Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 76-85).

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 185-199).

This study was undertaken to determine whether the gonads of pink salmon (Oncorhynchus gorbuscha), could be stimulated with exogenous hormones to reproductive maturity one year earlier than normal. This procedure, if successful, could be used as a method for repopulating ‘off’ year cycles of pink salmon in numerous rivers in British Columbia and Washington. In the juvenile males, complete sexual maturity was attained by September in the year of hatching with thrice-weekly treatments of 10.0 micrograms and of 1.0 micrograms salmon (Oncorhynchus tshawytscha) gonadotropin per gram body weight. Histological examination of the precociously mature testes, and comparison with testes from uninjected controls repealed that the time of onset of the mitotic division of spermatogonia to form the primary spermatocyte, and the process of active spermatogenesis were accelerated. At sexual maturity, a scattering of localizations of ∆5-3ß hydroxysteroid dehydrogenase activity was observed which corresponded to the distribution of the interstitial cells. A larger stock of pink salmon, in which injections were initiated 83 days later, developed mature testes in the same time interval as the normal-sized individuals. These gonads were four times larger, however. A small species difference in the action of the gonadotropin preparation was found when comparing its effect on the G.S.I., rate of induction of sexual maturity, and 3ß-ol dehydrogenase activity of immature Oncorhynchus tshawytscha. In the females, the yolk stage was induced first in fish treated three times a week with 1.0 µg/gram body weight salmon gonadotropin and 1.5 µg/gram body weight estradiol 17ß for 126 days. Oocytes containing yolk globules did not appear in pink salmon treated with 1.0 µg/gram body weight salmon gonadotropin alone for a further 42 days. Estradiol l7ß alone, or in combination with salmon gonadotropin at a dosage of 15 µg/gram body weight inhibited vitellogenesis. Formation of oocytes 2 mm in diameter required seven and one half months of treatment with 1.0 µg/gram body weight salmon gonadotropin and 1.5 µg/gram body weight estradiol 17ß, and nine months of injections with l.0µg/gram body weight salmon gonadotropin alone. Few large yolky oocytes were developed by any of the treatments. Large numbers of pre-ovulatory corpora atretica were observed in all of the treated fish. Little histochemically demonstrable ∆5-3ß hydroxysteroid dehydrogenase activity was present in ovaries from pink or spring salmon juveniles treated for 3 months with various dosages of salmon gonadotropin. The significance of the results in relation to the original problem are discussed. / Science, Faculty of / Zoology, Department of / Graduate

This study was undertaken to try to delay gonadal maturation of pink salmon for one year beyond their normal two year life cycle. This would allow these fish to spawn in years of low or nonexistent escapement and possibly increase these "poor" year populations. Three experiments were conducted to investigate the efficacy of the antigonadotropic drug, methallibure, in inhibiting gonadal maturation in pink salmon. Gonadosomatic index, oocyte diameter, and stages of cell maturation in the testis and oocyte maturation in the ovary were measured. The first or pilot experiment involved a range of doses of methallibure (0.10 mg., 0.32 mg., and 1.0 mg./gm./2wks.) to determine the optimal dose for subsequent experiments. All doses had only a slight slowing effect on maturation. This result and possible undesirable effects of higher doses prompted the decision to use the 0.10 mg./gm. dose for subsequent experiments. The second or long-term experiment investigated the effects of methallibure and a constant 12 hours light:12 hours dark photoperiod on gonadal maturation of males and females for a period of ten months. Methallibure completely inhibited testicular maturation by preventing the transformation of primary into secondary spermatogonia. Ovarian maturation, however, was only slowed. The treated ovaries possessed oocytes in the oil globule stage while control ovaries had oocytes in the secondary yolk globule stage. Methallibure had an antithyroidal effect under natural photoperiod but not under constant 12L:12D photoperiod or at a high dose (1.0 mg./gm). Stress from kidney disease may have been operative in this effect. Methallibure also slowed the rate of increase in body weight. The constant 12L:12D photoperiod slowed gonadal maturation in both males and females. It is suggested that a specific day-length and an endogenous rhythm stimulate the initiation, maintenance, and termination of gonadal maturation and that the seasonal daylength fluctuations function as a synchronizer. The difference in effect of methallibure on males and females may be due to treatment beginning prior to the start of testicular maturation but after the start of vitellogenesis. To investigate this possibility, methallibure treatment was begun at successive intervals prior to the start of vitellogenesis in the third or sequential experiment. This treatment had no effect on ovarian maturation which suggests that the females are less sensitive to methallibure than are the males. Treatment with a higher dose started early in juvenile life may inhibit ovarian maturation. From this study, only the males could be delayed and, therefore, possibly spawn in "poor" years. However, Funk and Donaldson (1972) were able to achieve the same goal by maturing males in the year of hatching, thus making a three year program impractical. The value of a long program would be the delay of ovarian maturation since Funk et al. (1973) were unable to advance maturation of females by one year. / Science, Faculty of / Zoology, Department of / Graduate

Anadromous pink salmon undergo several migratory movements between different habitats during their life history. These migrations are accurately timed on a seasonal basis. Annual rhythms or seasonally-timed events may result from interactions between daily rhythms and annual changes in environmental factors. Therefore, knowledge of daily behavioral rhythms in pink salmon may improve our current poor understanding of the seasonal timing of its migrations. Hence, the objective of this study was to investigate, in a seasonal context and mainly under laboratory conditions, diel rhythms of ecologically-relevant behavior in juvenile pink salmon, and their timing mechanisms. Fry emergence from a simulated gravel redd in fresh water was mainly nocturnal below 13°C. Diel emergence timing was synchronized with the onset of night, but was affected by temperature in a non-linear manner. Temperature affected negatively the duration of the intra-gravel alevin stage and the rate of emergence. Nocturnal emergence was considered an anti-predator adaptation. Fry exhibited mainly nocturnal rhythms of swimming activity and of vertical distribution during the first week after emergence. However, a gradual shift from a nocturnal to a diurnal swimming activity rhythm occurred 7 to 13 days after emergence, when wild fish are residing in estuaries and adjacent coastal waters. Coincident with this shift was an increasing tendency of the fry to swimnnear the water surface during the day. This suggested a weakening of their negative phototactic response during this period. Thereafter, the fish usually displayed diurnal rhythms of swimming activity and nocturnal rhythms of vertical distribution. The ontogenetic shift in the phase of the activity rhythm and in photobehavior was considered adaptive for schooling and feeding during the day. Wild fry fed mainly during daylight hours in littoral areas of two marine bays. However, their feeding rhythms varied among study sites. Laboratory experiments showed that hunger level affected fish feeding rate and ration consumed positively. Fish fed continuously on live copepods under idealized laboratory conditions. During a 12-h session they rapidly (< 30 min) filled their stomachs with prey; thereafter, they maintained their stomachs full by feeding at a rate that balanced the rate of evacuation of prey from the stomach. Hence, I concluded that pink salmon have flexible feeding activity rhythms, which may permit opportunistic exploitation of prey, and feed at a relatively low hunger threshold. This feeding strategy may explain in part their relatively high growth rates in nature. During the periods corresponding to their juvenile coastal and pelagic ocean phases, the fish exhibited generally diurnal rhythms of swimming activity and of aggression, and nocturnal rhythms of vertical distribution in response to simulated seasonal photoperiodic and temperature changes. These rhythms were synchronized with the artificial light-dark (LD) cycle throughout most of the year. Some parameters of these rhythms varied on a seasonal basis, but not according to the Aschoff-Wever model. Mean swimming speed, the degree of diurnalism of the swimming activity rhythm, and the timing of the daily peak of the rhythms were affected by daylength. Hence, photoperiod might be an important proximate factor that pink salmon use to time their oceanic migration on a seasonal basis. Some data suggested the existence of an endogenous, circadian activity rhythm, and thus a daily "clock", in pink salmon. However, this remains uncertain. The free-running period of their activity rhythm was not related negatively to constant light intensity, as predicted by the Circadian Rule. The LD cycle affected directly swimming activity (masking), rather than entraining an endogenous circadian system. Since the activity rhythm of pink salmon does not possess a strong endogenous component, it is doubtful that the seasonal timing of its migrations results from interactions between a circadian clock and seasonal changes in environmental factors. However, the flexibility and inter-individual variability of their behavioral rhythms may be adaptive responses to the instability and heterogeneity of the marine environment. / Science, Faculty of / Zoology, Department of / Graduate

Changes in population size are governed by the birthrate, the sex ratio and the death rate. In pink salmon the average egg-production per female is about 1700 and variations from this average are insufficient to account for observed changes in adult populations. The sex ratio is approximately 50-50. Survival during the freshwater phases of the life cycle has been found to vary from approximately 1% to 24%,the average survival being significantly different in different streams. Variation is relatively greater in streams in which average survival is low. Natural survival in the ocean is considered, to average about 5% of the number of young fish reaching the sea. In the central region of the British Columbia coast the annual catch averages about 60% of the adult fish, this percentage being relatively constant for both small and large runs. Pink salmon maturing in "even" and "odd" years represent separate populations. These populations vary in size independently but may maintain a relatively constant ratio for a series of generations. This ratio varies from near equality to extreme disparity. Marked changes in the level of abundance may occur suddenly. Three types of mortality are recognized: (a) mortality which becomes relatively heavier as populations increase in density (compensatory) (b) mortality which becomes relatively heavier as populations decrease in density (depensatory) (c) mortality which is independent of density (extrapensatory). (a) is especially identified with the period of spawning and incubation;(b) is considered to occur mainly during the period of fry migration and to be due to predation;(c) may occur at any stage but is probably most variable during the period between entrance of the adults into fresh water and emergence of the fry. Population changes initiated by extrapensatory factors, among which stream-flow conditions are considered to be important, are exaggerated by depensatdry factors (notably predation on fry) but tend to be resisted by the compensatory influences which operate during the period of spawning and incubation. Stabilization of a level of abundance depends on a balance between these processes. In general, freshwater mortality is more variable than ocean mortality and plays a greater part in inducing population changes. It is suggested that the average freshwater survival of an un-fished population would approximate 2.4% and that this efficiency must be raised to about 6% to permit a sustained catch of 60% of the adult population. A lower freshwater output is likely to result in a reduction in size of the stock. Large runs in both even and odd years are not fundamentally incompatible. The possibility, of promoting a low-level stock to a persisting higher level of abundance is indicated. Chum salmon are subject to the same types of mortality as pink salmon but the results are modified by the higher average egg-production (ca.2700) and the variable length of the life cycle. The species tends to occupy streams in which physical conditions are less stable. Compensatory influences are frequently obscured by these conditions, resulting in irregular fluctuations in abundance. In the application of remedial measures similar principles apply to both species. / Science, Faculty of / Zoology, Department of / Graduate

The ecological niche of a population is dynamic and will be affected by changes in the ecosystem and as a population migrates. An ontogenetic niche shift can also occur as organisms grow and can include changes in morphology, habitat, and feeding behaviour. Although they are the two most abundant salmon species, and are further augmented through hatchery stocking, it is unclear the degree to which the niches of juvenile pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) overlap. Furthermore, juvenile pink salmon and chum salmon undergo a period of rapid growth during their first summer at sea and it is unclear how their ecological niche changes with their ontogeny. Understanding the foodweb dynamics of juvenile salmon in the coastal marine environment is important because a large proportion of the overall mortality of salmon is thought to occur during their first summer at sea. The purpose of this study is to determine the degree to which the niches of juvenile pink salmon and chum salmon overlap, how their trophic position and food source changes as they grow into a new ontogenetic niche, and how these processes are affected by ocean conditions. I expected that years of poorer feeding conditions and increased competition would result in reduced trophic position and greater overlap of the niches of juvenile pink salmon and chum salmon. I hypothesized that juvenile salmon would shift their diet to a more offshore-based foodweb as they grew and that their trophic position would increase with size, but that the shift would be stronger when feeding conditions were improved. Statistical analysis showed evidence that the overlap of the niches of pink salmon and chum salmon increased when the abundance of salmon was high. Contrary to expectations, the trophic position of salmon appeared to decrease under favourable conditions. The trophic position of both pink salmon and chum salmon was higher in the southern portion of the study area, and increased when juvenile abundance was high. I suggest that the higher trophic position among juvenile salmon when there is more competition might result from increased reliance on gelatinous zooplankton, which are carnivorous, but a nutritionally poor food choice compared to other common prey items. The ontogenetic shift from summer to fall among juvenile salmon included a shift to a more offshore-based diet and a higher trophic position. In the northern portion of the study area, which was comprised of the southern reaches of the Alaska Coastal Current (ACC), the shift to an offshore-based food source was more pronounced than the trophic shift. In the southern portion of the study area, which included the Transition Domain (TD) between the ACC and the California Current System (CCS), the shift to a higher trophic position was more pronounced than the shift in food source. The results of this study suggest that if climate change leads to poorer feeding conditions, the niches of pink salmon and chum salmon may increasingly overlap when the abundance of these species is high. Hatchery stocking of these species may also contribute to this trend if it leads to a greater abundance of juvenile salmon in the coastal marine environment. There is evidence that the structure of the food web and the nature of the ontogenetic niche shift are very different in the ACC and the TD, and climate change and hatchery stocking will most likely affect these regions differently. / Graduate

In response to the increasing need for ecosystem services throughout the Southeast Alaska region, decision makers are tasked with balancing the need for natural resources with salmon conservation. However, accurate historical and current information on salmonid population abundance, freshwater distribution, and habitat quality are sparse with limited resolution for large portions of this remote and rugged landscape. Here, I created Intrinsic Potential (IP) models for chum and pink salmon to predict the potential for portions of coastal rivers to provide high-quality spawning habitat. I developed IP models for both species from field redd surveys and synthetic habitat variables derived from 1-m resolution digital elevation models. The surveys were performed at 49 study reaches in five coastal drainage basins on the north end of Chichagof Island, Southeast Alaska. I used a spatially balanced random sampling design that included field surveys for redds during two field seasons with contrasting precipitation patterns and disparate adult salmon escapements. The IP models predict probable spawning habitat for both species based on persistent landform characteristics and hydrologic processes that control the formation and distribution of spawning habitat across the landscape. Selection of persistent reach variables for both species IP models was informed by principal component analysis (PCA), resource selection ratios, random forest modeling, and regression models of field and synthetic variable comparisons. I observed primarily one spawning strategy by chum salmon associated with mainstem channels, and two distinct spawning strategies for pink salmon related to small moderate-gradient channels and tributaries, and lower drainage basin mainstem channels. The relationships suggest that chum and pink salmon primarily selected for unconstrained channel types in large-and small-size channels, with chum salmon being more selective toward the larger mainstem channels, and pink salmon selecting for smaller channels and tributaries. The prediction of chum salmon redd presence within a specific reach for both high and low streamflow regimes was explained by channel gradient, floodplain width, and mean annual flow in order of importance. In general, chum salmon redds were observed in larger unconstrained low-gradient floodplain reaches where accumulation of deposited gravels and adequate flow produce habitat heterogeneity suitable for spawning. Pink salmon redd presence for both survey years was explained by channel gradient, reach elevation, and mean annual flow, in order of importance. Specifically, when flows allowed upstream access, spawning pink salmon utilized smaller moderate-gradient channels where substrate size and flows were better suited to their smaller body size. Remotely sensed persistent fish habitat data is valuable information for helping understand fish population distributions across the landscape. These synthetic metrics enabled the identification and evaluation of persistent landscape features as probable predictors of IP. Validation of LiDAR-derived channel characteristics indicated channel lengths measured from the DEM were 12% longer than field measured channel length, primarily for channels wider than 10 meters. Thus, understanding the limitations of the data is important so that decision makers do not unintentionally set unrealistic objectives. This research highlights the utility of using IP models with high resolution remote sensing to expand known distributions and quality of spawning habitat for these two species in Southeast Alaska coastal streams.

<p>  </p> <p>Evolution is the foundation for all of biology. However, our approaches and understanding of evolution—simply, the change of allele frequencies from one generation to the next—have themselves evolved over time. In this dissertation I explore multiple approaches to understand evolution and the consequences of evolution across variable scales and study organisms. First, I use meta-analytic techniques and Bayesian hierarchical models to investigate the phenotypic consequences of two forms of cryptic local adaptation, co- and countergradient variation, by leveraging a decades-old quantitative genetics approach (Chapter 1). I find large effects for both co- and countergradient variation, however they are obscured in natural settings by concurrent large environmental effects. I also show that these large effects are ubiquitous across phenotypic traits, organisms, and environmental gradients, suggesting that while similar phenotypes may be the evolutionary end point, the mechanisms to achieve those phenotypes likely vary. In the following chapter I explore the rapid evolution of a unique and understudied species introduction, pink salmon (<em>Oncorhynchus gorbuscha</em>) in the Great Lakes. Pink salmon were introduced into Lake Superior in a single introduction event and have broken two obligate life histories, anadromy (though they treat the Great Lakes like surrogate oceans) and their fixed two-year life cycle, making them ripe subjects for contemporary evolution. Using whole-genome sequence data, I first investigate the effects of a genetic drift in the form of a bottleneck at introduction and characterize the subsequent loss of genetic diversity (Chapter 2). I show that despite a large loss of genetic diversity, pink salmon also rapidly adapted to their novel environment based on signals of putative selection across numerous regions of the genome, particularly in a period gene associated with their daily circadian clock (<em>per2</em>). Next, I explore how genome structure likely aided adaptation by pink salmon to the Great Lakes, providing evidence that a supergene (~29 Mbp) containing an inversion on chromosome 10 swept to near fixation in the Great Lakes (Chapter 3) and likely aided in osmoregulatory adaptation to this novel environment. Finally, I end with a short perspective chapter (Chapter 4) where I highlight potential future research directions for each of the previous chapters. Together, this research investigates the drivers and consequences of evolution across multiple scales and shows the powerful effect of genetic drift and genetic adaptation in shaping the genomic and phenotypic attributes of populations.</p>