ESA-listed Puget Sound rockfish: How did we get here and how do we assess progress towards recovery planning goals?

In Puget Sound, WA, rockfish abundance declined significantly over the last 50+ years as a result of fishing pressure, life-history characteristics and the isolated geography of Puget Sound. In 2010, three species of rockfish were listed under the Endangered Species Act (ESA): yelloweye rockfish, canary rockfish and bocaccio. Due to a general lack of data specific to these three species, data from other rockfish species were used to support the listings. Since the listings, targeted research and recovery planning has begun to address major data gaps for these three species. First, cooperative research with the recreational fishing community has revealed that yelloweye rockfish are genetically distinct from coastal populations, whereas canary rockfish are not distinct - which has led to canary rockfish being delisted, the first delisting of a marine fish. Second, an ROV survey has been designed specifically to provide a path forward to estimate changes in abundance of listed rockfish in Puget Sound. Third, the Rockfish Recovery Plan for yelloweye rockfish and bocaccio has been published. This plan provides, and we have begun to address, a list of research activities related to environmental conditions and human activities that might constrain rockfish recovery. Two ongoing studies examine whether specific environmental covariates (e.g. dissolved oxygen) alter the movement and foraging behavior of yelloweye rockfish and whether rockfish bycatch can be reduced in the recreational lingcod fishery by using specific bait types. Finally, we will discuss the criteria to be used for delisting these species under the ESA, including statistical methods and operational challenges

Climate shifts the interaction web of a marine plankton community

Climatic effects in the ocean at the community level are poorly described, yet accurate predictions about ecosystem responses to changing environmental conditions rely on understanding biotic responses in a food-web context to support knowledge about direct biotic responses to the physical environment. Here we conduct time-series analyses with multivariate autoregressive (MAR) models of marine zooplankton abundance in the Northern California Current from 1996 to 2009 to determine the influence of climate variables on zooplankton community interactions. Autoregressive models showed different community interactions during warm vs. cool ocean climate conditions. Negative ecological interactions among zooplankton groups characterized the major warm phase during the time series, whereas during the major cool phase, ocean transport largely structured zooplankton communities. Local environmental conditions (sea temperature) and large-scale climate indices (El Niño/Southern Oscillation) were associated with changes in zooplankton abundance across the full time series. Secondary environmental correlates of zooplankton abundance varied with ocean climate phase, with most support during the warm phase for upwelling as a covariate, and most support during the cool phase for salinity. Through simultaneous quantitation of community interactions and environmental covariates, we show that marine zooplankton community structure varies with climate, suggesting that predictions about ecosystem responses to future climate scenarios in the Northern California Current should include potential changes to the base of the pelagic food.Keywords: community interactions, California Current, marine zooplankton, time series analysis, MAR models, climate chang

Taxonomic Distinctness of Demersal Fishes of the California Current: Moving Beyond Simple Measures of Diversity for Marine Ecosystem-Based Management

BACKGROUND: Large-scale patterns or trends in species diversity have long interested ecologists. The classic pattern is for diversity (e.g., species richness) to decrease with increasing latitude. Taxonomic distinctness is a diversity measure based on the relatedness of the species within a sample. Here we examined patterns of taxonomic distinctness in relation to latitude (ca. 32-48 degrees N) and depth (ca. 50-1220 m) for demersal fishes on the continental shelf and slope of the US Pacific coast. METHODOLOGY/PRINCIPAL FINDINGS: Both average taxonomic distinctness (AvTD) and variation in taxonomic distinctness (VarTD) changed with latitude and depth. AvTD was highest at approximately 500 m and lowest at around 200 m bottom depth. Latitudinal trends in AvTD were somewhat weaker and were depth-specific. AvTD increased with latitude on the shelf (50-150 m) but tended to decrease with latitude at deeper depths. Variation in taxonomic distinctness (VarTD) was highest around 300 m. As with AvTD, latitudinal trends in VarTD were depth-specific. On the shelf (50-150 m), VarTD increased with latitude, while in deeper areas the patterns were more complex. Closer inspection of the data showed that the number and distribution of species within the class Chondrichthyes were the primary drivers of the overall patterns seen in AvTD and VarTD, while the relatedness and distribution of species in the order Scorpaeniformes appeared to cause the relatively low observed values of AvTD at around 200 m. CONCLUSIONS/SIGNIFICANCE: These trends contrast to some extent the patterns seen in earlier studies for species richness and evenness in demersal fishes along this coast and add to our understanding of diversity of the demersal fishes of the California Current

Vulnerability to climate change of managed stocks in the California Current large marine ecosystem

Introduction: Understanding how abundance, productivity and distribution of individual species may respond to climate change is a critical first step towards anticipating alterations in marine ecosystem structure and function, as well as developing strategies to adapt to the full range of potential changes. Methods: This study applies the NOAA (National Oceanic and Atmospheric Administration) Fisheries Climate Vulnerability Assessment method to 64 federally-managed species in the California Current Large Marine Ecosystem to assess their vulnerability to climate change, where vulnerability is a function of a species’ exposure to environmental change and its biological sensitivity to a set of environmental conditions, which includes components of its resiliency and adaptive capacity to respond to these new conditions. Results: Overall, two-thirds of the species were judged to have Moderate or greater vulnerability to climate change, and only one species was anticipated to have a positive response. Species classified as Highly or Very Highly vulnerable share one or more characteristics including: 1) having complex life histories that utilize a wide range of freshwater and marine habitats; 2) having habitat specialization, particularly for areas that are likely to experience increased hypoxia; 3) having long lifespans and low population growth rates; and/or 4) being of high commercial value combined with impacts from non-climate stressors such as anthropogenic habitat degradation. Species with Low or Moderate vulnerability are either habitat generalists, occupy deep-water habitats or are highly mobile and likely to shift their ranges. Discussion: As climate-related changes intensify, this work provides key information for both scientists and managers as they address the long-term sustainability of fisheries in the region. This information can inform near-term advice for prioritizing species-level data collection and research on climate impacts, help managers to determine when and where a precautionary approach might be warranted, in harvest or other management decisions, and help identify habitats or life history stages that might be especially effective to protect or restore

Spatio-temporal patterns in juvenile habitat for 13 groundfishes in the California Current Ecosystem.

Identifying juvenile habitats is critical for understanding a species' ecology and for focusing spatial fishery management by defining references like essential fish habitat (EFH). Here, we used vector autoregressive spatio-temporal models (VAST) to delineate spatial and temporal patterns in juvenile density for 13 commercially important species of groundfishes off the US west coast. In particular, we identified hotspots with high juvenile density. Three qualitative patterns of distribution and abundance emerged. First, Dover sole Microstomus pacificus, Pacific grenadier Coryphaenoides acrolepis, shortspine thornyhead Sebastolobus alascanus, and splitnose rockfish Sebastes diploproa had distinct, spatially-limited hotspots that were spatially consistent through time. Next, Pacific hake Merluccius productus and darkblotched rockfish Sebastes crameri had distinct, spatially limited hotspots, but the location of these hotspots varied through time. Finally, arrowtooth flounder Atheresthes stomias, English sole Parophrys vetulus, sablefish Anoplopoma fimbria, Pacific grenadier Coryphaenoides acrolepis, lingcod Ophiodon elongatus, longspine thornyhead Sebastolobus altivelis, petrale sole Eopsetta jordani, and Pacific sanddab Citharichthys sordidus had large hotspots that spanned a broad latitudinal range. These habitats represent potential, if not likely, nursery areas, the location of which will inform spatial management

Using multivariate state-space models to examine commercial stocks of redfish (Sebastes spp.) on the Flemish Cap

There are three different species of redfish (Sebastes spp.) in the waters of the Flemish Cap (Division 3M, NAFO Regulatory Area): S. fasciatus, S. mentella, and S. norvegicus. Historically, S. fasciatus and S. mentella have been managed together as a single stock because of similar biology and difficulty in species identification. Here we use multivariate autoregressive state-space models to examine the abundance trajectories of the three species and to determine whether they can be treated as a single stock for management purposes or whether they should be treaty separately. We also included covariates to evaluate relationships with climate, commercial catch, and the abundance of predators and (or) competitors and prey. We did two separate analyses: (i) a single-period analysis over the full time series and (ii) a blocked, two-period analysis over different regulatory periods. In both analyses, the best-fit model included separate trajectories for each species at each depth but one overall stock growth rate; both also included commercial catches as a covariate. These analyses suggest that a single assessment for the Sebastes complex is acceptable.S

Using multivariate state-space models to examine commercial stocks of redfish (Sebastes spp.) on the Flemish Cap

There are three different species of redfish (Sebastes spp.) in the waters of the Flemish Cap (Division 3M, NAFO Regulatory Area): S. fasciatus, S. mentella, and S. norvegicus. Historically, S. fasciatus and S. mentella have been managed together as a single stock because of similar biology and difficulty in species identification. Here we use multivariate autoregressive state-space models to examine the abundance trajectories of the three species and to determine whether they can be treated as a single stock for management purposes or whether they should be treaty separately. We also included covariates to evaluate relationships with climate, commercial catch, and the abundance of predators and (or) competitors and prey. We did two separate analyses: (i) a single-period analysis over the full time series and (ii) a blocked, two-period analysis over different regulatory periods. In both analyses, the best-fit model included separate trajectories for each species at each depth but one overall stock growth rate; both also included commercial catches as a covariate. These analyses suggest that a single assessment for the Sebastes complex is acceptable

Supplement 2. The depth and species-assemblage data used in the application.

<h2>File List</h2><blockquote> <p><a href="Lat33.csv">Lat33.csv</a></p> <p><a href="Lat33checksum.csv">Lat33checksum.csv</a></p> </blockquote><h2>Description</h2><blockquote> <p>Lat33.csv</p> <p>The depth and species-abundance data used in the application, from 68 demersal trawls at approximate latitude 33N. Column 1 contains the depth. Columns 2–118 contain the catch weight (kg) of each of 117 species. The species id numbers are not sequential, because some species were not caught at latitude 33N, and are not included.</p> <p>There are no missing values in this data set.</p> <p> </p> <p>Lat33checksum.csv </p> <p>The checksum values for the 118 columns in Lat33.csv.</p> </blockquote