Yevhenii Pakhomov


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Graduate Student Supervision

Doctoral Student Supervision

Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

Global distribution and biomass of the mesopelagic mesozooplankton and micronekton community (2024)

Despite the ecological importance of mesopelagic zooplankton, very little is known about their global distribution in the midwater realm, and even less information is available on global trends in their diversity. This study is the first attempt to explore the distribution, diversity gradients, and total biomass of mesopelagic mesozooplankton and micronekton in the global ocean. This study created the first quantitative Mesopelagic Mesozooplankton and Micronekton Database, organizing and standardizing a broad spectrum of literature sources for effective data analysis. Analyzing 861 mesozooplankton species using a range of species distribution models, the study found that the highest species richness was observed in the North Atlantic region, the west coast of India, and the Mediterranean Sea. Factors such as water temperature, euphotic zone depth, salinity, and dissolved nitrate concentration were essential for explaining their distribution. The results of this study indicate that NPP and POC are important factors that influence the biomass of mesopelagic mesozooplankton. The global mesozooplankton population in the mesopelagic zone was estimated using estimates of particulate organic carbon (POC) and primary productivity (NPP). Linear models fitted to predict mesopelagic mesozooplankton biomass using NPP and POC data were able to explain a moderate-to-substantial proportion of variance. The distribution patterns of mesopelagic mesozooplankton biomass showed enhanced values in certain regions, such as the Northern Hemisphere, west coasts of continents, and equatorial and 50°S bands. Global mesopelagic mesozooplankton biomass was estimated to range between 0.20-0.91 PgC, depending on the method used. Overall, this study provides an estimate of mesopelagic mesozooplankton biomass using the classical definition of the mesopelagic zone, and an estimate that considers the variable depth of this layer. The findings indicated that POC was a more reliable indicator of mesozooplankton biomass than NPP, particularly in more northerly latitudes. The research also showed that low mesopelagic mesozooplankton biomass is linked to low POC levels and low range-size rarity and species diversity, but higher biomass values are more often found in areas with moderate rarity values and high species diversity, combined with high POC.

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Hidden diversity in gelatinous zooplankton assemblages from selected Pacific Ocean ecosystems (2023)

Gelatinous and soft-bodied zooplankton (GZ) are critical components of almost all marine food webs. They act as intermediate predators and prey, contribute to nutrient cycling, and help shape microbial communities. Despite these characteristics, GZ were traditionally seen as ‘trophic dead-ends’ with limited ecosystem value. This view has changed in recent decades. As a result, improved representation of GZ in food web, fisheries, and biogeochemical models is now possible. Despite GZ assemblages being comparably well-studied in the Pacific Ocean, many questions beyond the taxonomic class or species levels remain unanswered. This dissertation aims to provide new insights into inter- and intraspecific differences in GZ biology, demography, stoichiometry, bioenergetics, and distribution in the subarctic Northeast Pacific and the Chatham Rise in the Southwest Pacific. This dissertation demonstrates that GZ organic content, elemental composition, and energy content vary among species, between life cycle stages, and with organism size. New species-resolved energy content data support previous in situ observations and reject the notion of GZ organisms as ‘trophic dead-ends’. GZ are also shown to utilise a stoichiometrically wide prey spectrum, challenging the linear carbon-to-phosphorus food web dogma. Moreover, in and ex situ observations of a widespread pelagic tunicate species (Salpa thompsoni), revealed size-specific growth rates and size- and stage-dependent differences in day and night vertical distributions. Corresponding demographic data suggest a life span shorter than previously estimated. Ontogenetic morphological changes were demonstrated to be highly comparable between several macromorphologically similar salp species. The salps’ abundance was subsequently shown to be sensitive to season, year, bottom depth, and some ocean-atmospheric indices. The causation and size- and stage-specific diel vertical migration (DVM) patterns of two cold-water salp species were studied using demography and size-frequency distribution data. The resulting analyses provide support for several DVM-related hypotheses. Overall, this dissertation contributes significantly to our understanding of GZ biology and ecology by highlighting key inter- and intraspecific characteristic differences. These new insights form a comprehensive baseline for the realistic parameterisation and inclusion of GZ in food web, fisheries, and biogeochemical models.

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Copepod dynamics of the Fraser River Estuary (2022)

How the zooplankton in estuaries of nival basins will respond to a warming water column and earlier peak flows is unknown. The goal of this dissertation is to increase our knowledge of zooplankton dynamics in snowmelt-dominated estuarine systems by studying the Fraser River Estuary (FRE). To describe the copepod community of the FRE and identify drivers of species composition and abundance, an intensive zooplankton sampling program was carried out over a period of 33 months, from August 2013 – May 2016. I coupled the sampling program with investigations of the depth distribution and egg production of the most abundant pelagic copepod in the estuary, Eurytemora affinis. Using the information gained in these studies and data from the literature, I built a stage-structured, concentration-based population model to explore the response of E. affinis abundance to projected changes in temperature and Fraser River discharge.The results outlined in this dissertation demonstrate that mesozooplankton abundance, biomass, and production in the FRE were low in comparison to other studied estuaries and limited by water residence times in the estuary. Targeted study of E. affinis provided evidence of tidal vertical migration behaviour and a first record of the production of resting eggs to bridge periods of rapid flushing and low salinity. The presence of these retention mechanisms highlights the role advection risk has played in shaping both the behaviour and life history of the E. affinis population in the FRE. Results of model simulations suggest that the response of E. affinis abundance to predicted changes in water temperature and river discharge is dependent on how those changes influence spring contributions to the egg bank. My simulations suggest that warming of 1.5 ℃, in combination with predicted changes to the Fraser River’s hydrograph, has the potential to lead to a near doubling (+ 92%) of abundance of E. affinis and significant changes in their phenology (from 50 days earlier to 25 days later, depending on the timeframe of the river discharge scenario). I suggest that zooplankton production in snowmelt-dominated estuarine systems may be sensitive to changes in hydrology, particularly where channelization has occurred.

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Mesozooplankton normalized biomass size spectra and production in the northeast Pacific (2021)

Mesozooplankton play a critical role in the World’s oceans, fundamentally linking primary producers to higher trophic levels, including species of commercial importance (e.g., Chinook salmon). Production reflects how much biomass is available in one trophic level to support organisms in the next level. Although estimates of primary production are readily available, those of secondary production (e.g., mesozooplankton) are limited. Due to the variable energy loss between trophic levels at the primary-secondary producer interface, improved representation of mesozooplankton in ecosystem models is essential to understand climate effects on pelagic ecosystems. The objective of this thesis is to develop, test, and implement a tool for estimating mesozooplankton production. As ecological rates (e.g., growth, mortality) scale with size, information on mesozooplankton size structure (normalized biomass size spectra; NBSS) derived using a bench-top laser optic particle counter (lab-LOPC) were paired with empirical growth rate models. To identify the best growth rate model for the region, a comparison study was conducted in Saanich Inlet, British Columbia, where model outputs were compared with chitobiase-derived estimates. I applied the approach to mesozooplankton collected as part of the Fisheries and Oceans Canada (DFO) Line P oceanographic time series between 2017-2019 using mesozooplankton collected with different mesh sizes, and between 1997-2019 using a single mesh. Data were paired with Chinook salmon productivity (Recruits/Spawner; hereafter ln(R/S)) data to build Bayesian Belief Networks (BBNs), which evaluated the association between variables.Findings of this study demonstrate that: (i) the Hirst and Bunker (2003) growth rate model agreed with the biochemical chitobiase approach; (ii) a single net mesh cannot be used to infer whole community size spectra and production, and can potentially lead to over-/underestimations; (iii) NE Pacific NBSS indicate progressively lower production and longer food chains moving offshore; (iv) NBSS are correlated with chlorophyll-a, zooplankton diversity, zooplankton water content, nitrate + nitrite, multivariate El Niño Southern Oscillation index (MEI), and species number; and (v) the associations between chlorophyll-a, mesozooplankton (biomass and production), and Chinook salmon productivity varied considerably across stocks. This research highlights the importance of including alternative hypotheses about linkages between mesozooplankton and higher trophic levels in ecosystem and fisheries models.

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Fractal analysis of fisheries and environmental time series for the development of early warning indicators (2015)

Fractal theory has been used in aquatic sciences to quantify scale-invariant relationships under the form of scaling or power laws, which represent patterns that help to understand the complex structure of exploited marine ecosystems and their populations through time. Fisheries time series are inherently variable and complex because they represent the interaction between population dynamics, oceanographic forcing’s and anthropogenic pressure (exploitation rates). Thus, to better understand the temporal dynamics of fisheries time series under the framework of fractal theory, smooth pink shrimp (Pandalus jordani) daily catch time series, daily sea surface temperature and wind stress time series from the west coast off Vancouver Island were analyzed. The ultimate goal of this thesis was the early detection of changes and critical thresholds levels over which a fishery move to a depleted or unhealthy state. This is a highly desirable objective because it gives fishery managers time to intervene in order to avoid a fishery collapse. I identified fractal patterns in smooth pink shrimp daily catches, sea surface temperature and wind stress time series. Those patterns were quantified through the Hurst coefficient (H), which integrates time series’ long-range dependence and intermittency into a single index. Inter-annual changes in Hurst coefficients from sea surface temperature appear to be related with major oceanographic anomalous conditions such regime shifts and El Niño events. Long-range dependence and intermittency were estimated for catch time series using the fractionally differenced parameter d and the Lévy index α and then combined into a single index (1/LHE indicator). Our proposed indicator, calculated using rolling windows across the history of the fishery, tracks well the vulnerable biomass for all years, which means that it is possible to have an indicator of major changes in the biomass of Pandalus jordani at the beginning and during the progress of each fishing season.

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An ecosystem study of the Prince Edward Archipelago (Southern Ocean) (2014)

This study brings together the wealth of data available for the Prince Edward Islands marine ecosystem and consolidates it into a network, mass-balanced model (using Ecopath). Biomass estimates for the land based top predators show penguins dominate the system for all three time periods assessed (1960s, 1980s and 2000s). The islands appear to have a carrying capacity which may be declining. A consumption model shows a change in prey for the land based top predators from one in which both crustaceans and myctophid fish were of equal importance in the 1960s, to one dominated by myctophids for the 2000s period. The contribution of the sources of primary production were assessed through the ecosystem model with open ocean productivity dominating at all but the smallest scale (shelf region), where the macrophyte production was important. The model describes the marine ecosystem for each of the above mentioned time periods at the scale of the Exclusive Economic Zone and, when compared to other subantarctic and Antarctic systems for which there are ecosystem models, the system was most similar to the neighbouring Kerguelen Islands. An investigation into the ecosystem boundary size was conducted, with all constituents able to satisfy their energetic requirements if considered at the scale of the EEZ. Using the dynamic temporal simulation approach (Ecosim), the model was able to successfully hindcast three past events: the fur seal exploitation, Patagonian toothfish fishery, and the effect of cat predation on small flying birds. In each instance the model performed well for the directly impacted groups. Potential ecosystem effects of climate change were explored through simulations of increasing and decreasing productivity. No single scenario was able to replicate observed patterns and a suite of drivers needs to be considered to reproduce observed patterns. The inclusion of energetic density of prey led to improvements in consumption rate estimates for the static models and should be incorporated into estimates to improve ecosystem model parameterization. The work constitutes the first ecosystem model for the PEIs that can be used as a tool for an ecosystem approach to marine resource management.

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Examining the environmental forcing of zooplankton population dynamics: a life history approach using data from a British Columbia fjord (2013)

Zooplankton play a pivotal role in marine ecosystem by cycling carbon and energy up the food chain. The species composition of a zooplankton community can influence such energy transfer pathways in a marine ecosystem. For example, when large calanoid copepods dominate a food web, more of the energy produced by phytoplankton is transferred up the food chain and high biomass of large, lipid-rich calanoid copepods or euphausiids has been associated with higher recruitment of upper trophic levels compared to a system dominated by smaller copepod species. Thus, understanding how environmental forcing drives fluctuations in zooplankton community composition is essential to assessing how the structure of marine ecosystems may vary in the future. However, knowledge of what zooplankton life history strategies or functional traits (e.g. feeding guild) make some species more successful under specific environmental conditions remains limited. Here, using three years of field data on zooplankton abundance, biomass, and species composition from a fjord in British Columbia, Canada, I identified the zooplankton seasonal succession cycle and the controlling effects of different environmental forcing factors on the recruitment success of various zooplankton functional traits. Zooplankton succession was delayed when the spring bloom was late. Furthermore, herbivorous, ontogenetically migrating copepods with a short reproductive season, such as Calanus marshallae and Eucalanus bungii, had reduced recruitment when the spring bloom was delayed or in years of high spring temperature, as compared to omnivorous copepods with a long reproductive season. A population dynamics model was employed to determine the environmental drivers of the observed temporal variability of C. marshallae and E. bungii. Interannual differences in mortality and advection drove the observed change in the recruitment of the two copepod species. High mortality was associated with conditions of low chlorophyll biomass and high temperatures. I suggest that the success of these copepod species may depend on the presence of a low predation-high chlorophyll window in early spring.

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The role of recreational boating in the introduction and spread of marine invasive species (2012)

Introduction and spread of non-indigenous species is a significant threat to the preservation of global biodiversity. Human-mediated vectors are responsible for transporting potentially invasive species to new habitats throughout the world. This research investigates the role of recreational boating movements as a vector for introduction and spread of invasive species. A baseline survey of subtidal fouling communities was conducted using artificial substrates in marinas of the southern Strait of Georgia, British Columbia. There was both a high presence of non-indigenous species and high non-indigenous species fouling cover in some marinas, indicating a likely negative impact on native communities. A dive survey which examined the species present on the underwater surfaces of recreational boats in marinas throughout British Columbia showed that more than two-thirds of boats examined had macrofouling present and one-quarter had one or more known non-indigenous species. In combination, a boater questionnaire was used to describe the movements and behaviours of the boaters themselves and behaviour patterns indicated a risk of non-indigenous species transport. The results of the dive survey and boater questionnaire were then used to develop a model that predicts the presence of fouling on boats based on three variables (age of antifouling paint, time in water and incidence of long trips). The biomechanical properties of non-indigenous species were compared to native species and non-indigenous species had both stronger attachment and lower drag than similar native species, indicating they have the ability to remain attached to fast-moving marine vessels. Finally, a statistical analysis was conducted comparing environmental, demographic and vector variables in explaining the spatial distribution of non-native species. The results showed that recreational boating played a stronger role in the distribution of subtidal non-native species than the original introduction vectors, aquaculture and shipping. This body of research demonstrates that recreational boating is a significant vector for the introduction and spread of invasive species in this region and around the world. It is the first comprehensive study of the recreational boating vector in Canadian marine waters and the results have important implications for the prevention of new introductions and the preservation of biodiversity.

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Master's Student Supervision

Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

The Galápagos penguin as the "canary in the coal mine" for microplastics research in the Galápagos Marine Reserve & plastic pollution perceptions in Ecuadorian mangrove communities (2023)

Microplastic pollution now threatens some of the world's most iconic locations for biodiversity, including the Galápagos Islands, Ecuador. This thesis highlights the pervasive and harmful nature of plastic pollution in our oceans, which has significant ecotoxicological implications for marine ecosystems, biodiversity, and human health.Using the Galápagos penguin as an indicator species, this study assessed the concentration of microplastics and other anthropogenic particles in surface seawater near Galápagos penguin colonies, penguin prey, zooplankton, and penguin scat, as well as microplastic bioaccumulation and biomagnification potentials in the Galápagos penguin using trophodynamic Ecopath with Ecosim (EwE) ecosystem modeling with the Ecotracer contaminant tracing routine. The study also investigated Ecuadorian mangrove communities' perceptions of plastic pollution's impact on the environment, economy, and human health, providing localized context for effective strategies to tackle this pervasive problem.Empirical evidence collected in the Galápagos in October 2021 revealed an average of 0.54±0.49 particles/L in surface seawater (
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The fate of salp blooms: decomposition and sinking of salp carcasses (2022)

Gelatinous zooplankton (GZ) biomass is an important, yet often overlooked, vector of particulate organic matter (POM) export in the ocean and a nutritional prey source for the mesopelagic and benthic environments. To better quantify the potential impact of their blooms on surrounding biogeochemistry and food webs, we performed decomposition and sinking experiments under two different temperature regimes, 6 and 12 °C using 260 Salpa aspera, sampled in the Northeast Pacific during May 2021. Salps were suspended in large seawater tanks with continuous water filtration systems and kept in the dark for a maximum of 30 days. Decay was exponential and occurred ~1.5 times faster in the warmer conditions. Comparison of GZ across literature studies supported the strong influence of temperature on their decomposition (Q₁₀ = 3.46) and revealed S. aspera to decay at a lower rate compared to most other GZ taxa. Carcass sinking rates were higher than previously reported for this species but slowed with prolonged decay. Biochemical (proteins, carbohydrates, lipids) and elemental (C: carbon, N: nitrogen) composition was determined for samples at various stages of degradation. Energetic content, estimated from total organics using published conversions, was typical of GZ but notably lower than common crustacean zooplankton. The high water (~97%) and low organic content of 27.8 ± 7.1 percent of dry weight (% DW) was typical of other thaliaceans. S. aspera carcasses were relatively rich in C (15.6 ± 1.66% DW) and somewhat low in N (2.42 ± 0.53% DW). Carbohydrates accounted for the majority of total organics (45.3%), followed by lipids (42.1%) and protein (13.3%). However, possible under-detection of protein could have served to overestimate lipid content and skew macromolecular ratios. The high C:N ratio (6.61 ± 1.14) of S. aspera, in comparison with a typical ratio of
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Strategies for coexisting: juvenile pink and chum salmon diets and interactions in a challenging section of coastal migration (2021)

The cultural and ecological contributions of salmon cannot be understated, as these keystone species have underpinned coastal ecosystems and societies from time immemorial. Despite this millennia-long intimate relationship with Pacific salmon, returns of stocks have become unpredictable and difficult to manage from overfishing and multiple complex stressors. Research has shown that juvenile salmon feeding is a crucial factor for growth and recruitment, and the ocean conditions driving prey availability are tightly coupled with survival of salmon. Pink and chum are abundant co-migratory species of salmon that may exert competitive pressure for food resources during their vulnerable early marine phase. However, competition research on juvenile pink and chum salmon is limited, especially within the complex British Columbia coast. This research aimed to fill gaps in understanding of juvenile pink and chum foraging strategies and interactions in areas of good and poor foraging conditions during their coastal outmigration. In the Discovery Islands and Johnstone Strait regions, there were foraging deserts and oases, where juvenile salmon mean stomach fullness values ranged from 6% body weight. In good foraging conditions, juvenile pink and chum both consumed the same high-quality crustacean prey with limited competition, but under poor foraging scenarios, salmon diets differed. Chum salmon consistently consumed gelatinous prey and pink salmon relied more heavily on copepods and nearshore zooplankton, differing in niche in response to competitive interactions. There was a match between predators and prey in 2015, when salmon fed on larger prey, and were in healthier condition (K = 1.0). There was a potential mismatch in 2016, when small prey taxa may have caused poorer condition for juvenile salmon (K = 0.94). Chum salmon had a stronger relationship to prey size than pink, when larger chum successfully consumed the largest prey. These foraging strategies of opportunistic specialization may indeed provide salmon with resilience to face the challenges of shifting climates. Pink and chum salmon can be monitored as indicators for ecosystem health and zooplankton availability. Salmon reflect the health of socio-ecological systems and require our understanding and care to view them holistically as they migrate through diverse, challenging habitats.

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Foraging ecology of juvenile Fraser River sockeye salmon across mixed and stratified regions of the early marine migration (2019)

Pacific salmon hold tremendous ecological, cultural, and economic value to communities and ecosystems throughout British Columbia. The productivity of several populations, however, has declined since the early 1990s. The cause of the decline is still not fully understood, though bottom-up drivers and trophic interactions during the early marine migration are believed to be contributing factors. For juveniles leaving the Fraser River, their migration crosses a range of stratified and well-mixed waters with varying levels of productivity. The purpose of this study is therefore to a) characterize the foraging ecology of juvenile sockeye salmon across the range of environmental conditions they encounter during the early marine migration, and b) test whether foraging success is lower in tidally mixed waters. In 2015 and 2016, environmental conditions, prey dynamics, and sockeye diets were sampled at high spatial and temporal resolution in the Discovery Islands and Johnstone Strait during the outmigration period. Analyses revealed two unique diet types, one dominated by meroplankton, cladocerans, and larvaceans in the warmer, fresher waters of the Discovery Islands and the other dominated by large calanoid copepods in the cooler, saltier waters of Johnstone Strait. In all diets, sockeye exhibited strong selection for prey items larger than 2 mm. Furthermore, foraging success was low throughout the tidally-mixed regions of the Discovery Islands and Johnstone Strait, providing strong support for the hypothesis that this region is a ‘trophic gauntlet’ for outmigrating salmon. Foraging hotspots were also discovered along the interface between mixed and stratified waters. These frontal areas may in fact be important foraging grounds for juveniles to facilitate their migration through otherwise challenging conditions. This research addresses a critical knowledge gap in the foraging ecology of juvenile salmon across different environmental conditions during their early marine migration and can be used to improve our ability to monitor fish condition, growth, survival, and ultimately recruitment.

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Zooplankton community composition across a range of productivity regimes in coastal British Columbia (2018)

Coastal British Columbia is composed of deep channels and shallow sills intricately wovenaround a collection of small islands, creating complex oceanographic conditions. Consequently,seasonal production varies up to several orders of magnitude throughout the region, with someregions undergoing large annual phytoplankton blooms, while others have permanently lowphytoplankton biomass. The region from the northern Strait of Georgia (SoG) to Johnstone Strait(JS) has been vastly understudied from the perspective of zooplankton despite its importance tomany higher trophic levels. The objectives of this study were to: a) describe the annual seasonalcycle of zooplankton in the northern SoG over the course of two years and examine howcommunities differed, and b) examine the spatial patterns in zooplankton communitycomposition and abundance from the northern SoG to JS, a region spanning seasonallyproductive / stratified areas (northern SoG, eastern Discovery Islands (DI)) as well aspermanently high-nutrient, low-chlorophyll (HNLC) regions (JS, western DI). There was astrong signal of intra-annual seasonality in zooplankton community dynamics in the northernSoG, separating into distinct winter, early spring, and summer – fall assemblages. Despite a sixweek difference in spring bloom timing between years, peak zooplankton abundance occurredwithin the same calendar week during both years and community composition was similarbetween years, indicating that there is likely resilience within the zooplankton seasonal cycle toshort scale interannual changes in environmental conditions. Our spatial analysis indicated thatthe northern SoG, DI, and JS each had distinct zooplankton communities with key species anddensities separating regions. We detected minimal overlap in the JS zooplankton communitywith the DI and northern SoG, indicating that while DI zooplankton are likely sourced from theSoG, JS zooplankton likely originate from Queen Charlotte Sound. The DI were comprised ofboth productive and HNLC regions, yet zooplankton abundance was highest in the mixedwestern DI channels. Intense tidal mixing in the DI likely supplies nutrients to stratified surfacewaters in the eastern DI, which in turn supply zooplankton to the western DI with low in-situproduction. These results provide insight into how feeding conditions for higher trophic levelsmay vary throughout the region.

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Temporal and spatial patterns of outmigration of juvenile sockeye salmon in Rivers Inlet (2017)

The sockeye salmon, Oncorhynchus nerka, is economically, ecologically and culturally important for British Columbia and Canada. Currently, ~75% of sockeye populations are declining with a precipitous decline reported in Rivers Inlet (RI). The purpose of this study was to investigate the variability of juvenile sockeye residence and growth in RI during their outmigration to the Pacific Ocean. The point of the marine entry was estimated by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) using otolith elemental composition (Sr:Ca ratio). A significant correlation was found between the day of entry and the duration of the migration. Average transit time through the inlet was ~ 2 weeks in 2011 and 2009, compared to ~ 4 weeks in 2008 and 2010. In terms of BL/s, the fish travel through RI with an average speed of 0.2– 0.5 BL/s. The size of the smolts at the entry to the inlet ranged between 54 and 83 mm. Detailed analysis of the full outmigration period in 2009 identified two possible migration behaviors, dependent on the day of entry and potentially the size of the smolts. Smaller fish that entered the inlet prior to mid-June exhibited a “holding” pattern at the head of the inlet, with an average residence time of 2-3 weeks. Smolts that entered the inlet later in the season swam continuously throughout the inlet. Using GAM models, it was determined that 78% of the weight at catch and 64% increase in weight were explained by the combination of water temperature, freshwater discharge, zooplankton densities and inlet entry size of smolts. The duration of the outmigration was dependent on river discharge and temperature, with 62% of the variation in outmigration duration explained by the model. Results suggest that there is a set of optimal environmental conditions for smolt growth during their outmigration. Outmigration timing was found to be the key determinant of conditions experienced and appeared to act as an equilibration mechanism between small and large smolts, resulting in similar size being attained by both by the inlet mouth.

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Stable Isotope Analysis of Rivers Inlet Sockeye Salmon (Oncorhynchus nerka): Investigating the Contribution of Environmental Conditions in the High Seas to British Columbia Population Declines (2015)

Sockeye salmon (Oncorhynchus nerka) populations in BC have undergone varying degrees of decline coinciding with a shift to a warmer phase of the Pacific Decadal Oscillation (PDO) in 1977. The PDO, and other climate cycles, have been shown to significantly affect the physical and biological characteristics of the North East Pacific Ocean. Changes in ocean productivity have implications for pelagic food webs and may cause shifts in the abundance of potential prey for sockeye salmon, impacting their long-term production patterns. We investigated the coupling of ocean conditions and population fluctuations using Rivers Inlet as a case study, a system that suffered probably the most catastrophic sockeye stock collapse in BC history. Stable isotope analysis was used to access information on ocean conditions stored in the carbon and nitrogen isotope ratios of archived sockeye scales for the period 1915-2013. Our results indicated that Rivers Inlet sockeye salmon experienced highly variable open ocean conditions during this period. Both decadal scale shifts in North Pacific climate (e.g., PDO) and interannual scale shifts in climate (e.g., El Niño/La Niña events) were reflected in the physical and biological environment of the offshore Gulf of Alaska. Positive phases of the PDO and El Niño events were associated with a warmer and less productive ocean, while negative phases of the PDO and La Niña events were associated with a colder and more productive ocean. Moreover, the carbon and nitrogen stable isotope time-series indicated that the foraging habits of Rivers Inlet sockeye salmon were affected by these shifts of North Pacific climate. A lengthening (shortening) of the food web was associated to warm (cold) and less productive (more productive) periods. In addition, the isotope data also supports Rivers Inlet sockeye salmon shifting diet depending upon prey availability. We concluded that a combination of the two factors was responsible for the changes in the feeding ecology of Rivers Inlet sockeye salmon during the period 1915-2013. Such variation in the feeding ecology of Rivers Inlet sockeye salmon could potentially have a negative effect in the overall survival rates of sockeye salmon.

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The life cycle of the pteropod Limecina hellicna in Rivers Inlet (British Columbia, Canada) (2014)

The life cycle of Limacina helicina has been continuously debated within the literature.We believe the current lack of consensus regarding fundamental aspects of its life cycle(e.g. seasonal times of spawning, seasonal development of the population size structure, as well as the life cycle longevity)is primarily due to using datasets of low temporal resolution. Using fort-nightly data, two population cohorts were identified using the mixdist statistical package and tracked for more than 400 days, throughout 2008 to 2010.From this, a life cycle longevity of 1.2--1.5 years was estimated for L. helicina in Rivers Inlet.Throughout the seasons, the population size structure showed a continually high presence of the smaller size-groups suggesting continuous spawning, however, based on total densities of > 600 ind.m^-³, the late spring was put forward as the period of peak spawning.Continuous spawning was confirmed with the use of daily data.Identification of a summer peak spawning established late spring and summer as two periods of enhanced spawning, although continuous spawning occurred throughout the season (in a limited fashion).Short-term periods of significant growth were observed prior to peak spawning in late spring and summer. This was not directly coupled with chlorophyll concentrations, possibly due to the time lag between periods of high chlorophyll biomass and zooplankton response.Attempts were made to estimate the instantaneous mortality of L. helicina, and the seasonal changes experienced from spring to summer.Our estimates were complicated by a combination of 1.) inherent patchiness of L. helicina, 2.) advection, and 3.) merged recruits.Generally, there were no cases of significant mortality throughout the seasons however, short term mortality was observed after peak spawning.It is plausible that the smallest size-groups of L. helicina experiences the highest mortality after peak spawning.Our findings show that in Rivers Inlet, L. helicina has a life cycle spanning 1--1.5 years with spring and summer peak spawning activities. The spring cohort is likely spawned by the summer cohort from the previous year. It utilizes the spring phytoplankton bloom to reach sexual maturity and spawn the summer cohort.

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Active carbon transport and feeding ecology of pelagic decapods in the North Pacific Subtropical Gyre (2012)

Pelagic decapods were collected during two cruises in the central North Pacific Subtropical Gyre (NPSG): in 2011 depth stratified samples with a MOCNESS-10 (10 m² Multiple Opening/Closing Net and Environmental Sensing System) were carried out at two stations to the west and north of the Hawaiian island of Oahu (21°20.6'N, 158°16.4'W and 22°45'N, 158°00'W), and in 2004 samples were collected using three different micronekton sampling gears in the shallow backscattering layer (SSL) and deep backscattering layer (DSL) off the southwest coast of Hawaii. A total of 40 decapod taxa were identified. Amongst the 22 species with sufficient representation, three migration classes were identified: full migrators (6 species); partial migrators (13 species); and non-migrators (3 species). Using measured local temperature profiles along with published models of respiration, excretion and mortality, the individual and total active downward carbon flux was calculated. From the 2004 samples, diets of nine pelagic decapod species were established through stomach content analysis. It was found that decapod diet varied not only with size, but also with taxonomy. All decapods fed more in the SSL at night than in the DSL during the day or night. However, decapods did not feed entirely at night in the SSL, a common assumption made in previous estimates of active flux for a wide variety of organisms. Instead, feeding in the DSL was equal to 9.67 – 44.69% of feeding in the SSL by weight. Using these feeding estimates, and assuming a micronekton sampling efficiency of 33.33% for the MOCNESS-10, the active flux due to decapod migrations was calculated to be 382.7 - 625.0 µgC/m²/day. Compared to the local passive flux, this active flux was equal to 4.8 - 7.8% of passive flux at the mean night time residence depth (710.7 m), 2.1 - 3.4% of passive flux at the mean daytime residence depth (261.8 m), and 1.5 - 2.4% of passive flux at the base of the euphotic zone (173 m).

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Spatial and Temporal Variation in Kelp-Derived Detritus and Its Dietary Importance to Consumers Along the West Coast of Vancouver Island, Canada (2012)

Stable isotope analysis was used to determine spatial and temporal patterns of suspended kelp-derived detritus (KDD) and its contribution to consumers along a gradient of kelp abundance driven by recovering sea otter (Enhydra lutris) populations along the west coast of Vancouver Island (WCVI). During the summer and winter, ocean surface size-fractionated particulate organic matter (POM), dominant kelp species (order Laminariales), surface plankton and benthic organisms were sampled along offshore transects (0 – 30 km), and analyzed for carbon and nitrogen stable isotopes. Phytoplankton isotope fractionation characteristics were utilized along with principal component analysis to determine seasonally and size fraction specific δ¹³C and δ¹⁵N values. Blooming size fractions of phytoplankton were enriched in ¹³C by 2.5 to 5.4 ‰ and enriched by 0.3 to 3.1 ‰ in ¹⁵N. There were significant within and among region, and between season differences in kelp isotopic values. For example, during the summer, the otter-present Macrocystis pyrifera mean δ¹³C value (-13.17 ± 1.12 ‰) was more enriched than Nereocystis luetkeana (-16.89 ± 1.88 ‰; p 40 %) and similar with size, among regions and between seasons, with the exception of red turban snails (Astraea gibberosa) in the otter-present region where KDD contribution was 41.2 to 96.6 % lower than the otter-absent region.These results indicate that kelp abundance is not the only driver of KDD dispersal spatially and temporally. Factors such as local oceanography, kelp forest community composition, large variation in kelp isotope values, and similarity between kelp and phytoplankton isotope values may affect these patterns and lead to high uncertainty in modeled KDD contributions.

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The growth and diet composition of sockeye salmon smolts in Rivers Inlet, British Columbia (2012)

In the early life history of sockeye salmon smolts, prey availability (quality and quantity) and growth are strongly linked. During this critical period, when ~ 90% of their mortality occurs, they must attain a critical size at which they have sufficient energy stores to survive their long migration with little predation impact, leading to better survival and higher returns. To determine patterns of growth of out-migrating sockeye salmon and to link inter-annual variations in growth to diet and seasonality of the zooplankton community, seine netting and zooplankton tows were conducted in May-June 2008, 2009, and 2010 in Rivers Inlet, British Columbia, a fjord with estuarine circulation. Growth rate, condition factor and mass-length relationships were calculated from length and mass data obtained from fresh fish. Stomachs were analyzed for total prey composition in terms of biomass and abundance. Growth rates were faster in 2009 and 2010 than in 2008; however, the condition factor was highest in 2010, and similar in 2009 and 2008. Mass-length relationships indicated that sockeye smolts were significantly heavier per unit length in 2010 (p
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Assessing intertidal marine non-indigenous species in Canadian ports (2011)

The establishment of non-indigenous species in natural ecosystems is a growing concern at global, national, and regional scales. Over 100 known marine non-indigenous species (NIS) are found along the Pacific and Atlantic coasts of Canada. It is widely believed that commercial shipping activities associated with international ports (e.g. ballast water discharge, hull fouling) could expose native communities to a variety of NIS. Thus, harbours are recognized as critical entry points for NIS and, pending establishment, can serve as invasion hubs for secondary dispersal vectors (e.g. recreational boats). The aim of this study was to characterize intertidal NIS distributions among ports on the Pacific and Atlantic coasts of Canada and to determine if commercial shipping activities (ballast water discharge, vessel arrivals) can be directly linked to the observed patterns of established NIS. Sixteen major international ports in Canada were surveyed for species composition and abiotic conditions, including both environmental and anthropogenic factors. Species diversity for both NIS and native species were found to be significantly different between the Pacific and the Atlantic intertidal communities. Although both NIS and native species had higher diversity on the Pacific coast, the Invasion index, a novel measurement of the degree of invasion developed in this thesis, demonstrated that the Atlantic coast was actually more invaded by NIS than the Pacific. No direct link was found between commercial shipping activities and the distribution patterns of established intertidal NIS in Canadian ports. Instead, NIS distributions were found to be strongly related to salinity, sediment type, human population, aquaculture and latitude on the Pacific coast and human disturbance at docks, latitude and salinity on the Atlantic coast. In contrast to what was previously suggested, these results demonstrated that ballast water discharge and vessel arrival frequency were not detected as the main variables towards NIS establishment success. However, this study highlighted the importance of environmental conditions and local anthropogenic vectors in the establishment of NIS in new regions. Future research in conservation and management of invaded communities should include environmental conditions and the risk posed by anthropogenic activities, in addition to commercial shipping, when characterizing invasion dynamics.

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Changing jellyfish populations: trends in large marine ecosystems (2011)

Although there are various indications and claims that jellyfish have been increasing at a global scale in recent decades, a rigorous demonstration to this effect has never been presented. As this is mainly due to scarcity of quantitative time series of jellyfish abundance from scientific surveys, an attempt is presented here to complement such data with non-conventional information from other sources. This was accomplished using the analytical framework of fuzzy logic, which allows the combination of information with variable degrees of cardinality, reliability, and temporal and spatial coverage. Data were aggregated and analysed at the scale of Large Marine Ecosystem (LME). Of the 66 LMEs defined thus far, which cover the world’s coastal waters and seas, trends of jellyfish abundance (increasing, decreasing, or stable/variable) were identified (occurring after 1950) for 45, with variable degrees of confidence. Of these 45 LMEs, the overwhelming majority (31 or 69%) showed increasing trends. Recent evidence also suggests that the observed increases in jellyfish populations may be due to the effects of human activities, such as overfishing, global warming, pollution, and coastal development. Changing jellyfish populations were tested for links with anthropogenic impacts at the LME scale, using a variety of indicators and a generalized additive model. Significant correlations were found with several indicators of ecosystem health, as well as marine aquaculture production, suggesting that the observed increases in jellyfish populations are indeed due to human activities and the continued degradation of the marine environment.

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