No description available.

The current study had two overriding and inter-related aims. The first was to describe the biology of C. hesperia the dominant scavenging subtidal cirolanid found in temperate waters off the Perth metropolitan coastline and thereby extend our knowledge and test several hypotheses regarding the biology of scavenging crustaceans in general. The second was to use the biological information generated to develop fishing practices that reduce the amount of bait used by trap based fisheries without reducing the overall catch. Fulfilling the latter aim has the potential to greatly reduce some of the deleterious effects of fishing practices around the world. A survey was designed to determine whether the anecdotal evidence that commercial rocklobster fishers believe sea lice have a negative impact on the ratio of bait used to rocklobster landed was widespread across the fishery and, if so, whether they associated particular factors with increases or decreases in lice numbers. The response rate of over 40% was high for a survey of this type and had similar return rates across all zones of the fishery. Such a high return rate, in addition to the responses confirms that commercial fishers, regardless of zone, consider that sea lice have adverse effects on the ratio of bait used to rocklobster landed. The findings of the survey allowed the following conclusions to be drawn and hypotheses developed. Commercial fishers believe particular temporal and spatial factors are associated with increased numbers of sea lice predating on rocklobster baits. For example, fishing in depth ranges of 20 - 30 fathoms (40 – 60 metres) and greater, fishing on a sand bottom, fishing during the months of November, December, March and April, fishing during the full and new moons and lastly during periods of weak current and high water temperature were all felt to increase the number of sea lice scavenging on baits. Laboratory growth trials demonstrated significant differences in the mean body lengths of starved and fed manca and adult C. hesperia after three and seven months, respectively. Despite these findings, starved adult C. hesperia continued to moult and grow after approximately 300 days of fasting. The relatively short period of time before differences in starved and fed manca C. hesperia growth parameters arose is probably due to early life stages of cirolanids being more reliant on regular food sources than their adult counterparts. An increase in water temperature from 16 ºC to 24 ºC resulted in no significant increase in mean body length of manca C. hesperia. However, the mean inter-moult period of fed manca housed at 24 ºC was significantly lower (25-50%) than both the fed treatment group housed at 16 ºC and the starved treatment group within the first two months of the trial. This reduction in mean inter-moult period is indicative of an animal which is growing quickly as a result of increased metabolic rate albeit at reduced increments. The 24 hour activity rhythms of C. hesperia in shallow waters in the metropolitan zone of the Western Rocklobster Fishery were determined in order to identify those factors which modulate the emergence and/or swimming activity of this dominant scavenger. It was concluded that the presence of a circadian rhythm of spontaneous nocturnal activity induced by the end of the diurnal period of photo-inhibition,regardless of tidal regime or lunar cycle, is evident in adult C. hesperia. In contrast, circa-tidal rhythms of emergence centered around spring tides were found to exist in juvenile C. hesperia with similar mean numbers trapped across all sampling times (see Chapter 3, tables 3.4-3.8) with the exception of high water spring tides (HWS), which resulted in significantly greater mean numbers. It was concluded that mature cirolanids found off the Western Australian coastline adopt a strictly nocturnal and facultative necrophage mode of existence despite carrion generally being regarded as a much less crucial food resource in relatively shallow, productive, inshore waters. However, juvenile cirolanids found off the Western Australian coastline were recognised as relying on a more opportunistic scavenger mode of existence being active during both day and night. This perpetual foraging strategy employed in cirolanids at manca and juvenile stages is possibly due to the lack of the well developed chemosensory and or olfactory capabilities found in their adult stages. In addition to this reduced foraging efficiency, a smaller gut size combined with higher metabolic rates and lower assimilation efficiencies ensures their ongoing search for sustenance. Analyses of the number of C. hesperia collected during three years of trapping in C zone of the Western Rocklobster Fishery clearly demonstrated that the numbers of cirolanids caught in rocklobster pots were significantly affected by bottom type, moon phase and depth. With respect to bottom type, the greatest numbers of C. hesperia were trapped in rocklobster pots deployed on weed/rock and sand bottoms while significantly lower numbers of C. hesperia were trapped on rock or weed bottoms. In regards to moon phase, rocklobster pots deployed during the new and last quarter of the moon phase trapped significantly greater numbers of both C. hesperia and the Western Rocklobster, P. cygnus than those deployed during the full and first quarter phases. Rocklobster pots containing lice traps deployed in depths ranging from 10-19 and 20-29 fathoms (20-39 and 40-59 metres respectively) caught significantly greater numbers of C. hesperia and P. cygnus than pots deployed in the 1-19 metre depth range. Lastly, the catchability of both C. hesperia and P. cygnus was greatest when either Australian salmon or blue mackerel was deployed in pots indicating these scavengers do exercise a degree of selectivity with respect to particular bait types. Whilst ovigerous C. hesperia were present in each month of the year, peaks in their abundance and/or catchability occurred at the height of summer (January to March). These peaks in mpm, i.e. morphological parturial moult stage, C. hesperia were then followed by corresponding peaks in recruitment from April to June. I hypothesise that peaks in the reproductive intensity of C. hesperia can be attributed to peaks in water temperature and also the seasonal influx of carrion due to both recreational and commercial charter fishing and the commencement of the rocklobster season all occurring predominately within a similar time frame, i.e. the warmer months. The current study has clearly demonstrated that a plethora of factors attract high numbers of both C. hesperia and P. cygnus. Thus, it is apparent that those practices employed by commercial fishers to land the greatest number of P. cygnus will also attract significant numbers of C. hesperia to rocklobster baits. Irrespective of key factors driving C. hesperia abundance, the high market price received for P. cygnus in conjunction with the relatively low price payed for bait, ensures fishers will continue to deploy rocklobster pots in the manner which maximises their landings. Thus for a reduction in bait usage to offer significant economic savings to the industry, different methods of bait deployment that do not result in a decrease in the catch of P. cygnus must be developed. A series of baitsaver trials were conducted in order to determine whether baitsavers deployed containing reduced quantities of bait would catch the same numbers of rocklobster as conventional pots using the typical amounts of bait employed in the fishery. During the start of the season the majority of fishers concentrate their efforts in shallow waters and employ predominantly one day soaks as they target rocklobster migrating from the shallows to offshore habitats (whites phase – November to February). In the later parts of the season (reds phase – March to June) fishing effort becomes less concentrated as some fishers continue to fish the inshore grounds whilst others move out into deeper waters. The season long trial demonstrated that packing large quantities of bait in both baitboxes in the pot (traditional method) caught significantly more rocklobster than pots using a baitsaver in one bait box while the other bait box was packed in traditional fashion (combined method) during the first two months of the whites phase. However, during the remainder of the season there was no significant difference in catches between the two methods. Thus, the season-long trial found that the use of traditional methods of bait deployment in the first two months of the season in conjunction with the combined method of bait deployment from January until the end of the commercial season has the potential to save inshore and offshore based fishers $34,000 and $36,000 each year.

The close proximity of net-pen salmon farms and wild Pacific salmon stocks in British Columbia (BC) is an incentive for precautionary management of the environmentally and economically damaging parasites known as sea lice. Bivalves cultured as part of an integrated multi-trophic aquaculture (IMTA) system may contribute natural, preventative louse control through the ingestion of planktonic sea lice larvae. A field trial was conducted to test sea lice mitigation by bivalves at a commercial Atlantic salmon (Salmo salar) farm in BC using Pacific oysters (Crassostrea gigas). Oysters were cultured in trays around one end of the farm and at a reference site approximately 150 m away from August 2013 until August 2014. Parasitic and planktonic sea lice (Lepeophtheirus salmonis and Caligus clemensi) were monitored before and during oyster deployment, beginning in December 2012. Parasite abundance peaked in January 2013 (6.5 lice/fish, >85% C. clemensi), and the following year in February 2014 (3.3 lice/fish, >80% L. salmonis). Larval density within cages peaked in January, both in 2013 (1.28 larvae/m3) and 2014 (0.96 larvae/m3). Parasite abundance was significantly correlated with both surface salinity (r2= 0.28, p=0.04) and sea lice larval density (r2= 0.65, p=0.01). Observed densities were significantly lower (t=3.41, p=0.009) than those calculated for the site based on water temperature and salinity, the number of adult female lice present, and the approximate number of fish. Sea lice mitigation by oysters was assessed by comparing monthly sea lice larval densities inside bivalve and non-bivalve fish cages, and by analyzing preserved oyster digestive tracts from January 2014 (when larval densities were highest) for presence of L. salmonis DNA using PCR. Using these methods, no significant evidence of sea lice mitigation was detected. Oyster growth was monitored by measuring whole wet weight, soft tissue wet, dry, and ash-free dry weight, and shell length, width, and height approximately every four months. Oysters were sampled equally across different sides of the farm and at the reference site (~150 m away from the farm) at three depths: 1, 3, and 6 m. All seven measurements increased significantly over time. Effects of side and depth varied by growth parameter; in general, oysters at 1 and 3 m were significantly larger than those at 6 m, and oysters cultured at the reference site were either significantly smaller or the same size as those cultured around the farm. Oysters from select sides were consistently, significantly larger than those from other sides and from the reference site. Overall, the findings suggest that sea lice larvae quickly dispersed away from the farm after hatching and were not significantly impacted by bivalve presence around the fish cages. Bivalves grew significantly larger over time and size was significantly impacted by both depth and side of the fish cage. While no evidence of larval sea lice reduction/ingestion by cultured bivalves was detected, this study provides information on all sea lice stages present throughout an Atlantic salmon production cycle, as well as the first detailed growth analysis of Pacific oysters cultured alongside farmed Atlantic salmon in BC. / Graduate / 0792 / byrneaa@gmail.com

Pacific salmon (Oncorhynchus spp.) are key elements of ecological systems, and play an important role in the cultural foundation of human societies. All species of wild salmon face multiple, simultaneous threats, with habitat degradation likely playing a key role in survival. Open net-pen salmon farms can degrade important nursery marine habitat for wild juvenile salmon by disrupting natural salmonid host-parasite dynamics. The first two chapters in this thesis examine louse parasitism of wild juvenile chum (Oncorhynchus keta), pink (O. gorbuscha), and sockeye salmon (O. nerka) in relation to their marine migration past salmon farms. I compare sites of low and high exposure to salmon farms, and include two areas without farms on British Columbia’s central and north coasts to assess baseline infection levels. Louse prevalence and abundance were lowest and most similar to natural baseline levels at low exposure sites, and highest at high exposure sites in all farm regions. A significantly greater proportion of the lice infecting juvenile chum and pink salmon were Lepeophtheirus salmonis at high exposure sites. Caligus clemensi was the principal louse species infecting all juveniles in areas without salmon farms, and at low exposure sites within salmon farm regions; C. clemensi was also the dominant louse to infect juvenile sockeye that migrated past farms. Mixed-effects modelling results showed that exposure to salmon farms was the most consistent factor to explain the variation in louse infection levels, and support my hypothesis that salmon farms are a major source of sea lice on juvenile wild salmon in regions with salmon farms. I discovered that juvenile sockeye at one particular location within the Georgia Strait hosted unusually high lice levels; this location was situated at a distance from salmon farms, but near a farm salmon processing facility. Upon further investigation, I found live sea lice, Lepeophtheirus salmonis, mucus, and fish tissue in effluent discharged from the processing facility. Sea lice transmitted from this source may pose a threat to wild salmon populations, and the release of potentially untreated offal, including blood water, is of considerable concern. These results form the third chapter in my thesis. Given the challenges facing juvenile salmon in general, and sockeye from the Fraser River in particular (i.e., 2009 was the lowest return on record), and because poor habitat conditions within Georgia Strait are considered the major cause of the recent decline in Fraser River sockeye, this raises the question as to whether food limitations are a factor. The final chapter in my thesis examines the prey assemblage, diet composition, and foraging selectivity of juvenile sockeye, and investigates whether food limitations can be detected during early migration through Georgia Strait. Juvenile sockeye demonstrated high prey diversity, with preference for particular prey. Prey were more concentrated in the north, which may help explain migratory behavior of juveniles through the study region, and temporal similarities in sockeye foraging success may reflect short-term food resource stability. Moreover, I could not find evidence of food limitations that might suggest juvenile sockeye were strongly food deprived during the years of this study. Finally, my thesis explores how best to conserve salmon populations given the multitude of stressors. Because stressors often interact to produce compound effects and unpredictable results, ranking the overall threats in order of severity may not be useful. Instead, the most successful ranking system may be in terms of reducing harm where possible. For juvenile salmon during their early marine migration, risks posed by salmon farms can be more easily mitigated than the far-reaching effects on ocean productivity of climate change and ocean acidification, or predator removal. I recommend we begin here. / Graduate

British Columbia salmon aquaculture operations use the chemotherapeutant emamectin benzoate (EMB trade name SLICE®), a synthesized avermectin compound, delivered through feed to decrease sea lice (Lepeophtheirus salmonis) parasite abundance on production fish. Avermectins bind to ion channels in crustaceans and disrupts nerve impulse transmission. Detectable amounts of EMB can accumulate in the depositional area around farms during SLICE® treatment periods, thus presenting potential for exposure to populations of proximate non-target species. The distribution of spot prawn (Pandalus platyceros), an economically important crustacean, overlaps with areas of intensive salmon farm activity. The primary objective of this research was to determine if EMB exposure had a measurable biological effect on spot prawns in the field and in the laboratory. The field component was conducted in the Broughton Archipelago, BC, to determine if emamectin benzoate residues could be detected near actively treating salmon farms, and whether farm proximity affected spot prawn size distribution. Three laboratory experiments tested the mortality, molting and behavioural response of spot prawns to SLICE® feed pellet exposure and acute exposure to EMB through sediment over ten, 30 and 45-day durations. Measurable amounts of EMB was detected in the marine sediment near five farm sites during the field survey and was found to persist between treatment periods. Male and transitional stage spot prawns captured near farm sites attained a greater size and had better body condition compared to reference sites, indicating prawns may benefit from direct or indirect farm food subsidies. However, at several farm sites the size distribution of prawns changed over the sampling period, a trend not observed at reference sites, demonstrating that farm activity may alter prawn population dynamics. Laboratory results indicated that only prawns that had been starved prior to exposure would initially consume SLICE® pellets, but feeding rates declined with subsequent exposures. Depressed consumption rates was not a residual effect of EMB, but rather an aversion to the SLICE® pellet diet as prawns resumed feeding when offered a preferred diet. Sediment EMB exposures to doses 808 µg kg-1 and greater increased prawn mortality, largely due to the inability of molting individuals to successfully complete ecdysis. Exposed individuals accumulated EMB in their abdomen tissue with levels increasing with exposure dose. Prawns exposed to EMB through sediment at concentrations 1419 and 3330 µg kg-1 displayed a significant reduction in olfactory detection and orientation behaviours to food stimuli. This research highlights that spot prawns may avoid SLICE® pellets for preferential food sources, and that only short term EMB exposure 50 to 200 magnitude greater than levels present in the marine environment elicited a measurable response in spot prawn mortality rates, molting success and behaviour. However, preliminary trends in the field survey data indicate that there may be population differences occurring in spot prawns inhabiting areas near treating salmon farms that are not observed in reference populations. These results signify the inherent pitfalls in current management policy that base decisions on short-term acute toxicity laboratory exposure results that may not be indicative of the response of marine populations near active salmon farms to long-term chronic EMB exposure. / Graduate / 0792 / 0329 / 0768

The objective of the work described in the current thesis was to provide a better understanding of some of the key factors associated with sea louse, Lepeophtheirus salmonis, infection of farmed Atlantic salmon. In Chapter 2, initial work focused on establishing the vertical and horizontal distribution of sea lice copepodids and spatial patterns of on-farm infections. The louse distribution was investigated along the main current gradient across adjacent salmon production pens at three commercial sites. A depth profile for the distribution of larval lice was also established for the top 12 m of the water column at three different locations in close proximity to commercial salmon farms. Within all multi-pen sites there were clear patterns of distribution and infection along the main water current gradient with the abundance of lice in end pens at each site appearing to be different from the central pens. The vertical distribution pattern of free swimming L. salmonis larvae (nauplii and copepodids) showed that the surface 6 m harboured 85.5 ± 1.6 % of the lice present in the water body analysed (0 – 12 m depth), irrespective of sampling date and location. In Chapter 3, further environmental effects / influences on attachment success of the copepodids were analysed using controlled infection challenges. A flume with adjustable flow rates, and controlled light conditions was designed for this study. Flume current velocity was observed to be a significant factor in infection success, with higher infection levels observed at lower current velocities, while higher current velocities were demonstrated to reduce settlement success. At fixed velocity, higher copepodid exposure levels gave rise to higher infection levels, this having a linear relationship suggestive of a lack of competitive effects for space on the fish. Light was also shown to play an important role in host settlement. A positive correlation between increasing light intensity and higher louse attachment success was found for all tested light spectra / wavelengths (white - Halogen, blue 455 nm, green 530 nm and red 640 nm). Observation of an infecting cohort of copepodids showed maximal infection at four days post-moulting with a tail-off of infection by six days post-moulting. However, even under the optimal conditions represented by a flume challenge, including linear water flow, the constraint of copepodids to pass close to the salmon host and the very high exposure levels of copepodids per fish, louse attachment success was still relatively low. Chapter 4 examined implementation of a possible management approach based upon some of the environmental influences observed. This chapter described a study in which environmental manipulation of salmon swimming depth was employed on-site in an attempt to reduce farm infection of Atlantic salmon. The effects of submerged artificial lighting in combination with submerged feeding were tested with respect to salmon swimming depth and sea lice infection, following the hypothesis that L. salmonis infection in a commercial salmon population could be reduced through exposure to deep lighting and feeding. The results of the study suggest that swimming depth manipulation can indeed be used at a commercial scale to reduce salmon lice burdens on Atlantic salmon by physically minimising spatial interactions between the two animals. In the final research chapter (Chapter 5), this thesis examines the question of whether ploidy of the host impacts on sea louse infection levels and whether susceptibility of individual fish is consistent between replicate infections. Results showed that triploid salmon are not subject to higher sea louse infection levels under experimental challenge and farm infection conditions compared to diploid hosts. In addition, triploid fish subject to initial infection, did not become more or less resistant to infection compared to diploids when comparing repeated sea louse infections. In summary, this thesis describes work conducted to analyse key infection pathways and factors influencing infection of Atlantic salmon by sea lice and suggestions made as to how findings may be exploited to reduce louse burdens in Atlantic salmon farming. The practical solutions presented to exploit the results found in this work are currently under consideration by the Scottish salmon industry.

Salmon aquaculture can be a potential solution to bridge the gap between declining capture fisheries and increasing seafood demand. However, the environmental impacts it creates have generated criticism. The overall objectives of this dissertation are to examine the economic consequences of environmental issues associated with salmon aquaculture, and to explore policy implications and recommendations for reducing environmental impacts. These objectives are addressed in five main analyses. The growth of salmon aquaculture is analyzed based on farmed salmon production in the four leading producing countries and the sector as a whole. Analyses indicate that salmon aquaculture is unlikely to continue to grow at its current pace. A joint production function approach is used to estimate pollution abatement costs for the salmon aquaculture industry. Results reveal that pollution abatement costs vary among observations and models. On average, pollution abatement cost is estimated at 3.5% in terms of total farmed salmon production, and 6.5% in terms of total revenue of farmed salmon. The ecological and economic impacts of sea lice from salmon farms on wild salmon population and fisheries are also studied. Analyses suggest that these effects are minor when the sea lice induced mortality rate is below 20%, while they can be severe if the mortality is greater than 30%. Sea lice have greater ecological and economic impacts on pink salmon than on chum salmon. These effects are greater under a fixed exploitation rate than under a target escapement policy. The economic performance of open netcage and sea-bag production systems for salmon aquaculture is compared. Netcage systems appear to be more economically profitable than sea-bag systems when environmental costs are either not or only partially included. Sea-bag systems can be financially profitable only when the salmon they produce can achieve a price premium. Finally, policy implications are explored and recommendations are made for sustaining salmon aquaculture in a holistic manner based on the results from previous chapters. Technologies, economic-based instruments and more stringent environmental policies can be employed to reduce environmental impacts. However, there is no single solution to solve these environmental impacts, and a combination of policy options is needed.

Salmon aquaculture can be a potential solution to bridge the gap between declining capture fisheries and increasing seafood demand. However, the environmental impacts it creates have generated criticism. The overall objectives of this dissertation are to examine the economic consequences of environmental issues associated with salmon aquaculture, and to explore policy implications and recommendations for reducing environmental impacts. These objectives are addressed in five main analyses. The growth of salmon aquaculture is analyzed based on farmed salmon production in the four leading producing countries and the sector as a whole. Analyses indicate that salmon aquaculture is unlikely to continue to grow at its current pace. A joint production function approach is used to estimate pollution abatement costs for the salmon aquaculture industry. Results reveal that pollution abatement costs vary among observations and models. On average, pollution abatement cost is estimated at 3.5% in terms of total farmed salmon production, and 6.5% in terms of total revenue of farmed salmon. The ecological and economic impacts of sea lice from salmon farms on wild salmon population and fisheries are also studied. Analyses suggest that these effects are minor when the sea lice induced mortality rate is below 20%, while they can be severe if the mortality is greater than 30%. Sea lice have greater ecological and economic impacts on pink salmon than on chum salmon. These effects are greater under a fixed exploitation rate than under a target escapement policy. The economic performance of open netcage and sea-bag production systems for salmon aquaculture is compared. Netcage systems appear to be more economically profitable than sea-bag systems when environmental costs are either not or only partially included. Sea-bag systems can be financially profitable only when the salmon they produce can achieve a price premium. Finally, policy implications are explored and recommendations are made for sustaining salmon aquaculture in a holistic manner based on the results from previous chapters. Technologies, economic-based instruments and more stringent environmental policies can be employed to reduce environmental impacts. However, there is no single solution to solve these environmental impacts, and a combination of policy options is needed.

The sea louse (Lepeophtheirus salmonis), whose larvae are planktonic and disseminated in the water column, is an economically important parasite of Atlantic salmon (Salmo Salar). The effect of temperature (5, 10, 15°C), diet (larvae alone, larvae plus phytoplankton), and bivalve size (small, medium, large) on the amount of L. salmonis larvae ingested by various species of filter-feeding bivalves (Pacific oysters, Pacific scallops, blue/Gallo’s mussel hybrids, basket cockles) was examined in a series of laboratory experiments. Four separate temperature/diet experiments were conducted (one for each species) in which large bivalves were individually placed in 2-L containers holding 750 ml of aerated, filtered seawater and fed one of three treatment diets: (1) phytoplankton: ~7.1 x 104 cells ml-1 of Isochrysis sp. (Tahitian strain, TISO); (2) sea lice larvae: ~431 larvae (mostly nauplii); and (3) phytoplankton and larvae (at the levels mentioned above). There was also a control treatment of phytoplankton and larvae, but no bivalve. After feeding for 1 h, the bivalve soft tissues were excised and preserved, the digestive system was dissected, and sea lice larvae were removed and counted to provide direct evidence of ingestion. The larvae remaining free swimming in the container were iv preserved and counted. The proportion missing from the container was used to estimate ingested larvae in statistical analyses. Two additional experiments investigating the effect of bivalve size (small, medium, large) on the ingestion of sea lice larvae were conducted with Pacific oysters and Pacific scallops. The heights for oysters (anterior-posterior axes) were 19.2, 44.2, and 84.0 mm, and scallops (dorsal hinges to ventral margins) were 40.3, 64.1, 102.7 mm. The methodology for the size experiments was as previously described for the temperature/diet experiments with the following changes: (1) the diet of larvae alone was not used; (2) the mean number of larvae in each container was ~498; (3) the mean concentration of TISO added to each container was ~7.8 x104 cells ml-1, and (4) the mean water temperature was 10.4°C. The data for the four temperature/diet experiments indicate that all four bivalve species ingested sea lice larvae, whether their diet included phytoplankton or not, and that temperature had no significant effect. The data for the two size experiments indicated that all three sizes of oysters and scallops ingested sea lice larvae and that there was a significant size effect. Large shellfish consumed a significantly greater proportion of the sea lice larvae than the small shellfish. Bivalves grown at salmon net pens as part of an IMTA (Integrated Multi-Trophic Aquaculture) system may be able to reduce the number of sea lice larvae as well as being an additional crop of market value. Future research, conducted at a commercial scale at a salmon farm, is warranted in order to determine if bivalves can serve in this role. / Graduate

Parasitic copepods including Lepeophtheirus salmonis have been the focus of strong concern for the health of wild and farmed salmonids in the Pacific and Atlantic Oceans. Salmon are highly valuable species from both socioeconomic and ecological perspectives. The host-parasite dynamics of Lepeophtheirus salmonis and the Atlantic and Pacific salmonids have changed over evolutionary time to the point that both Atlantic and Pacific salmon and Atlantic and Pacific Lepeophtheirus salmonis are genetically distinct. Recent human interference with the natural population dynamics of this parasite and its hosts may have altered the population genetic structure of Lepeophtheirus salmonis, particularly because salmon farms may provide more stable conditions for parasite population growth. High abundance of Lepeophtheirus salmonis on salmon farms causes damage to the farmed salmon and leads to increased infection intensities in nearby wild hosts. Some Atlantic Lepeophtheirus salmonis have developed resistance to the anti-parasitic drugs they are repeatedly exposed to. No drug resistance has yet been detected within the Pacific Ocean, where only one drug is available, and heavily relied on, to treat Lepeophtheirus salmonis infections. Control of Lepeophtheirus salmonis abundance on Pacific salmon farms is important to maintain the health of farmed salmon and is also important to protect wild salmonids from increased infections originating from salmon farms. The goal of this thesis was to characterize and employ a large suite of molecular markers to assess the population structure of Lepeophtheirus salmonis in the Pacific Ocean. Until this point, the primary focus of Lepeophtheirus salmonis population genetics research has been limited to the Atlantic Ocean and has relied on a small number of available molecular markers. Available expressed sequence tag DNA libraries were screened to identify putative polymorphic loci, which were then experimentally evaluated. We characterized 22 novel microsatellite loci and 87 single nucleotide polymorphisms within 25 nuclear loci for Lepeophtheirus salmonis. We used these genetic markers, as well as 5 microsatellite loci previously developed for use in Atlantic Lepeophtheirus salmonis population studies, to genotype 562 Lepeophtheirus salmonis that were collected from12 Pacific Ocean sampling locations. We compared Lepeophtheirus salmonis genotypes among: (1) seven wild host populations and five farmed host populations within the Pacific Ocean; (2) geographically separated wild host populations, ranging from the Bering Sea to the southwest end of Vancouver Island, British Columbia; and (3) temporally separated cohorts of farmed Atlantic salmon from two geographically distant farm locations on the northwest coast of Vancouver Island and the Campbell River area east of central Vancouver Island. Our analyses failed to resolve significant population structure among sampled Pacific Lepeophtheirus salmonis and, therefore, supports a hypothesis of high gene flow throughout the Northeast Pacific Ocean. It is important to understand the biology and population dynamics of Lepeophtheirus salmonis because it is a consequential parasite of wild and farmed salmonids in the Pacific Ocean. Both the molecular tools developed for this study and the population genetics information generated from this study have contributed to our overall understanding of the evolutionary history and population dynamics of Lepeophtheirus salmonis. / Graduate