The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations....
Cephalopods are increasingly viewed as sentient animals that require the same welfare consideration as their vertebrate counterparts. In this study, an observational welfare assessment tool developed by the EU Directive was revised to be species-specific for the giant Pacific octopus, Enteroctopus dofleini. This E. dofleini health and welfare assessment tool...
Dynamic marine environments can shape complex spatial and temporal patterns in the population connectivity of marine species, and this is often exemplified in species with long larval phases. Here, we used a genotyping-by-sequencing (GBS) approach to examine fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits...
The California Current Ecosystem (CCE) is a dynamic marine ecosystem from which many socioeconomically important fisheries species are harvested. Here, a genotyping-by-sequencing (GBS) approach was used to examine genomic variation in an early life stage (megalopae) of the Dungeness crab (Cancer magister), which constitutes the most valuable single-species commercial fishery...
Skin condition assessment of wildlife can provide insight into individual and population health. Yet, logistics can limit skin condition assessment of large whales. We developed a standardized, quantitative protocol using photographs to assess skin condition of blue whales in New Zealand, and demonstrate the value gained by testing hypotheses, documenting...
The phenotypic identification of sex in Sebastes rockfish is difficult and often impractical from a management perspective, and the genetic basis of sex determination in the genus is currently uncertain. We tested a previously developed sex identifi- cation polymerase chain reaction restriction fragment length polymorphism (PCR–RFLP) assay in eight species...
A critical seasonal event for anadromous Chinook salmon (Oncorhynchus tshawytscha) is the time at which adults migrate from the ocean to breed in freshwater. We investigated whether allelic variation at the circadian rhythm genes, OtsClock1a and OtsClock1b, underlies genetic control of migration timing among 42 populations in North America. We...
Arctic freshwater ecosystems have been profoundly affected by climate change. Given that the Arctic charr (Salvelinus alpinus) is often the only fish species inhabiting these ecosystems, it represents a valuable model for studying the impacts of climate change on species life‐history diversity and adaptability. Using a genotyping‐by‐se‐ quencing approach, we...
Little is known about intraspecific variation within the deacon rockfish (Sebastes di‐ aconus), a recently described species found in the northeast Pacific Ocean. We in‐ vestigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50‐km2 area...
The California Current Ecosystem (CCE) is a dynamic marine ecosystem from which many socioeconomically important fisheries species are harvested. Here, a genotyping- by-sequencing (GBS) approach was used to examine genomic variation in an early life stage (megalopae) of the Dungeness crab (Cancer magister), which constitutes the most valuable single-species commercial...
Ocean acidification (OA) has had significant negative effects on oyster populations on the west coast of North America over the past decade. Many studies have focused on the physiological challenges experienced by young oyster larvae in high pCO₂/low pH seawater with reduced aragonite saturation state (Ωarag), which is characteristic of...
Recognisable debris from the Great Tōhoku Earthquake and Tsunami of March 2011 began arriving on the coasts of Oregon and Washington, USA in June 2012. This debris often carried fouling Japanese marine algae, and there was concern that these species might recruit and invade northeast Pacific shores. From June 2012...
Using a combination of population‐ and individual‐based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic...
Limited approaches exist for studying population connectivity in widely dispersing marine benthic invertebrates. Genetic techniques can provide important insights toward identifying recruitment trajectories. Here, 10 microsatellite loci were used to examine connectivity among Oregon Dungeness crabs (Cancer magister, Dana, 1852) in the California Current System (CCS) (n = 801) as...
Bird scaring lines (BSLs) protect longline fishing gear from seabird attacks, save bait, reduce incidental seabird mortality and are the most commonly prescribed seabird bycatch mitigation measure worldwide. We collaborated with fishermen to assess the efficacy of applying BSL regulations from the demersal longline sablefish fishery in Alaska to a...
Two species of burrowing shrimp occur in high densities in US West Coast estuaries, the ghost shrimp, Neotrypaea californiensis, and the blue mud shrimp, Upogebia pugettensis. Both species of shrimp are considered ecosystem engineers as they bioturbate and irrigate extensive galleries within the sediment. While their burrows comprise a dominant...
Understanding connectivity of marine organisms is necessary for determining the appropriate scale of conservation and management strategies. For species that inhabit both the coastal ocean and partially enclosed water bodies (i.e., estuaries or fjords), this information is even more critical since estuaries and fjords are often characterized by hydrological complexities...
Periodic weighing of seabird chicks is labour-intensive and repeated handling can cause high levels of disturbance to chicks. Although automatic weighing systems using a fibreglass nest have been designed for albatross species with a pedestal nest made of mud, this approach is inappropriate for great albatross species (genus Diomedea) whose...
Identification and classification of behavior states in animal movement data can be complex, temporally biased, time-intensive, scale-dependent, and unstandardized across studies and taxa. Large movement datasets are increasingly common and there is a need for efficient methods of data exploration that adjust to the individual variability of each track. We...
In the face of dramatic declines in groundfish populations and a lack of sufficient stock assessment information, a need has arisen for new methods of assessing groundfish populations. We describe the integration of seafloor transect data gathered by a manned submersible with high-resolution sonar imagery to produce a habitat- based...
The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured...
Accurate estimation of historical abundance provides an essential baseline for judging the recovery of the great whales. This is particularly challenging for whales hunted prior to twentieth century modern whaling, as population-level catch records are often incomplete. Assessments of whale recovery using pre-modern exploitation indices are therefore rare, despite the...
Interannual variability in salmon (Oncorhynchus spp.) production in the northeast Pacific is understood to be driven by oceanographic variability and bottom-up processes affecting prey availability to juvenile salmon. Scyphozoan jellyfish have an important role in shaping the pathways of energy flow through pelagic food webs. While jellyfish obtain high production...
While sophisticated tools are used to monitor behavioral changes of large marine vertebrates, determining whether these changes are meaningful for management and conservation is challenging. The Population Consequences of Disturbance model proposed a bioenergetics model to detect biologically meaningful population responses, where disturbance costs are linked to lost energy. The...
Heceta Bank is a large reef on the edge of the central Oregon continental shelf that supports a wide variety of commercial fisheries. Using the research submersible Delta, we studied fish abundances on Heceta Bank and the relationship between species composition of fish assemblages and bottom types. Cluster analysis indicated...
Submersible belt-transect surveys along a rocky bottom were combined with acoustic surveys of the water column to estimate depth distribution and density of fishes at Stonewall Bank, Oregon in the northeastern Pacific Ocean from September through October 1991. The objectives of the study were to determine the proportion of fish...
Rockfishes, Sebastes spp.. were the most numerous and speciose fishes seen during 16 submersible dives from 64 to 305 m depth in the vicinity of Heceta Bank off the coast of Oregon. Dense schools of juvenile rockfishes and large yellowtail rockfish, S. flavidus, were observed only over rocky, high relief...
A majority of the world’s largest net-based fisheries target planktivorous forage fish that serve as a critical trophic link between the plankton and upper-level consumers such as large predatory fishes, seabirds, and marine mammals. Because the plankton production that drives forage fish also drives jellyfish production, these taxa often overlap...
We evaluated the external signs of barotrauma and 48-h post-recompression survival for 17 54 canary and 81 yelloweye rockfish captured at depths of 46-174 m, much deeper than a 18 similar prior experiment, but within the depth range of recreational fishery catch and 19 discard. Survival was measured using specialized...
We evaluated how the use of bait as a fish attractant influenced the species and size composition 20 of demersal fishes viewed with a stereo video lander, at 160 sampling sites at Stonewall Bank, a 21 deepwater rocky reef complex in Oregon waters. We also studied the effectiveness of stereo...
We combine high-resolution bathymetry acquired using the Autonomous Underwater Vehicle ABE with digital seafloor imagery collected using the remotely operated vehicle ROPOS across the axial valley of the Southern Explorer Ridge (SER) to infer the recent volcanic and tectonic processes. The SER is an intermediate spreading ridge located in the...
Superpopulation capture–recapture models are useful for estimating the abundance of long-lived, migratory species because they are able to account for the fluid nature of annual residency at migratory destinations. Here we extend the superpopulation POPAN model to explicitly account for heterogeneity in capture probability linked to reproductive cycles (POPAN-τ). This...
Differences in the chemical composition of calcified skeletal structures (e.g. shells, otoliths) have proven useful for reconstructing the environmental history of many marine species. However, the extent to which ambient environmental conditions can be inferred from the elemental signatures within the vertebrae of elasmobranchs (sharks, skates, rays) has not been...
We used a combination of seabird data (both fishery-dependent and fishery-independent) and fishing-effort data to evaluate the relative fisheries risk of five west coast groundfish fisheries and oneshrimp fishery to black-footed (Phoebastria nigripes), short-tailed (P. albatrus) and Laysan albatrosses(P. immutabilis). To assess risk, an overlap index was derived as the...
Similarly structured food web models of four coastal ecosystems (Northern California Current, Central Gulf of Alaska, Georges Bank, southwestern Antarctic Peninsula) were used to investigate competition among whales, fishes, pinnipeds, and humans. Two analysis strategies simulated the effects of historic baleen and odontocete whale abundances across all trophic levels: food...
Authors listed on this Accepted Manuscript vary slightly from those listed on the Version of Record. Harold L. Gibson is an additional author on the published version.
We examined the genetic structure of double-crested cormorants (Phalacrocorax auritus) across their range in the United States and Canada. Sequences of the mitochondrial control region were analyzed for 248 cormorants from 23 breeding sites. Variation was also examined at eight microsatellite loci for 409 cormorants from the same sites. The...
In the California Current coastal boundary zone, the spring transition between downwelling and upwelling conditions, along with the fluctuating structure of the Columbia River plume, creates highly dynamic interactions. In this study, we investigated whether the surface distribution of brachyuran larvae and ichthyoplankton would track the dynamics of the Columbia...
Populations of blue king crab (BKC) (Paralithodes platypus Brandt, 1850) have declined in Alaskan waters
over recent decades, and substantial effort is being made to rehabilitate the once important fishery with releases
of hatchery-reared juveniles. However, little is known about the species' first year of post-settlement
life. This study was...
Diets of juvenile coho Oncorhynchus kisutch and Chinook O. tshawytscha salmon
are made up primarily of winter-spawning fish taxa in the late-larval and early juvenile stages that
are undersampled in plankton and larger trawl nets. Although we have no direct measure of the
availability of fish prey important to juvenile...
Lithothamnion rnuelleri is reported for the first time as one of the main components of rhodolith beds along the Eastern Pacific Ocean based on samples from Washington State (USA), Pacific Baja California (Mexico), southern Nicaragua, and Costa Rica. Individual rhodoliths ranged from fruticose to lumpy in morphology, and bi-sporangial, tetrasporangial,...
conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting
animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However,
many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce...
Density estimation for marine mammal species is performed primarily using
visual distance sampling or capture-recapture. Minke whales in Hawaiian waters
are very difficult to sight; however, they produce a distinctive “boing” call, making
them ideal candidates for passive acoustic density estimation. We used an array of
14 bottom-mounted hydrophones, distributed...
The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in...
To directly determine mortality and predation in the endangered western Steller sea lion Eumetopias jubatus, we deployed implanted, satellite-linked post-mortem data transmitters in 21 juveniles. Data recovered from 4 of 5 detected mortalities exhibited precipitous drops in ambient temperatures followed by immediate onset of transmissions (N = 3), or gradual...
A significant step transition between seasonally stratified and destratified hydrographic conditions occurred during an October 2008 cruise to the Florida Panhandle Shelf along a cross-shelf transect that was sampled before and after a cold front passed through the area. Meteorological measurements from nearby ocean and land-based stations characterized the event....
A survey of the Brothers caldera volcano (Kermadec arc) with the autonomous underwater vehicle ABE has revealed new details of the morphology and structure of this submarine frontal arc caldera and the geologic setting of its hydrothermal activity. Brothers volcano has formed between major SW-NE–trending faults within the extensional field...
Polar ecosystems are sensitive to climate forcing, and we often lack baselines to evaluate changes. Here we report a nearly 50-year study in which a sudden shift in the population dynamics of an ecologically important, structure-forming hexactinellid sponge, Anoxycalyx joubini was observed. This is the largest Antarctic sponge, with individuals...
Marine protected areas (MPAs) are increasingly being used as a conservation tool for highly mobile marine vertebrates and the focus is typically on protecting breeding areas where individuals are aggregated seasonally. Yet movements during the non-breeding season can overlap with threats that may be equally as important to population dynamics....
Species distribution models (SDMs) are currently being used to identify essential fish habitat and guide
fisheries management worldwide. We present SDMs based on generalized linear mixed models (GLMM) of
the fall distribution or occurrence of juvenile American shad (Alosa sapidissima) and juvenile striped bass
(Morone saxatilis) in the Hudson River...