Gulf States Marine Fisheries Commission

This review considers the effect of anthropogenic sound on beaked whales2. Two major conclusions are presented: (1) gas-bubble disease, induced in supersaturated tissue by a behavioural response to acoustic exposure, is a plausible pathologic mechanism for the morbidity and mortality seen in cetaceans associated with sonar exposure and merits further investigation; and (2) current monitoring and mitigation methods for beaked whales are ineffective for detecting these animals and protecting them from adverse sound exposure. In addition, four major research priorities, needed to address information gaps on the impacts of sound on beaked whales, are identified: (1) controlled exposure experiments to assess beaked whale responses to known sound stimuli; (2) investigation of physiology, anatomy, pathobiology and behaviour of beaked whales; (3) assessment of baseline diving behaviour and physiology of beaked whales; and (4) a retrospective review of beaked whale strandings.

Improved management approaches are needed to reduce the rate at which humans are depleting exploited marine populations and degrading marine ecosystems. Networks of no-take marine reserves are promising management tools because of their potential to (1) protect coastal ecosystem structure and functioning, (2) benefit exploited populations and fisheries, (3) improve scientific understanding of marine ecosystems, and (4) provide enriched opportunities for non-extractive human activities. By protecting marine ecosystems and their populations, no-take reserve networks can reduce risk by providing important insurance for fishery managers against overexploitation of individual populations. Replicated reserves also foster strong scientific testing of fishery and conservation management strategies. Reserve networks will require social acceptance, adequate enforcement, and effective scientific evaluation to be successful. Processes for reserve establishment should accommodate adaptive management so boundaries and regulations can be modified to enhance performance. However, even well-designed reserve networks will require continued conservation efforts outside reserve boundaries to be effective. Establishing networks of no-take reserves is a process-oriented, precautionary management strategy that protects functional attributes of marine ecosystems. As an addition to fishery management practices and other conservation efforts, no-take reserve networks may improve the status of exploited populations while conserving marine resources for future generations.

Since 1995, several stocks of Fraser River sockeye salmon (Oncorhynchus nerka) have begun upriver spawning migrations significantly earlier than previously observed. In some years, the timing of peak migration has shifted more than 6 weeks. Coincident with this early migration are high levels of en route and pre-spawning mortality, occasionally exceeding 90%. These phenomena pose risks to the perpetuation of these fisheries resources. At present, although there are many competing hypotheses (e.g., energetics, osmoregulatory dysfunction, oceanic conditions, parasites) that may account for early migration and high mortality, there are no definitive answers, nor any causal evidence that link these issues. With poor predictive ability in the face of uncertainty, fisheries managers have been unable to effectively allocate harvest quotas, while ensuring that sufficient fish are able to not only reach the spawning sites, but also successfully reproduce. If trends in mortality rates continue, several important sockeye salmon fisheries and stocks could collapse. Indeed, one sockeye stock has already been emergency listed as endangered under Canadian legislation.

The Wadeable Streams Assessment (WSA) provided the first statistically sound summary of the ecological condition of streams and small rivers in the US. Information provided in the assessment filled an important gap in meeting the requirements of the US Clean Water Act. The purpose of the WSA was to: 1) report on the ecological condition of all wadeable, perennial streams and rivers within the conterminous US, 2) describe the biological condition of these systems with direct measures of aquatic life, and 3) identify and rank the relative importance of chemical and physical stressors affecting stream and river condition. The assessment included perennial wadeable streams and rivers that accounted for 95% of the length of flowing waters in the US. The US Environmental Protection Agency, states, and tribes collected chemical, physical, and biological data at 1392 randomly selected sites. Nationally, 42% of the length of US streams was in poor condition compared to best available reference sites in their ecoregions, 25% was in fair condition, and 28% was in good condition. Results were reported for 3 major regions: Eastern Highlands, Plains and Lowlands, and West. In the West, 45% of the length of wadeable flowing waters was in good condition. In the Eastern Highlands, only 18% of the length of wadeable streams and rivers was in good condition and 52% was in poor condition. In the Plains and Lowlands, almost 30% of the length of wadeable streams and rivers was in good condition and 40% was in poor condition. The most widespread stressors observed nationally and in each of the 3 major regions were N, P, riparian disturbance, and streambed sediments. Excess nutrients and excess streambed sediments had the highest impact on biological condition; streams scoring poor for these stressors were at 2 to 3× higher risk of having poor biological condition than were streams that scored in the good range for the same stressors. Condition of stream ecosystems in the US: an overview of the first national assessment (PDF Download Available). Available from: http://www.researchgate.net/publication/250078770_Condition_of_stream_ecosystems_in_the_US_an_overview_of_the_first_national_assessment [accessed Jul 9, 2015].

Abstract Ainsworth, C. H., Samhouri, J. F., Busch, D. S., Cheung, W. W. L., Dunne, J., and Okey, T. A. 2011. Potential impacts of climate change on Northeast Pacific marine foodwebs and fisheries. – ICES Journal of Marine Science, 68: 1217–1229. Although there has been considerable research on the impacts of individual changes in water temperature, carbonate chemistry, and other variables on species, cumulative impacts of these effects have rarely been studied. Here, we simulate changes in (i) primary productivity, (ii) species range shifts, (iii) zooplankton community size structure, (iv) ocean acidification, and (v) ocean deoxygenation both individually and together using five Ecopath with Ecosim models of the northeast Pacific Ocean. We used a standardized method to represent climate effects that relied on time-series forcing functions: annual multipliers of species productivity. We focused on changes in fisheries landings, biomass, and ecosystem characteristics (diversity and trophic indices). Fisheries landings generally declined in response to cumulative effects and often to a greater degree than would have been predicted based on individual climate effects, indicating possible synergies. Total biomass of fished and unfished functional groups displayed a decline, though unfished groups were affected less negatively. Some functional groups (e.g. pelagic and demersal invertebrates) were predicted to respond favourably under cumulative effects in some regions. The challenge of predicting climate change impacts must be met if we are to adapt and manage rapidly changing marine ecosystems in the 21st century.

BACKGROUND: One of the greatest obstacles to moving ecosystem-based management (EBM) from concept to practice is the lack of a systematic approach to defining ecosystem-level decision criteria, or reference points that trigger management action. METHODOLOGY/PRINCIPAL FINDINGS: To assist resource managers and policymakers in developing EBM decision criteria, we introduce a quantitative, transferable method for identifying utility thresholds. A utility threshold is the level of human-induced pressure (e.g., pollution) at which small changes produce substantial improvements toward the EBM goal of protecting an ecosystem's structural (e.g., diversity) and functional (e.g., resilience) attributes. The analytical approach is based on the detection of nonlinearities in relationships between ecosystem attributes and pressures. We illustrate the method with a hypothetical case study of (1) fishing and (2) nearshore habitat pressure using an empirically-validated marine ecosystem model for British Columbia, Canada, and derive numerical threshold values in terms of the density of two empirically-tractable indicator groups, sablefish and jellyfish. We also describe how to incorporate uncertainty into the estimation of utility thresholds and highlight their value in the context of understanding EBM trade-offs. CONCLUSIONS/SIGNIFICANCE: For any policy scenario, an understanding of utility thresholds provides insight into the amount and type of management intervention required to make significant progress toward improved ecosystem structure and function. The approach outlined in this paper can be applied in the context of single or multiple human-induced pressures, to any marine, freshwater, or terrestrial ecosystem, and should facilitate more effective management.

Understanding changes in the migratory and reproductive phenology of fish stocks in relation to climate change is critical for accurate ecosystem-based fisheries management. Relocation and changes in timing of reproduction can have dramatic effects upon the success of fish populations and throughout the food web. During anomalously warm conditions (1-4°C above normal) in the northeast Pacific Ocean during 2015-2016, we documented shifts in timing and spawning location of several pelagic fish stocks based on larval fish samples. Total larval concentrations in the northern California Current (NCC) during winter (January-March) 2015 and 2016 were the highest observed since annual collections first occurred in 1998, primarily due to increased abundances of Engraulis mordax (northern anchovy) and Sardinops sagax (Pacific sardine) larvae, which are normally summer spawning species in this region. Sardinops sagax and Merluccius productus (Pacific hake) exhibited an unprecedented early and northward spawning expansion during 2015-16. In addition, spawning duration was greatly increased for E. mordax, as the presence of larvae was observed throughout the majority of 2015-16, indicating prolonged and nearly continuous spawning of adults throughout the warm period. Larvae from all three of these species have never before been collected in the NCC as early in the year. In addition, other southern species were collected in the NCC during this period. This suggests that the spawning phenology and distribution of several ecologically and commercially important fish species dramatically and rapidly changed in response to the warming conditions occurring in 2014-2016, and could be an indication of future conditions under projected climate change. Changes in spawning timing and poleward migration of fish populations due to warmer ocean conditions or global climate change will negatively impact areas that were historically dependent on these fish, and change the food web structure of the areas that the fish move into with unforeseen consequences.

Preamble: Executive Order (EO) 13112 —defines an invasive species as “ an alien species whose introduction does or is likely to cause economic or environmental harm or harm to human health. ” In the Executive Summary of the National Invasive Species Management Plan (NISMP) the term invasive species is further clarified and defined as “ a species that is non-native to the ecosystem under consideration and whose introduction causes or is likely to cause economic or environmental harm or harm to human health. ” To provide guidance for the development and implementation of the NISMP, the National Invasive Species Council (NISC) and the Invasive Species Advisory Committee (ISAC) adopted a set of principles outlined in Appendix 6 of the NISMP. Guiding Principle #1 provides additional context for defining the term invasive species and states “ many alien species are non-invasive and support human livelihoods or a preferred quality of life. ”

Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of hatchery broodstock and uses parentage assignments to identify the origin and brood year of their progeny. In this study we empirically confirmed that fewer than 100 single nucleotide polymorphisms (SNPs) were needed to accurately conduct PBT, we demonstrated that our selected panel of SNPs was comparable in accuracy to a panel of microsatellites, and we verified that stock assignments made with this panel matched those made using CWTs. We also demonstrated that when sampling of spawners was incomplete, an estimated PBT rate for the offspring could also be predicted with fewer than 100 SNPs. This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly in the region, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of parentage-based research and management questions.

The species composition of benthic diatoms was related to environmental conditions in streams throughout the western US to develop diatom traits, indicators for assessment of biological condition and indicators for diagnosing stressors. We hypothesized that indicators based on species traits determined for subsets of streams with similar natural landscape features would be more precisely related to environmental conditions than would be indicators calculated based on species traits for all streams in the data set. The ranges of many environmental conditions were wide among western streams, and these conditions covaried greatly along a major environmental gradient characterized by positive correlations among % watershed disturbed by agricultural and urban land uses (% WD), conductivity, total N, total P, and % fine sediments. Species traits were calculated for 242 diatom taxa. Weighted average (WA) methods were used to define species environmental optima, and regression approaches were used to determine whether species were sensitive or tolerant to environmental conditions indicated by % WD, total P, total N, a nutrient multivariate index, pH, conductivity, % fine sediments, % embeddedness, and a watershed disturbance multivariate index. Indicators based on WA optima and sensitive/tolerant traits were highly correlated with these environmental conditions. Natural and anthropogenic conditions varied greatly among classes of streams grouped by climate regions, but indicators developed for the entire western US were consistently more accurate than were regional indicators. Indicators for individual stressors, such as total P, conductivity, and % embeddedness, were highly correlated with values of respective stressors, but covariation among all indicators and stressors indicated that only 1 environmental gradient was reliably reflected by the indicators. Thus, robust indicators of the biological condition of diatom assemblages were developed for streams of the western US, but development of stressor-specific indicators will require application of additional analytical approaches.

Effective conservation and restoration of estuarine wetlands require accurate maps of their historical and current extent, as well as estimated losses of these valued habitats. Existing coast-wide tidal wetland mapping does not explicitly map historical tidal wetlands that are now disconnected from the tides, which represent restoration opportunities; nor does it use water level models or high-resolution elevation data (e.g. lidar) to accurately identify current tidal wetlands. To better inform estuarine conservation and restoration, we generated new maps of current and historical tidal wetlands for the entire contiguous U.S. West Coast (Washington, Oregon, and California). The new maps are based on an Elevation-Based Estuary Extent Model (EBEEM) that combines lidar digital elevation models (DEMs) and water level models to establish the maximum historical extent of tidal wetlands, representing a major step forward in mapping accuracy for restoration planning and analysis of wetland loss. Building from this new base, we also developed an indirect method for mapping tidal wetland losses, and created maps of these losses for 55 estuaries on the West Coast (representing about 97% of historical West Coast vegetated tidal wetland area). Based on these new maps, we estimated that total historical estuary area for the West Coast is approximately 735,000 hectares (including vegetated and nonvegetated areas), and that about 85% of vegetated tidal wetlands have been lost from West Coast estuaries. Losses were highest for major river deltas. The new maps will help interested groups improve action plans for estuarine wetland habitat restoration and conservation, and will also provide a better baseline for understanding and predicting future changes with projected sea level rise.

Identifying the existence and magnitude of density dependence is one of the oldest concerns in ecology. Ecologists have aimed to estimate density dependence in population and community data by fitting a simple autoregressive (Gompertz) model for density dependence to time series of abundance for an entire population. However, it is increasingly recognized that spatial heterogeneity in population densities has implications for population and community dynamics. We therefore adapt the Gompertz model to approximate, local densities over continuous space instead of population-wide abundance, and allow productivity to vary spatially using Gaussian random fields. We then show that the conventional (nonspatial) Gompertz model can result in biased estimates of density dependence (e.g., identifying oscillatory dynamics when not present) if densities vary spatially. By contrast, the spatial Gompertz model provides accurate and precise estimates of density dependence for a variety of simulation scenarios and data availabilities. These results are corroborated when comparing spatial and nonspatial models for data from 10 years and -100 sampling stations for three long-lived rockfishes (Sebastes spp.) off the California, USA coast. In this case, the nonspatial model estimates implausible oscillatory dynamics on an annual time scale, while the spatial model estimates strong autocorrelation and is supported by model selection tools. We conclude by discussing the importance of improved data archiving techniques, so that spatial models can be used to reexamine classic questions regarding the existence and magnitude of density. dependence in wild populations.

Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. We identified that 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. Given that the primary purpose of surveys is to provide independent data to inform stock assessment of commercially important populations, we further highlight that single surveys do not cover the full range of the main commercial demersal fish species. An average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.

As with other species, frequency-dependent selection during reproduction has long been proposed as an important mechanism in maintaining alternative male reproductive phenotypes in Pacific salmon ( Oncorhynchus spp.). Jack salmon mature one year earlier than the youngest females in a population and are much smaller than older “adult” males. We tested the hypothesis that mating success of both phenotypes is consistent with the frequency-dependent selection model. By holding male density constant and varying the frequency of adults and jacks in eight separate breeding groups, we found that adult male access to females, participation in spawning events, and adult-to-fry reproductive success increased with their decreasing frequency in a breeding group. Jacks exhibited the same pattern (increasing success with decreasing frequency), although the relationships were not as strong as for adults. Overall, jack and adult males mated with a similar number of females, but jacks sired only 20% of all offspring. Observational data suggested that adult males benefited from sperm precedence associated with their ability to court females and enter the nest first at the time of spawning. Our work provides the first experimental evidence of frequency-dependent selection during mating in the family Salmonidae.

The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has 'grown up' with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de-list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.

After spawning their first nest, female chinock salmon Oncorhynchus tshawytscha paired with small males ( c. 46% of female weight) spent an average of 16·2 h between spawning of successive nests compared with 9·6 h for females paired with large males ( c. 112% of female weight) ( P< 0·05). Neither frequencies of female nest construction behaviours (digging and probing) nor male courtship behaviour (crossovers and quivers) differed between large‐ and small‐male pairs. Male quivering frequencies were correlated significantly with female digging and probing frequencies, whereas the crossover frequencies were not. It is suggested that delayed spawning by females in the presence of relatively small males is a primary mechanism by which females in the genus Oncorhynchus exhibit mate choice.

Dietary intake surveys of rural and urban communities in three Pacific Island countries were conducted using an adjusted 24-hour dietary recall method. Dietary survey samples were drawn from noncommunicable disease surveys of Melanesians and Indians in Fiji, Micronesians in Kiribati and Melanesians in Vanuatu. Comparisons of total energy and macronutrient intakes and of obesity, hypertension, diabetes mellitus, serum cholesterol and physical activity levels revealed similar rural/urban trends. Urban subjects were more obese than rural ones, had higher prevalence rates of diabetes and hypertension, and generally had higher cholesterol levels. Rural subjects were leaner, suffered less from diabetes and hypertension, and had greater total energy intakes than urban dwellers. Rural people ate a greater proportion of carbohydrates, while urban subjects ate proportionally more protein and fat, apart from the outer Kiribati atolls with high coconut intakes. Rural subjects in all three studies had higher levels of physical activity. These studies provide persuasive evidence that exercise as well as diet has a significant effect on rural/urban differentials in obesity and noncommunicable disease, and that energy intake reflects energy expenditure.

Steelhead Oncorhynchus mykiss fry reared in an enriched hatchery environment (overhead cover, submerged structures and underwater feeders) and a natural stream both achieved significantly greater social dominance ranks than fry reared in a conventional hatchery environment. Dominant fry from enriched tanks and natural stream exhibited greater frequencies of threat displays than dominant fry reared in conventional tanks. Fry reared in the natural stream exhibited greater territory overlap than fry from either hatchery environment. Overall, the results suggest that enriched hatchery environments may act to ameliorate some but not all changes in social behaviour that result from hatchery rearing.

Abstract Parentage-based tagging (PBT), an innovative and large-scale application of genetic parentage assignments, is transforming how fisheries managers determine the age and origin of sampled fish. PBT is an efficient alternative for mass tagging and has been widely implemented in the Pacific Northwest. While still an emerging technology, PBT is being used to provide information to managers in state, federal, and tribal agencies on the harvest, research, and conservation of Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss in this region. We review the development of PBT in the Pacific Northwest focusing on the technical and logistical challenges for implementing a regional PBT program. We also showcase recent results and review management efforts that made use of PBT-derived data.

Abstract: To evaluate anthropogenic sedimentation in United States (U.S.) Pacific Northwest coastal streams, we applied an index of relative bed stability ( LRBS *) to summer low flow survey data collected using the U.S. Environmental Protection Agency’s Environmental Monitoring and Assessment Program field methods in a probability sample of 101 wadeable stream reaches. LRBS * is the log of the ratio of bed surface geometric mean particle diameter ( D gm ) to critical diameter ( D* cbf ) at bankfull flow, based on a modified Shield’s criterion for incipient motion. We used a formulation of LRBS * that explicitly accounts for reductions in bed shear stress that result from channel form roughness due to pools and wood. LRBS * ranged from −1.9 to +0.5 in streams within the lower quartile of human riparian and basin disturbance, and was substantially lower (−4.2 to −1.1) in streams within the upper quartile of human disturbance. Modeling results suggest that the expected range of LRBS* in streams without human disturbances in this region might be generally between −0.7 and +0.5 in either sedimentary or volcanic lithology. However, streams draining relatively soft, erodible sedimentary lithology showed greater reductions in LRBS * associated with disturbance than did those having harder, more resistant volcanic (basalt) lithology with similar levels of basin and riparian disturbance. At any given level of disturbance, smaller streams had lower LRBS * than those with larger drainages. In sedimentary lithology (sandstone and siltstone), high‐gradient streams had higher LRBS* than did low‐gradient streams of the same size and level of human disturbance. High gradient streams in volcanic lithology, in contrast, had lower LRBS * than low‐gradient streams of similar size and disturbance. Correlations between D gm and land disturbance were stronger than those observed between D * cbf and land disturbance. This pattern suggests that land use has augmented sediment supplies and increased streambed fine sediments in the most disturbed streams. However, we also show evidence that some of the apparent reductions in LRBS *, particularly in steep streams draining small volcanic drainages, may have resulted in part from anthropogenic increases in bed shear stress. The synoptic survey methods and designs we use appear adequate to evaluate regional patterns in bed stability and sedimentation and their general relationship to human disturbances. More precise field measurements of channel slope, cross‐section geometry, and bed surface particle size would be required to use LRBS * in applications requiring a higher degree of accuracy and precision, such as site‐specific assessments at individual streams.