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Management of protected species is difficult when objectives include the recovery of both predator and its prey. Ideally, identifying trade-offs between competing objectives involves evaluating management alternatives with a quantitative model that integrates information on both species, but data are often limited. We used new predator diet data and simulation modeling to update our understanding of seal predation on juvenile Chinook (Oncorhynchus tshawytscha) and coho salmon (Oncorhynchus kisutch) in the Puget Sound. Under prey size assumptions used by previous studies, estimates suggest predation could be a significant source of mortality for Chinook salmon (mean: 37% of ocean age-0 juveniles), but varied considerably among years (range of median estimates: 22%-49%). However, when we estimated prey size from otoliths recovered from seal scats, the impact (numbers of fish consumed) decreased by 71%. Predation on coho salmon was estimated to be relatively low under both scenarios (6%-8% of ocean age-0 juveniles) with a 21% decrease in consumption using otolith-derived prey size. Our analysis highlights the importance of updating model inputs and re-evaluating assumptions of multi-species models used for ecosystem-based fisheries management. La gestion d'especes protegees est difficile quand les objectifs comprennent le retablissement tant d'un predateur que de sa proie. Si, idealement, la determination des compromis entre objectifs concurrents comprend l'evaluation de differentes options de gestion a l'aide d'un modele quantitatif qui integre de l'information sur les deux especes, les donnees sont souvent limitees. Nous utilisons de nouvelles donnees sur le regime alimentaire de predateurs et la modelisation de simulation afin d'actualiser la comprehension de la predation par les phoques de saumons chinooks (Oncorhynchus tshawytscha) et cohos (Oncorhynchus kisutch) juveniles dans le Puget Sound. Des estimations etablies a partir d'hypotheses sur la taille des proies utilisees dans des etudes anterieures indiqueraient que la predation pourrait constituer une source de mortalite significative de saumons chinooks (moyenne : 37 % des juveniles de moins de 1 an en ocean), mais varie considerablement d'une annee a l'autre (fourchette de valeurs medianes estimees : 22 %-49 %). Cependant, quand nous estimons la taille des proies a partir d'otolites recuperes d'excrements de phoque, l'impact (le nombre de poissons consommes) diminue de 71 %. Il est estime que la predation de saumons cohos est relativement faible dans les deux scenarios (6 %-8 % des juveniles de moins de 1 an en ocean), et la taille des proies etablie sur la base des otolites indique une diminution de 21 % de la consommation. Notre analyse souligne l'importance d'actualiser les intrants des modeles et de reevaluer les hypotheses des modeles multispecifiques utilises pour la gestion ecosystemique des peches. [Traduit par la Redaction], Introduction Management conflicts between protected marine species are increasing, and successful resolution requires identification of competing objectives and evaluating the ecological, social, and economic trade-offs associated with various management scenarios [...]

Knowing the species and life stages of prey that predators consume is important for understanding the impacts that predation may have on prey populations, but traditional methods for determining diets often cannot provide sufficient detail. We combined data from two methods of scat analysis (DNA metabarcoding and morphological prey ID) to quantify the species and life stages of salmon (Oncorhynchus spp.) consumed by harbour seals (Phoca vitulina) in the Strait of Georgia, Canada, where juvenile Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon survival is poor. Harbour seals primarily consumed adult salmon of lesser conservation concern in the fall (August-November): chum (Oncorhynchus keta: 18.4%), pink (Oncorhynchus gorbuscha: 12.6%), sockeye (Oncorhynchus nerka: 7.4%), Chinook (7.1%), and coho (1.8%). However, the opposite species trend occurred during the spring when seals preferred juvenile salmon of greater conservation concern (April-July): coho (2.9%), Chinook (2.9%), sockeye (2.5%), pink (1.4%), and chum (0.8%)--percentages that can equate to many individuals consumed. Our data suggest that harbour seals select juveniles of salmon species that out-migrate at ages >1 year and provide evidence of a potential causal relationship between harbour seal predation and juvenile salmon survival trends. Il importe de connaitre l'espece et l'etape du cycle biologique des proies que les predateurs consomment afin de comprendre les impacts que la predation peut avoir sur les populations de proies. Dans bien des cas, les methodes traditionnelles de determination du regime alimentaire ne peuvent toutefois fournir assez de details. Nous avons combine des donnees de deux methodes d'analyse d'excrements (meta-codes-barres d'ADN et identification morphologique des proies) pour quantifier l'espece et l'etape du cycle biologique de saumons (Oncorhynchus spp.) consommes par des phoques communs (Phoca vitulina) dans le detroit de Georgia (Canada), ou la survie des saumons quinnats (Oncorhynchus tshawytscha) et cohos (Oncorhynchus kisutch) juveniles est faible. Les donnees indiquent que, a l'automne (d'aout a novembre), les phoques communs consomment principalement des saumons adultes dont la conservation est moins preoccupante, a savoir des saumons ketas (Oncorhynchus keta : 18,4 %), roses (Oncorhynchus gorbuscha : 12,6%), rouges (Oncorhynchus nerka : 7,4%), quinnats (7,1%) et cohos (1,8%). Cependant, cette tendance est inversee au printemps (d'avril a juillet), alors que les phoques privilegient des saumons juveniles dont la conservation est plus preoccupante, a savoir des saumons cohos (2,9%), quinnats (2,9%), rouges (2,5%), roses (1,4%) et ketas (0,8%), ces pourcentages pouvant equivaloir a de nombreux individus consommes. Nos donnees laissent croire que les phoques communs choisissent des juveniles d'especes de saumon qui migrent vers la mer a des ages de plus d'un an et indiqueraient une possible relation de causalite entre la predation par les phoques communs et les tendances de survie des saumons juveniles. [Traduit par la Redaction], Introduction Predators can have different net effects on ecological communities depending on the life stage of prey they consume (Hastings 1983; 1988; Werner and Gilliam 1984). This is because prey [...]

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi‐quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa‐specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low‐level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population‐level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research. [ABSTRACT FROM AUTHOR]

Abstract: Species monitoring using environmental DNA (eDNA) is a powerful new technique for natural resource scientists and the number of research groups employing eDNA detection is growing rapidly. However, current eDNA sampling technologies consist mainly of do‐it‐yourself solutions, and the lack of purpose‐built sampling equipment is limiting the efficiency and standardization of eDNA studies. Here, we describe the first fully integrated sampling system (ANDe™) designed by a team of molecular ecologists and engineers for high‐throughput eDNA sample collection. It consists of a backpack portable pump that integrates sensor feedback, a pole extension with remote pump controller, custom‐made filter housings in single‐use packets for each sampling site and onboard sample storage. The system is optimized for sampling speed and replicability, while minimizing risk of contamination. We present an example pilot study designed to identify optimal ANDe™ system parameter values (i.e. pump pressure, flow rate, filter pore size, sample volume) in a new sampling environment. We identified a peak in filtration efficiency at a flow rate threshold of 1.0 L/m, and found that 5 μm filters captured significantly more target eDNA than 1 μm filters. Results also suggest that high filtration pressures may reduce eDNA retention, which implies that pressure should be standardized to avoid biasing detection data. Similar to the technological evolution of backpack electrofishers, eDNA sampling technology is in the process of transitioning from a nascent phase to professionally engineered research tools. Such innovations will be essential as eDNA monitoring becomes one of the industry standard methods used for species detection and management. [ABSTRACT FROM AUTHOR]

Brucella ceti and Brucella pinnipedialis have been documented as occurring in marine mammals, and B. ceti has been identified in 3 naturally acquired human cases. Seroconversion and infection patterns in Pacific Northwest harbor seals (Phoca vitulina richardii) and North Atlantic hooded seals (Cystophora cristata) indicate post-weaning exposure through prey consumption or lungworm infection, suggesting fish and possibly invertebrates play an epizootiologic role in marine Brucella transmission and possible foodborne risk to humans. We determined if real-time quantitative PCR (qPCR) assays can detect marine Brucella DNA in fish DNA. Insertion sequence (IS)711 gene and sequence type (ST)27 primer–probe sets were used to detect Brucella associated with marine mammals and human zoonotic infections, respectively. First, DNA extracts from paired-species fish (containing 2 species) samples were tested and determined to be Brucella DNA negative using both IS711 and ST27 primer–probe sets. A representative paired-species fish DNA sample was spiked with decreasing concentrations of B. pinnipedialis DNA to verify Brucella detection by the IS711 primer–probe within fish DNA. A standard curve, developed using isolated DNA from B. pinnipedialis, determined the limit of detection. Finally, the IS711 primer–probe was used to test Atlantic cod (Gadus morhua) DNA extracts experimentally infected with the B. pinnipedialis hooded seal strain. In culture-positive cod tissue, the IS711 limit of detection was ~1 genome copy of Brucella. Agreement between culture and PCR results for the 9 positive and 9 negative cod tissues was 100%. Although a larger sample set is required for validation, our study shows that qPCR can detect marine Brucella in fish. [ABSTRACT FROM AUTHOR]

DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors ( RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal ( Phoca vitulina) prey species ( RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives. [ABSTRACT FROM AUTHOR]

Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals ( Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors ( TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% ( TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors ( DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis. [ABSTRACT FROM AUTHOR]

The article discusses an 11-year study that examined stranding data on the Great Shearwater (Puffinus Gravis), an abundant pelagic seabird that undertakes transequatorial migrations between the North and South Atlantic Ocean. It says that this was prompted by 12 separate mortality events where the cause of death was not attributed to infectious disease or heavy metals. It adds that the cause of death was an apparent increase in strandings, leading to large-scale mortality of emaciated birds.