Tesis para optar al Grado de Magíster en Ciencias de la Acuicultura / Se entregan los parámetros genéticos de heredabilidad, correlaciones genéticas, y ganancia genética estimados para peso alevín, peso smolt y peso cosecha de dos líneas, año par e impar, de salmón Coho (Oncorhynchus kisutch), a partir de seis y cuatro generaciones respectivamente, del programa de reproducción de un núcleo comercial, en Chiloé, Región de Los Lagos. Se estima el nivel de consanguinidad alcanzado para cada línea en las cinco generaciones. La metodología utilizada considera el desove de reproductores individualizados, la incubación de ovas y desarrollo inicial de alevines en unidades segregadas por cada familia generada, marcaje individual de ejemplares juveniles y crecimiento en comunidad, con muestreos periódicos de peso corporal. La metodología de evaluación para la estimación de los parámetros genéticos fue el ‘modelo animal’ y los softwares Pedigree Viewer y MTDFREML.

A deterministic simulation model is used to explore the relationship between juvenile pink, chum and coho salmon growth and size-related survival in the Fraser River estuary. Parameters most sensitive to change are identified and the results related to proposals for enhancement. These results suggest that increasing the initial size of enhancement pink and chum fry, relative to the size of wild fry, prior to seaward migration and releasing them early in the spring may increase their chances of survival. If increasing total (enhancement plus wild) fry density decreases fry growth rate, the presence of enhancement fry in the estuary could reduce the survival chances of wild fry. The decrease in wild stock survival may not be apparent from estimates of adult return for many years due to errors in measurement and to the effect on survival of environmental variability. The model can be used to suggest and evaluate enhancement proposals. Areas needing further research are also indicated. / Science, Faculty of / Zoology, Department of / Graduate

Pacific salmon

This thesis examines the ontogeny of plasma sodium regulation (an indicator of osmoregulatory ability), current or rheotactic response (an indicator of emigration timing) and salinity preference in juvenile coho salmon (Oncorhynchus kisutch). The purpose of the study was to determine if there are inherited differences in the development of these traits between coastal and interior British Columbia populations of coho. An interior (Cold water River) and a coastal (Rosewall Creek-Big Qualicum River) population were monitored for the above traits throughout the year. Both wild and laboratory groups were included in the study. The laboratory raised populations were divided into two incubation treatment groups: one incubated under a coastal temperature regime, and the other incubated under an interior temperature regime. There were no differences in the development of sodium regulatory ability between wild populations when the data were sorted by coho weight. Coastal coho, however, physiologically smolted after one year in the natal streams, while interior coho smolted after at least two years of freshwater growth. No obvious differences were noted between wild resident populations in the timing of downstream movement or the shift in salinity preference from hypotonic to isotonic and hypertonic salinities. Both of these behavioural responses typically occurred in the spring (April-May) of each year. Fyke net catches, however, sugqested that, in addition to the spring emigrations observed in both populations, a portion of the interior population migrated in the fall (November). No differences in the development of sodium regulatory ability were observed either within or between laboratory raised populations. Ion regulatory ability increased to a plateau in the fall and winter following emergence, and increased to smolting levels during the following spring (April-May). There were differences between coastal and interior populations in the pattern of development of both nocturnal current responses and the preference for isotonic or hypertonic salinities. Interior laboratory raised coho developed negative nocturnal rheotaxis and a preference for isotonic salinities about three months earlier (November) than laboratory raised coastal coho (late February-March). Within populations, no differences were observed in the ontogeny of these traits in the groups reared under different temperature regimes. Because these interpopulation ontogenetic behavioural differences persisted in fish reared under identical laboratory conditions, they probably have some genetic basis. Such an innate component in behaviour implies an adaptive role and in juvenile coho these behavioural traits may allow populations to use a variety of habitats at different distances from the sea, even though a major physiological schedule (in this case the development of ion regulatory capabilities) appears to be fixed within the species. Perhaps variations in migratory timing and salinity preference in juvenile coho evolved to assure survival in a relatively unstable and often severe environment by optimizing habitat use within the constraints of an overriding physiological schedule. / Science, Faculty of / Zoology, Department of / Graduate

Highly unsaturated marine lipids are common ingredients in salmon diets, and they are prone to oxidative change. The present study was undertaken to examine the growth and health of coho salmon (Oncorhynchus kisutch) fed diets containing herring oil autoxidized to different degrees. The efficacy of dietary vitamin E in ameliorating any adverse effect on performance was investigated. Herring oil was oxidized to one of two levels (relative to a control) by aeration and mild heating (40 °C). Peroxide values and iodine numbers were recorded to monitor the extent of autoxidation. Depletion of dietary linolenic acid series fatty acids (n3FA), and the labile vitamins A, C, and E, provided further evidence of the progress of lipid oxidation. The mean initial body weight was 5.1 g/fish, and growth (weight and length) was measured at 3 or 6 week intervals for 28 weeks. Experimental diets contained 16.8% lipid, primarily as herring oil. One diet was made with corn oil replacing herring oil, and another contained a combination of low and highly oxidized oil. Vitamin E (as dl-ɑ-tocopheryl acetate) was added at either 30 IU/kg dry diet or 1000 IU/kg dry diet. At 23 weeks, 1/3 of the fish were vaccinated against vibriosis. At 28 weeks the fish were twice challenged with live Vibrio sp. Immunocompetence was estimated by mortality and by plasma agglutination. The inclusion of autoxidized herring oil reduced the nutritive value of the diets. The poorer growth and feed efficiency of fish fed diets containing oxidized oils appears to have resulted from a combination of appetite suppression and nutrient deficiency. The relative importance of these factors in influencing growth and feed efficiency depended upon the extent of the oxidation, with appetite suppression being most apparent in fish fed diets containing moderately oxidized oil. Dietary supplementation with a high level of vitamin E had no ameliorating effect on growth or feed efficiency. Health and immunocompetence were not impaired by the presence of oxidized dietary lipid, or improved by the addition of vitamin E. / Land and Food Systems, Faculty of / Graduate

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No. of bitstreams: 1 yoshida_gm_dr_jabo.pdf: 1722466 bytes, checksum: 3b9d699968bdca5ed4d5856648c5403d (MD5) Previous issue date: 2018-02-26 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Os objetivos deste trabalho foram: (i) testar a eficiência do algoritmo de seleção de acasalamento (MS) em controlar o nível de endogamia e coascendência, além de aumentar os ganhos genéticos; (ii) incluir a variabilidade genética da futura progênie como componente de otimização na função objetiva de seleção de acasalamento usando dados de dois programas de melhoramento aquícolas; e (iii) comparar a MS com a seleção truncada (TS) e contribuição genética ótima (OCS), combinados com diferentes estratégias de acasalamentos para controlar a endogamia e manter os mesmo níveis de ganhos genéticos. Para os objetivos (i) e (ii), o total de 8.782 tilápias do Nilo (NT) de cinco gerações e 79.144 salmões coho (CS) de oito gerações foram utilizados para otimizar as funções objetivos e vinte gerações discretas foram simuladas para o objetivo (iii), considerando 50 famílias e 2.000 filhos por geração, e uma característica com herdabilidade igual a 0.30. As OFs foram otimizadas considerando a coascendência média dos pais, o mérito genético esperado, a endogamia da futura progênie para os objetivos (i) e (iii) e a variabilidade genética da futura progênie foi adicionada na OF para o objetivo (ii). Para o objetivo (i), a MS permitiu reduzir a endogamia em até 73% para tilápia do Nilo, em comparação com a seleção truncada e até 20% para o salmão coho, em comparação com o cenário real de acasalamento. No objetivo dois, a MS permitiu produzir progênie com maior (DP = 0.77 e 0.30 para NT e CS, respectivamente) ou menor (DP = 0.25 e 0.14 para NT e CS, respectivamente) dispersão dos valores genéticos, dependendo da função objetivo otimizada. A seleção de acasalamentos superou a seleção truncada e o cenário real de acasalamento e também foi possível alterar a variabilidade genética da futura progênie, quando esse componente foi considerado na OF utilizado os dados reais. Para os dados simulados, a MS teve melhor performance comparada com a TS e a OCS combinada com acasalamentos aleatórios. A curto-prazo, a MS foi mais eficiente do que a OCS combinada com os acasalamentos que minimizam a endogamia em controlar a endogamia sob o mesmo nível de ganho genético. Porém, a longo prazo os resultados entre as duas estratégias foram muito semelhantes. De forma geral, o algoritmo de seleção de acasalamentos foi eficiente e flexível em otimizar a função objetiva usando diferentes componentes, em diferentes aplicações práticas na aquicultura. / The aims of this work were: (i) test the efficiency of mate selection (MS) algorithm in controlling the inbreeding and coancestry level, as well, increase the genetic gain; (ii) include the genetic variability of the future progeny as component for the optimization of the MS objective function in two aquaculture real dataset; and (iii) compare MS among truncation selection (TS) and optimum contribution selection (OCS) scenarios combined to different mating strategies to assess the best method in controlling inbreeding and maintain the genetic gain, for aquaculture breeding using simulated dataset. For objective (i) and (ii), a total of 8,782 Nile tilapias (NT) from five generations and 79,144 coho salmon (CS) from eight generations were used to optimize the objective functions (OF) and twenty discrete generations were simulated for the objective (iii), considering 50 families and 2,000 offspring per generation, and a trait with heritability of 0.30. The OFs were optimized accounting to coancestry of parents, expected genetic merit and inbreeding of the future progeny for the objective (i) and (iii) and in addition the genetic variability of the future progeny was considered for the objective (ii). For the objective (i), the mate selection allowed reducing inbreeding up to 73% for NT, compared with truncation selection, and up to 20% for CS, compared with realized scenario. In the objective (ii), MS allowed producing animals with higher (SD = 0.77 and 0.30 for NT and CS, respectively) or lower (SD = 0.25 and 0.14 for NT and CS, respectively) dispersion of estimated breeding value, depending on the objective function optimized. For real data set the MS outperformed the real mates and truncation selection and in addition the genetic variability of the future progeny could be changed when this component was considered in the OF. For the simulated dataset, the MS outperformed the TS and OCS followed by random mating. In the short-term, MS was more efficient than OCS + inbreeding minimizing in controlling inbreeding under the same genetic gain. However, in the long-term, OCS and MS resulted in similar genetic progress and average inbreeding, under the same weight on coancestry. In general, the mate selection algorithm was efficient and flexible to optimize objective functions accounting for different components, under practical applications in aquaculture breeding. / 14/20626-4 e 15/25232-7

An investigation was initiated in southern British Columbia during 1984 to determine the degree of similarity between populations of coho salmon, in terms of their demographic traits and exploitation patterns. Fourteen stocks of wild or hatchery origin were subject to coded-wire tagging in nine different streams located within a 150 km region of southeast Vancouver Island during 1985,1986, and 1987. Escapement enumeration and tag recovery were conducted during the 1985-1988 period in all streams by means of counting fences and stream surveys. A new mark-recapture model was formulated specifically for estimating escapement levels in natural streams where only a partial enumeration of spawners is possible. Estimates of the number of tags recovered in various sport and commercial fisheries were generated primarily on the basis of catch and sampling records extracted from the Mark-Recovery Program database, located at the Pacific Biological Station of the Canadian Department of Fisheries and Oceans. Estimates of sampling rates in the Strait of Georgia sport fishery were determined from simulation studies based on catch and sampling statistics associated with the Georgia Strait Creel Survey and Head Recovery programs. Populations were contrasted in terms of their juvenile migration patterns, smolt-to-adult survival, catch distributions, straying rates, escapement patterns, run composition, adult sizes, and exploitation rates. Considerable variation in smolt size and juvenile migration time was detected among populations each year. The most pronounced difference was the consistently shorter migration period of smolts released from public hatcheries. Estimates of ocean survival was highly variable across years and streams, and even among stocks within the same stream. No particular stock or stock type had consistently higher survival, but hatchery fish from the Big Qualicum River exhibited consistently lower survival. Considerable variation was observed in the duration and timing of various runs within the study area. On average, the contribution of strays to each spawning population was relatively small (< 2%), but strays could account for as much as 50% of the escapement to a given stream. Average exploitation rates were in the neighborhood of 80% each year, but were as high as 96% for some stocks. Substantial differences in exploitation rate were detected between stocks from the same stream, and between stocks from adjacent streams, but exploitation rates were not consistently higher or lower for any particular stock or stock type. The influence of specific factors upon straying rates, survival rates and exploitation patterns was estimated by means of log-linear models. Stock contributions to various fisheries appeared to be related to the release location, and two stock assemblages were identified within the study area based on the level of similarity among stocks in fishery contribution. Attempts to quantify the level of co-variation among stocks in survival and exploitation rates were hampered by the lack of sufficiently long time series of data, but preliminary results gave no indication of a high level of similarity among stocks or stock types. Still, it was possible to identify stocks which could be used as indicators of the general status of all stocks in the study area in terms of escapement trends, smolt-to-adult survival and exploitation rates. Based on the level of similarity observed, indicator stocks are considered to be useful stock-assessment tools, and can provide useful information for management purposes. / Science, Faculty of / Zoology, Department of / Graduate

Co-evolution between parasites and their hosts result in extremely well-orchestrated and intimate relationships that are characterized by remarkable adaptations in the attack response of the parasite and the defense response of the host. To fully understand host-parasite interactions, these adaptations must be considered in the context of the ecological constraints in which they evolved. As a serious pest to salmon mariculture, Lepeophtheirus salmonis has been extensively studied; however, there are still several areas that require further research. Of utmost importance, and the topic of this thesis, is molecular basis for resistance to sea lice. The following chapters investigate this phenomena under the umbrella of ecological immunology using combined modern technologies of transcriptomics, proteomics and functional immunology with a focus on the primary interaction site. In the first chapter, I describe the key players involved in this host-parasite relationship with a focus on the primary interaction site, the louse-salmon interface, where there are responses by the louse (attack) and the salmon host (defense). Previous research indicated that an early aggressive inflammatory response at the louse-skin interface contributes to resistance in coho salmon; however, there are no data characterizing a site-specific response in resistant (pink and coho) and susceptible (Atlantic, chum) species. Accordingly in Chapter 2, I define site-specific cutaneous responses in Atlantic, pink and chum salmon to establish genetic biomarkers of resistance. Chapter 3 focuses on identification of cellular effectors using histochemical localization of biomarkers to characterize cellular populations activated at the louse-attachment site, while broadening the gene targets. Our notion of pink salmon as a resistant species is challenged by the common observation of migrating pink salmon supporting large populations of L. salmonis in the field. Thus the purpose of chapter 4 was to investigate potential mechanisms to explain variations in susceptibility as a function of life history. Host-parasite relationships are a product of both host and parasite responses; therefore, in chapters 5 and 6, I shift focus to the level of the parasite. In chapter 5 I present the first documented large-scale transcriptomic profiling of L. salmonis during feeding on both resistant (coho) and susceptible (Atlantic, sockeye) salmon. This was followed (chapter 6) by describing the proteomic profile of L. salmonis secretions after feeding on Atlantic salmon. In the seventh and final chapter, I present my conclusions on the molecular mechanisms for resistance to sea lice and discuss potential applications of this information for future louse control strategies. / Graduate

Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. / Graduate / 2019-04-19

Aquatic ecosystems continue to be increasingly affected by climate warming. For salmonids in the Pacific Northwest of North America, increasing temperatures pose tighter thermal constraints on their habitat use as well as aspects of their individual performance, such as disease resistance. This thesis examines the effect of temperature on the phenology of the Ceratomyxa shasta life cycle, the effect of thermal refugia on disease risk in juvenile salmonids in the Klamath River, CA, and the spatial and temporal distribution of C. shasta in the Willamette River, OR. We developed a biological model that predicts an acceleration of the C. shasta life cycle development due to climate shifts in the Klamath River, resulting in more generations per year and earlier seasonal parasite occurrence. We showed that in early summer the Beaver Creek-Klamath River confluence provides juvenile Chinook and coho salmon an area of lower parasite doses and cooler temperatures than the main stem, thus lessening disease risk. By accelerating the development of C. shasta in its hosts, increasing temperatures will result in earlier parasite transmission to juvenile salmonids and a longer season of infectivity. These fish may find disease refuge at cold tributary inflows to the main stem of the Klamath River in early summer, further adding to the benefit of these important thermal habitats. To determine if similar disease patterns occur in other rivers with the parasite, we described spatial and temporal occurrence of C. shasta in the Willamette River. By collecting weekly water sampling at four sites over 28 months we characterize seasonal and annual differences of parasite abundance, which varies with weekly temperature. We also collected samples along the length of the main stem and its tributaries and identified spatial differences in C. shasta spore densities. Identification of spatial and temporal variation of C. shasta in the Willamette River provides a foundation for understanding future patterns of disease occurrence in this river where conservation of anadromous fisheries is also of concern. This thesis identifies likely responses of C. shasta to climate warming in the Klamath River, with useful application to other rivers in the Pacific Northwest. / Graduation date: 2013