Arrowtooth Flounder Research Articles

Spatially varying coefficients can improve parsimony and descriptive power for species distribution models

Species distribution models (SDMs) are widely used to relate species occurrence and density to local environmental conditions, and often include a spatially correlated variable to account for spatial patterns in residuals. Ecologists have extended SDMs to include spatially varying coefficients (SVCs), where the response to a given covariate varies smoothly over space and time. However, SVCs see relatively little use perhaps because they remain less known relative to other SDM techniques. We therefore review ecological contexts where SVCs can improve the interpretability and descriptive power from SDMs, including local responses to regional indices that represent ecological teleconnections; density‐dependent habitat selection; spatially varying detectability; and context‐dependent covariate responses that represent interactions with unmeasured covariates. We then illustrate three additional examples in detail using the vector autoregressive spatio‐temporal (VAST) model. First, a spatially varying decadal trends model identifies decadal trends for arrowtooth flounder Atheresthes stomias density in the Bering Sea from 1982 to 2019. Second, a trait‐based joint SDM highlights the role of body size and temperature in spatial community assembly in the Gulf of Alaska. Third, an age‐structured SDM for walleye pollock Gadus chalcogrammus in the Bering Sea contrasts cohorts with broad spatial distributions (1996 and 2009) and those that are more spatially constrained (2002 and 2015). We conclude that SVCs extend SDMs to address a wide variety of ecological contexts and can be used to better understand a range of ecological processes, e.g. density dependence, community assembly and population dynamics.

Climate‐informed models benefit hindcasting but present challenges when forecasting species–habitat associations

Although species distribution models (SDMs) are commonly used to hindcast fine‐scale population metrics, there remains a paucity of information about how well these models predict future responses to climate. Many conventional SDMs rely on spatially‐explicit but time‐invariant conditions to quantify species distributions and densities. We compared these status quo ‘static' models with more climate‐informed 'dynamic' SDMs to assess whether the addition of time‐varying processes would improve hindcast performance and/or forecast skill. Here, we present two groundfish case studies from the Bering Sea – a high latitude system that has recently undergone considerable warming. We relied on conventional statistics (R2, % deviance explained, UBRE or GCV) to evaluate hindcast performance for presence–absence, numerical abundance and biomass of arrowtooth flounder Atheresthes stomias and walleye pollock Gadus chalcogrammus. We then used retrospective skill testing to evaluate near‐term forecast skill. Retrospective skill testing enables direct comparisons between forecasts and observations through a process of fitting and forecasting nested submodels within a given time series. We found that the inclusion of time‐varying covariates improved hindcasts. However, dynamic models either did not improve or decreased forecast skill relative to static SDMs. This is likely a result of rapidly changing temperatures within the ecosystem, which required models to predict species responses to environmental conditions that were outside the range of observed values. Until additional model development allows for fully dynamic predictions, static model forecasts (or persistence forecasts from dynamic models) may serve as reliable placeholders, especially when anomalous conditions are anticipated. Nonetheless, our findings demonstrate support for the use of retrospective skill testing rather than selecting forecast models a priori based on their ability to quantify species–habitat associations in the past.

Shifting fish distributions impact predation intensity in a sub‐Arctic ecosystem

An abundance of studies in marine systems have documented species range shifts in response to climate change, and many more have used species distribution models to project species ranges under future conditions. However, there is increasing interest in moving beyond a single‐species focus to understand how species redistribution alters ecosystem dynamics via changes in trophic interactions. We employed spatiotemporal models to characterize decadal‐scale changes in spatial overlap between the distribution of juvenile walleye pollock Gadus chalcogrammus and the distributions of four of its groundfish predators: arrowtooth flounder Atheresthes stomias, Pacific cod Gadus macrocephalus, Pacific halibut Hippoglossus stenolepis and adult walleye pollock. These fishes represent ecologically and commercially important species in a rapidly changing sub‐Arctic ecosystem, the eastern Bering Sea, Alaska, USA. We then examined whether changes in spatial overlap corresponded to changes in predation, using spatiotemporal models of predator stomach contents. We found marked shifts in spatial overlap between juvenile pollock and two predators (arrowtooth flounder and Pacific halibut) over 34 years, with changes in overlap corresponding to increases in population‐scale predation pressure. By contrast, we did not find clear relationships between spatial overlap and predation for Pacific cod and adult pollock, the two predators for which juvenile pollock constitute a much smaller diet proportion. Our findings highlight the complexity of predicting predation dynamics for generalist marine species and suggest a need for better process‐based methods for understanding the potential future ecological impacts of coupled species range shifts. However, simple metrics of spatial overlap between relatively specialized predators and their prey offer promise as a means to integrate predictions from species distribution models into ecosystem‐based fisheries management.

Synthesizing integrated ecosystem research to create informed stock-specific indicators for next generation stock assessments

Over the past two decades, numerous ecosystem surveys and process studies have emerged to monitor and assess the large marine ecosystems of Alaska. Several regional collaborative integrated ecosystem research projects (IERPs) were conducted to gain understanding of fish population fluctuations in relation to the surrounding environment. The Gulf of Alaska (GOA) IERP is one example of such an effort. Products of this program include a suite of in situ observations from fully integrated ecosystem surveys, laboratory experiments of physical thresholds for fish condition, and high-resolution oceanographic, planktonic, and habitat distribution models. When coupled, the synthesis products of this program can be utilized to understand system connectivity and highlight the primary ecosystem drivers of the GOA. Much of this information was included in annual GOA ecosystem status reports through individual indicator contributions. However, assimilation of these data into single-species stock assessments has remained limited. We provide a clear and direct avenue for including the products of these IERPs through the new ecosystem and socioeconomic profile (ESP) framework that identifies mechanistic relationships and tests ecosystem linkages within the stock assessment process. We present a case study using a data synthesis of the five commercially and ecologically valuable focal species of the GOAIERP (sablefish, pollock, Pacific cod, arrowtooth flounder, and Pacific ocean perch). Information was organized along the categories of distribution, phenology, and condition by life history stage to develop life history narratives for each species. These narratives identified critical ecosystem processes that could impact survival of each species. We then used habitat distribution models, seasonal phenology, and energy allocation strategies to sequentially reduce two gridded temperature datasets to reflect the life experience of the stock. This method essentially aligns ecosystem information at a spatial and temporal scale relevant to a stock and creates informed indicators that could then be related to a stock assessment parameter of interest, such as recruitment. Informed temperature indicators differed in magnitude and variability when compared to non-informed indicators and demonstrating species and stage-specific thermal preferences. The difference between the informed indicators and the non-informed indicators can also highlight thresholds and trends in habitat preference that could be further investigated with targeted process studies or laboratory experiments. The coordinated nature of the IERP allowed for the creation of these informed indicators that would not be possible with the results of any one process study. Both the stock-specific narratives and the informed indicators can be included into the ESPs for further monitoring and development. This integration ensures that the identified ecosystem linkages are evaluated concurrently with the stock assessment and ultimately transferred to fishery managers in an efficient and effective format for informing management decisions.

An ensemble approach to understand predation mortality for groundfish in the Gulf of Alaska

There is increasing consensus of the need for ecosystem-based fisheries management (EBFM), which accounts for trophic interactions and environmental conditions when managing exploited marine resources. Continued development and testing of analytical tools that are expected to address EBFM needs are essential for guiding the management of fisheries resources in achieving and balancing multiple social, economic, and conservation objectives. To address these needs, we present and compare alternative climate-informed multi-species statistical catch-at-age models to account for spatio-temporal differences in stock distributions, with application to four groundfish species (walleye pollock Gadus chalcogrammus, Pacific cod Gadus macrocephalus, arrowtooth flounder Atheresthes stomias, and Pacific halibut Hippoglossus stenolepis) in the Gulf of Alaska, USA. We integrate across multiple forms of uncertainty regarding the data and distribution of Pacific halibut using an ensemble modelling approach. Models developed here can be used to supplement current tactical fisheries management and inform on the trade-offs between harvesting across groundfish in the Gulf of Alaska. This approach may be applicable for other situations where spatial and temporal overlap is extensive among closely coupled species.

Food habit variability of arrowtooth flounder (Atheresthes stomias) along the U.S. west coast

A diet study of arrowtooth flounder (Atheresthes stomias) was undertaken to provide current information on their food habits and predator-prey relationships in the California Current Ecosystem. Arrowtooth flounder stomachs (n = 573) were collected between 2013 and 2018 from 397 trawls during the Northwest Fisheries Science Center’s West Coast Groundfish Bottom Trawl Survey. A total of 357 stomachs (62.3%) contained prey, which revealed a highly piscivorous diet across all lengths examined (14 – 77 cm) and described a regionalized and opportunistic feeding behavior. Increased predator length correlated both with an increase in percentage of fish prey consumed and an increase in depth of capture. Smaller (< 43 cm) and shallower (≤ 183 m) arrowtooth flounder consumed a relatively high percentage of euphausiids and shrimp, while larger arrowtooth flounder (≥ 43 cm) captured at greater depths (> 183 m) consumed more fish and fewer shrimp and euphausiids. Arrowtooth flounder diet varied by geographic area, likely resulting from regional differences in prey availability. North of the mean latitude of capture (44.45°N), Pacific hake (Merluccius productus) and Pacific herring (Clupea pallasii) were the predominant fish in arrowtooth flounder diets, while arrowtooth flounder caught south of the mean latitude consumed mostly Pacific hake and rockfishes (Scorpaenidae). Unidentified teleost fish contributed much to the diet across all size, depth, and latitude ranges.

The effects of climate, oceanography, and habitat on the distribution and abundance of northern California Current continental shelf groundfishes

AbstractThe California Current Ecosystem has experienced variable climate regimes, hypoxia, and marine heatwave events that have the potential to impact groundfishes and their associated fisheries. Using bottom trawl survey data collected by NOAA Fisheries, we assessed changes over the last four decades in northern California Current continental shelf (≤200 m) groundfish assemblage composition, species' presence, and relationships to environmental and habitat variables. We focus on the currently understudied continental shelf area, due to its ecological and economic importance, especially after the recent opening of historically important areas to trawling. We found a temporally consistent separation in groundfish assemblages between depth zones based on NMS analysis using species found in over 1% of samples, with shallow, mid‐, and deep shelf groupings. Grain size, species richness, and diversity were associated with assemblage composition. Then, focusing on petrale sole, rex sole, lingcod, arrowtooth flounder, sablefish, English sole, Pacific sanddab, and Dover sole, we examined what factors impact groundfish presence and abundance on the shelf. Bottom temperature, sediment characteristics, and depth were correlated with abundance for all species. These results corroborate previous work indicating recent reductions in presence of hypoxia‐intolerant species. Shallow‐water groundfishes known to tolerate warmer water and low dissolved oxygen concentrations exhibit reductions offshore, possibly a result of low recruitment. There have been significant spatiotemporal changes in the shelf groundfish populations over the past several decades, and while assemblage composition over most of the shelf remains consistent, single species distributional shifts may impact access to target species in newly reopened areas.

Modern state of stocks for demersal and pelagic fishes on the shelf of Olyutorsky-Navarin area

Stocks of demersal and pelagic fish species are assessed for the bottom layer over the outer shelf and upper continental slope between Cape Olyutorsky and Cape Navarin (northwestern Bering Sea) on the data of bottom trawl survey conducted aboard RV Professor Levanidov over the isobaths 20-400 m in the summer of 2019. The total biomass of demersal fish in the surveyed polygon was estimated as 682,262 t; the portion of pacific cod was 51.50 %, arrowtooth flounder — 9.80 %, great sculpin — 9.64 %, rock sole — 4.60 %, alaska skate — 4.57 %, flathead flounders — 2.56 %, yellow irish lord — 2.30 %, and &lt; 2 % for other species. The total biomass of pelagic fish species in the bottom layer was estimated as 759,639 t (species-specific coefficients of catchability were used); the portion of adult walleye pollock was 85.12 %, its juveniles — 9.94 %, pacific herring — 4.67 %, and other pelagic species — 0.27 % in sum. Mean ratios of the species stock between the surveyed polygon and other areas of the northwestern Bering Sea, as the Gulf of Anadyr and the deeper continental slope (below 400 m), were evaluated using the data of bottom trawl surveys conducted in 2005-2017. Some species as yellow irish lord, saffron cod, pacific halibut, arrowtooth flounder, great sculpin, kamchatka flounder, rock sole, and aleutian skate distributed mostly within the polygon and their mean biomass in the outside areas varied from 0.5 % to 69.2 % relative to the biomass in the polygon surveyed in 2019. On the contrary, the portions of pacific cod, greenland halibut, alaska skate, and walleye pollock were larger outside the polygon — from 102.9 to 190.4 %, and almost entire stocks were in the outside areas for alaska plaice, flathead flounders, and pacific herring — from 533.4 % to 1380.5 % relative to the biomass accounted within the polygon. The stocks assessed in 2019 reflected both the state of populations and their spatial and bathymetric redistribution, mostly because of the St. Lawrence Cold Water Pool shrinkage at the bottom of the Gulf of Anadyr. The stocks fluctuations are reasoned mainly by natural factors, rather than fishery impact.

The Role of Size in Trophic Niche Separation between Two Groundfish Predators in Alaskan Waters

AbstractTo minimize negative effects of competition, predators must divide resources along one or more niche dimensions. Trophic niche separation is a principal method of resource partitioning in marine environments and is often assessed by quantifying diets of fishes with similar lengths. Taxonomic differences in allometric growth, however, suggest that the degree of gape limitation at a given body size varies among species. We studied resource overlap between two potential competitors in Southeast Alaska: Pacific Halibut Hippoglossus stenolepis and Arrowtooth Flounder Atheresthes stomias. We quantified length–gape relationships and assessed effects of fork length (FL; cm), gape height (GH; mm), and gape width (GW; mm) on interpretations of trophic niche separation. Gape sizes for Arrowtooth Flounder were nearly twice those of Pacific Halibut at similar FLs. Predators with smaller gapes exhibited moderate to high dietary overlap ( = 0.554; = 0.731), whereas those with larger gapes had lower dietary overlap and distinct diet compositions ( = 0.421; = 0.265). These findings suggest that the greatest potential for food competition is among small‐bodied Arrowtooth Flounder and relatively large‐bodied Pacific Halibut, with trophic niche separation increasing as these predators progress throughout their ontogeny. When comparing resource use among predators with similar FLs, we found high dietary overlap but significantly different diet compositions ( = 0.657). Thus, we postulate that GW is more appropriate than FL when quantifying trophic niche separation among sympatric fishes, especially when disparate length–gape relationships are detected. Studies of resource partitioning would benefit from examining multiple size metrics and explicitly considering differences in allometric growth, thereby addressing potential mechanisms for resource overlap among hypothesized competitors.

Forecasting community reassembly using climate‐linked spatio‐temporal ecosystem models

Ecosystems are increasingly impacted by human activities, altering linkages among physical and biological components. Spatial community reassembly occurs when these human impacts modify the spatial overlap between system components, and there is need for practical tools to forecast spatial community reassembly at landscape scales using monitoring data. To illustrate a new approach, we extend a generalization of empirical orthogonal function (EOF) analysis, which involves a spatio‐temporal ecosystem model that approximates coupled physical, biological and human dynamics. We then demonstrate its application to five trophic levels for the eastern Bering Sea by fitting to multiple, spatially unbalanced datasets measuring physical characteristics (temperature measurements and climate‐linked forecasts), primary producers (spring and fall size‐fractionated chlorophyll‐a), secondary producers (copepods), juveniles (age‐0 walleye pollock), adult consumers (five commercially important fishes), human activities (seasonal fishing effort) and mobile predators (seabirds). We identify the spatial niche for each ecosystem component, as well as dominant modes of variability that are highly correlated with a known bottom–up driver of dynamics. We then measure spatial overlap between interacting variables (using Schoener's‐D) and identify that age‐0 pollock have decreased spatial overlap with copepods and increased overlap with adult pollock during warm years, and also that adult pollock have increased overlap with arrowtooth flounder and decreased overlap with catcher–processor fishing effort during these warm years. Given the warming conditions that are projected for the coming decade, the model forecasts increased prey and competitor overlap involving adult pollock (between age‐0 pollock, adult pollock and arrowtooth flounder) and decreased overlap with the copepod forage base and with the catcher–processor fishery during future warming. We recommend that joint species distribution models be extended to incorporate ‘ecological teleconnections' (correlations between distant locations arising from known mechanisms) arising from behavioral adaptation by mobile animals as well as passive advection of nutrients and planktonic juvenile stages.

Improving estimates of species distribution change by incorporating local trends

A common goal in ecology and its applications is to better understand how species' distributions change over space and time, yet many conventional summary metrics (e.g. center of gravity) of distribution shifts may offer limited inference because such changes may not be spatially homogenous. We develop a modeling approach to estimate a spatially explicit temporal trend (i.e. local trend), alongside spatial (temporally constant) and spatiotemporal (time‐varying) components, to compare inferred spatial shifts to those indicated by conventional metrics. This method is generalizable to many data types including presence–absence data, count data and continuous data types such as density. To demonstrate the utility of this new approach, we focus on the application of this model to a community of well‐studied marine fish species on the US west coast (19 species, representing a wide range of presence–absence and densities). Results from conventional model selection indicate that the use of the model accounting for local trends is clearly justified for over 89% of these species. In addition to making more parsimonious and accurate predictions, we illustrate how estimated spatial fields from the local trend model can be used to classify regions within the species range where change is relatively homogenous. Conventional summary metrics, such as center of gravity, can then be calculated on each such region or within previously defined biogeographic boundaries. We use this approach to illustrate that change is more nuanced than what is expressed via global metrics. Using arrowtooth flounderAtheresthes stomiasas an example, the observed southward shift over time in the center of gravity is not reflective of a uniform shift in densities but local trends of decreasing density in the northern region and rapidly increasing density at the southern edge of the species' range. Thus, estimating local trends with spatiotemporal models improves interpretation of species distribution change.

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.

Development of a predation index to assess trophic stability in the Gulf of Alaska.

Predation can have substantial and long‐term effects on the population dynamics of ecologically important prey. Diverse predator assemblages, however, may produce stabilizing (i.e., portfolio) effects on prey mortality when consumption varies asynchronously among predators. We calculated spatiotemporal variation in predation on a dominant forage species to quantify synchrony and portfolio effects in a food web context and better understand diversity–stability relationships in a large marine ecosystem that has undergone considerable changes in community composition. We selected Walleye Pollock (Gadus chalcogrammus) as our case study because they support some of the largest, most valuable commercial fisheries in the world and serve as essential prey for an array of economically and culturally important species. Thus, there are sufficient data for Pollock with which to test ecological theories in an empirical setting. Spatially explicit predation indices accounted for annual variation in predator biomass, bioenergetics‐based rations, and age‐specific proportions of Pollock consumed by a suite of groundfishes in the Gulf of Alaska (1990–2015). We found that Arrowtooth Flounder (Atheresthes stomias) was, by far, the dominant Pollock predator (proportional consumption: 0.74 ± 0.14). We also found synchronous trends in consumption among predator species, indicating a lack of portfolio effects at the basin scale. This combination of a single dominant predator and synchronous consumption dynamics suggests strong top‐down control over Pollock in the Gulf of Alaska, though the degree of synchrony was highly variable at all spatial scales. Whereas synchrony generally increased in the western subregion, consumption in the central Gulf of Alaska became less synchronous through time. This suggests diminished trophic stability in one area and increased stability in another, thereby emphasizing the importance of spatiotemporal heterogeneity in maintaining food web structure and function. Finally, total Pollock consumption was highly variable (ranging from 1.87 to 7.63 Tg) and often exceeded assessment‐based estimates of productivity. We assert that using our holistic and empirically derived predation index as a modifier of assumed constant natural mortality would provide a practical method for incorporating ecological information into single‐species stock assessments.

Eddy retention and seafloor terrain facilitate cross‐shelf transport and delivery of fish larvae to suitable nursery habitats

AbstractFor marine fish with ontogenetic shifts in habitat requirements, survival is dependent upon oceanographic transport of pelagic larvae from spawning locations and the arrival of settlement‐stage larvae to nursery habitats. Settlement success for fish with nurseries on the continental shelf, such as many flatfish, relies on routes of transport that facilitate the delivery of larvae from offshore to suitable inshore habitats. To address spatial and temporal coupling between spawning, transport, and settlement, we utilized an individual‐based biophysical model for the years 2000–2011 in combination with a juvenile habitat suitability model for arrowtooth flounder (Atheresthes stomias), an abundant predatory flatfish in the oceans off Alaska. Settlement success was inversely related to the availability of nursery habitat, but oceanographic variability dictated interannual patterns in larval supply to nurseries. Paradoxically, the majority of larvae were advected offshore and arrived to nurseries on the continental shelf. Shoreward bathymetric steering through glacial troughs that resulted in directed transport to nurseries was minimal despite the high proportion of larvae that accessed trough features. Based on modeling results and empirical observations, mesoscale eddies and retention near suitable settlement habitats enhanced settlement and recruitment magnitude. In advective ecosystems such as the Gulf of Alaska, settlement success and cross‐shelf transport are augmented by transient retentive features that influence recruitment by facilitating the delivery of larvae to nursery habitats on the continental shelf.

Identification of four new Kudoa spp. (Myxozoa: Myxosporea: Multivalvulida) in commercial fishes collected from South China Sea, Atlantic Ocean, and Bering Sea by integrated taxonomic approach.

Members of the myxosporean genus Kudoa are defined as having a myxospore with four or more shell valves (SVs) and a corresponding number of polar capsules (PCs). Here, we employed integrated taxonomic approaches to four kudoid isolates from Acentrogobius chlorostigmatoides and Konosirus punctatus from the South China Sea, off Guangdong, Pentanemus quinquarius from the Southeast Atlantic Ocean, off West African coast, and Atheresthes stomias from the Bering Sea, off Alaska, and concluded that all these kudoids were novel species, named Kudoa acentrogobia n. sp., Kudoa guangdongensis n. sp., Kudoa iidae n. sp., and Kudoa aburakarei n. sp., respectively. Kudoa guangdongensis n. sp., forming pseudocysts in the trunk muscle myofibers of K. punctatus, had large-sized tripod myxospores with three wing-like SV extensions and three PCs (one prominent PC and two rudimentary PCs). Phylogenetic analyses based on the 18S and 28S ribosomal RNA gene (rDNA) demonstrated its affinity to the genus Kudoa, not to Unicapsula characterized by a myxospore with one prominent PC and two rudimentary PCs, suggesting the atypical nature of this new species in the context of myxospore morphology. Three other kudoid isolates had four SVs and PCs in a semi-quadrated, ray-like, or cruciform myxospore, respectively, forming pseudocysts in the trunk muscle myofibers. Kudoa iidae n. sp. forming pseudocysts in the muscles of P. quinquarius from Southeast Atlantic Ocean had unique myxospores with ray-like form, showing close morphological resemblance to Kudoa rayformis, which were recorded from the muscle of Scomberomorus sierra from the Pacific Ocean off Panama. These two species had a phylogenetic relationship of morphological convergence, evolving separately in different sea areas. It is fairly difficult to differentiate K. acentrogobia n. sp. and K. aburakarei n. sp., prevalent in their host fishes, from kudoid species with similar myxospore morphology (e.g., Kudoa nova and Kudoa thyrsites, respectively), but distinct in phylogeny from known Kudoa spp. Combined taxonomic identification of multivalvulid myxosporeans based on both morphological criteria of isolated myxozoans and their molecular characterization could disclose their real biodiversity and phylogeny.

MinION sequencing of seafood in Singapore reveals creatively labelled flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans

Food mislabelling is a growing world-wide problem that can be addressed through the authentication of ingredients via techniques like mass spectrometry or DNA sequencing. However, unfortunately traditional DNA sequencing methods are slow, expensive, and require well-equipped laboratories. We here test whether these problems can be overcome through the use of Nanopore sequencing. We sequenced 92 single and 13 mixed-species samples purchased in Singapore. We successfully obtained DNA barcodes for 94% and 100% of the single- and mixed-species samples respectively by applying a bioinformatics pipeline that was optimised for this purpose. We find comparatively low levels of clear-cut mislabelling for single-species samples (7.6%), while the rates are higher for mixed-species samples (38.5%). The low rates for single-species samples are somewhat deceptive, however, because of the use of vague species names. With regard to the clearly mislabelled single-species products, higher-value products (e.g., prawn roe, wild-caught Atlantic salmon, halibut) are replaced with lower-value ingredients (e.g., fish roe, Pacific salmon, arrowtooth flounder) while more serious problems are observed for mixed-species samples. Cuttlefish and prawn balls repeatedly contained pig DNA and all but one of the mixed samples labelled as containing crustaceans (‘crab’, ‘prawn’, ‘lobster’) lacked a significant number of crustacean signals. We conclude that there is a need for more regular testing of seafood samples and suggest that due to speed and low-cost, MinION would be a good instrument for this purpose. We also emphasize the need for developing clearer labelling guidelines.

Биологические исследования в российских дальневосточных и арктических морях в трансарктической экспедиции ВНИРО

The results of biological research on the RV “Professor Levanidov” in the Bering, Chukchi, East Siberian, Laptev and Kara seas, July 6 — October 2, 2019 are presented. Expatriates from the Pacific and Atlantic oceans made a significant contribution to the biomass of plankton communities in the Arctic seas. Plankton biomass was depended on the distance from the Bering Strait in the east, the Fram Strait and the Barents Sea in the west. A noticeable level of biomass was maintained by local Arctic plankton species. In megabenthos, crustaceans dominated in the Kara and Chukchi seas, and echinoderms in the Laptev and East Siberian seas. The biomass of demersal fishes (mostly Pacific cod, Saffron cod, yellowfin flounder, great sculpin and starry flounder) in the Karaginskaya subzone was 318 thousand tons, pollock biomass was 539–1349 thousand tons. The biomass of demersal fishes (mostly cod, great sculpin, and arrowtooth flounder) in the Olyutorsko-Navarinsky area was 768 thousand tons, pollock biomass 359–897 thousand tons. Representatives of Cottidae, Zoarcidae, Liparidae, Gadidae, Pleuronectidae, and Agonidae families comprised the bulk of catches in Arctic seas. Polar cod dominated in all seas, with exception of the Chukchi Sea, where pollock biomass increased many times compared to previous years. In the Laptev Sea, the abundance of Greenland halibut increased significantly. In the Chukchi Sea, Polar cod biomass was 117 thousand tons, flathead sole 43 thousand tons, pollock 897 thousand tons, snow crab 51 thousand tons. In the Kara Sea, Polar cod biomass was 171 thousand tons, snow crab 67 thousand tons. Significant differences in food composition and feeding intensity of pollock, Polar cod, capelin and Greenland halibut of different sizes revealed the existence of a complex trophic system. Anthropogenic pollution was assessed, the distribution of species-indicators of vulnerable marine ecosystems was studied, and materials for genetic research were collected.

Defining indices of ecosystem variability using biological samples of fish communities: A generalization of empirical orthogonal functions

Multivariate data reduction techniques are widely used to describe modes of variability in atmospheric and oceanographic conditions for the world’s oceans. Dominant modes of variability such as the Pacific Decadal Oscillation (PDO) are typically defined as a statistical summary of physical measurements, and include both principle components representing modes of variability over time, and an empirical orthogonal function (EOF) giving the spatial pattern associated with a positive or negative phase for each mode. Typically, these indices are compared with biological conditions to describe or predict physical drivers of ecological dynamics. In some circumstances, however, it may instead be useful to apply EOF analysis directly to biological measurements, estimating indices of biological variability as well as maps of biological response associated with each index. We therefore develop a generalization of EOF analysis that can be applied directly to multispecies biological samples using a multivariate spatio-temporal model. These biologically derived indices can then be compared with relevant indices derived from physical data, or used as covariates in spatially-varying coefficient models. We first show that a spatio-temporal model can replicate previous EOF estimates of the PDO and North Pacific Gyre Oscillation. We then identify three axes of variability in the eastern Bering Sea using biomass-sampling data for fourteen bottom-associated fishes and decapod crustaceans from 1982 to 2017. The first axis represents habitat preferences that are stable over time, and the second represents a multi-decadal trend in distribution for most species; for example, showing an increasing density for Alaska skate and arrowtooth flounder in the middle and inner domain. Finally, the third axis shows high interannual variability from 1982 to 1998 switching to multiyear stanzas from 1999 to 2017 and is highly correlated (0.87) with the extent of the cold bottom temperatures in this region and associated impacts on Alaska pollock and Pacific cod. These axes represent ecological dynamics for adult fishes and therefore integrate the impact of bottom-up and top-down processes, and they also confirm the importance of cold-pool extent for fish distribution in the Bering Sea while visualizing its varied impact on individual species. Moreover, this spatio-temporal approach allows oceanographers to define annual indices representing modes of variability in diverse biological communities from widely available field-sampling data.

Multispecies biomass dynamics models reveal effects of ocean temperature on predation of juvenile pollock in the eastern Bering Sea

AbstractWalleye pollock (Gadus chalcogrammus) supports one of the largest commercial fisheries in the world. Juvenile pollock are important forage fish in the eastern Bering Sea (EBS) ecosystem, often representing the largest fraction in the diets of major Bering Sea piscivores. Large variability in the EBS pollock stock biomass in recent years has been attributed primarily to fluctuations in recruitment. It has been hypothesized that predation rates on forage fishes increase when the cold pool (a body of cold water &lt; 2°C) is extensive and covers much of the middle continental shelf, which tends to concentrate larger predatory fishes in the outer shelf and slope regions. In contrast, young pollock appear to tolerate colder temperatures than older fish and can stay in the cold pool, thereby reducing predation. We used a multispecies modeling approach to examine the effects of the cold pool size on predation of juvenile pollock. We found that predation on age‐1 pollock by age‐3+ pollock decreased, and predation on age‐1 and age‐2 pollock by arrowtooth flounder increased with increasing bottom temperature, which was used as a proxy for the cold pool size. These results suggest that the cold pool creates spatial separation between juvenile pollock and arrowtooth flounder, but not between adult and juvenile pollock. The model developed in this study could be used to examine the effects of other covariates on interspecific interactions, help explain observed changes in fish communities, and understand implications of climate change on ecosystems and their productivity.

Trade‐offs in covariate selection for species distribution models: a methodological comparison

Species distribution models (SDMs) are a common approach to describing species’ space‐use and spatially‐explicit abundance. With a myriad of model types, methods and parameterization options available, it is challenging to make informed decisions about how to build robust SDMs appropriate for a given purpose. One key component of SDM development is the appropriate parameterization of covariates, such as the inclusion of covariates that reflect underlying processes (e.g. abiotic and biotic covariates) and covariates that act as proxies for unobserved processes (e.g. space and time covariates). It is unclear how different SDMs apportion variance among a suite of covariates, and how parameterization decisions influence model accuracy and performance. To examine trade‐offs in covariation parameterization in SDMs, we explore the attribution of spatiotemporal and environmental variation across a suite of SDMs. We first used simulated species distributions with known environmental preferences to compare three types of SDM: a machine learning model (boosted regression tree), a semi‐parametric model (generalized additive model) and a spatiotemporal mixed‐effects model (vector autoregressive spatiotemporal model, VAST). We then applied the same comparative framework to a case study with three fish species (arrowtooth flounder, pacific cod and walleye pollock) in the eastern Bering Sea, USA. Model type and covariate parameterization both had significant effects on model accuracy and performance. We found that including either spatiotemporal or environmental covariates typically reproduced patterns of species distribution and abundance across the three models tested, but model accuracy and performance was maximized when including both spatiotemporal and environmental covariates in the same model framework. Our results reveal trade‐offs in the current generation of SDM tools between accurately estimating species abundance, accurately estimating spatial patterns, and accurately quantifying underlying species–environment relationships. These comparisons between model types and parameterization options can help SDM users better understand sources of model bias and estimate error.