Permissible Home Range Estimation (PHRE) in Restricted Habitats: A New Algorithm and an Evaluation for Sea Otters

The role of spatial structure in at-risk metapopulation recoveries

Metapopulations are often managed as a single contiguous population despite the spatial structure underlying their local and regional dynamics. Disturbances from human activities can also be spatially structured with mortality impacts concentrated to just a few local populations among the aggregate. Scale transitions between local and regional processes can generate emergent properties whereby the whole system can fail to recover as quickly as expected for an equivalent single population. Here, we draw on theory and empirical case studies to ask: what is the consequence of spatially structured ecological and disturbance processes on metapopulation recoveries? We suggest that exploring this question could help address knowledge gaps for managing metapopulations including: Why do some metapopulations recover quickly while others remain collapsed? And, what risks are unaccounted for when metapopulations are managed at aggregate scales? First, we used model simulations to examine how scale transitions among ecological and disturbance conditions interact to generate emergent metapopulation recovery outcomes. In general, we found that the spatial structure of disturbance was a strong determinant of recovery outcomes. Specifically, disturbances that unevenly impacted local populations consistently generated the slowest recoveries and highest conservation risks. Ecological conditions that dampened metapopulation recoveries included low dispersal, variable local demography, sparsely connected habitat networks, and spatially and temporally correlated stochastic processes. Second, we illustrate the unexpected challenges of managing metapopulations by examining the recoveries of three USA federally listed endangered species: Florida Everglade snail kites, California and Alaska sea otters, and Snake River Chinook salmon. Overall, our results show the pivotal role of spatial structure in metapopulation recoveries whereby the interplay between local and regional processes shapes the resilience of the whole system. With this understanding, we provide guidelines for resource managers tasked with conserving and managing metapopulations and identify opportunities for research to support the application of metapopulation theory to real-world challenges.

Satellite telemetry reveals habitat selection decisions by black oystercatchers across seasonal, diel, and tidal cycles

Habitat use of indicator species is used to prioritize management activities. However, habitat use can vary temporally in response to changes in predation risk and foraging rewards. We deployed satellite tags on 20 black oystercatchers (Haematopus bachmani) in four regions of British Columbia, Canada, to examine habitat use and selection decisions across seasonal, diel and tidal cycles. We characterized the shoreline in each region and used GLMMs to investigate how habitat characteristics influenced shoreline use by tracked birds. For individuals, we estimated home range size and the frequency key features of the shoreline were re-visited. Black oystercatchers generally made greater-than-expected use of rocky islets and shoreline with freshwater outflows, less tree cover and greater intertidal area. However, while black oystercatchers preferred islets and shoreline with less tree cover at most/all time periods, they only exhibited preferences for greater intertidal area during low tides, and preferences for shoreline with freshwater outflows during the nonbreeding season, day, and high tides. Individual home ranges, on average, contained 46 km of shoreline (range: 12-156 km) and individuals used 10.4 km (range: 6.7-13.9 km). Individuals made greater use of larger islets with less tree cover that were closer to outflows, and greater use of outflows associated with larger streams, greater intertidal areas and gravel substrates. Black oystercatchers' habitat preferences likely reduce predation risk (rocky islets and shoreline with less tree cover) and increase foraging rewards (shoreline with freshwater outflows, greater intertidal area, and gravel substrates). However, habitat preferences appear sensitive to constraints on movement in the breeding season and changes in foraging rewards across the diel and tidal cycle, highlighting the importance of examining habitat use at multiple temporal scales. Black oystercatchers are considered indicators of rocky intertidal health; therefore, critical habitat is expected to be important for a suite of wildlife dependent on safe and productive coastline.

Southeast Alaskan kelp forests: inferences of process from large-scale patterns of variation in space and time

Humans were considered external drivers in much foundational ecological research. A recognition that humans are embedded in the complex interaction networks we study can provide new insight into our ecological paradigms. Here, we use time-series data spanning three decades to explore the effects of human harvesting on otter-urchin-kelp trophic cascades in southeast Alaska. These effects were inferred from variation in sea urchin and kelp abundance following the post fur trade repatriation of otters and a subsequent localized reduction of otters by human harvest in one location. In an example of a classic trophic cascade, otter repatriation was followed by a 99% reduction in urchin biomass density and a greater than 99% increase in kelp density region wide. Recent spatially concentrated harvesting of otters was associated with a localized 70% decline in otter abundance in one location, with urchins increasing and kelps declining in accordance with the spatial pattern of otter occupancy within that region. While the otter-urchin-kelp trophic cascade has been associated with alternative community states at the regional scale, this research highlights how small-scale variability in otter occupancy, ostensibly due to spatial variability in harvesting or the risk landscape for otters, can result in within-region patchiness in these community states.

Investigating Associations Among Relatedness, Genetic Diversity, and Causes of Mortality In Southern Sea Otters (Enhydra lutris nereis)

Southern sea otter (Enhydra lutris nereis) population recovery is influenced by a variety of factors, including predation, biotoxin exposure, infectious disease, oil spills, habitat degradation, and resource limitation. This population has also experienced a significant genetic bottleneck, resulting in low genetic diversity. We investigated how two metrics, familial relatedness and genetic diversity, are correlated with common causes of mortality in southern sea otters, including cardiomyopathy, acanthocephalan (Profilicollis spp.) peritonitis, systemic protozoal infection (Toxoplasma gondii and Sarcocystis neurona), domoic acid intoxication, end-lactation syndrome, and shark bite. Microsatellite genetic markers were used to examine this association in 356 southern sea otters necropsied from 1998 to 2012. Significant associations with genetic diversity or familial relatedness (P<0.05) were observed for cardiomyopathy, acanthocephalan peritonitis, and sarcocystosis, and these associations varied by sex. Adult male cardiomyopathy cases (n=86) were more related than the null expectation (P<0.049). Conversely, female acanthocephalan peritonitis controls (n=110) were more related than the null expectation (P<0.004). Including genetic diversity as a predictor for fatal acanthocephalan peritonitis in the multivariate logistic model significantly improved model fit; lower genetic diversity was associated with reduced odds of sea otter death due to acanthocephalan peritonitis. Finally, male sarcocystosis controls (n=158) were more related than the null expectation (P<0.011). Including genetic diversity in the multivariate logistic model for fatal S. neurona infection improved model fit; lower genetic diversity was associated with increased odds of sea otter death due to S. neurona. Our study suggests that genetic diversity and familial relatedness, in conjunction with other factors such as age and sex, may influence outcome (survival or death) in relation to several common southern sea otter diseases. Our findings can inform policy for conservation management, such as potential reintroduction efforts, as part of species recovery.

Protected area use by two sympatric marine predators repopulating their historical range

As large carnivores recover from over-exploitation, managers often lack evidence-based information on species habitat requirements and the efficacy of management practices, particularly where species repopulate areas from which they have long been extirpated. We investigated the movement and habitat use by 2 semi-aquatic carnivores (Australian fur seals Arctocephalus pusillus doriferus and New Zealand fur seals A. forsteri) at the northern end of their distributions in Australia, where after a long absence both are recolonising their historic range. We also assessed male fur seal habitat use overlap with terrestrial and marine protected areas (PAs). While at the margin of the range during winter and early spring, the males remained inshore close to terrestrial sites and where interactions with humans often occur. From early spring, the males from the range margin showed uniform movement toward colonies in the core of the species’ range prior to their breeding seasons. This contrasts with males tracked from the core of the species’ range that returned periodically to colonies during the year, and highlights the importance of range-wide monitoring of a species to inform conservation planning. Habitat use by some males included over 90% of a marine PA at the margin of the species’ range. Most terrestrial haul-outs used were within terrestrial PAs, while sites not protected were on the margin of the range. Despite wide-ranging habits, their dependence on coastal sites, where human access and activities can be regulated and more readily enforced, suggests that terrestrial and marine PAs will continue to play an important role in managing the recovery of these fur seals.

Informing sea otter reintroduction through habitat and human interaction assessment

Sea otters Enhydra lutris have been absent from Oregon, USA, following their extirpation over a century ago. Stakeholder groups and native tribes are advocating for reintroduction to restore historic populations. We investigated the potential for successful reintroduction by: (1) estimating expected equilibrium sea otter densities as a function of habitat variables to assess sea otter habitat in Oregon; and (2) spatially relating areas of high expected densities to human activities (e.g. fisheries, recreation, vessel activity, protected areas) to anticipate potential disturbance or fishery resource competition. We estimated that 4538 (1742-8976; 95% CI) sea otters could exist in Oregon, with higher expected abundance (N = 1551) and densities (x̄ = 2.45 km-2) within the southern region. Most core habitat areas (97%), representing clusters of high expected densities, overlapped with some form of human activity. While commercial shipping and tow lanes overlapped little (1%) with core habitat areas, recreational activities (58%) and fisheries (76%) had a higher degree of overlap, posing higher disturbance risk. We anticipate higher resource competition potential with the commercial red sea urchin fishery (67% of harvest areas) than the commercial Dungeness crab fishery (9% of high-catch crabbing grounds). Our study presents the first published carrying capacity estimate for sea otters in Oregon and can provide population recovery targets, focus attention on ecological and socioeconomic considerations, and help to inform a recovery plan for a resident sea otter population. Our findings suggest current available habitat may be sufficient to support a sea otter population, but resource managers may need to further investigate and consider whether current human activities might conflict with reestablishment in Oregon, if plans for a reintroduction continue.

Exposure to domoic acid is an ecological driver of cardiac disease in southern sea otters✰

Harmful algal blooms produce toxins that bioaccumulate in the food web and adversely affect humans, animals, and entire marine ecosystems. Blooms of the diatom Pseudo-nitzschia can produce domoic acid (DA), a toxin that most commonly causes neurological disease in endothermic animals, with cardiovascular effects that were first recognized in southern sea otters. Over the last 20 years, DA toxicosis has caused significant morbidity and mortality in marine mammals and seabirds along the west coast of the USA. Identifying DA exposure has been limited to toxin detection in biological fluids using biochemical assays, yet measurement of systemic toxin levels is an unreliable indicator of exposure dose or timing. Furthermore, there is little information regarding repeated DA exposure in marine wildlife. Here, the association between long-term environmental DA exposure and fatal cardiac disease was investigated in a longitudinal study of 186 free-ranging sea otters in California from 2001 - 2017, highlighting the chronic health effects of a marine toxin. A novel Bayesian spatiotemporal approach was used to characterize environmental DA exposure by combining several DA surveillance datasets and integrating this with life history data from radio-tagged otters in a time-dependent survival model. In this study, a sea otter with high DA exposure had a 1.7-fold increased hazard of fatal cardiomyopathy compared to an otter with low exposure. Otters that consumed a high proportion of crab and clam had a 2.5- and 1.2-times greater hazard of death due to cardiomyopathy than otters that consumed low proportions. Increasing age is a well-established predictor of cardiac disease, but this study is the first to identify that DA exposure affects the risk of cardiomyopathy more substantially in prime-age adults than aged adults. A 4-year-old otter with high DA exposure had 2.3 times greater risk of fatal cardiomyopathy than an otter with low exposure, while a 10-year old otter with high DA exposure had just 1.2 times greater risk. High Toxoplasma gondii titers also increased the hazard of death due to heart disease 2.4-fold. Domoic acid exposure was most detrimental for prime-age adults, whose survival and reproduction are vital for population growth, suggesting that persistent DA exposure will likely impact long-term viability of this threatened species. These results offer insight into the pervasiveness of DA in the food web and raise awareness of under-recognized chronic health effects of DA for wildlife at a time when toxic blooms are on the rise.

Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.

Assessing anthropogenic risk to sea otters (Enhydra lutris nereis) for reintroduction into San Francisco Bay

Southern sea otters have been actively managed for their conservation and recovery since listing on the federal Endangered Species Act in 1977. Still, they remain constrained to a geographically small area on the central coast of California relative to their former coast-wide range, with population numbers far below those of the estimated optimal sustainable population size. Species managers have discussed reintroducing southern sea otters into parts of their historic range to facilitate sustained population growth and geographic range expansion. San Francisco Bay (SFB), historically home to several thousand sea otters, is one location identified as a candidate release site for these reintroductions. The return of sea otters to SFB could bring benefits to local ecosystem restoration and tourism, in addition to spurring sea otter population growth to meet recovery goals. However, this is a highly urbanized estuary, so sea otters could also be exposed to serious anthropogenic threats that would challenge a successful reintroduction. In light of these potential detriments we performed a spatially-explicit risk assessment to analyze the suitability of SFB for southern sea otter reintroduction. We looked at threats to sea otters specific to SFB, including: the impacts of vessel traffic from commercial shipping, high-speed ferries, and recreational vessels; environmental contaminants of methylmercury and polychlorinated biphenyls; major oil spills; and commercial fishing. Factors that influenced the relative threat imposed by each stressor included the spatio-temporal extent and intensity of the stressor and its mitigation potential. Our analysis revealed the complex spatial and temporal variation in risk distribution across the SFB. The type and magnitude of anthropogenic risk was not uniformly distributed across the study area. For example, the central SFB housed the greatest cumulative risk, where a high degree of vessel traffic and other stressors occurred in conjunction. The individual stressors that contributed to this risk score varied across different parts of the study area as well. Whereas vessel traffic, particularly of fast ferries, was a high scoring risk factor in in the north and central bay, in the south bay it was environmental contaminants that caused greater risk potential. To help identify areas within the study area that managers might want to target for release efforts, the spatially-explicit risk map revealed pockets of SFB that could provide both suitable habitat and relatively low overall risk. However in some cases these were adjacent or in close proximity to identified high-risk portions of habitat in SFB. This predictive suitability and risk assessment can be used by managers to consider the spatial distribution of potential threats, and risk abatement that may be necessary for sea otters to re-occupy their historic home range in SFB.

A new selection criterion for statistical home range estimation

The home range of an animal describes the geographic area where this individual spends most of the time while doing its usual activities. From a statistical viewpoint, the problem of home range estimation can be considered as a set estimation one. In the ecological literature, there are a variety of home range estimators. We address the open question of choosing the 'best' home range from a collection of them constructed on the same sample. We introduce the penalized overestimation ratio, a numerical index to rank the estimated home ranges. The key idea is to balance the excess area covered by the estimator (with respect to the sample) and a shape descriptor measuring the over-adjustment of the home range to the data. To our knowledge, apart from computing the home range area, our ranking procedure is the first one both applicable to real data and to any type of home range estimator. Further, optimization of the selection index provides a way to select the tuning parameters of nonparametric home ranges. For illustration purposes, we apply our selection proposal to a dataset of a Mongolian wolf and we carry out a simulation study.

Robust age estimation of southern sea otters from multiple morphometrics

Reliable age estimation is an essential tool to assess the status of wildlife populations and inform successful management. Aging methods, however, are often limited by too few data, skewed demographic representation, and by single or uncertain morphometric relationships. In this study, we synthesize age estimates in southern sea otters Enhydra lutris nereis from 761 individuals across 34 years of study, using multiple noninvasive techniques and capturing all life stages from 0 to 17 years of age. From wild, stranded, and captive individuals, we describe tooth eruptions, tooth wear, body length, nose scarring, and pelage coloration across ontogeny and fit sex-based growth functions to the data. Dental eruption schedules provided reliable and identifiable metrics spanning 0.3-9 months. Tooth wear was the most reliable predictor of age of individuals aged 1-15 years, which when combined with total length, explained >93% of observed age. Beyond age estimation, dental attrition also indicated the maximum lifespan of adult teeth is 13‒17 years, corresponding with previous estimates of life expectancy. Von Bertalanffy growth function model simulations of length at age gave consistent estimates of asymptotic lengths (male Loo  = 126.0‒126.8 cm, female Loo  = 115.3‒115.7 cm), biologically realistic gestation periods (t 0 = 115 days, SD = 10.2), and somatic growth (male k = 1.8, SD = 0.1; female k = 2.1, SD = 0.1). Though exploratory, we describe how field radiographic imaging of epiphyseal plate development or fusions may improve aging of immature sea otters. Together, our results highlight the value of integrating information from multiple and diverse datasets to help resolve conservation problems.

Species recovery and recolonization of past habitats: lessons for science and conservation from sea otters in estuaries

Recovering species are often limited to much smaller areas than they historically occupied. Conservation planning for the recovering species is often based on this limited range, which may simply be an artifact of where the surviving population persisted. Southern sea otters (Enhydra lutris nereis) were hunted nearly to extinction but recovered from a small remnant population on a remote stretch of the California outer coast, where most of their recovery has occurred. However, studies of recently-recolonized estuaries have revealed that estuaries can provide southern sea otters with high quality habitats featuring shallow waters, high production and ample food, limited predators, and protected haul-out opportunities. Moreover, sea otters can have strong effects on estuarine ecosystems, fostering seagrass resilience through their consumption of invertebrate prey. Using a combination of literature reviews, population modeling, and prey surveys we explored the former estuarine habitats outside the current southern sea otter range to determine if these estuarine habitats can support healthy sea otter populations. We found the majority of studies and conservation efforts have focused on populations in exposed, rocky coastal habitats. Yet historical evidence indicates that sea otters were also formerly ubiquitous in estuaries. Our habitat-specific population growth model for California's largest estuary-San Francisco Bay-determined that it alone can support about 6,600 sea otters, more than double the 2018 California population. Prey surveys in estuaries currently with (Elkhorn Slough and Morro Bay) and without (San Francisco Bay and Drakes Estero) sea otters indicated that the availability of prey, especially crabs, is sufficient to support healthy sea otter populations. Combining historical evidence with our results, we show that conservation practitioners could consider former estuarine habitats as targets for sea otter and ecosystem restoration. This study reveals the importance of understanding how recovering species interact with all the ecosystems they historically occupied, both for improved conservation of the recovering species and for successful restoration of ecosystem functions and processes.

Measures of effective population size in sea otters reveal special considerations for wide-ranging species

Conservation genetic techniques and considerations of the evolutionary potential of a species are increasingly being applied to species conservation. For example, effective population size (N e) estimates are useful for determining the conservation status of species, yet accurate estimates of current N e remain difficult to obtain. The effective population size can contribute to setting federal delisting criteria, as was done for the southern sea otter (Enhydra lutris nereis). After being hunted to near extinction during the North Pacific fur trade, the southern sea otter has recovered over part of its former range, but remains at relatively low numbers, making it desirable to obtain accurate and consistent estimates of N e. Although theoretical papers have compared the validity of several methods, comparisons of estimators using empirical data in applied conservation settings are limited. We combined thirteen years of demographic and genetic data from 1,006 sea otters to assess multiple N e estimators, as well as temporal trends in genetic diversity and population genetic structure. Genetic diversity was low and did not increase over time. There was no evidence for distinct genetic units, but some evidence for genetic isolation by distance. In particular, estimates of N e based on demographic data were much larger than genetic estimates when computed for the entire range of the population, but were similar at smaller spatial scales. The discrepancy between estimates at large spatial scales could be driven by cryptic population structure and/or individual differences in reproductive success. We recommend the development of new delisting criteria for the southern sea otter. We advise the use of multiple estimates of N e for other wide-ranging species, species with overlapping generations, or with sex-biased dispersal, as well as the development of improved metrics of genetic assessments of populations.

Defining the risk landscape in the context of pathogen pollution: Toxoplasma gondii in sea otters along the Pacific Rim

Pathogens entering the marine environment as pollutants exhibit a spatial signature driven by their transport mechanisms. The sea otter (Enhydra lutris), a marine animal which lives much of its life within sight of land, presents a unique opportunity to understand land-sea pathogen transmission. Using a dataset on Toxoplasma gondii prevalence across sea otter range from Alaska to California, we found that the dominant drivers of infection risk vary depending upon the spatial scale of analysis. At the population level, regions with high T. gondii prevalence had higher human population density and a greater proportion of human-dominated land uses, suggesting a strong role for population density of the felid definitive host of this parasite. This relationship persisted when a subset of data were analysed at the individual level: large-scale patterns in sea otter T. gondii infection prevalence were largely explained by individual exposure to areas of high human housing unit density, and other landscape features associated with anthropogenic land use, such as impervious surfaces and cropping land. These results contrast with the small-scale, within-region analysis, in which age, sex and prey choice accounted for most of the variation in infection risk, and terrestrial environmental features provided little variation to help in explaining observed patterns. These results underscore the importance of spatial scale in study design when quantifying both individual-level risk factors and landscape-scale variation in infection risk.