Acoustic survey techniques are widely used to quantify abundance and distribution of a variety of pelagic fish such as herring (Clupea harengus). The information provided is becoming increasingly important for stock assessment and ecosystem studies, however, the data collected are used as relative indices rather than absolute measures, due to the uncertainty of target strength (TS) estimates. A fish’s TS is a measure of its capacity to reflect sound and, therefore, the TS value will directly influence the estimate of abundance from an acoustic survey. The TS is a stochastic variable, dependent on a range of factors such as fish size, orientation, shape, physiology, and acoustic frequency. However, estimates of mean TS, used to convert echo energy data from acoustic surveys into numbers of fish, are conveniently derived from a single metric - the fish length (L). The TS used for herring is based on TS-L relationships derived from a variety of experiments on dead and caged fish, conducted 25-30 years ago. Recently, theoretical models for fish backscatter have been proposed to provide an alternative basis for exploring fish TS. Another problem encountered during acoustic surveys is the identification of insonified organisms. Trawl samples are commonly collected for identification purposes, however, there are several selectivity issues associated with this method that may translate directly into biased acoustic abundance estimates. The use of different acoustic frequencies has been recognised as a useful tool to distinguish between different species, based on their sound reflection properties at low and high frequencies. In this study I developed theoretical models to describe the backscatter of herring at multiple frequencies. Data collected at four frequencies (18, 38, 120 and 200 kHz) during standard acoustic surveys for herring in the North Sea were examined and compared to model results. Multifrequency backscattering characteristics of herring were described and compared to those of Norway pout, a species also present in the survey area. Species discrimination was attempted based on differences in backscatter at the different frequencies. I examined swimbladder morphology data of Baltic and Atlantic herring and sprat from the Baltic Sea. Based on these data, I modelled the acoustic backscatter of both herring stocks and attempted to explain differences previously observed in empirical data. I investigated the change in swimbladder shape of herring, when exposed to increased water pressures at deeper depths, by producing true shapes of swimbladders from MRI scans of herring under pressure. The swimbladder morphology representations in 3-D were used to model the acoustic backscatter at a range of frequencies and water pressures. I developed a probabilistic TS model of herring in a Bayesian framework to account for uncertainty associated with TS. Most likely distributions of model parameters were determined by fitting the model to in situ data. The resulting probabilistic TS was used to produce distributions of absolute abundance and biomass estimates, which were compared to official results from ICES North Sea herring stock assessment. Modelled backscatter levels of herring from the Baltic Sea were on average 2.3 dB higher than those from herring living in northeast Atlantic waters. This was attributed to differences in swimbladder sizes between the two herring stocks due to the lower salinity Baltic Sea compared to Atlantic waters. Swimbladders of Baltic herring need to be bigger to achieve a certain degree of buoyancy. Morphological swimbladder dimensions of Baltic herring and sprat were found to be different. Herring had a significantly larger swimbladder height at a given length compared to sprat, resulting in a modelled TS that was on average 1.2 dB stronger. Water depth, and therefore the increase in ambient pressure, was found to have a considerable effect on the size and shape of the herring swimbladder. Modelled TS values were found to be around 3 dB weaker at a depth of 50 m compared to surface waters. At 200 m, this difference was estimated to be about 5 dB. The Bayesian model predicted mean abundances and biomass were 23 and 55% higher, respectively, than the ICES estimates. The discrepancy was linked to the depth-dependency of the TS model and the particular size-dependent bathymetric distribution of herring in the survey area.

Thesis (Ph.D.)--Pennsylvania State University, 2008. / Includes bibliographical references (leaves [202]-219)

Harmful algal blooms (HABs) of the brevetoxin-producing dinoflagellate Karenia brevis occur periodically along the central west coast of Florida. Mass mortalities of marine birds have long been associated with these blooms, yet there is little data documenting the accumulation of brevetoxins in the tissues of birds and their prey items. An intense HAB event impacted the region from Tampa Bay to Charlotte Harbor during most of 2005. More than one hundred marine birds, representing twenty three species, were collected during this bloom. All birds sampled were found dead or had died within 24 hours of admittance to local wildlife rehabilitation centers. In order to determine if fish were vectors for brevetoxin ingestion, the stomach contents of all birds were examined and any recovered fish were identified to the extent possible. The gastrointestinal tissues and contents from all avian samples were analyzed for brevetoxin levels, with results ranging from Shorebirds and gulls may also be exposed to brevetoxins via scavenging of red tide-killed fish deposited on beaches during blooms. Samples from scavenged fish were found to have brevetoxin levels ranging from 31 to 95,753 ng PbTx per gram tissue.

Presence of Triaenophorus crassus Forel in the flesh of lake whitefish (Coregonus clupeaformis (Mitchill)) and cisco (C. artedi Lesueur) can be an important economic problem for commercial coregonine fisheries. This study was initiated during the development of native fisheries in northern Quebec. Coregonine populations from 6 lakes of the Nottaway watershed were sampled to determine infection patterns of T. crassus in relation to age and size of fish, and to document interlake differences in prevalence and number of T. crassus. Interspecific and interlake differences in the infection dynamics of T. crassus were described in relation to capsule types, sizes and plerocercoid conditions. Infection dynamics were also investigated with age of fish. All coregonine populations were infected with T. crassus, and cisco more so than lake whitefish where the two species co-occurred. Prevalence and number of T. crassus were independent of fish age and size in most lake whitefish populations. Number of T. crassus increased with fish age and size in all cisco populations, but prevalence increased only in the populations from the largest lakes. Interlake differences in prevalence and number of T. crassus were detected for both coregonine species, and were related to feeding behaviour of the fish and lake biophysical characteristics. Heavy infections in one lake whitefish population were mainly associated with piscivory. Interspecific and interlake differences in the infection dynamics of T. crassus were also observed. Differences in the proportions of capsule types, sizes, and plerocercoid conditions suggest that population turnover of T. crassus in cisco is faster than in lake whitefish. In contrast to previous studies, plerocercoid condition was found to be independent of capsule size. Coregonine populations, which did not differ in prevalence and number of T. crassus, showed some differences in the proportions of capsule types, sizes and plerocercoid conditions, suggesting

Ecosystems are linked by spatial subsidies, the bi-directional flows of nutrients, materials and energy that cross ecosystem boundaries. Considered one of the planet’s most productive and diverse meta-ecosystems, the broad interface between land and sea is crossed by innumerable abiotic and biotic spatial subsidies, including migratory animals. Routinely crossing ecological boundaries, migrants play significant roles in subsidizing receiving ecosystems, including influencing ecosystem productivity, diversity, community structure and trophic cascades. On the Pacific coast of North America, spatial subsidies driven by migratory Pacific salmon have been intensively studied. Like many of the world’s migrants, however, salmon populations have declined considerably and most of our scientific knowledge has been gained from a diminished subsidy. Other subsidies, including those driven by migratory species in decline, remain relatively unknown. Each year, Pacific herring (Clupea pallasii) migrate to shallow waters to spawn on nearshore and intertidal substrates. Despite suggestions in the literature that herring, an abundant, nearshore/intertidal spawning forage fish, subsidizes coastal ecosystems, there had been no investigation of cross-ecosystem interactions. Just as stable isotopes and fatty acids have been used to explore wrack (drift macrophytes) subsidies to intertidal ecosystems, we combined both approaches to trace the input of Pacific herring and wrack to semi-terrestrial amphipods (Traskorchestia spp.), which are highly abundant detritivores in beach ecosystems. Brown algae and seagrass were major contributors to amphipods but when available, herring was also a significant resource. Because amphipods are prey for terrestrial consumers, including bears (Ursus spp.), we also identified indirect trophic linkages between herring and terrestrial ecosystems. Bears are major consumers and vectors of salmon into terrestrial ecosystems, but little is known regarding their involvement in other spatial subsidies. Using a model-based inference approach paired with remote cameras to monitor intertidal black bear (U. americanus) activity, we determined that the best predictors of black bear intertidal activity were major intertidal prey items (herring and amphipod biomass) and Julian day. Bears positively responded to herring and amphipod biomass on beaches but it was the analysis of scats that determined the contribution of herring eggs to the diets of bears. In 2010, the herring spawn was relatively poor and consumption of eggs was negligible, with amphipods constituting a major portion of bear diets. In following years, herring egg loading was relatively high and eggs were the dominant dietary item in bear scats. Tracing the contribution of herring into terrestrial areas proved challenging and instead, we furthered knowledge of the within-watershed spatiotemporal influences of salmon on conifer tree ring growth and δ15N signatures. Both tree ring growth and δ15N signatures tracked the known spatial distribution of salmon carcasses. Using a model-based inference approach, salmon abundance and interaction terms of salmon*temperature and salmon*distance into the forest best predicted tree growth. In contrast, salmon abundance was not a leading predictor of δ15N. By broadening our understanding of the fine-scale influence of salmon on a stand of ancient trees, this research is expected to contribute to future exploration of the terrestrial influences of Pacific herring. / Graduate / 0329 / cfox@uvic.ca

The condition of juvenile fish relates to their overall health and is a strong predictor of survival and eventual recruitment. Condition can be quantified and interpreted in a variety of ways covering different time scales and levels of biological organization. Here I (i) quantify interannual variability in the condition in Young-of-Year (YOY) Pacific herring (Clupea pallasi) in the Strait of Georgia, BC, from 2013-2016, and (ii) examine the extent to which the condition of an individual fish varies depending on which condition metric is used. Chapter 1 provides a general background on the concept of measuring condition in fish, as well as the basic biology of Pacific herring and their importance in Strait of Georgia ecosystem. In Chapter 2, I report the condition of YOY herring from 2013-2016 using six metrics: (i) Fulton’s K, (ii) the residuals from a length:weight regression, (iii) the RNA:DNA ratio, (iv) recent growth estimated via otolith microstructure analysis, (v) lipid content, and (vi) the ratio of two essential acids DHA:EPA. Four of these metrics (Fulton’s K, length:weight residuals, and growth from RNA:DNA and otolith increments) indicate a decrease in condition over the four years. In contrast, lipid content suggests an increase across the four years, while DHA:EPA suggests a decrease in 2015 but no change over the other three years. The observed interannual variability in condition can be partly linked to unfavourable changes in temperature and zooplankton community composition in 2015 and 2016, and to the propensity of juvenile fish to prioritize energy storage over somatic growth before a period of prey scarcity, such as their first winter. This dataset is further examined in Chapter 3, wherein I examine variability in condition of individual fish based on the different metrics used. Individual herring are ranked based on their scores from the six different metrics of condition, and the distribution of these rankings are examined to assess the degree of intercorrelation among the metrics. Based on this model, as well as pairwise Spearman rank correlations between the six metrics, I conclude that there is little intercorrelation between metrics, and that a fish that scores highly in terms of condition in any one metric will not necessarily score highly for the other metrics. These findings underscore the importance of choosing condition metrics carefully, based on the nature of the question being asked. / Graduate / 2019-07-04

Tidal freshwater wetlands provide valuable ecosystem services such as nutrient cycling, coastal flood control, and reproductive habitat for early life stages of economically and ecologically important fishes. The nutrient rich environments that tidal freshwater wetlands occur in support high levels of primary productivity of phytoplankton and vegetation that provide essential reproductive habitat for anadromous clupeid fishes (Alosa spp., Brevoortia tyrannus) in Chesapeake Bay tributaries. Seasonal retention of clupeid eggs and larvae within tidal freshwater habitats may enhance early growth, survival, and year class strength. The primary goal of the present study was to characterize the relative importance of tidal freshwater wetlands to the early life history stages of anadromous, migratory, and resident clupeid fishes in the lower James River. From 2014-2018, conical tow nets were used to collect ichthyoplankton samples from representative locations within the tidal freshwater marsh-creek complex of Curles Neck Creek, Virginia during the period of February through May. Boat electrofishing was used to sample juvenile target clupeids within the marsh-creek complex during March through November 2014-2018. A strong positive correlation between larval and juvenile Blueback Herring and Atlantic Menhaden, supported the hypothesis of seasonal in-system retention. This was the first published study to describe spatial and temporal patterns of occurrence of clupeid fishes with varying life history strategies in a tidal freshwater marsh and highlighted the importance of tidal freshwater marshes as nursery habitat.

No description available.

Understanding, quantifying, and comparing the temporal distribution of anadromous fish spawning migrations is an important yet vexing problem for fisheries research, management, and conservation. Central to this problem is the lack of a representative and comprehensive standardized suite of quantitative metrics to characterize the complex, multidimensional temporal distribution of migrating anadromous fish. Without this, it is not possible to develop effective sampling regimes, extrapolate counts to accurate population estimates, understand the basic ecology and behavior of anadromous fish, or make the comparisons through time and across river systems that are fundamental to sustainable conservation. In this thesis, I define, calculate, and compare 17 metrics that characterize the temporal distribution of migrating adult river herring [two closely related clupeids, the alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis)] as they return to spawn. These metrics are based on fish counts from three southeastern Massachusetts river systems that were obtained through a low-cost video monitoring system.

Nature-like fish passes have been designed with the intent to re-connect river corridors and provide passage for all species occurring in a system. Nature-like fish pass designs have been constructed in Europe and elsewhere with some success, but performance of these designs has not been evaluated for North American species. Re-establishing passage for adult anadromous clupeids to their spawning areas is critical considering their recent dramatic population declines. Two nature-like fish pass designs in New England were evaluated for passage of anadromous adult alewives (Alosa pseudoharengus) using passive integrated transponder (PIT) telemetry and showed differing results. At Town Brook in Plymouth, Massachusetts the 32 m long perturbation boulder rock ramp with a 1:24 slope passed 94% of attempting fish with most ascending in under 22 minutes. At East River in Guilford, Connecticut the 48 m long steppool bypass design with a 1:14 slope passed only 40% of attempting fish with a median transit time of 75 minutes. Two technical fishway designs at the field sites were also evaluated and showed contrasting performance. At Town Brook a 14 m long 1:7 slope pool and weir fishway exhibited attraction and passage deficiencies. At East River two 3.05 m long steeppass fishways both passed the majority of attempting fish but one steeppass fishway may have had poor attraction efficiency. At both sites tagged fish passed rapidly downstream through the fish passes after spawning. Nature like fish pass designs are suitable for the passage of alewife but further evaluations are required to more precisely identify the influence of vertical drop per pool and specific local hydraulics on behaviors and passage performance for this species.