M. Bradley Hanson

Distinguishing the Impacts of Inadequate Prey and Vessel Traffic on an Endangered Killer Whale (Orcinus orca) Population

Managing endangered species often involves evaluating the relative impacts of multiple anthropogenic and ecological pressures. This challenge is particularly formidable for cetaceans, which spend the majority of their time underwater. Noninvasive physiological approaches can be especially informative in this regard. We used a combination of fecal thyroid (T3) and glucocorticoid (GC) hormone measures to assess two threats influencing the endangered southern resident killer whales (SRKW; Orcinus orca) that frequent the inland waters of British Columbia, Canada and Washington, U.S.A. Glucocorticoids increase in response to nutritional and psychological stress, whereas thyroid hormone declines in response to nutritional stress but is unaffected by psychological stress. The inadequate prey hypothesis argues that the killer whales have become prey limited due to reductions of their dominant prey, Chinook salmon (Oncorhynchus tshawytscha). The vessel impact hypothesis argues that high numbers of vessels in close proximity to the whales cause disturbance via psychological stress and/or impaired foraging ability. The GC and T3 measures supported the inadequate prey hypothesis. In particular, GC concentrations were negatively correlated with short-term changes in prey availability. Whereas, T3 concentrations varied by date and year in a manner that corresponded with more long-term prey availability. Physiological correlations with prey overshadowed any impacts of vessels since GCs were lowest during the peak in vessel abundance, which also coincided with the peak in salmon availability. Our results suggest that identification and recovery of strategic salmon populations in the SRKW diet are important to effectively promote SRKW recovery.

Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

Estimation of a Killer Whale (Orcinus orca) Population's Diet Using Sequencing Analysis of DNA from Feces.

Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population’s summer diet.

The Relationship between Vessel Traffic and Noise Levels Received by Killer Whales (Orcinus orca)

Whale watching has become increasingly popular as an ecotourism activity around the globe and is beneficial for environmental education and local economies. Southern Resident killer whales (Orcinus orca) comprise an endangered population that is frequently observed by a large whale watching fleet in the inland waters of Washington state and British Columbia. One of the factors identified as a risk to recovery for the population is the effect of vessels and associated noise. An examination of the effects of vessels and associated noise on whale behavior utilized novel equipment to address limitations of previous studies. Digital acoustic recording tags (DTAGs) measured the noise levels the tagged whales received while laser positioning systems allowed collection of geo-referenced data for tagged whales and all vessels within 1000 m of the tagged whale. The objective of the current study was to compare vessel data and DTAG recordings to relate vessel traffic to the ambient noise received by tagged whales. Two analyses were conducted, one including all recording intervals, and one that excluded intervals when only the research vessel was present. For all data, significant predictors of noise levels were length (inverse relationship), number of propellers, and vessel speed, but only 15% of the variation in noise was explained by this model. When research-vessel-only intervals were excluded, vessel speed was the only significant predictor of noise levels, and explained 42% of the variation. Simple linear regressions (ignoring covariates) found that average vessel speed and number of propellers were the only significant correlates with noise levels. We conclude that vessel speed is the most important predictor of noise levels received by whales in this study. Thus, measures that reduce vessel speed in the vicinity of killer whales would reduce noise exposure in this population.

Twenty-Five Years of Rehabilitation of Odontocetes Stranded in Central and Northern California, 1977 to 2002

Rehabilitation of stranded cetaceans is receiving increasing attention and involves considerable financial and personnel resources, although the survival rate appears to be low. To evaluate rehabilitation success, we examined 25 years (1977 to 2002) of data on live-stranded odontocetes (n = 70) from northern California that were rescued for rehabilitation. Thirty-five animals (50%) died within the first 24 h of being rescued, 13 animals (19%) died within the first week, seven animals (10%) died within a month, and five animals (7%) survived longer than one month, but subsequently died. Three animals (4%) were deemed nonreleasable and placed into captivity, whereas five animals (7%) were released back into the wild. Two animals (3%) were relocated and released; these animals were never seen again. Clinical signs were nonspecific, and it was difficult to differentiate medical problems that resulted from stranding from those that may have caused the stranding. Causes of death included pneumonia (n = 16), septicemia (n = 6), encephalitis (n = 3), maternal separation (n = 7), and blunt trauma (n = 6). No morbilliviral inclusion bodies or typically associated lesions were detected. Cause of death was unknown for 23 cases. Myocardial degeneration and contraction band necrosis (n = 9) and nephrosis (n = 4) probably resulted from the stress of stranding. Ulcerative glossitis and esophagitis were observed in most animals that were tube-fed in rehabilitation. Four animals that had been in rehabilitation for more than 1 wk had rhabdomyolysis and one had scoliosis. These data indicate that the success of rehabilitating and releasing stranded odontocetes in California is minimal, and the stress of stranding and rehabilitation in addition to pre-existing disease can result in morbidity and mortality. Of the animals released, two common dolphins (Delphinus delphis) and one harbor porpoise (Phocoena phocoena) were tagged with satellite transmitters. Transmissions were received for up to 5 mo after release. Increased use of telemetry is essential for post-release monitoring and evaluating rehabilitation success.

Respiratory Microbiome of Endangered Southern Resident Killer Whales and Microbiota of Surrounding Sea Surface Microlayer in the Eastern North Pacific

In the Salish Sea, the endangered Southern Resident Killer Whale (SRKW) is a high trophic indicator of ecosystem health. Three major threats have been identified for this population: reduced prey availability, anthropogenic contaminants, and marine vessel disturbances. These perturbations can culminate in significant morbidity and mortality, usually associated with secondary infections that have a predilection to the respiratory system. To characterize the composition of the respiratory microbiota and identify recognized pathogens of SRKW, exhaled breath samples were collected between 2006–2009 and analyzed for bacteria, fungi and viruses using (1) culture-dependent, targeted PCR-based methodologies and (2) taxonomically broad, non-culture dependent PCR-based methodologies. Results were compared with sea surface microlayer (SML) samples to characterize the respective microbial constituents. An array of bacteria and fungi in breath and SML samples were identified, as well as microorganisms that exhibited resistance to multiple antimicrobial agents. The SML microbes and respiratory microbiota carry a pathogenic risk which we propose as an additional, fourth putative stressor (pathogens), which may adversely impact the endangered SRKW population.

Modulation in Persistent Organic Pollutant Concentration and Profile by Prey Availability and Reproductive Status in Southern Resident Killer Whale Scat Samples

Persistent organic pollutants (POPs), specifically PCBs, PBDEs, and DDTs, in the marine environment are well documented, however accumulation and mobilization patterns at the top of the food-web are poorly understood. This study broadens the understanding of POPs in the endangered Southern Resident killer whale population by addressing modulation by prey availability and reproductive status, along with endocrine disrupting effects. A total of 140 killer whale scat samples collected from 54 unique whales across a 4 year sampling period (2010-2013) were analyzed for concentrations of POPs. Toxicant measures were linked to pod, age, and birth order in genotyped individuals, prey abundance using open-source test fishery data, and pregnancy status based on hormone indices from the same sample. Toxicant concentrations were highest and had the greatest potential for toxicity when prey abundance was the lowest. In addition, these toxicants were likely from endogenous lipid stores. Bioaccumulation of POPs increased with age, with the exception of presumed nulliparous females. The exceptional pattern may be explained by females experiencing unobserved neonatal loss. Transfer of POPs through mobilization of endogenous lipid stores during lactation was highest for first-borns with diminished transfer to subsequent calves. Contrary to expectation, POP concentrations did not demonstrate an associated disruption of thyroid hormone, although this association may have been masked by impacts of prey abundance on thyroid hormone concentrations. The noninvasive method for measuring POP concentrations in killer whales through scat employed in this study may improve toxicant monitoring in the marine environment and promote conservation efforts.

Competing tradeoffs between increasing marine mammal predation and fisheries harvest of Chinook salmon

Many marine mammal predators, particularly pinnipeds, have increased in abundance in recent decades, generating new challenges for balancing human uses with recovery goals via ecosystem-based management. We used a spatio-temporal bioenergetics model of the Northeast Pacific Ocean to quantify how predation by three species of pinnipeds and killer whales (Orcinus orca) on Chinook salmon (Oncorhynchus tshawytscha) has changed since the 1970s along the west coast of North America, and compare these estimates to salmon fisheries. We find that from 1975 to 2015, biomass of Chinook salmon consumed by pinnipeds and killer whales increased from 6,100 to 15,200 metric tons (from 5 to 31.5 million individual salmon). Though there is variation across the regions in our model, overall, killer whales consume the largest biomass of Chinook salmon, but harbor seals (Phoca vitulina) consume the largest number of individuals. The decrease in adult Chinook salmon harvest from 1975–2015 was 16,400 to 9,600 metric tons. Thus, Chinook salmon removals (harvest + consumption) increased in the past 40 years despite catch reductions by fisheries, due to consumption by recovering pinnipeds and endangered killer whales. Long-term management strategies for Chinook salmon will need to consider potential conflicts between rebounding predators or endangered predators and prey.

Assessing the coastal occurrence of endangered killer whales using autonomous passive acoustic recorders

Using moored autonomous acoustic recorders to detect and record the vocalizations of social odonotocetes to determine their occurrence patterns is a non-invasive tool in the study of these species in remote locations. Acoustic recorders were deployed in seven locations on the continental shelf of the U.S. west coast from Cape Flattery, WA to Pt. Reyes, CA to detect and record endangered southern resident killer whales between January and June of 2006-2011. Detection rates of these whales were greater in 2009 and 2011 than in 2006-2008, were most common in the month of March, and occurred with the greatest frequency off the Columbia River and Westport, which was likely related to the presence of their most commonly consumed prey, Chinook salmon. The observed patterns of annual and monthly killer whale occurrence may be related to run strength and run timing, respectively, for spring Chinook returning to the Columbia River, the largest run in this region at this time of year. Acoustic recorders provided a unique, long-term, dataset that will be important to inform future consideration of Critical Habitat designation for this U.S. Endangered Species Act listed species.

Coping with variation in aerial survey protocol for line-transect sampling

Altitude and flight speed affect detection probability and they typically vary during the course of most aerial surveys. We demonstrate how these sources of variation can be accommodated with covariates in a line-transect analysis using data from a pronghorn (Antilocapra americana) survey in Wyoming and a survey of Antarctic ice seals (Lobodon carcinophaga, Leptonychotes weddellii, Hydrurga leptonyx, Ommatophoca rossii). We also show how the likelihood for binned distance data can be modified to allow for variation in altitude. As an alternative, we develop an estimator for aerial line-transect sampling based on vertical angles rather than distance. With a small simulation study, we show that our estimators are unbiased and are preferable to using biased estimators based on fixed-distance intervals derived from average altitude.