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Objective: Coho Salmon Oncorhynchus kisutch provide an important resource for recreational, commercial, and Indigenous fisheries in the Pacific Northwest. The goal of this study was to improve our understanding of how marine mammal predation may be impacting the survival and productivity of Coho Salmon in the Strait of Georgia, British Columbia. Specifically, we quantified the impact of harbor seal Phoca vitulina predation on juvenile Coho Salmon during their first several months at sea. Early marine survival is believed to be the limiting factor for the recovery of Coho Salmon populations in this region. Methods: To estimate the number of juvenile Coho Salmon consumed by harbor seals, we developed a mathematical model that integrates predator diet data and salmon population and mortality dynamics. Result: Our analysis estimated that harbor seals consumed an annual average of 46−59% of juvenile Coho Salmon between 2004–2016, providing the first quantitative estimate of seal predation in the Strait of Georgia. Conclusion: Marine mammal predation on juvenile Coho Salmon is potentially a very important factor limiting survival and recovery of Coho Salmon in the Strait of Georgia. Impact statementCoho Salmon populations in the Strait of Georgia have experienced precipitous declines in marine survival over the last four decades. In this study, we used predator diet data to quantify the potential impact of harbor seals on juvenile Coho Salmon. Our results suggest seal predation may strongly influence survival of young salmon during their first several months at sea, and should be considered in future recovery efforts. [ABSTRACT FROM AUTHOR]

Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal (Phoca vitulina) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon (Oncorhynchus spp.). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided. Measurement(s) diet Technology Type(s) DNA metabarcoding diet analysis Sample Characteristic - Organism Phoca vitulina Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.19077809 [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Fisheries & Aquatic Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sex-biased predation, a predator's bias for one prey sex over the other, can have important demographic impacts on prey species of conservation concern. Yet, it is difficult to measure in the wild. Molecular scatology has been used to indirectly determine the proportion of prey items consumed in the diet, and it may be possible to apply similar approaches to determine the sex-biased consumption of prey items. We developed a molecular method to indirectly examine sex-specific predation employing scat, focusing on predator–prey interactions between Chinook salmon (Oncorhynchus tshawytscha) and harbor seals (Phoca vitulina richardii). We established that the proportions of male and female Chinook DNA can be determined in a controlled sample by measuring a Y-linked marker, growth hormone pseudogene, using qPCR. We then applied the assay to harbor seal scat samples. Although the assay amplified in 83% of scat samples, 27% of samples quantified had an estimated male proportion > 1, which may have been due to a lack of robustness of the PCR assay in samples. Lastly, we constructed a biomass calibration curve to determine whether DNA measurements could estimate the proportions of male and female biomass consumed. The calibration curve was skewed by high male DNA density precluding our ability to quantify the relative amounts. We demonstrated that nuclear prey markers can be amplified in predator scat, however, contamination and extreme DNA density differences between the prey sexes may pose practical difficulties to estimate the relative amounts of male to female biomass consumed. [ABSTRACT FROM AUTHOR]

eDNA studies often rely on water filtration in the field and immediate sample preservation to prevent DNA degradation during sample transport. However, filter membrane transfer steps for preservation can increase risk of sample contamination and the reliance on typical single‐use filter housings produces significant plastic waste.We created a new eDNA filter housing (compatible with any suction pump) partially comprised of a biodegradable, hydrophilic material that functions to automatically preserve captured eDNA via desiccation—no filter membrane transfer steps, no chemical or cold storage required.We tested the self‐preservation capabilities of the desiccating filter housings by filtering replicate samples in an eDNA mesocosm study and compared with ethanol preservation. Self‐preserving filters were placed back into original packaging for storage, and samples for both preservation methods were kept at room temperature until extraction at prescribed time points (11 days, 18 days, 25 days, 32 days, 60 days, 88 days, 172 days) post‐filtration. Paired field samples were also collected from six pond locations targeting an additional species to demonstrate field performance.Quantitative PCR results from the mesocosm study indicated that both methods effectively preserved eDNA over a 6‐month storage period, with the self‐preserving filters yielding slightly more target DNA on average (SQ = 329 copies) than ethanol‐preserved samples (SQ = 288 copies) (F1,38 = 4.050, p = 0.051). Neither method showed signs of degradation after 172 days. Results from field sampling indicated a larger difference between preservation methods, with the self‐preserving filters containing approximately 2X the eDNA of ethanol‐preserved samples on average (paired t test, p = 0.020).These data suggest that self‐preserving eDNA filter housings are a viable alternative to standard ethanol preservation methods and may provide higher detection sensitivity in some circumstances. The new filter housings should also help in reducing the risk of sample contamination, minimize protocol steps and result in less plastic waste. Such innovations are important to assure eDNA data quality and to help in facilitating the inclusion of non‐expert sample collectors (e.g. citizen scientists) in research programs. [ABSTRACT FROM AUTHOR]

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]

Advances in technology are making it easier for rapid field detection of microbes in aquaculture. Specifically, real‐time quantitative PCR (qPCR) analysis, which has traditionally been confined to laboratory‐based protocols, is now available in a handheld, field‐portable system. The feasibility of using the Biomeme handheld qPCR system for rapid (<50 min) on‐site detection and monitoring of Flavobacterium psychrophilum from filtered water samples was evaluated. Paired water samples were collected over a 23‐d period from microcosm tanks that housed fish injected with known levels of F. psychrophilum. Water samples were filtered through 0.45‐μm nitrocellulose filters and were analyzed with both the Biomeme qPCR platform and a traditional bench qPCR protocol. The two methods identified similar fluctuations in F. psychrophilum DNA throughout the study. Standard curves relating quantification cycles to the number of F. psychrophilum colony‐forming units (CFU) were constructed and analyzed; results indicated that CFU increased rapidly between days 6 and 8 of the trial and then progressively decreased during the remaining 15 d. Average calculated log10(CFU/mL) values were significantly correlated between the two platforms. Rapid, field‐based qPCR can be incorporated into daily water quality monitoring protocols to help detect and monitor microbes in aquaculture systems. [ABSTRACT FROM AUTHOR]

Sex‐specific diet information is important in the determination of predator impacts on prey populations. Unfortunately, the diet of males and females can be difficult to describe, particularly when they are marine predators. We combined two molecular techniques to describe haul‐out use and prey preferences of male and female harbor seals (Phoca vitulina) from Comox and Cowichan Bay (Canada) during 2012–2013. DNA metabarcoding quantified the diet proportions comprised of prey species in harbor seal scat, and qPCR determined the sex of the individual that deposited each scat. Using 287 female and 260 male samples, we compared the monthly sex ratio with GLMs and analyzed prey consumption relative to sex, season, site, and year with PERMANOVA. The sex ratio between monthly samples differed widely in both years (range = 12%–79% males) and showed different patterns at each haul‐out site. Male and female diet differed across both years and sites: Females consumed a high proportion of demersal fish species while males consumed more salmonid species. Diet composition was related to both sex and season (PERMANOVA: R2 = 27%, p < 0.001; R2 = 24%, p < 0.001, respectively) and their interaction (PERMANOVA: R2 = 11%, p < 0.001). Diet differences between males and females were consistent across site and year, suggesting fundamental foraging differences, including that males may have a larger impact on salmonids than females. Our novel combination of techniques allowed for both prey taxonomic and spatiotemporal resolution unprecedented in marine predators. Sex‐specific diet information is important for determining predator impacts on prey populations, but diet of males and females can be difficult to describe, particularly in marine predators. We combined prey DNA metabarcoding and predator molecular sex identification from scat to describe prey preferences of male and female harbor seals. The male diet was less diverse than the female diet and suggested a greater male than female impact on salmon species of conservation concern. [ABSTRACT FROM AUTHOR]

Anthropogenic disturbances can constrain the realized niche space of wildlife by inducing avoidance behaviors and altering community dynamics. Human activity might contribute to reduced partitioning of niche space by carnivores that consume similar resources, both by promoting tolerant species while also altering behavior of species (e.g. activity patterns). We investigated the influence of anthropogenic disturbance on habitat and dietary niche breadth and overlap among competing carnivores, and explored if altered resource partitioning could be explained by human‐induced activity shifts. To describe the diets of coyotes, bobcat, and gray foxes, we designed a citizen science program to collect carnivore scat samples in low‐ (‘wildland’) and high‐ (‘interface’) human‐use open space preserves, and obtained diet estimates using a DNA metabarcoding approach. Habitat use was determined at scat locations. We found that coyotes expanded habitat and dietary niche breadth in interface preserves, whereas bobcats and foxes narrowed both niche breadth measures. High human use was related to increased dietary niche overlap among all mesocarnivore pairs, increased coyote habitat overlap with bobcats and foxes, and a small reduction in habitat overlap between bobcats and foxes. The strongest increase in diet overlap was among coyotes and foxes, which was smaller in magnitude than their habitat overlap increase. Finally, coyote scats were more likely to contain nocturnal prey in interface preserves, whereas foxes appeared to reduce consumption of nocturnal prey. Our results suggest that dominant and generalist mesocarnivores may encroach on the niche space of subordinate mesocarnivores in areas with high human activity, and that patterns in resource use may be related to human‐induced activity shifts. [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]

Copyright of Canadian Journal of Fisheries & Aquatic Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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]

A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals ( Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis. [ABSTRACT FROM AUTHOR]