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Environmental laws around the world require some version of an environmental‐impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon‐sequencing—also called metabarcoding—of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental‐impact analysis for development projects. Here, we analyze an 18‐month time series of water samples taken before, during, and after two culvert removals in a salmonid‐bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species‐specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court‐mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental‐impact reporting using eDNA that is widely applicable in environments worldwide. [ABSTRACT FROM AUTHOR]

Understanding the process of recruitment is fundamental to fisheries biology and management. However, recruitment in natural populations is highly variable and rarely well described by classical stock-recruitment relationships (SRRs). Recent analyses suggest that the age composition of the spawning biomass may play an important role in the mismatch between SRRs and data. Here we develop a generalization of the Ricker SRR that incorporates age structure by allowing mortality and fecundity rates to depend on maternal age. We provide a flexible SRR with biologically interpretable parameters that can be estimated from existing fisheries time series and use a Bayesian framework that enables parameters to be informed by experimental data. We apply our method to the Icelandic population of Atlantic cod (Gadus morhua) and show models that include age structure effects outperform the classical Ricker SRR that ignores age structure. Our results indicate a strong effect of spawning stock age structure on recruitment dynamics in this population. Our approach provides a biologically interpretable and immediately applicable method for investigating the consequences for spawning stock age structure on recruitment. La comprehension du processus de recrutement est un aspect essentiel de la biologie et de la gestion des peches. Le recrutement au sein de populations naturelles est toutefois tres variable et les relations stock-recrutement (SSRs) classiques en fournissent rarement une description adequate. Des analyses recentes suggerent que la composition par age de la biomasse de frai pourrait etre un important facteur explicatif de la non- concordance des SSR et des donnees. Nous presentons une generalisation de la SRR de Ricker qui integre la structure par age en permettant que les taux de mortalite et de fecondite dependent de l'age maternel. Nous fournissons ainsi une SRR souple contenant des parametres pouvant etre interpretes d'un point de vue biologique et qui peuvent etre estimes a partir de series chronologiques existantes sur les peches et nous utilisons un cadre bayesien qui permet la definition des parametres a partir de donnees experimentales. Nous appliquons cette methode a la population islandaise de morue franche (Gadus morhua) et demontrons que les modeles qui integrent les effets de la structure par age donnent de meilleurs resultats que la SSR de Ricker classique, qui n'en tient pas compte. Nos resultats indiquent un effet marque de la structure par age des stocks reproducteurs sur la dynamique du recrutement dans cette population. Notre approche offre une methode pouvant etre appliquee immediatement et permettant des interpretations biologiques pour etudier les repercussions de la structure par age des stocks reproducteurs sur le recrutement. [Traduit par la Redaction], Introduction The fundamental law of population biology is that species cannot increase without bound. When viewed in a single species context, this means that density dependence must act on survival, [...]

Accurate landing statistics are among the most important data for the management of sustainable fisheries. For many fisheries, however, estimating species-specific landings and the associated uncertainty can be difficult, especially in the case of complex multispecies fisheries. Here we develop general and flexible methods for estimating species- specific landings, motivated by the mixed-species California groundfish fishery. We describe Bayesian generalized linear and hierarchical models for estimating species compositions from port sampling data and illustrate the application of each to several examples from California fisheries. Our hierarchical modeling approach provides a coherent statistical framework that can provide estimates of landings and uncertainty in the face of sparse and missing sampling data that compliment existing procedures for estimating landings. Furthermore, our methods provide ways to compare alternative model formulations and to maintain estimates of uncertainty when landings are aggregated across temporal or spatial scales. Our model structure is applicable to fisheries worldwide. Les statistiques precises sur les debarquements sont parmi les donnees les plus importantes pour la gestion des peches durables. Pour plusieurs peches, cependant, l'estimation des debarquements en fonction des especes et l'incertitude qui leur est associee peut s'averer difficile, particulierement dans le cas de peches complexes et multispecifiques. Nous mettons au point ici des methodes generales et flexibles pour estimer les debarquements en fonction des especes, a cause de notre interet pour la peche multispecifique des poissons de fond de la Californie. Nous decrivons des modeles bayesiens generalises lineaires et hierarchiques pour estimer la composition en especes a partir de donnees d'echantillonnage dans les ports; nous illustrons l'utilisation de chacun des modeles avec plusieurs exemples provenant des peches de Californie. Notre methodologie de modelisation hierarchique fournit un cadre statistiquement coherent qui peut produire des estimations des debarquements ainsi que de l'incertitude dans les cas de donnees d'echantillonnage rares ou manquantes; elle sert donc de complement aux procedures actuelles d' estimation des debarquements. De plus, nos methodes fournissent des facons de comparer les differentes formulations des modeles et de maintenir les estimations de l' incertitude lorsque les debarquements sont repartis de maniere contagieuse aux echelles temporelles ou spatiales. Notre structure de modelisation peut s'appliquer aux peches a l' echelle mondiale. [Traduit par la Redaction], Introduction Historical landing records and catch-effort statistics derived from landing records form the backbone of most fisheries stock assessments. Therefore, the accuracy and reliability of landings statistics underlie sustainable management [...]

Balancing trade‐offs amongst social–ecological objectives is a central aim of natural resource management. However, objectives and resources often have spatial dimensions, which are usually ignored in trade‐off analyses. We examine how simultaneously integrating social–ecological benefits and their spatial complexities can improve trade‐off analysis. We use Pacific herring (Clupea pallasii, Clupeidae)—an ecologically important forage fish with social, cultural and economic value to communities and commercial fisheries—as a case study. By combining spatial management strategy evaluation with social benefits analysis, we illustrate when policies aimed at aggregate stocks versus spatially segregated substocks of fish fail to balance trade‐offs amongst social–ecological objectives. Spatial measures (e.g. area‐based closures) may achieve some objectives but produce alternative trade‐offs that are sensitive to assumptions about fish population dynamics and social complexities. Our analyses identify policies that are inefficient (e.g. yielding economic costs without producing social or ecological gains), highlight management strategies that generate trade‐offs and indicate when costs are distributed unequally for different user groups. We also point to strategies with outcomes that are robust to spatial uncertainties and reveal research priorities by identifying which performance metrics exhibit sensitivity to spatial ecological assumptions. Collectively, our analyses demonstrate how incorporating social objectives and spatial dynamics into management strategy evaluation can reveal trade‐offs and the implications of management decisions. [ABSTRACT FROM AUTHOR]

We explore a "Go With the Older Fish" (GWOF) mechanism of learned migration behaviour for exploited fish populations, where recruits learn a viable migration path by randomly joining a school of older fish. We develop a non-age-structured biomass model of spatially independent spawning sites with local density dependence, based on Pacific herring (Clupea pallasii). We compare a diffusion (DIFF) strategy, where recruits adopt spawning sites near their natal site without regard to older fish, with GWOF, where recruits adopt the same spawning sites, but in proportion to the abundance of adults using those sites. In both models, older individuals return to their previous spawning site. The GWOF model leads to higher spatial variance in biomass. As total mortality increases, the DIFF strategy results in an approximately proportional decrease in biomass among spawning sites, whereas the GWOF strategy results in abandonment of less productive sites and maintenance of high biomass at more productive sites. A DIFF strategy leads to dynamics comparable to non-spatially structured populations. While the aggregate response of the GWOF strategy is distorted, non-stationary and slow to equilibrate, with a production curve that is distinctly flattened and relatively unproductive. These results indicate that fishing will disproportionately affect populations with GWOF behaviour. [ABSTRACT FROM AUTHOR]

Abstract: Theory and previous studies have shown that commercial fishers with a diversified catch across multiple species may experience benefits such as increased revenue and reduced variability in revenue. However, fishers can only increase the species diversity of their catch if they own fishing permits that allow multiple species to be targeted, or if they own multiple single‐species permits. Individuals holding a single permit can only increase catch diversity within the confines of their permit (e.g. by fishing longer or over a broader spatial area). Using a large dataset of individual salmon fishers in Alaska, we build a Bayesian variance function regression model to understand how diversification impacts revenue and revenue variability, and how these effects have evolved since the 1970s. Applying these models to six salmon fisheries that encompass a broad geographic range and a variety of harvesting methods and species, we find that the majority of these fisheries have experienced reduced catch diversity through time and increasing benefits of specialization on mean individual revenues. One factor that has been hypothesized to reduce catch diversity in salmon fisheries is large‐scale hatchery production. While our results suggest negative correlations between hatchery returns and catch diversity for some fisheries, we find little evidence for a change in variability of annual catches associated with increased hatchery production. Synthesis and applications. Despite general trends towards more specialization among commercial fishers in Alaska, and more fishers exclusively targeting salmon, we find that catching fewer species can have positive effects on revenue. With increasing specialization, it is important to understand how individuals buffer against risk, as well as any barriers that prevent diversification. In addition to being affected by environmental variability, fishers are also affected by economic factors including demand and prices offered by processors. Life‐history variation in the species targeted may also play a role. Individuals participating in Alaskan fisheries with high contributions of pink salmon — which have the shortest life cycles of all Pacific salmon — also have the highest variability in year‐to‐year revenue. [ABSTRACT FROM AUTHOR]

Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez oil spill (EVOS) for demersal fish. We delineate areas across a range of exposure to EVOS and use spatio-temporal models to quantify the abundance of 53 species-groups over 31 years. We compare multiple community metrics for demersal fish in EVOS and Control areas. We find that areas more exposed to EVOS have more negative trends in total groundfish biomass than non-EVOS areas, and that this change is driven primarily by reductions in the abundance of the apex predator guild. We show no signature of increased variability or increased levels of synchrony within EVOS areas. Our analysis supports mild consequences of EVOS for groundfish communities, but suggests that long time-series and assessments of changes at the community level may reveal sub-lethal effects in marine communities. [ABSTRACT FROM AUTHOR]

Forage fish undergo dramatic changes in abundance through time. Long-term fluctuations, which have historically been attributed to changes in recruitment, may also be due to changes in adult mortality. Pacific herring, a lightly exploited forage fish in Puget Sound, WA, have exhibited shifts in age structure and decreases in spawning biomass during the past 30 years. Here, we investigate changes in adult mortality as a potential explanation for these shifts. Using a hierarchical, age-structured population model, we indicate that adult natural mortality for Puget Sound Pacific herring has increased since 1973. We find that natural mortality has increased for every age class of adult (age 3+), especially age 4 fish, whose estimated mortality has doubled over the survey time period (from M = 0.84-1.76). We demonstrate that long-term shifts in mortality explain changes in age structure, and may explain biomass declines and failure to reach management thresholds for two spawning sites in Puget Sound (Cherry Point and Squaxin Pass). Temporal shifts in natural adult mortality could have negative implications for herring and herring predators. We demonstrate that adult mortality, in addition to recruitment variation, is an important driver for forage fish, which face exceptionally high natural mortality compared with other fishes. [ABSTRACT FROM AUTHOR]