Use of state‐space modelling to identify ecological covariates associated with trends in pinniped demography

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Upscaling as ecological information transfer: a simple framework with application to Arctic ecosystem carbon exchange

Transferring ecological information across scale often involves spatial aggregation, which alters information content and may bias estimates if the scaling process is nonlinear. Here, a potential solution, the preservation of the information content of fine-scale measurements, is highlighted using modeled net ecosystem exchange (NEE) of an Arctic tundra landscape as an example. The variance of aggregated normalized difference vegetation index (NDVI), measured from an airborne platform, decreased linearly with log(scale), resulting in a linear relationship between log(scale) and the scale-wise modeled NEE estimate. Preserving three units of information, the mean, variance and skewness of fine-scale NDVI observations, resulted in upscaled NEE estimates that deviated less than 4% from the fine-scale estimate. Preserving only the mean and variance resulted in nearly 23% NEE bias, and preserving only the mean resulted in larger error and a change in sign from CO₂ sink to source. Compressing NDVI maps by 70–75% using wavelet thresholding with the Haar and Coiflet basis functions resulted in 13% NEE bias across the study domain. Applying unique scale-dependent transfer functions between NDVI and leaf area index (LAI) decreased, but did not remove, bias in modeled flux in a smaller expanse using handheld NDVI observations. Quantifying the parameters of statistical distributions to preserve ecological information reduces bias when upscaling and makes possible spatial data assimilation to further reduce errors in estimates of ecological processes across scale.     

Effects of cage netting colour and density on the skin pigmentation and stress response of Australian snapper Pagrus auratus (Bloch & Schneider, 1801)

The unnaturally dark pigmentation of cultured Australian snapper Pagrus auratus can be improved through dietary astaxanthin supplementation and by holding fish in tanks with a white background. The practical application of these laboratory‐based findings was examined with two experiments to establish if the advantages of transferring fish to light coloured tanks before harvest could be achieved on‐farm using white cages and to determine the effects of fish density on skin colour. For the first experiment, snapper (mean TL=29.7 cm) were transferred from a commercial snapper sea cage to black or white netted cages and fed diets supplemented with unesterified astaxanthin (supplied as Lucantin^® Pink, BASF) at 0 or 39 mg kg^?1 for 42 days. Skin colour was measured using the CIE (black–white), (green–red), (blue–yellow) colour scale. Snapper held in white netting cages became significantly lighter (higher ) than snapper held in black cages; however, values were not as high as previous laboratory‐based studies in which snapper were held in white plastic‐lined cages. Snapper fed astaxanthin displayed significantly greater and values, and total carotenoid concentrations after 42 days. In addition, total carotenoids were higher in fish from black than white cages. The second experiment was designed to investigate whether density reduced the improvements in skin colour achieved by holding fish in white coloured cages and whether cage colour affected stress. Snapper (mean weight=435 g) were acclimated to black cages and fed 39 mg kg^?1 astaxanthin for 44 days before transferring to black or white plastic‐lined cages at 14 (low), 29 (mid) or 45 (high) kg m^?3 for 7 days after which time skin colour, plasma cortisol and plasma glucose concentrations were measured. Skin lightness () was greater in snapper transferred to white plastic‐lined cages with the lightest coloured fish obtained from the lowest density after 7 days. Density had no effect on plasma cortisol or glucose levels after 7 days, although plasma cortisol was elevated in snapper from black cages. For improved skin colouration we recommend feeding unesterified astaxanthin at 39 mg kg^?1 for approximately 6 weeks and transferring snapper to white plastic‐lined cages or similar at low densities for short periods before harvest rather than producing fish in white netting sea cages subject to biofouling.     

Effect of electrical stunning at slaughter on the quality of farmed turbot (Psetta maxima)

Food quality aspects of farmed turbot (Psetta maxima) were compared following two methods of slaughter: the current commercial method, by immersion in an ice slurry, which is then dewatered after approximately 20 min, or by first humanely, electrically stunning the fish using a prototype commercial stunner, before immersion in an ice slurry, which is dewatered after 20 min. Quality was assessed for up to 10 days of storage on ice following slaughter. No differences were found between the slaughter methods in terms of an overall carcass quality: overall appearance, haemorrhage, damage, burst gall bladder, staining of the body cavity by leakage from the gut or damage to the spine. No detectable difference was found between the treatments using the industry standard freshness scoring system, the Quality Index Method. Both groups of fish were classified as ‘Fresh’ after 10 days of storage on ice. Using objective measurements of colour, no differences between fish from either treatment were found in fillet colour. Changes in flesh pH were similar in electrically stunned and traditionally killed fish with a mean pH (±SE) at 2 h post‐mortem of 6.80±0.027 declining to 6.44±0.032 at 24 h post‐mortem. Humane electrical stunning of turbot at slaughter neither detectably improved nor decreased product quality as measured between 1 and 10 days of storage on ice.     

Effects of dietary astaxanthin concentration and feeding period on the skin pigmentation of Australian snapper Pagrus auratus (Bloch & Schneider, 1801)

A single‐factor experiment was conducted to investigate the effects of dietary astaxanthin concentration on the skin colour of snapper. Snapper (mean weight=129 g) were held in white cages and fed one of seven dietary levels of unesterified astaxanthin (0, 13, 26, 39, 52, 65 or 78 mg astaxanthin kg^?1) for 63 days. Treatments comprised four replicate cages, each containing five fish. The skin colour of all fish was quantified using the CIE L^*, a^*, b^* colour scale after 21, 42 and 63 days. In addition, total carotenoid concentrations of the skin of two fish cage^?1 were determined after 63 days. Supplementing diets with astaxanthin strongly affected redness (a^*) and yellowness (b^*) values of the skin at all sampling times. After 21 days, the a^* values increased linearly as the dietary astaxanthin concentration was increased before a plateau was attained between 39 and 78 mg kg^?1. The b^* values similarly increased above basal levels in all astaxanthin diets. By 42 days, a^* and b^* values increased in magnitude while a plateau remained between 39 and 78 mg kg^?1. After 63 days, there were no further increases in measured colour values, suggesting that maximum pigmentation was imparted in the skin of snapper fed diets >39 mg kg^?1 after 42 days. Similarly, there were no differences in total carotenoid concentrations of the skin of snapper fed diets >39 mg kg^?1 after 63 days. The plateaus that occurred in a^* and b^* values, while still increasing in magnitude between 21 and 42 days, indicate that the rate of astaxanthin deposition in snapper is limited and astaxanthin in diets containing >39 mg astaxanthin kg^?1 is not efficiently utilized. Astaxanthin retention after 63 days was greatest from the 13 mg kg^?1 diet; however, skin pigmentation was not adequate. An astaxanthin concentration of 39 mg kg^?1 provided the second greatest retention in the skin while obtaining maximum pigmentation. To efficiently maximize skin pigmentation, snapper growers should commence feeding diets containing a minimum of 39 mg unesterified astaxanthin kg^?1 at least 42 days before sale.     

QTL for IHNV resistance and growth identified in a rainbow (Oncorhynchus mykiss) × Yellowstone cutthroat (Oncorhynchus clarki bouvieri) trout cross

Infectious hematopoietic necrosis virus (IHNV) is a major constraint to rainbow trout culture. Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri) have greater resistance to this virus than do rainbow trout (O. mykiss), but the genetic mechanism of this resistance is not understood. We conducted a genome scan using a backcross of cutthroat trout into a rainbow trout background to estimate the number and locations of quantitative trait loci (QTL) associated with IHNV resistance and growth in trout. IHNV resistance was considered in terms of both survival (binary trait) and days to death (quantitative trait). The genetic map was scanned using interval mapping via two different approaches: one model considered survival alone and a second two-part model combined both survival and days to death. Three QTL were significantly (P ≤ 0.05) associated with virus resistance genome-wide, explaining 32.5% of the phenotypic variation. Cutthroat alleles at two of these QTL resulted in increased resistance to the pathogen, as expected. No growth QTL were detected in this cross. We suggest that these traits are genetically independent.     

A review of cyanobacterial odorous and bioactive metabolites: Impacts and management alternatives in aquaculture

Increased demand has pushed extensive aquaculture towards intensively operated production systems, commonly resulting in eutrophic conditions and cyanobacterial blooms. This review summarizes those cyanobacterial secondary metabolites that can cause undesirable tastes and odors (odorous metabolites) or are biochemically active (bioactive metabolites) in marine and freshwater, extensive and intensive aquaculture systems. For the scope of this paper, biochemically active metabolites include (1) toxins that can cause mortality in aquaculture organisms or have the potential to harm consumers via accumulation in the product (hepatotoxins, cytotoxins, neurotoxins, dermatoxins, and brine shrimp/molluskal toxins), (2) metabolites that may degrade the nutritional status of aquaculture species (inhibitors of proteases and grazer deterrents) or (3) metabolites that have the potential to negatively affect the general health of aquaculture species or aquaculture laborers (dermatoxins, irritant toxins, hepatotoxins, cytotoxins). Suggestions are made as to future management practices in intensive and extensive aquaculture and the potential exposure pathways to aquaculture species and human consumers are identified.     

Differences in swimbladder volume between Baltic and Norwegian spring-spawning herring: Consequences for mean target strength

Fish swimbladders, where present, contribute most to the scattering of sound by fish, as measured by the target strength (TS). The volumes of the swimbladders of two different European stocks of Atlantic herring were compared to consider the effect on estimates of TS. Swimbladder volumes of Baltic and Norwegian spring-spawning herring (Clupea harengus) were measured, together with individual herring fat content. Swimbladder volumes were found to differ significantly between the two herring stocks. Baltic herring have a larger swimbladder volume, which is suggested to be associated with the fish's low fat content, which in turn may be linked to its specific energy budget and the low salinity of the Baltic Sea. A buoyancy model that considered the different salinity conditions and fat proportions was used to evaluate the observed differences in swimbladder volume. The swimbladder volume data were subsequently used to model the mean target strength as a function of depth and growth pattern. Backscattering of the swimbladder was modelled using the modal-series-based deformed-cylinder model (MSB-DCM), describing the swimbladder as a gas-filled, elongated prolate spheroid. The fish body component was modelled as a fluid-filled ellipsoid using the distorted wave Born approximation (DWBA). Modelling results support a different TS-to-size relationship for Baltic herring, with a stronger echo, due to the larger swimbladder. Depth- and length-dependent TS relationships based on the model results are suggested.     

The role of flatfishes in the organization and structure of the eastern Bering Sea ecosystem

We evaluated the role of flatfishes in the organization and structure of the eastern Bering Sea ecosystem using the Ecopath/Ecosim approach. As basic input data for the Ecopath/Ecosim model, we used estimates of biomass from bottom trawl surveys and age-structured population models, production/biomass (P/B) ratio, consumption/biomass (Q/B) ratio, diet composition (DC), and fisheries harvests for each component of species or species groups. We estimated the trophic level of each component, niche overlaps among flatfishes, and the impacts of competition and predation on flatfish species in the eastern Bering Sea ecosystem. Based on those estimates, we developed the tropho-dynamic structure of the ecosystem, and the model was used to simulate ecological effects of fishery exploitation patterns. No single flatfish species appeared to have a profound and uniquely important role in the organization and structure of the ecosystem. Instead, the most important component among the guild of flatfish species appeared to be yellowfin sole Pleuronectes asper, which had greater biomass than other flatfish and a relatively diverse diet among the small flatfish species. Pacific halibut Hippoglossus stenolepis, Greenland turbot Reinhardtius hippoglossoides, and arrowtooth flounder Atheresthes stomias were important keystone predators in the eastern Bering Sea ecosystem together with some groups of marine mammals and sea birds. Intra flatfish complex cannibalism was not observed, however, substantial diet overlaps were common in the flatfish guild system.     

Angling for endangered fish: conservation problem or conservation action?

Recreational angling has been implicated in population declines of some marine and freshwater fish, but this activity is rarely considered as a threat or even halted when endangered species are targeted. Indeed, in some cases, anglers are drawn to fish for rare or endangered species. Conservation‐oriented behaviours such as catch‐and‐release are often practiced voluntarily due to the ethics of anglers, yet even in these cases, some fishing mortality occurs. Nonetheless, there are many indirect conservation benefits associated with recreational angling. Here, we present a series of case‐studies and consider whether catch‐and‐release angling for endangered fish is a conservation problem or a conservation action. If recreational angling activities contribute to population‐level consequences that are contrary to recovery strategies, then angling for endangered species would seem to be a poor option. However, as revealed by several case‐studies, there is much evidence that anglers are vocal and effective proponents of fish and habitat conservation, and for endangered species, they are often the only voice when other stakeholders are not engaged. Anglers may contribute directly to conservation actions via user fees (e.g. licences), philanthropic donations or by volunteering in research, education and restoration activities. However, it is important to quantify post‐release mortality as well as understand the full suite of factors influencing a given population or species to know the potential risks. A risk assessment approach outlined in the paper may be used by managers to determine when the benefits of angling for endangered species outweigh the risks.