Observed properties of the internal wave groups which occur in the southern Strait of Georgia are summarized, with particular emphasis on those properties which must be explained by any theory of generation. Current measurements within Boundary Pass are described. These measurements suggest a generation mechanism in the form of impulsive disturbances to the stratified water mass within the Strait, caused by the abrupt changes in current speed which are observed to characterize the tidal flow close to both turns of the tide. Such a mechanism is shown to explain the most important observed properties: origin in space near the mouths of the passes between the Gulf Islands, origin in time near both turns of the tide, uni-directional propagation into the Strait, and origin of a varying number of groups on one turn of the tide. The form of wave groups which result from the initial-value problem for a stratified fluid is examined. A linear model is shown to result in wave groups which are of the same general form as the groups observed in the Strait, but much less compact, indicating the necessity of some effect to counteract dispersion. Since observed waves are of distinctly finite amplitude, nonlinear effects were included and time-dependent theory developed for "long-short" waves in a thin-layer system, characteristic of the southern Strait. For a restricted class of initial conditions, solutions are obtained by a comparison technique, using known solutions of the Korteweg-deVries equation. This class of solutions suggests that the general initial-value problem results, for large x and t, in a number of "solitons", individual solitary waves of the thin-layer system. Surface effects associated with the internal waves in the Strait are described, and the reflectivity changes examined in some detail. The usual explanation of the effect of shallow internal waves on the surface wave field is in terms of wave damping by a surface organic film which is periodically expanded and contracted by internal wave-induced motions. It is shown that, under certain conditions, the effect may equally well, be-due to periodic changes in-surface wave amplitude and vector wave number caused-by radiation stress effects induced by the presence of internal waves. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Climate is emerging as a primary determinant of marine survival and migratory behaviour for Pacific salmon. For example, a regime shift in the mid-1990s was correlated to a major change in the migratory behaviour of coho salmon (Oncorhynchus kisutch) in the Strait of Georgia, BC. The details of this new behaviour pattern remain relatively unknown. Furthermore, many coho stocks have been declining during the past three decades. Mitigative strategies –such as hatchery programs— have done little to reverse the trend, and little is known about how hatchery fish are affecting wild populations. The objective of this dissertation was to identify key mortality areas and provide the first look at the migratory behaviour of juvenile wild and hatchery coho in southwestern British Columbia using new telemetry technologies. As coho pre-smolts are relatively small compared with other salmonid species that are typically studied using acoustic telemetry, the identification of the appropriate sizes of fish and tags to use was critical. The first study tested the effects of surgically implanting the three smallest sizes of acoustic tags available on the growth, survival, performance and condition of coho pre-smolts. The first of three field studies to follow investigated the early migratory behaviour and survival of an endangered coho population. The second field study examined differences in physiology, survival and migratory behaviour between wild and hatchery-reared coho smolts. Finally, the third study analysed the altered marine migratory behaviour of juvenile coho in the Strait of Georgia. This dissertation provides the first evidence of high freshwater mortality rates in the endangered coho population, which has implications for the management and conservation of this and other at-risk stocks. I found differences in migratory behaviour and physiology between wild and hatchery-reared coho, suggesting that mitigative strategies need further evaluation. Finally, the timing of the anomalous coho migration out of the Strait of Georgia confirmed that population changes in the strait are a consequence of ecosystem-related impacts. These findings demonstrate how new technologies could be used to fill major information gaps and improve the management and conservation of Pacific salmon.

Climate is emerging as a primary determinant of marine survival and migratory behaviour for Pacific salmon. For example, a regime shift in the mid-1990s was correlated to a major change in the migratory behaviour of coho salmon (Oncorhynchus kisutch) in the Strait of Georgia, BC. The details of this new behaviour pattern remain relatively unknown. Furthermore, many coho stocks have been declining during the past three decades. Mitigative strategies –such as hatchery programs— have done little to reverse the trend, and little is known about how hatchery fish are affecting wild populations. The objective of this dissertation was to identify key mortality areas and provide the first look at the migratory behaviour of juvenile wild and hatchery coho in southwestern British Columbia using new telemetry technologies. As coho pre-smolts are relatively small compared with other salmonid species that are typically studied using acoustic telemetry, the identification of the appropriate sizes of fish and tags to use was critical. The first study tested the effects of surgically implanting the three smallest sizes of acoustic tags available on the growth, survival, performance and condition of coho pre-smolts. The first of three field studies to follow investigated the early migratory behaviour and survival of an endangered coho population. The second field study examined differences in physiology, survival and migratory behaviour between wild and hatchery-reared coho smolts. Finally, the third study analysed the altered marine migratory behaviour of juvenile coho in the Strait of Georgia. This dissertation provides the first evidence of high freshwater mortality rates in the endangered coho population, which has implications for the management and conservation of this and other at-risk stocks. I found differences in migratory behaviour and physiology between wild and hatchery-reared coho, suggesting that mitigative strategies need further evaluation. Finally, the timing of the anomalous coho migration out of the Strait of Georgia confirmed that population changes in the strait are a consequence of ecosystem-related impacts. These findings demonstrate how new technologies could be used to fill major information gaps and improve the management and conservation of Pacific salmon.

Climate is emerging as a primary determinant of marine survival and migratory behaviour for Pacific salmon. For example, a regime shift in the mid-1990s was correlated to a major change in the migratory behaviour of coho salmon (Oncorhynchus kisutch) in the Strait of Georgia, BC. The details of this new behaviour pattern remain relatively unknown. Furthermore, many coho stocks have been declining during the past three decades. Mitigative strategies –such as hatchery programs— have done little to reverse the trend, and little is known about how hatchery fish are affecting wild populations. The objective of this dissertation was to identify key mortality areas and provide the first look at the migratory behaviour of juvenile wild and hatchery coho in southwestern British Columbia using new telemetry technologies. As coho pre-smolts are relatively small compared with other salmonid species that are typically studied using acoustic telemetry, the identification of the appropriate sizes of fish and tags to use was critical. The first study tested the effects of surgically implanting the three smallest sizes of acoustic tags available on the growth, survival, performance and condition of coho pre-smolts. The first of three field studies to follow investigated the early migratory behaviour and survival of an endangered coho population. The second field study examined differences in physiology, survival and migratory behaviour between wild and hatchery-reared coho smolts. Finally, the third study analysed the altered marine migratory behaviour of juvenile coho in the Strait of Georgia. This dissertation provides the first evidence of high freshwater mortality rates in the endangered coho population, which has implications for the management and conservation of this and other at-risk stocks. I found differences in migratory behaviour and physiology between wild and hatchery-reared coho, suggesting that mitigative strategies need further evaluation. Finally, the timing of the anomalous coho migration out of the Strait of Georgia confirmed that population changes in the strait are a consequence of ecosystem-related impacts. These findings demonstrate how new technologies could be used to fill major information gaps and improve the management and conservation of Pacific salmon. / Land and Food Systems, Faculty of / Graduate

Cohorts of larval Pacific herring, Clupea harengus pallasi Valenciennes 1847, were studied from hatch during the spring of 1985, 1986, and 1987 in the Strait of Georgia, British Columbia. The main objectives were to study the patterns in the larval dispersal process, to study a major spawning area for Pacific herring to determine whether this site may act as a nursery area for the resulting year-class, and to evaluate the current hypotheses concerning survival of the larval year-class for their applicability to Pacific herring. Results indicated a significant proportion of larval herring which hatched in Lambert Channel quickly dispersed into Baynes Sound, probably through a combination of tidal movements and wind driven surface currents. Baynes Sound was shown to be much more stable than Lambert Channel due to strong stratification through freshwater input and protection from wind mixing by the surrounding land masses which may also have resulted in an earlier spring plankton bloom. Baynes Sound also had significantly higher densities of microzooplankton important to the early feeding herring larvae than Lambert Channel and outside waters. The suite of potential predators was also different between the two channels with Baynes Sound having more hydromedusae and Lambert Channel having more chaetognaths and polychaetes. Analysis of larval growth rates using an RNA/DNA ratio technique on individuals from the yolk sac stage onwards indicated the larvae initially grew very slowly but, by postflexion were growing over 25 %•d⁻¹ in protein. Starvation did not appear to play an important role in mortality. The RNA/DNA ratio was demonstrated to be directly correlated with a morphometric condition factor Pacific herring larvae indicating it can also be used as a condition factor. There was a significant positive correlation between the mean protein growth rate measured with RNA/DNA ratios and the mean nauplii density. Feeding larvae in Baynes Sound were found to be growing faster than those in Lambert Channel suggesting Baynes Sound was being used as a nursery area. Analysis of otoliths suggested there was a significant increase in survival of larval herring having higher growth rates over as little as a 3-week period. / Science, Faculty of / Zoology, Department of / Graduate

The main objective of this thesis was to evaluate the use of Moderate Resolution Imaging Spectroradiometer (MODIS) Aqua imagery to estimate chlorophyll-a (chl) concentrations in the surface waters of the Strait of Georgia, located off the southwest coast of Canada. To meet this objective two components were addressed: (1) evaluate chl algorithms using ship-based radiometric and biophysical measurements, (2) evaluate atmospheric correction methods in conjunction with chl algorithms using MODIS Aqua imagery. In Chapter 2, biophysical and above-water reflectance measurements collected in 2006 were used to evaluate the OC3M, standard Garver-Siegel-Maritorena version~1 (GSM01), and a modified version of the GSM01 algorithms for estimating chl concentrations in the Strait. The Strait was generally classified as a case 2 water body, transitioning from chromophoric dissolved organic matter (CDOM) dominant in the central region to possibly particulate dominant in the Fraser River plume region. From these biophysical measurements, results showed that the OC3M algorithm was somewhat effective (r^2 = 0.552) outside the most turbid areas of the Fraser River plume. However, a systematic overestimation of lower chl concentrations was found, which may have been related to the higher CDOM absorption observed throughout the Strait. The standard GSM01 algorithm had moderately good agreement with measured CDOM absorption (r^2 = 0.584) and total suspended solids (TSS) concentrations (r^2 = 0.866), but was ineffective at estimating chl concentrations. Localized characterization of the CDOM absorption, through a hyperbolic CDOM model, improved the modified GSM01 results by providing better agreement with measured CDOM absorption (r^2 = 0.620) and TSS concentrations (r^2 = 0.935). By limiting the GSM01 algorithm to regions with lower combined CDOM and non-algal particulate absorption, the statistical relationship between measured and estimated chl improved (r^2 = 0.690). The further re-interpretation of phytoplankton absorption from the modified GSM01 algorithm with a two-component phytoplankton model resulted in a chl relationship with an r^2 = 0.702 and a linear slope closer to one. However, due to the nature of the GSM01 algorithm, its effectiveness is dependent the accurate characterization of the absorption and backscattering of the optically significant water constituents, which is not always available. Furthermore, the GSM01 algorithm effectiveness is contingent upon the accurate atmospheric correction of the shorter blue wavelengths within satellite imagery. Using unattended fluorometric chl measurements, different atmospheric correction approaches in conjunction with the standard OC3M chl algorithm and modified GSM01 algorithm from Chapter 2 were evaluated in Chapter 3. Atmospheric correction methods that were evaluated included: the standard near infrared (NIR) correction, a shortwave infrared (SWIR) correction, and an adapted version of the correction developed at the Management Unit of the North Sea Mathematical Models (MUMM). The NIR correction with the OC3M algorithm was statistically significant with an adjusted r^2 = 0.759 outside the most turbid portions of the Strait, but had a relatively large RMSE of 0.523, was limited to chl < 21 mg m^-3, and only estimated concentrations for 63% of the pixels. Effectiveness of the SWIR correction was limited with the OC3M algorithm because of the low percentage of estimated chl concentrations (21% of the pixels) and a lower adjusted r^2 = 0.572 outside the more turbid portion of the Strait. The adapted MUMM correction was the most effective, using the spatially averaged aerosol properties from the SWIR correction with the fixed NIR water-reflectance ratio defined by the MUMM method. The MUMM correction with the OC3M algorithm, when limited to pixels outside the Fraser River influence, had an adjusted r^2 = 0.720 and provided chl estimates for 84% of the pixels. The modified GSM01 algorithm was ineffective with all three atmospheric corrections due to the overcorrection of the 412 nm band. Several possible reasons for this overcorrection were identified, including the presence of absorbing aerosols and absorption from atmospheric nitrogen dioxide. When comparing spatial-temporal patterns in the MUMM corrected OC3M image with chl measurements, general spatial patterns and temporal trends match, with some explainable exceptions. Firstly, turbidity typically found near Fraser River plume makes the OC3M algorithm ineffective. Secondly, under lower aerosol reflectance conditions, the signal-to-noise ratio of the SWIR bands can make the spatial identification of the aerosol properties difficult.

Although food quality is thought to play an important role in the survival of marine copepods, the extent of natural variability in food quality remains poorly characterized. Here I characterize the different scales at which food quality varies in copepods of the Strait of Georgia, British Columbia, Canada. Significant interannual variability occurs in the diet of Neocalanus plumchrus in the Strait of Georgia. Between 2001-06 the fatty acid profiles of N. plumchrus switched from omnivorous, oceanic signatures to herbivorous, diatom-dominated signatures. An index of food quality (DHA/EPA) is strongly correlated to the abundance of diapausing N. plumchrus, suggesting that the relative proportion of essential fatty acids provided by dinoflagellates and diatoms are related to the survival of this species. Combined fatty acid and stable isotope analysis indicated that the spring calanoid copepods of the Strait of Georgia occupy three trophic positions: Eucalanus bungii is herbivorous, Calanus marshallae and N. plumchrus are omnivorous, while Euchaeta elongata is carnivorous. Oceanic conspecifics of Strait of Georgia copepods experience a more omnivorous diet, as indicated by the presence of higher proportions of flagellate and carnivory markers, and lower proportions of diatom-based markers in their fatty acids. Despite spatial differences in the quality of their diets, the relative trophic positions of these copepods are constant as indicated by their stable isotope signatures. There is a correlation between the trophic information provided by stable isotopes and fatty acids. However, stable isotopes are not sensitive enough to capture the range of dietary variability observed in fatty acids, and fatty acids do not always provide reliable markers of carnivory and trophic position. Over the span of a season, copepods can utilize a wide range of dietary items including diatoms, flagellates, bacteria, detritus and microzooplankton. Copepods can switch from herbivory to carnivory in response to declining chlorophyll concentrations after the spring bloom, and are occasionally able to utilize detrital and bacterial sources. I conclude that the quality of copepod diets in the SoG varies on interannual, interspecific and seasonal scales. The implications of these findings are discussed in relation to ecosystem models of the area, and to copepod physiology.

Estimating the efficiency with which energy is transferred to higher trophic levels demands estimates of adult and juvenile copepod biomass production rates. Adult rates (egg production) are well studied; however. our knowledge of how juvenile biomass production rates (BPR) vary in situ remains incomplete and has been limited by difficulties associated with measuring somatic growth rate in the field. This problem may be resolved with the application of new methods that either: a) directly estimate BPR without additional estimates of growth or biomass, and/or: h) improve estimates of development and growth rate that may then be applied to estimates of biomass. The objective of this thesis is to develop a routinely applicable method that may be used to gain greater insight into how production of juvenile copepods is regulated in the field. I have developed a field method for estimating BPR, development and growth of marine copepods that is based on measuring the in situ rate of decay of the crustacean moulting enzyme, chitobiase. The method may be generalized to the community level because the relationship between chitobiase activity liberated into seawater after moult and individual body size was found to be common to three calanoid and one harpacticoid copepod species. This relationship. and the rate of decay of chitobiase in the water column, can be used to estimate the community-level BPR and size-class specific stage durations. Estimates of stage duration based on the turnover rate of chitobiase in the water column were in good agreement (within 5-15%) with both conventional incubation techniques and literature-based estimates. The approach was also used to estimate community-level BPR during a two-year time series in the Straight of Georgia (2004 and 2005) and two broad-scale spatial surveys encompassing shelf, slope and open ocean regions in the subarctic NE Pacific during the spring and late summer of 2004. This thesis presents the development and field validation of a novel method of estimating rates of juvenile copepod production. development, and growth that may be used to further characterize how variation of these rates is regulated in the field. The results of field studies using this approach suggest that: (i) the chitobiase-based method can be routinely used to estimate production rates that are broadly applicable to copepod communities; (ii) even when food is abundant. poor food quality can negatively influence copepod community production rates over relatively short timescales and; (iii) contemporary predictive models of in situ copepod growth rate may not be globally applicable because the relative influence of temperature. individual body weight, and chlorophyll a concentration on in situ growth rate varies with region and copepod community composition.

Although food quality is thought to play an important role in the survival of marine copepods, the extent of natural variability in food quality remains poorly characterized. Here I characterize the different scales at which food quality varies in copepods of the Strait of Georgia, British Columbia, Canada. Significant interannual variability occurs in the diet of Neocalanus plumchrus in the Strait of Georgia. Between 2001-06 the fatty acid profiles of N. plumchrus switched from omnivorous, oceanic signatures to herbivorous, diatom-dominated signatures. An index of food quality (DHA/EPA) is strongly correlated to the abundance of diapausing N. plumchrus, suggesting that the relative proportion of essential fatty acids provided by dinoflagellates and diatoms are related to the survival of this species. Combined fatty acid and stable isotope analysis indicated that the spring calanoid copepods of the Strait of Georgia occupy three trophic positions: Eucalanus bungii is herbivorous, Calanus marshallae and N. plumchrus are omnivorous, while Euchaeta elongata is carnivorous. Oceanic conspecifics of Strait of Georgia copepods experience a more omnivorous diet, as indicated by the presence of higher proportions of flagellate and carnivory markers, and lower proportions of diatom-based markers in their fatty acids. Despite spatial differences in the quality of their diets, the relative trophic positions of these copepods are constant as indicated by their stable isotope signatures. There is a correlation between the trophic information provided by stable isotopes and fatty acids. However, stable isotopes are not sensitive enough to capture the range of dietary variability observed in fatty acids, and fatty acids do not always provide reliable markers of carnivory and trophic position. Over the span of a season, copepods can utilize a wide range of dietary items including diatoms, flagellates, bacteria, detritus and microzooplankton. Copepods can switch from herbivory to carnivory in response to declining chlorophyll concentrations after the spring bloom, and are occasionally able to utilize detrital and bacterial sources. I conclude that the quality of copepod diets in the SoG varies on interannual, interspecific and seasonal scales. The implications of these findings are discussed in relation to ecosystem models of the area, and to copepod physiology.

The goal of this research was to construct a time series of accurate chlorophyll-a concentration for the Strait of Georgia (SoG), Canada, using an improved atmospheric correction scheme and workflow for the Moderate Resolution Imaging Spectroradiometer AQUA (MODIS) satellite instrument to describe the chla dynamics and spring bloom phenology in the SoG. In situ radiometric samples were acquired via Aerosol Robotic Network (AERONET), and hyperspectral data collected from a Hyperspectral Surface Acquisition System (HyperSAS) to assess three potential atmospheric correction schemes. Water property samples including total suspended material (TSM), chromophoric dissolved organic matter (CDOM), and chlorophyll concentrations (chla) were collected to further assess atmospheric corrections and the applied ‘Ocean Color 3 Modis’ (OC3M) standard chlorophyll algorithm. Regression, Absolute percentage difference (APD), Relative Percentage difference (RPD), and Root mean squared error (RMSE) analysis revealed the most appropriate method to be the ‘Management Unit of the North Seas Mathematical Models’ (MUMM) using the shortwave infrared spectrum (SWIR) to determine NIR-derived aerosol model. This method was used to construct a time series (July 2002-June 2014) of daily chlorophyll maps for all available imagery. Files were spatially binned into 8-day composites for the North and Central SoG where a modified threshold-based definition was used to determine the start of the spring phytoplankton bloom period, as well as timing of maxima and duration of the largest spring bloom. Results indicate Central SoG start dates range from late February to late April, with an average start date at the last week of March. These results compare favorably to Hindcast predictive modelling of bloom start dates. The Northern SoG bloom phenology starts on average 9 days earlier, and experiences lower chlorophyll-a magnitudes. Hierarchical clustering with correlation similarity of spring seasons indicate 2008 and 2007 were anomalous, while 2009 and 2012 were the most correlated for blooms occurring in the spring season. / Graduate / 0366 / 0416 / 0752 / 0368 / carswell@uvic.ca