Over the last century, wild populations of salmonids in the Columbia River basin have significantly declined. Several of these populations have been listed as "threatened" under the Endangered Species Act and collaborative multi-state, multi-agency efforts have been established to manage and restore at-risk populations. A thorough understanding of a species' life history is necessary for effective conservation. A tool widely implemented to collect information during juvenile salmonid life stages is a rotary screw trap. Rotary screw traps sample juvenile salmonids as they migrate to the ocean but environmental conditions, low species abundances, and complex life histories can lead to sparse data. In this study I implemented a hierarchical Bayesian model to obtain abundance estimates from rotary screw traps with large periods of missing data and utilized this information to explore two predominant life history assemblages of juvenile Chinook salmon that have strong implications on survival and reproductive success.
From guppies to Galapagos finches and from adaptive landscapes to haldanes, this compilation of contributed works provides reviews, perspectives, theoretical models, statistical developments, and empirical demonstrations exploring the tempo and mode of microevolution on contemporary to geological time scales. New developments, and reviews, of classic and novel empirical systems demonstrate the strength and diversity of evolutionary processes producing biodiversity within species. Perspectives and theoretical insights expand these empirical observations to explore patterns and mechanisms of microevolution, methods for its quantification, and implications for the evolution of biodiversity on other scales. This diverse assemblage of manuscripts is aimed at professionals, graduate students, and advanced undergraduates who desire a timely synthesis of current knowledge, an illustration of exciting new directions, and a springboard for future investigations in the study of microevolution in the wild.
For many fish and wildlife species, a mosaic of available habitats is required to complete their life cycle, and is considered necessary to ensure population stability and persistence. Particularly for young animals, nursery habitats provide opportunities for rapid growth and high survival during this vulnerable life stage. My thesis focuses on juvenile Chinook salmon (Oncorhynchus tshawytscha) and their use of estuarine wetlands as nursery habitat. Estuaries are highly productive systems representing a mosaic of habitats connecting rivers to the sea, and freshwater tidal estuaries provide abundant prey communities, shade, refuge from predation and transitional habitat for the osmoregulatory changes experienced by anadromous fishes. I will be discussing the freshwater tidal wetland habitat use of juvenile Chinook salmon in the Columbia River estuary, which are listed under the Endangered Species Act. I used otolith microstructural growth estimates and prey consumption to measure rearing habitat quality. This sampling effort was designed to target as much genetic diversity as possible, and individual assignment to regional stocks of origin was used to describe the diversity of juvenile Chinook salmon groups inhabiting the estuary. Diversity is important for resilience, and in salmon biocomplexity within fish stocks has been shown to ensure collective productivity despite environmental change. However much of the research which links diversity to resilience in salmon has focused on the adult portion of the life cycle and many resource management policies oversimplify juvenile life history diversity. When this oversimplification of juvenile life history diversity is applied to salmon conservation it may be ignoring critical indicators for stability. Therefore in addition to genetic diversity I also explore methods for better defining juvenile life history diversity and its application in salmon management, such as permitting requirements, habitat restoration, hydropower practices and hatchery management. This study addresses how juvenile salmon growth changes among a range of wetland habitats in the freshwater tidal portion of the Columbia River estuary and how growth variation describes and contributes to life history diversity. To do this, I incorporated otolith microstructure, individual assignment to regional stock of origin, GIS habitat mapping and diet composition, in three habitats (mainstem river, tributary confluence and backwater channel) along ~130 km of the upper estuary. For my first chapter I employed a generalized linear model (GLM) to test three hypotheses: juvenile Chinook growth was best explained by (1) temporal factors, (2) habitat use, or (3) demographic characteristics, such as stock of origin or the timing of seaward migration. I found that variation in growth was best explained by habitat type and an interaction between fork length and month of capture. Juvenile Chinook salmon grew faster in backwater channel habitat and later in the summer. I also found that mid-summer and late summer/fall subyearlings had the highest estuarine growth rates. When compared to other studies in the basin these juvenile Chinook grew on average 0.23, 0.11-0.43 mm/d in the freshwater tidal estuary, similar to estimates in the brackish estuary, but ~4 times slower than those in the plume and upstream reservoirs. However, survival studies from the system elucidated a possible tradeoff between growth and survival in the Columbia River basin. These findings present a unique example of the complexity in understanding the influences of the many processes that generate variation in growth rate for juvenile anadromous fish inhabiting estuaries. In my second chapter, I used otolith microstructure and growth trends produced in a dynamic factor analysis (DFA, a multivariate time series method only recently being used in fisheries) to identify the life history variation in juvenile Chinook salmon caught in the Columbia River estuary over a two-year period (2010-2012). I used genetic assignment to stock of origin and capture location and date with growth trajectories, as a proxy for habitat transitions, to reconstruct life history types. DFA estimated four to five growth trends were present in juvenile Chinook salmon caught in the Columbia River estuary, diversity currently being simplified in many management practices. Regional stocks and habitats did not display divergent growth histories, but the marked hatchery fish did ordinate very similarly in the trend loadings from the DFA analysis, suggesting that hatchery fish may not experience the same breadth of growth variability as wild fish. I was not able to quantify juvenile life history diversity, and juvenile Chinook life history diversity remains difficult to catalog and integrate into species conservation and habitat restoration for resource management. However, by expanding our understanding of how juvenile Chinook salmon experience their freshwater rearing environment we improve our capacity to conserve and manage salmon populations. The findings from my thesis provide the necessary information for a restoration framework to link habitat features with salmon management goals, such as juvenile growth, wild and genetic origin and life history diversity.
Pacific salmon are an important biological and economic resource of countries of the North Pacific rim. They are also a unique group of fish possessing unusually complex life histories. There are seven species of Pacific salmon, five occurring on both the North American and Asian continents (sockeye, pink, chum, chinook, and coho) and two (masu and amago) only in Asia. The life cycle of the Pacific salmon begins in the autumn when the adult female deposits eggs that are fertilized in gravel beds in rivers or lakes. The young emerge from the gravel the following spring and will either migrate immediately to salt water or spend one or more years in a river or lake before migrating. Migrations in the ocean are extensive during the feeding and growing phase, covering thousands of kilometres. After one or more years the maturing adults find their way back to their home river, returning to their ancestral breeding grounds to spawn. They die after spawning and the eggs in the gravel signify a new cycle. Upon this theme Pacific salmon have developed many variations, both between as well as within species. Pacific Salmon Life Histories provides detailed descriptions of the different life phases through which each of the seven species passes. Each chapter is written by a scientist who has spent years studying and observing a particular species of salmon. Some of the topics covered are geographic distribution, transplants, freshwater life, ocean life, development, growth, feeding, diet, migration, and spawning behaviour. The text is richly supplemented by numerous maps, illustrations, colour plates, and tables and there is a detailed general index, as well as a useful geographical index.
The Behavior and Ecology of Pacific Salmon and Trout explains the patterns of mate choice, the competition for nest sites, and the fate of the salmon after their death. It describes the lives of offspring during the months they spend incubating in gravel, growing in fresh water, and migrating out to sea to mature. This thorough, up-to-date survey should be on the shelf of everyone with a professional or personal interest in Pacific salmon and trout. Written in a technically accurate but engaging style, it will appeal to a wide range of readers, including students, anglers, biologists, conservationists, legislators, and armchair naturalists.
Juvenile Chinook salmon (Oncorhynchus tshawytscha) exhibit an array of life history tactics in Oregon's Willamette River Basin, yet we do not know to what extent it is driven by phenotypic plasticity or whether it is predetermined and how conditions in the early rearing environment may affect phenotype expression. We have found hatchery-origin fry sort themselves into distinct surface and bottom oriented phenotypes within days of first feeding and this orientation persists after separation. Surface and bottom phenotypes demonstrated differences in head and body morphology at 2 months post-swim up across three brood years (BY). The surface phenotype exhibits a shorter head and deeper body compared to bottom phenotype. The BY 2012 surface phenotype spent 3 times longer, on average, interacting with their mirror image in an open arena than the bottom phenotype. Tests conducted with BY 2013 fish indicated that bottom-oriented fish engaged in swimming-against-mirror behavior 5 times more than the surface phenotype when the mirror was near gravel refuge. After 8 months of rearing, the BY 2012 surface phenotype was 10% larger than bottom fish and morphometric differences persisted. Surface and bottom phenotypes from BY 2013, were reared under two temperatures and as either separate or combined phenotype groups. The two phenotypes grew at the same rate at 12°C, irrespective of separate or combined rearing, but at 7°C surface fish were significantly larger than bottom fish after three months until temperatures increased after which the two phenotypes converged. While equal in size, the morphologies of the BY 2013 orientation phenotypes were consistent with previous findings. These differences seen in body shape between the surface and bottom oriented groups are similar to differences exhibited between wild subyearling and yearling life history types in the basin. Such phenotypic differences may offer potential for predicting juvenile life history trajectory early in life.
This work gives a critical overview on the evolution and population biology of salmon and their relatives. It should appeal to investigators in each of the scientific disciplines it integrates - evolutionary biology, ecology, salmonid biology, management and conservation. Variation in salmonids can be used to illustrate virtually all evolution.
