In the spirit of so-called "sightability models" for estimating population abundance, we developed a Bayesian hierarchical model that combines survey counts for animals (or plants) and a separate data set for detection to account for individuals that were missed during surveys. Our case study consisted of harbor seal (Phoca vitulina richardii) aerial survey counts from 1996 to 2023 for the Prince William Sound (PWS) stock in Alaska and haul-out data from bio-logged individuals. Detection (i.e., haul-out probability) was modeled using logistic regression with temporally autocorrelated latent random effects. The probability of detection informed binomial count models, where true abundances were temporally autocorrelated Poisson models, leading to a logistic-binomial-Poisson hierarchical model. To speed computations, we coupled a two-stage sampling with first-order autoregressive (AR1) and random walk models for autocorrelation. We found time-of-year and time-from-low-tide to be the most important predictors for detection, and our population abundance analysis showed a significant decline (1996-2001), followed by an increase (2001-2015), and then another decline (2015-2023) for the PWS stock. Our approach can be used for other organisms and surveys that have separate detection and count data sets, such as those commonly used in sightability models, as part of long-term population monitoring programs.

Tidewater glacial fjords support the largest populations of harbor seals (Phoca vitulina richardii) in Alaska and are a prime destination for tour ships. Chronic disturbance from ships, however subtle, could impact long-term population stability. We examined variation in abundance and distribution of harbor seals on floating ice in Disenchantment Bay, Alaska, a tour ship destination for over a century with near daily visitation by ships in the spring/summer over the last decade. Counts of seals by aerial transect showed a sharp decline in May, prior to pupping and the first ships arriving; counts rebounded by the end of June remaining high until August. Seal distribution and abundance peaked in 5-7 tenths ice cover; total area of ice cover showed no effect. Despite regular flushing of seals by ships, we found no broad-scale patterns in seal abundance and distribution that could be explained by ship presence. We cannot rule out mechanisms of long-term disturbance, difficult to detect and that might explain notable differences with other, similar sites. Population declines at disturbed glacial sites and the still rising popularity of vessel-based tourism indicate a need for individual-based studies on how seals respond to the dynamics of glacial ice environments and human-caused stresses.

Monitoring plant and animal populations is an important goal for both academic research and management of natural resources. Successful management of populations often depends on obtaining estimates of their mean or total over a region. The basic problem considered in this paper is the estimation of a total from a sample of plots containing count data, but the plot placements are spatially irregular and non-randomized. Our application had counts from thousands of irregularly spaced aerial photo images. We used change-of-support methods to model counts in images as a realization of an inhomogeneous Poisson process that used spatial basis functions to model the spatial intensity surface. The method was very fast and took only a few seconds for thousands of images. The fitted intensity surface was integrated to provide an estimate from all unsampled areas, which is added to the observed counts. The proposed method also provides a finite area correction factor to variance estimation. The intensity surface from an inhomogeneous Poisson process tends to be too smooth for locally clustered points, typical of animal distributions, so we introduce several new overdispersion estimators due to poor performance of the classic one. We used simulated data to examine estimation bias and to investigate several variance estimators with overdispersion. A real example is given of harbor seal counts from aerial surveys in an Alaskan glacial fjord.

Tidewater glacial fjords in Alaska provide habitat for some of the largest aggregations of harbor seals (Phoca vitulina), with calved ice serving as platforms for birthing and nursing pups, molting, and resting. These fjords have also been popular destinations for tour ships for more than a century, with dramatic increases in vessel traffic since the 1980s. Seals on ice are known to flush into the water when approached by tour ships, but estimating the exposure to disturbance across populations is difficult. Using aerial transect sampling while simultaneously tracking vessel movements, we estimated the spatial overlap between seals on ice and cruise ships in Disenchantment Bay, Alaska, USA. By integrating previously estimated rates of disturbance as a function of distance with an ‘intensity surface’ modeled spatially from seal locations in the surveys, we calculated probabilities of seals flushing during three separate ship visits. By combining our estimate of seals flushed with a modeled estimate of the total fjord population, we predict that up to 14% of the seals (up to 11% of pups) hauled out would have flushed into the water, depending on the route taken by ships relative to seal aggregations. Such high potential for broad-scale disturbance by single vessels (when up to 4 ships visit per day) was unexpected and underscores the need to 1) better understand long-term effects of disturbance; 2) regularly monitor populations exposed to high vessel traffic; and 3) develop conservation measures to reduce seal-ship overlap.

Marine birds spend most of their lives at sea; consequently, it is important to evaluate where they spend time at sea, especially when breeding areas are not known or their breeding habits prevent study at colonies (e.g. solitary nesting species). In addition, assessing human impacts, including fisheries bycatch (e.g. Zydelis et al. 2009), oil spills (e.g. Carter & Kuletz 1995), pollution (e.g. Laist 1987) and climate change (e.g. Hoegh-Guldberg & Bruno 2010), is vital for a timely response to risks and successful conservation of marine birds.

Abstract The largest aggregations of harbor seals (Phoca vitulina) in Alaska, USA, haul out on floating ice in tidewater glacial fjords. Seals use these fjords in peak numbers during the critical periods of pupping, breeding, and molting when visits by tour ships also peak. Documented and suspected declines of harbor seals in fjords with rising vessel traffic underscore the need to better understand possible impacts, particularly in areas where ship visits have risen substantially in the past 2 decades. We examined the interruption of haul-out bouts of harbor seals due to approaching cruise ships in Disenchantment Bay, Alaska. We conducted observations from cruise ships and focused on disturbance of seals as evidenced by seals flushing into the water from the floating ice on which they rested. We investigated rate of flushing in relation to vessel distance, approach angle, group size, and seal type (mother, pup, or other). Using a survival-regression analysis, we found that the risk of disturbing harbor seals increased when ships approached within 500 m; seals approached as close as 100 m were 25 times more likely to enter the water than seals 500 m from a ship. Seals were 4 times more prone to enter the water when ships were approaching directly rather than passing abeam. Seals responded similarly regardless of group size or seal type. Energetic models indicated a potential to disrupt energy balance and cause thermal stress in disturbed pups if they spent >50% of their time in ice-chilled water. Studies at non-glacial sites suggest that pups spend 40–70% of their time in the water. Voluntary guidelines for approaching seals in Alaska recommend that cruise ships approach ≥91 m (100 yards), a distance at which we show 90% of seals would flush into the water. Our findings indicate a need to develop regulations to maintain a 500-m separation between cruise ships and seals in all Alaskan glacial fjords.

-The effects of radio transmitter attachment on foraging trip duration and reproductive success of breeding Chinstrap Penguins (Pygoscelis antarctica) were studied on Seal Island, South Shetland Islands, Antarctica. Attachment of transmitters having a cross-sectional area 0.9% that of the penguin had no significant effect on foraging trip duration, nest visit duration or the number of foraging trips per nest per day. Adults equipped with transmitters had significantly lower chick survival rates than control animals, however. This difference resulted from a higher nest failure rate of transmitter-equipped adults. Most of these failures occurred in the early part of the guard period. The average number of chicks raised to the creche stage in successful nests was similar for control and transmitter-equipped animals. Thus, chick mortality occurred as a result of failure of the entire nest (i.e., abandonment by the adults) rather than lowered chick survival in individual nests. Nests at which both members were equipped with transmitters failed at a higher rate than nests at which one member was equipped with a transmitter. The transmitters used in this study may be considered a maximum size to be used for foraging trip duration experiments of medium-sized penguins. CONDUCTA DE FORRAJEO Y tXITO REPRODUCTIVO EN PYGOSCEUIS ANTARCTICAEFECTO DE RADIOTRANSMISORES Sinopsis.-Se llev6 a cabo un estudio del efecto de radiotransmisores en la duraci6n de viajes de forrajeo y 6xito reproductivo en el pingffino Pygoscelis antarctica. El trabajo se llev6 a cabo en Seal Island, South Shetland. El radiotransmisor no tuvo efecto significativo en la duraci6n de los viajes de forrajeo, la duraci6n de las visitas a los nidos y el ndmero de viajes/ nido/dia. Los adultos equipados con radiotransmisores tuvieron una tasa de sobrevivencia de polluelos menor que el grupo control. La diferencia fue el resultado de una tasa de fracasos mayor en los pingfiinos equipados con transmisores. La mayoria de los fracasos de anidamiento ocurrieron temprano en el periodo de vigilancia. El nuimero promedio de polluelos criados hasta el etapa de "creche", en nidos exitosos, fue similar para el grupo ex'Current address: Institute of Marine Sciences, University of California, Santa Cruz, California 95064 USA. 2] D. A. Croll et al. J. Field Ornithol. Winter 1996 perimental y el control. La mortalidad de polluelos ocurrio como resultado del fracaso de nido per se (ej. abandono de este por parte de los adultos). Los nidos en donde ambos adultos tenian radiotransmisores tuvieron una tasa mayor de fracaso que aquellos nidos en donde tan solo uno de los adultos tenia transmisor. E1 transmisor uiilizado en este estudio pudiera considerarse del tamano maximo (9% del area del ave) a ser uiilizado en pinguinos de tamano mediano, para experimentos sobre la duracion de viajes de forrajeo. Use of radio telemetry permits measuring behavior in a manner not previously possible, often eliminating the need for long hours of vigil. It has been demonstrated, however, that attaching such devices to marine animals may significantly alter their behavior, leading to biased parameter estimates (e.g., Croll et al. 1991; Wanless et al. 1988; Wilson et al. 1986, 1989). The attachment of devices may lead to changes in behavior of the study animal through increased drag (Wilson et al. 1986) or the discomfort of the presence of the attached instrument package (Wilson et al. 1990). Croll et al. (1991) reported that attaching radio transmitters led to a significant increase in the duration of foraging trips of Chinstrap Penguins (Pygoscelis antarctica). It is important to understand the possible biases that might result from the use of animal-borne devices to collect behavioral information. Unfortunately, in many instances (e.g., diving behavior), it is difficult to assess accurately the impact of the attached device because comparable data from non-instrumented animals are not available. Some parameters, however, such as foraging trip duration and reproductive success, can be measured for birds with and without attached devices to assess instrument effects. The use of radio transmitters has been accepted by the CCAMLR (Commission for the Conservation of Antarctic Marine Living Resources) Ecosystem Monitoring Program (CEMP) as a standard method with which to monitor foraging trip duration in penguins (Scientific Committee for the Conservation of Antarctic Marine Living Resources (SC-CEMP) 1991) . In accepting this method, it was acknowledged that biases might potentially result from transmitter attachment, and that differences in foraging patterns might result from the attachment of transmitters to one or both members of a breeding pair. It was also noted that factors affecting variability in foraging trip duration should be examined to evaluate the utility of this method for monitoring ecosystem variability. This paper reports on: (1) the effects of radio transmitter attachment on nest attendance, foraging trip duration, nest failure and reproductive success in Chinstrap Penguins; (2) differences in these parameters when transmitters are applied to one or both members of a nest; and (3) variability in foraging patterns of penguins unencumbered by transmitters within the brood period. The present study extends our earlier work (Croll et al. 1991).

Central-place foragers that must return to a breeding site to deliver food to offspring are faced with trade-offs between prey patch quality and distance from the colony. Among colonial ani- mals, pinnipeds and seabirds may have different provisioning strategies, due to differences in their ability to travel and store energy. We compared the foraging areas of lactating Antarctic fur seals and chinstrap penguins breeding at Seal Island, Antarctica, to investigate whether they responded differ- ently to the distribution of their prey (Antarctic krill and myctophid fish) and spatial heterogeneity in their habitat. Dense krill concentrations occurred in the shelf region near the colony. However, only brooding penguins, which are expected to be time-minimizers because they must return frequently with whole food for their chicks, foraged mainly in this proximal shelf region. Lactating fur seals and incubating penguins, which can make longer trips to increase energy gain per trip, and so are expected to be energy-maximizers, foraged in the more distant (>20 km from the island) slope and oceanic regions. The shelf region was characterized by more abundant, but lower-energy-content immature krill, whereas the slope and oceanic regions had less abundant but higher-energy-content gravid krill, as well as high-energy-content myctophids. Furthermore, krill in the shelf region under- took diurnal vertical migration, whereas those in the slope and oceanic regions stayed near the sur- face throughout the day, which may enhance the capture rate for visual predators. Therefore, we sug- gest that the energy-maximizers foraged in distant, but potentially more profitable feeding regions, while the time-minimizers foraged in closer, but potentially less profitable regions. Thus, time and energy constraints derived from different provisioning strategies may result in sympatric colonial predator species using different foraging areas, and as a result, some central-place foragers use sub- optimal foraging habitats, in terms of the quality or quantity of available prey.

Environmental data are spatial, temporal, and often come with many zeros. In this paper, we included space‐time random effects in zero‐inflated Poisson (ZIP) and ‘hurdle’ models to investigate haulout patterns of harbor seals on glacial ice. The data consisted of counts, for 18 dates on a lattice grid of samples, of harbor seals hauled out on glacial ice in Disenchantment Bay, near Yakutat, Alaska. A hurdle model is similar to a ZIP model except it does not mix zeros from the binary and count processes. Both models can be used for zero‐inflated data, and we compared space‐time ZIP and hurdle models in a Bayesian hierarchical model. Space‐time ZIP and hurdle models were constructed by using spatial conditional autoregressive (CAR) models and temporal first‐order autoregressive (AR(1)) models as random effects in ZIP and hurdle regression models. We created maps of smoothed predictions for harbor seal counts based on ice density, other covariates, and spatio‐temporal random effects. For both models predictions around the edges appeared to be positively biased. The linex loss function is an asymmetric loss function that penalizes overprediction more than underprediction, and we used it to correct for prediction bias to get the best map for space‐time ZIP and hurdle models. Published in 2007 by John Wiley & Sons, Ltd.

This report does not constitute a publication and is for information only. All data herein are to be considered provisional. 1) Behavioral response of seals to approaching vessels (fine scale); 2) Variation in local seal abundance and distribution in relation to environmental factors including vessel traffic (medium scale); and 3) Comparing variation in seal abundance between nearby bays with and without cruise ship traffic (large scale) The mention of trade names, commercial products, or vendors in this report does not constitute endorsement or recommendation for use by the United States Government ii Executive Summary Cruise tourism in Alaska has been growing rapidly since the early 1970s. Over the last decade there has been increasing concern about possible impacts on sensitive coastal ecosystems. Attention has focused most recently on the possible effects of tour vessels, particularly cruise ships, on subsistence resources that have been critically important to Alaska Natives for many generations. Harbor seals that haul out year-round on floating ice near tidewater glaciers are one such resource of concern because their habitat is a popular destination for tourism. This study examined the potential effects of cruise ships on the behavior, abundance, and distribution of harbor seals in Disenchantment Bay, Alaska, from early May 2002, at the onset of seal pupping, to mid-August 2002, during the molting season. Analyses presented here of the behavioral observations – conducted from cruise ships – indicate that the likelihood of harbor seals vacating ice floes rose steeply when ships approached to less than 500 m; seals approached by a ship at 100 m were 25 times more likely to enter the water than seals approached at 500 m. Seals were also four times more prone to enter the water when ships approached them directly rather than passing abeam. The proportion of seals that entered the water when ships passed within 200 m was nearly 75% compared to less than 10% entering the water at distances where seals showed no apparent overt response to vessels (i.e., > 600 m). Analysis of aerial strip-transect sampling (by video playback) showed pronounced shifts in seal abundance, with a decline of 75% in mid-May during early pup-rearing. Abundance rebounded to peak levels in late June, as cruise ship traffic reached maximum levels. Sightings of mother-pup pairs also peaked in late June. Seal abundance then stabilized at near-peak levels from late June until the end of the study in early August. …

Whether parents are able to adapt food gathering to rising offspring demands, or if they are controlled largely by extrinsic factors, is important for understanding key limits on fitness. Over seven breeding seasons, we studied the provisioning behavior of chinstrap penguins, Pygoscelis antarctica, at Seal Island, Antarctica, during parents' transition to leave broods of one or two chicks unguarded. By measuring the frequency, duration, and diel timing of foraging trips and the quantity of prey brought to chicks, we examined the extent to which variation in parents' feeding behavior could be attributed to provisioning costs which increase with chick growth. Estimates of the energy content of food loads were combined with foraging patterns and brood requirements to model parents' seasonal provisioning budget. The frequency of foraging trips increased from the guard to post-guard phase and was higher, and the seasonal effect larger, in parents with two chicks. The duration of overnight trips (~16 h) increased with seasonally increasing night length; diurnal trip duration (~8 h) showed no seasonal pattern. Birds exhibited a seasonal shift to diurnal foraging, a trend that was generally weaker in parents of smaller broods. Food loads increased with chick mass only in parents of one chick; parents of two chicks had larger but more constant food loads. Based on per trip calculations, parents foraging overnight could not have delivered to two-chick broods enough food to meet their demands unless chicks were small. Diurnal foragers (regardless of brood size) and overnight foragers with one chick could meet brood demands at chicks' peak mass. The combined daily effort of parents indicated that mated pairs on average had ample resources to meet chick demands through most of rearing. A brief period when demands could not be met was predicted in two-chick broods just before chicks were left unguarded and again as they neared fledging. Our findings suggest that penguins both increased provisioning frequency and favored foraging under higher light intensity in conjunction with increasing chick demands, tactics which required parents to leave chicks unattended. The ability to maintain intrinsic control over provisioning has bearing on how penguins may be limited by extrinsic constraints. Prey surveys conducted annually near colonies show abundant resources 10–20 km offshore with no consistent seasonal shifts in abundance. These findings support a prominent role for intrinsic factors in the foraging decisions of chinstrap penguins.

Chinstrap penguins (Pygoscelis antarctica) normally lay two eggs, but brood size is often reduced by mortality during incubation or after hatching. We hypothesized that this variation in brood size would affect the parents’ foraging behavior and their chick provisioning performance. We studied patterns of adult foraging trip duration and frequency, food load delivery, and chick growth rates in relation to brood size during the guard phase in four breeding seasons (1991–1994) on Seal Island, Antarctica. Within a given year, parents with two chicks made more frequent foraging trips to sea and may have transported larger food loads to the nest; however, the duration of foraging trips was unrelated to brood size. Overall, parents with two chicks spent ∼15% more time at sea than parents with only one chick. Both the frequency and duration of foraging trips varied between years. Foraging trip duration may partly reflect the birds’ foraging radius, which probably varies with time in response to shifts in krill distribution. Chick growth rate varied betwen years, but was related to brood size only in 1992, when chicks from two-chick broods grew significantly more slowly than chicks from one-chick broods. Food loads transported to chicks, as well as chick growth rates, were highest in 1994, when concurrent hydroacoustic studies indicated that regional krill biomass was severely depressed. This apparent anomaly suggests that the spatial scale of the krill survey may have been too coarse to detect some high-density krill aggregations within the penguins’ foraging range.