The recent rise of 'omics and other molecular research technologies alongside improved techniques for tissue preservation have broadened the scope of marine mammal research. Collecting biological samples from wild marine mammals is both logistically challenging and expensive. To enhance the power of marine mammal research, great effort has been made in both the field and the laboratory to ensure the scientific integrity of samples from collection through processing, supporting the long-term use of precious samples across a broad range of studies. However, identifying the best methods of sample preservation can be challenging, especially as this technological toolkit continues to evolve and expand. Standardizing best practices could maximize the scientific value of biological samples, foster multi-institutional collaborative efforts across fields, and improve the quality of individual studies by removing potential sources of error from the collection, handling, and preservation processes. With these aims in mind, we summarize relevant literature, share current expert knowledge, and suggest best practices for sample collection and preservation. This manuscript is intended as a reference resource for scientists interested in exploring collaborative studies and preserving samples in a suitable manner for a broad spectrum of analyses, emphasizing support for 'omics technologies.

Chemical pollution can degrade aquatic ecosystems. Chinook salmon in contaminated habitats are vulnerable to health impacts from toxic exposures. Few studies have been conducted on adverse health outcomes associated with current levels and mixtures of contaminants. Fewer still address effects specific to the juvenile life-stage of salmonids. The present study evaluated contaminant-related effects from dietary exposure to environmentally relevant concentrations and mixture profiles in juvenile Chinook salmon from industrialized waterways in the U.S. Pacific Northwest using two end points: growth assessment and disease susceptibility. The dose and chemical proportions were reconstituted based on environmental sampling and analysis using the stomach contents of juvenile Chinook salmon recently collected from contaminated, industrialized waterways. Groups of fish were fed a mixture with fixed proportions of 10 polychlorinated biphenyls (PCBs), 3 dichlorodiphenyltrichloroethanes (DDTs), and 13 polycyclic aromatic hydrocarbons (PAHs) at five concentrations for 35 days. These contaminant compounds were selected because of elevated concentrations and the widespread presence in sediments throughout industrialized waterways. Fork length and otolith microstructural growth indicators were significantly reduced in fish fed environmentally relevant concentrations of these contaminants. In addition, contaminant-exposed Chinook salmon were more susceptible to disease during controlled challenges with the pathogen Aeromonas salmonicida. Our results indicate that dietary exposure to contaminants impairs growth and immune function in juvenile Chinook salmon, thereby highlighting that current environmental exposure to chemicals of potential management concern threatens the viability of exposed salmon.

Abstract Ecosystem-based fisheries management requires an understanding of the interactions between managed and unmanaged species and the connections they have with their habitats. Although aquatic plants are known to provide important shelter for a variety of species, an often-overlooked component is the extent to which primary producers contribute to their diet. In this study, we reconstructed the dietary connections between 18 consumers, including vulnerable rockfish species, and several primary producers. Two of these primary producers, Zostera marina (eelgrass) and Nereocystis luetkeana (bull kelp), have experienced spatial variation in abundance and substantial declines, respectively, within Puget Sound, Washington, USA. Using stable isotope ratio data, we estimated that both bull kelp and Smithora naiadum (an epiphytic algae) were the most important sources of carbon in consumer diets, followed by particulate organic matter and eelgrass. Our results indicated strong dietary connections for certain consumers, such that epiphytic algae was found to comprise greater than 40% of the diets of copper rockfish (Sebastes caurinus), while bull kelp contributed most to the diets of Pacific staghorn sculpin (Leptocottus armatus) and quillback rockfish (S. maliger). For several consumers, we observed habitat-mediated prey choice because the relative importance of bull kelp or epiphytic algae in their diets increased when these consumers were collected from sites dominated by kelp or eelgrass, respectively. Understanding the strength of these trophic relationships is an important step for predicting ecosystem consequences following perturbations within these habitats, and such information is vital to managers making decisions related to the conservation of valuable populations.

The Lower Duwamish River is a highly industrialized waterway flowing into the densely urbanized Puget Sound waterfront of Seattle, Washington, USA. The river has been profoundly altered from its natural state following more than a century of channelization, recurrent dredging, shoreline armoring, and pollution discharges. As part of a Natural Resource Damage Assessment addressing historical pollution at three designated Superfund sites (i.e., the assessment area), juvenile Pacific staghorn sculpin (Leptocottus armatus) were sampled throughout the lower river in order to evaluate injury from exposure to polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDTs), and butyltins (BTs). Sculpin live in close association with the river sediments within and upriver of the assessment area. Fish were collected for analysis of contaminant concentrations in composited whole bodies and stomach contents, as well as individual fish health metrics including daily somatic growth rates measured from otoliths. Sediment contaminant concentrations were also measured at sites near to fishing locations. Fish growth rates varied from 0.65 to 1.05 mm/day, and were significantly lower at unremediated downriver sites compared to upriver and remediated locations. Sculpin growth rates were negatively correlated with concentrations of PCBs in fish bodies, PAHs in stomach contents, as well as PCBs, DDTs and PAHs in sediment. Mixed effects models for whole-body and stomach content contaminants showed positive correlations between growth rate and water temperature. Temperature was not a significant confounding variable for the relationship between growth rate and sediment contaminants. Overall, these results show that juvenile sculpin are harmed by contaminant exposure in the Lower Duwamish River. Furthermore, this study demonstrates the utility of using paired biological and chemical indicators of pollutant-induced injury in a resident fish to inform a complex Natural Resource Damage Assessment and associated restoration efforts.

Effective species management often requires understanding patterns of movement and habitat use. A common approach in identifying where individuals reside relies upon chemical tracers from the environment that are incorporated into an individual's tissues. For fish, isotopes in their otoliths, specifically the portion of their otolith formed during their larval stage, have been used to identify the natal origin. Complicating this work, however, is the fact that during this life stage, there is a shift in the source of isotopes deposited onto the growing otolith from maternally to environmentally derived. The objective of this study was to identify the portion of the otolith representing this transition to environmentally derived isotopes so as to accurately investigate questions of natal origin for a threatened population of fall Chinook salmon (Oncorhynchus tshawytscha). We exposed developing larvae to four treatments that differed in terms of their water strontium isotope ratio (Sr-87/Sr-86) and used change-point analysis of otolith Sr-87/Sr-86 and strontium to calcium ratio (Sr/Ca) to identify the otolith radius corresponding to the transition to environmentally derived isotopes. Our results indicated this transition occurred, on average, at 132 mu m (Sr-87/Sr-86; +/- 50 mu m standard deviation) and 127 mu m (Sr/Ca; +/- 29 mu m) from the otolith core, which corresponded to the developmental time between hatching and exogenous feeding. A substantial proportion of our otoliths (i.e., 61%) did not show convergence between otolith and water Sr-87/Sr-86 by the end of the 113-day experiment, which was likely due to the dietary contribution of marine-based feed. Therefore, we were unable to recommend an otolith radius to target for the purposes of reconstructing natal origin apart from being beyond approximately 130 mu m.

Declines in fish body size have been reported in many populations and these changes likely have important ramifications for the sustainability of harvested species and ecosystem function.Pacific hake, Merluccius productus, have shown declines in size over the last several decades for populations located in Puget Sound (PS), Washington, U.S.A., and Strait of Georgia (SoG), British Columbia, Canada.To examine this decrease in size, we used archived otoliths from both populations to assess when the decrease in somatic growth occurred and explored what factors and processes might explain the decline, including otolith microchemistry to infer the environment experienced by fish at different ages.Results indicated that substantial changes in juvenile somatic growth have occurred across decades.The divergence in body size occurred in the second summer, whereby SoG fish grew, on average, 18% more than PS fish.Within the PS population, somatic growth differed significantly among fish that hatched in the 1980s, 1990s, and 2010s, such that the more recently hatched fish grew 26% more in their first summer and 71% less in their second summer relative to those that hatched in the 1980s.In comparison, growth of SoG fish did not differ between those that hatched in 1970s and 1990s.For both populations growth in the first and third summer was positively and negatively related, respectively, to the abundance of harbor seals, while growth in the first and second summer was negatively related to salinity.Overall, this study highlights the complicated nature of Pacific hake population recovery under dynamic, and typically uncontrollable, variation in biotic and abiotic conditions.

We investigated dietary preferences in Pigeon Guillemot (Cepphus columba) across different breeding stages in Puget Sound, WA. Observations of prey delivered to chicks were conducted during the breeding season (June–September) at 28 colonies on Whidbey Island over a 12-y period (2008–2019). We conducted stable isotope analysis on discarded eggshells collected below active Pigeon Guillemot burrows distributed across 9 colonies on Whidbey Island during the 2019 breeding season. We estimated the relative percent contribution of fish and invertebrates to the diet of pre-laying adult Pigeon Guillemot using the δ15N and δ13C in eggshell membrane tissue. Results of our mixing model showed that adults derive nearly 75% of their energy and nutrients from demersal fish species (rockfish, gunnel, and sculpin) during the pre-laying period, and prey-delivery observations showed that Pigeon Guillemot preferentially deliver gunnel (Pholidae) to chicks. These results demonstrate a consistent foraging pattern and dietary preference in this population over the course of 2 different stages during the breeding season.

Declines in fish body size have been reported in many populations and these changes likely have important ramifications for the sustainability of harvested species and ecosystem function. Pacific hake, Merluccius productus, have shown declines in size over the last several decades for populations located in Puget Sound (PS), Washington, USA, and Strait of Georgia (SoG), British Columbia, Canada. To examine this decrease in size, we used archived otoliths from both populations to assess when the decrease in somatic growth occurred and explored what factors and processes might explain the decline, including otolith microchemistry to infer the environment experienced by fish at different ages. Results indicated that substantial changes in juvenile somatic growth have occurred across decades. The divergence in body size occurred in the second summer, whereby SoG fish grew, on average, 18% more than PS fish. Within the PS population, somatic growth differed significantly among fish that hatched in the 1980s, 1990s, and 2010s, such that the more recently hatched fish grew 26% more in their first summer and 71% less in their second summer relative to those that hatched in the 1980s. In comparison, growth of SoG fish did not differ between those that hatched in 1970s and 1990s. For both populations growth in the first and third summer was positively and negatively related, respectively, to the abundance of harbor seals, while growth in the first and second summer was negatively related to salinity. Overall, this study highlights the complicated nature of Pacific hake population recovery under dynamic, and typically uncontrollable, variation in biotic and abiotic conditions.

The industrial waterway in Portland Harbor, Oregon, is a migration corridor for a distinct population segment of Chinook Salmon (Upper Willamette River) currently protected by the U.S. Endangered Species Act. Juveniles are exposed to a suite of contaminants during outmigration including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and dichlorodiphenyltrichloroethanes. We collected natural origin subyearling Chinook salmon from sites in and around the industrial harbor to evaluate growth (otolith microstructural analysis) in relation to measured chemical concentrations in tissue. A reduced growth rate was associated with higher tissue contaminant concentrations, particularly mixtures represented by PAHs and certain PCBs, which were elevated in juvenile Chinook collected throughout sites within Portland Harbor relative to those captured upstream. First-year growth is an established predictor of individual survival and eventual reproductive success in Chinook salmon. Therefore, our results indicate that legacy pollution may be limiting the population abundance of threatened Willamette River Chinook salmon, and future habitat remediation or restoration actions may benefit ongoing species recovery efforts.

Blubber and muscle were collected from male bowhead whales (n = 71) landed near Utqiaġvik (Barrow), Alaska, between 2006 and 2015 and analyzed for lipid content and concentrations of persistent organic pollutants (POPs) in order to determine levels and trends over the collection period. Collection year was a significant predictor of blubber concentrations for most classes of POPs, while for a few classes, animal length (proxy for age) was also a significant predictor. This is the first report on levels of PBDEs in bowhead whales; concentrations of these compounds are low (≤55 ng/g wet weight). Blubber concentrations were lower than those reported in samples collected between 1992 and 2000, and many POP classes in blubber declined significantly between 2006 and 2015. Concentrations of POPs in bowhead whale tissues, which are subsistence foods for Native Alaskan communities, appear to be declining at rates comparable with previously reported temporal trends in Arctic biota.

An animal's performance during its early life stage can greatly influence its survival to adulthood. Therefore, understanding aspects of early life history can be informative, particularly when designing management plans to rebuild a population. For a threatened population of fall Chinook salmon (Oncorhynchus tshawytscha) in the Snake River of Idaho, we reconstructed the early life history for 124 returning wild and hatchery adults using information recorded in their otoliths. Of our sampled wild adults (n = 61), 43% and 49% reared within the Snake River and Clearwater/Salmon rivers. We also found that only 21% of our sampled wild adults exhibited the historically common subyearling out-migration strategy, in which juveniles exit freshwater shortly after hatching, while the remaining wild adults exhibited the yearling out-migration strategy (i.e., individuals delay their freshwater exit). As expected, yearlings had, on average, a significantly larger body size than subyearlings at ocean entry. However, 35% of wild yearlings overlapped in size with wild subyearlings suggesting that spending more time in freshwater might not necessarily result in a larger body size. Lastly, we observed that variability in fork length at Snake River egress and ocean entry were best explained by migration strategy and where it reared, followed by hatch year and sex. Results from this study highlight the utility of adult otoliths in providing details about early life history, an understanding of which is critical to the conservation of Snake River fall Chinook salmon.

In the western United States, the long-term recovery of many Pacific salmon populations is inextricably linked to freshwater habitat quality. Industrial activities from the past century have left a legacy of pollutants that persist, particularly near working waterfronts. The adverse impacts of these contaminants on salmon health have been studied for decades, but the population-scale consequences of chemical exposure for salmonids are still poorly understood. We estimated acute and delayed mortality rates for seaward migrating juvenile Chinook salmon that feed and grow in a Superfund-designated area in the Lower Willamette River in Portland, Oregon. We combined previous, field-collected exposure data for juvenile Chinook salmon together with reduced growth and disease resistance data from earlier field and laboratory studies. Estimates of mortality were then incorporated into a life cycle model to explore chemical habitat-related fish loss. We found that 54% improved juvenile survival—potentially as a result of future remediation activities—could increase adult Chinook salmon population abundance by more than 20%. This study provides a framework for evaluating pollution remediation as a positive driver for species recovery.

Connecting maternal migratory behavior with the behavior and ecology of their progeny can reveal important details in the ecology of a population. One method for linking maternal migration to early juvenile life history is through maternal chemistry recorded in otoliths. Despite the wide use of maternal signatures to infer anadromy, the duration and dynamics of maternal otolith signatures are not well understood. Shifts in the elemental ratios and strontium isotope (87Sr/86Sr) chemistry in otoliths from juvenile Chinook salmon (Oncorhynchus tshawytscha) correlate with the timing of hatch and emergence, respectively, indicating a chemical marker of these ontological stages. Additionally, analysis of maternal signatures show that maternally derived87Sr/86Sr may be influenced by equilibration of the mother to fresh water, and in some cases the87Sr/86Sr signatures of the eggs can shift substantially after being laid. These results provide guidance in separating maternal and juvenile signatures as researchers increasingly target early juvenile otolith chemistry. These results also caution against the use of87Sr/86Sr alone as a marker of anadromy in populations with major inland migrations.

Estuarine habitats provide rearing opportunities for the juvenile life stage of anadromous fishes. Because survival is positively correlated with juvenile performance, these estuarine habitats play an important role in population abundance and productivity. To provide information for the recovery of several depressed stocks of Chinook salmon in the Columbia River Basin, we sought to identify the factors that explain variability in performance. Using otolith-derived estimates of juvenile somatic growth rate as an index of recent performance, we observed a negative nonlinear relationship between growth rate and day of year, and a decreasing and increasing trend of growth rate over the 8years of this study and distance from the river mouth respectively. Using a generalised linear modelling approach, we found that variability in juvenile somatic growth rate was best explained by where and when individuals were collected, their body size, contaminant loads, stock of origin, and whether a fish was hatchery produced or unmarked. Lastly, we argue that a considerable improvement to the growth rate of juveniles in estuarine habitats is physiologically possible. The results of this 8-year study provide a baseline of the performance of juvenile Chinook salmon to evaluate habitat restoration programs and to compare against future anthropogenic conditions.

Increments of a fish otolith are commonly used to estimate age and somatic growth; yet the accuracy of such estimates first requires an understanding of the periodicity with which increments are formed. We conducted a rearing experiment to evaluate daily formation of increments in otoliths from spring Chinook salmon (Oncorhynchus tshawytscha), an anadromous fish from the Yakima River, Washington. Specifically, we compared the known number of post-emergence days that fish were alive to the number of otolith increments formed after an emergence check. Our results indicated daily formation of otolith increments, thus corroborating previous studies and supporting the use of otolith increments to estimate age and somatic growth of individual Chinook salmon. Given the positive relationship between body size and survival to adulthood, continued use of otolith microstructure to quantify age and growth will help identify factors critical for the recovery of listed Chinook salmon populations.