced the impacts of a global invader. Our investigation highlights that investment in recovery of top predators can increase beneficial food web interactions and resilience of the entire ecosystem.

The measurement of stable isotope values of individual compounds, such as amino acids (AAs), has become a powerful tool in animal ecology and ecophysiology. As with any emerging technique, questions remain regarding the capabilities and limitations of this approach, including how metabolism and tissue synthesis impact the isotopic values of individual AAs and subsequent multivariate patterns. We measured carbon isotope (δ13C) values of essential (AAESS) and nonessential (AANESS) AAs in bone collagen, whisker, muscle, and liver from ten southern sea otters (Enhydra lutris nereis) that stranded in Monterey Bay, California. Sea otters in this population exhibit high degrees of individual dietary specialization, making this an excellent dataset to explore differences in AA δ13C values among tissues in a wild population. We found the δ13C values of the AANESS glutamic acid, proline, serine, and glycine and the AAESS threonine differed significantly among tissues, indicating possible isotopic discrimination during tissue synthesis. Threonine δ13C values were higher in liver relative to bone collagen and muscle, which may indicate catabolism of threonine for gluconeogenesis, an interpretation further supported by correlations between the δ13C values of threonine and its gluconeogenic products glycine and serine in liver. This intraindividual isotopic variation yielded different ecological interpretations among tissues; for 6/10 of the sea otter individuals analyzed, at least one tissue indicated reliance on a different primary producer source than the other tissues. Our results highlight the importance of gluconeogenesis in a carnivorous marine mammal and indicate that metabolic processes influence AAESS and AANESSδ13C values and multivariate AA δ13C patterns.

Differences in diet composition among conspecifics (dietary specialization) have been documented across a broad range of taxonomic groups and habitats, and such variation at the individual level is increasingly recognized as an important component of diversity in trophic interactions. Accurate identification of individual dietary specialization, however, requires longitudinal dietary records that are labor-intensive and cost-prohibitive to obtain for many species. Here we explore the use of stable isotopes (δ¹³C and δ¹⁵N) as a promising technique for detecting and quantifying patterns of individual dietary specialization. Southern sea otters (Enhydra lutris nereis) offer a unique opportunity for testing this approach because (1) they consume a wide variety of prey that span multiple trophic levels, habitats, and ecologically defined functional groups; and (2) individual diet specialization can be validated with existing observational data. We analyzed the isotopic composition of sea otter vibrissae (n = 31) in order to characterize inter- and intra-individual variation in sea otter diets at Monterey Bay, California, USA. At the population level, sea otters showed substantial variation in both δ¹³C and δ¹⁵N values, occupying nearly all of the \"isotopic space\" created by the diversity of isotopic signatures of potential prey taxa. Most of the variation in sea otter vibrissae was accounted for by differences between individuals, with much less contributed by within-individual variation. A majority of sea otters (∼80%) showed relatively little temporal variability in isotopic composition, suggesting that the proportional composition of most individuals' diets is relatively constant over time; a few individuals (∼20%) exhibited a high degree of intra-vibrissa isotopic variability, suggesting seasonal shifts in diet composition. These results and our interpretation of them were supported by long-term observational data on the diets of radio-tagged sea otters from the same population (n = 23). Our results demonstrate that stable isotopes can provide an efficient tool for measuring individual- and population-level dietary breadth and may be useful for studying populations where longitudinal data on individuals would otherwise be impossible to acquire. This will be critical for examining the causes and consequences of dietary variation within and among consumer populations, thereby improving our understanding of these important ecological and evolutionary processes at the community level.

Translocation and rehabilitation programmes are critical tools for wildlife conservation. These methods achieve greater impact when integrated in a combined strategy for enhancing population or ecosystem restoration. During 2002–2016 we reared 37 orphaned southern sea otter Enhydra lutris nereis pups, using captive sea otters as surrogate mothers, then released them into a degraded coastal estuary. As a keystone species, observed increases in the local sea otter population unsurprisingly brought many ecosystem benefits. The role that surrogate-reared otters played in this success story, however, remained uncertain. To resolve this, we developed an individual-based model of the local population using surveyed individual fates (survival and reproduction) of surrogate-reared and wild-captured otters, and modelled estimates of immigration. Estimates derived from a decade of population monitoring indicated that surrogate-reared and wild sea otters had similar reproductive and survival rates. This was true for males and females, across all ages (1–13 years) and locations evaluated. The model simulations indicated that reconstructed counts of the wild population are best explained by surrogate-reared otters combined with low levels of unassisted immigration. In addition, the model shows that 55% of observed population growth over this period is attributable to surrogate-reared otters and their wild progeny. Together, our results indicate that the integration of surrogacy methods and reintroduction of juvenile sea otters helped establish a biologically successful population and restore a once-impaired ecosystem.

Southern sea otters (Enhydra lutris nereis) face numerous risks to population recovery from infectious disease, shark attacks, and biotoxins. Recently, the most significant contributor to fatal infectious disease in sea otters has been acanthocephalan peritonitis (AP) caused by Profilicollis altmani. Despite the importance of AP‐associated otter mortality, long‐term and seasonal risks for spillover of this parasite from its avian definitive hosts (seabirds and shorebirds) and crustacean intermediate hosts, Pacific mole crabs (Emerita analoga), are poorly resolved. We analyzed a 30‐year dataset of sea otter strandings (n = 4460 cases) within the extant southern sea otter range to assess the contributions of temporal, demographic, geographic, and environmental risk factors to the prevalence of AP in southern sea otters. We found the incidence of AP was driven by high prevalence in immature otters near or in Morro and Monterey Bays, primarily in the late spring. The seasonal fluctuations in AP prevalence aligned closely with the presence of Pacific mole crabs in the gastrointestinal tracts of stranded otters. For Monterey Bay otters, AP prevalence was also higher during El Niño years. Long‐term trend analyses suggest that seasonal, demographic, and geographic patterns of AP prevalence in southern sea otters have shifted. Southern sea otter population recovery efforts can be informed by long‐term monitoring that assesses the evolving risks of AP and other sources of mortality.

Sea otters (Enhydra lutris kenyoni) historically occurred in Washington State, USA, until their local extinction in the early 1900s as a result of the maritime fur trade. Following their extirpation, 59 sea otters were translocated from Amchitka Island, Alaska, USA, to the coast of Washington, with 29 released at Point Grenville in 1969 and 30 released at La Push in 1970. The Washington Department of Fish and Wildlife has outlined 2 main objectives for sea otter recovery: a target population level and a target geographic distribution. Recovery criteria are based on estimates of population abundance, equilibrium abundance (K), and geographic distribution; therefore, estimates of these parameters have important management implications. We compiled available survey data for sea otters in Washington State since their translocation (1977–2019) and fit a Bayesian state-space model to estimate past and current abundance, and equilibrium abundance at multiple spatial scales. We then used forward projections of population dynamics to explore potential scenarios of range recolonization and as the basis of a sensitivity analysis to evaluate the relative influence of movement behavior, frontal wave speed, intrinsic growth, and equilibrium density on future population recovery potential. Our model improves upon previous analyses of sea otter population dynamics in Washington by partitioning and quantifying sources of estimation error to estimate population dynamics, by providing robust estimates of K, and by simulating long-term population growth and range expansion under a range of realistic parameter values. Our model resulted in predictions of population abundance that closely matched observed counts. At the range-wide scale, the population size in our model increased from an average of 21 independent sea otters (95% CI = 13–29) in 1977 to 2,336 independent sea otters (95% CI = 1,467–3,359) in 2019. The average estimated annual growth rate was 12.42% and varied at a sub-regional scale from 6.42–14.92%. The overall estimated mean K density of sea otters in Washington was 1.71 ± 0.90 (SD) independent sea otters/km² of habitat (1.96 ± 1.04 sea otters/km², including pups), and estimated densities within the current range correspond on average to 87% of mean sub-regional equilibrium values (range = 66–111%). The projected value of K for all of Washington was 5,287 independent sea otters (95% CI = 2,488–8,086) and 6,080 sea otters including pups (95% CI = 2,861–9,300), assuming a similar range of equilibrium densities in currently un-occupied habitats. Sensitivity analysis of simulations of sea otter population growth and range expansion suggested that mean K density estimates in currently occupied sub-regions had the largest impact on predicted future population growth (r² = 0.52), followed by the rate of southward range expansion (r² = 0.26) and the mean K density estimate of currently unoccupied sub-regions to the south of the current range (r² = 0.04). Our estimates of abundance and sensitivity analysis of simulations of future population abundance and geographic range help determine population status in relation to population recovery targets and identify the most influential parameters affecting future population growth and range expansion for sea otters in Washington State.

This article reviews the known methods for counting the sea otter Enhydra lutris (Linnaeus, 1758) of the Commander Islands population that has been steadily declining for the past 15 years. The relationship between the total abundance and the abundance at the northwestern haul-out site on Bering Island is shown: the long-term trend in population size is accurately identified using one rather large model haul-out site as an example. The results of different methods for counting sea otters at the haul-out site are presented. The use of a thermal imaging camera has been found to increase the efficiency of drive counts at night, especially in snow-free weather, being independent of light conditions. It is shown that counts of body prints in the snow at the haul-out site can be an alternative to drive counts.