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Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.

A three stream irradiance model is implemented and tested to determine its utility for bio-geochemical data assimilation of remote sensing reflectance, Rrs(λ), data in the California Current System. Two different numerical methods were tested to solve the model, but the shooting method using a 4th order classical Runge Kutta scheme was implemented. The optical model solves for Rrs(λ) from the concentrations of variable optical constituents and their respective wavelength dependent light scattering and absorption properties. Using single phytoplankton type absorption and scattering estimates, the optical model produces Rrs values that correlate to satellite observed Rrs more closely for certain phytoplankton types than others. The model produced accurate downward irradiance fields when using observed absorption and scattering profiles obtained from the Ocean Observatories Initiative’s Oregon Shelf Surface Piercing Profiler Mooring. Through this forward modeling based comparison to observations it was found that the optical model can produce accurate profiles under certain conditions, making it promising for data assimilation of Rrs, but outstanding issues remain to be addressed, including accurately resolving community structure, improvements to the parametrization of constituents other than phytoplankton, and atmospheric influence on surface boundary conditions.

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure and speciation (Dascyllus). The genus Dascyllus includes a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex. This complex is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus is a widespread, common, and well-studied coral reef fish species found across the tropical Indo-Pacific that has served as a model species for coral reef fish research. In this dissertation, we expand on what is known of population dynamics of the complex while providing valuable genomic resources to support future research into this model system. In Chapter 1 of this dissertation, we explore populations at the margins of a species’ distribution which tend to be smaller, more isolated, and importantly, exist in habitats at the edge of the species’ physiological limit. These conditions make such populations particularly vulnerable to extirpation, especially amid accelerating environmental changes. We focus on population structure based on mitochondrial DNA markers and inferred dynamics of an understudied, potentially vulnerable, population of an otherwise well studied and widespread coral reef fish. We present phylogeographic results using the most robust set of samples collected in the Ryukyu Archipelago and gain insight into edge population dynamics by comparing to another more well-studied edge population in French Polynesia. We found that despite its proximity to the Coral Triangle and position along the Kuroshio Current, the Ryukyu population of D. trimaculatus seems to be a relatively young and closed, suggesting that it may be more vulnerable to extinction than might be otherwise expected. In Chapter 2 we present the first genome assembly of Dascyllus trimaculatus. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the BUSCO score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. This assembly was a necessary resource for research in Chapter 3 and will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade. In Chapter 3, we use low coverage whole genome sequencing to examine the population structure of its Pacific distribution, and again, focus on dynamics of the Ryukyu Archipelago in southern Japan. We find evidence of clear divergence between the Pacific and Indian Ocean populations as well as between the Pacific and the restricted edge population in the Society Islands at the eastern edge of its range. We see a clear signal of introgression of one species within the complex, D. auripinnis described from the Line and Phoenix islands into D. trimaculatus that extends across to the west Pacific - further than previously reported. We also find that there is directional but restricted gene flow of Philippine genotypes into the Ryukyu Archipelago. While we have not yet identified specific isolation and speciation mechanisms, we propose some likely scenarios. This dissertation builds upon previous research of this complex which had made it a model system in its own right and adds genomic resources to ensure that we continue to further our understanding of this important model system in this genomic age. There are now resources for endless directions and questions to follow regarding this species complex and evolutionary processes. Understanding mechanisms of dispersal, the role of selection, and the capabilities of local adaptation in a species with relatively restricted gene flow are some of the exciting questions that this project has uncovered, thus placing Dascyllus trimaculatus as an ideal model species to address fundamental questions in the ecology and evolution of coral reef fishes.

Understanding fish diversity patterns is critical for fisheries management amidst overfishing and climate change. Fish egg surveys have been used to characterize pelagic spawning fish communities, estimate biomass, and track population trends in response to perturbations. Environmental DNA (eDNA) metabarcoding has been implemented to rapidly and non-invasively survey marine ecosystems. To understand the efficacy of eDNA metabarcoding for assessing pelagic spawning fish community composition, concurrent eDNA metabarcoding and fish egg DNA barcoding off Scripps Institution of Oceanography’s Pier (La Jolla, CA) were conducted. Both methods revealed seasonal patterns in agreement with previous fish and fish egg surveys. Species richness was highest in late spring and summer. The presence and spawning of commercially important species and species of conservation concern were detected. Both methods showed overlap for pelagic spawning fishes for broadcast spawners, schooling fish, and locally abundant species. Some actively spawning species were not co-detected with eDNA, likely due to different sampling strategies, taxonomic biases, and abiotic/biotic factors influencing eDNA transport, shedding, and degradation. We identified key advantages and disadvantages of each method. Fish egg barcoding provided information on spawning trends but did not detect taxa with alternate reproduction strategies. Metabarcoding eDNA detected species not found in fish egg sampling, including demersal and viviparous bony fishes, non-spawning adults, Chondrichthyan, and Mammalian species, but missed abundant pelagic fish eggs. This study demonstrates that DNA barcoding of fish eggs and eDNA metabarcoding work best in tandem as each method identified unique fish taxa and provided complementary ecological and biological insight.

The western North Atlantic is a dynamic region characterized by the Gulf Stream western boundary current and inhabited by a diverse host of odontocete, or toothed whale, top predators. Their habitats are highly exploited by commercial fisheries, shipping, marine energy extraction, and naval exercises, subjecting them to a variety of potentially harmful interactions. Many of these species remain poorly understood due to the difficulties of observing them in the pelagic environment. Their habitat utilization and the impacts of anthropogenic activities are not well known. Over the past decade, passive acoustic data has become increasingly utilized for the study of a wide variety of marine animals, and offers several advantages over traditional line-transect visual survey methods. Passive acoustic devices can be deployed at offshore monitoring sites for long periods of time, enabling detection of even rare and cryptic species across seasons and sea states, and without altering animal behaviors. Here we utilized a large passive acoustic data set collected across a latitudinal habitat gradient in the western North Atlantic to address fundamental knowledge gaps in odontocete ecology. I approached the problem of discriminating between species based on spectral and temporal features of echolocation clicks by using machine learning to identify novel click types, and then matching these click types to species using spatiotemporal correlates. I was able to identify novel click types associated with short-beaked common dolphins, Risso’s dolphins, and short-finned pilot whales in this way. Next I characterized temporal patterns in presence and activity for ten different species across our monitoring sites at three different temporal scales: seasonal, lunar, and diel. I observed spatiotemporal separation of apparent competitors, and complex behavioral patterns modulated by interactions between the seasonal, lunar, and diel cycles. Finally I investigated the relationships between species presence and oceanographic covariates to predict habitat suitability across the region, and explored niche partitioning between potentially competitive species. The insights gained here significantly advance our understanding of toothed whale ecology in this region, and can be used for more effective population assessments and management in the face of anthropogenic threats and climate change.

Parasites and pathogens exert strong selection on their hosts and alter the structure, diversity, and productivity of communities of ecosystems. This paper presents results of a survey of parasite composition and prevalence observed on and within the freshwater hybrids Owens (Siphateles bicolor snyderi) and Lahontan (Siphateles bicolor obesa) Tui Chubs, a native minnow species, in the Eastern Sierra Nevada mountains of California. The Owen and Lahontan Tui Chub is present in many lakes and rivers in Northern California and its parasite community has yet to be characterized. My thesis asks what kinds of parasites are found in the freshwater Tui Chub, which lakes or streams held the highest parasitic loads, and which features of individual fish and the habitat influence parasite density and/or types of parasites. Fish samples were collected in Summer 2019 by PhD student Henry Baker at 10 different sampling sites including freshwater lakes and streams that vary in size, temperature, water chemistry and species present across Owens Valley, California. I dissected 134 individual fish to characterize the ecto- and endo-parasite communities. My results show that two of the locations had significantly higher parasite infection rates than the others, where few macroscopic parasites were observed. These two locations were both geothermal with warmer waters and distinct water chemistry with high salinity and alkalinity. This pattern suggests that some aspects of geothermal habitat favor the parasite life cycle and makes fish in these sites more easily accessible as a host, though the mechanism behind the pattern is unknown. Four main types of visually distinct parasites were found: one adult life-stage tapeworm, one adult life- stage nematode and two metacercaria trematodes, though none were identified taxonomically. The greater parasite infection rates in geothermal habitats may be related to the greater abundance of snails in these sites, which may serve as intermediate hosts to fish parasites. No differences in parasite infection rates or composition were observed between lake and stream habitats. My thesis suggests that the atypical thermal and chemical environment of geothermal springs promotes parasitism in Tui Chub, but that lakes and streams are similar in containing low rates of infection by any parasites among fish.

Gut microbes provide vital functions for animal hosts. While it is known that host ecology and evolutionary history play a role in shaping gut microbiomes, a majority of studies have focused on mammal hosts. Other vertebrates, including fish, have received little attention. Coral reef fish, in particular, exhibit a wide range of distinct feeding behaviors, evolutionary histories, and geographic distributions that likely correlate with gut microbiome composition and diversity. They also inhabit a fragile ecosystem that is highly sensitive to anthropogenic disturbance—disturbances that are known to impact coral microbiomes but may or may not affect fish gut microbiomes. My thesis leverages a large unprecedented coral reef fish gut microbiome dataset (N=550), where I sampled the gut microbiomes of 20 host species of fish with robust replication spanning three islands across the South Pacific, to better understand how host phylogeny, host diet, and host environment shape vertebrate gut microbiomes. Comparing the gut microbiomes of distantly related hosts can reveal evolutionary and ecological dynamics that govern gut microbiomes across the animal kingdom. Chapter 1 investigates the possible similarities between coral reef fish and mammal gut microbiomes to elucidate any microbial features that may have converged between the two distantly related hosts. Through multivariate and Bayesian analyses, I show that fish and mammal gut microbiomes exhibit striking similarities in composition, particularly within carnivores and herbivores. Specifically, carnivores and herbivore gut microbiomes show more similarities within their diet groups than within their host phylogenies, and share a significant number of ASVs. Herbivore fish and mammal gut microbiomes, in particular, share a significant number of amplicon sequence variants (ASVs) associated with the functional requirements of herbivory, such as Ruminococcus and Treponema. My results indicate that despite 365 million years of evolution and two drastically distinct habitats (terrestrial vs. marine), fish and mammal gut microbiomes have converged on the basis of diet. Expanding on Chapter 1, Chapter 2 moves beyond host phylogeny and diet and aims to isolate and analyze the effects of host habitat on gut microbiome composition and diversity. Previous work on environmental effects acting on animal gut microbiomes largely focused on captive hosts or wild hosts of a single species, potentially ignoring any interactions between host environment and host phylogeny in the wild. Here, I leverage my dataset of coral reef fish gut microbiomes from a diverse range of hosts from three geographically distinct habitats to better understand how host habitat shapes vertebrate gut microbiomes. I find that host habitat significantly shapes fish gut microbiome composition and diversity and these effects are highly dependent on host phylogeny. For example, within the same analyses, a fish such as R. aculeatus, had significantly different gut microbiomes between the three islands, whereas E. merra gut microbiomes were largely unaffected by island location. For the fish gut microbiomes that were significantly impacted by host habitat, many of the associated ASVs were ASVs found in Chapter 1, suggesting that host habitat may also shape gut microbiome function. While comparative approaches on wild hosts are crucial in elucidating generalizable rules that govern animal gut microbiomes, experimental approaches are also imperative to unpack the finer-scale qualities and mechanisms of these rules. Chapter 3 builds on Chapter 2 by leveraging a simulated nutrient enrichment experimental design to further investigate the effects of host environment on gut microbiome composition and diversity. Nutrient enrichment is one of the most threatening consequences of anthropogenic stress on coral reef ecosystems, and the effects of nutrient enrichment on reef fauna gut microbiomes are largely unknown. Here, I artificially enrich the territories (N=40) of a highly abundant, territorial gardening fish, Stegastes nigricans, and use multivariate and differential abundance analyses to elucidate how nutrient enrichment impacts animal gut microbiome composition and diversity. I find that nutrient enrichment effectively “enriches” the gut microbiome, with S. nigricans gut microbiomes in enriched territories exhibiting significantly higher alpha diversities than those in control territories. I also find that these changes are specific to the hindgut and do not occur in the microbiomes of the food source that S. nigricans gardens.

In late 2019, at multiple hatcheries in California’s Central Valley (CCV), offspring of recently spawned fall-run Chinook salmon (Oncorhynchus tshawytscha) exhibited abnormalities in swimming, lethargy, and high early life-stage mortality; the combination of these symptoms is commonly referred to as thiamine deficiency complex (TDC). The cause of thiamine deficiency in Pacific salmonids is hypothesized to be due to a lack of diet heterogeneity and reliance on northern anchovies (Engraulis mordax), containing high levels of thiaminase, a thiamine-cleaving enzyme. Of CCV’s four runs, the endangered Sacramento River winter-run Chinook salmon (WRCS) is perhaps the most vulnerable to thiamine deficiency as any additional stressor will exacerbate current threats to survival. The goal of this study was to evaluate the effect of thiamine supplementation in pre-spawn WRCS females on their offspring egg thiamine concentrations, survival, prevalence of TDC-related symptoms, and physiological performance and behavioral traits. Sixty female WRCS at Livingston Stone National Fish Hatchery were randomly administered either a thiamine injection (n=33; 500 mg/ml thiamine hydrochloride) at a dose of 50 mg/kg body weight or a sham injection (n=27; sterile saline solution) at a volume of 0.127 ml/kg body weight. After spawn, a subset of fertilized eggs from each female were analyzed for thiamine concentration. Eyed embryos were transferred to the University of California, Davis and kept for observations of TDC, survival, and to assess the effects of maternal thiamine treatments on offspring physiology and behavior. Upper thermal tolerance, routine metabolic rate, spontaneous swimming activity, boldness, and anti-predator responses were evaluated in swim-up fry. On average, total egg thiamine concentrations were 5.02 and 34.91 nmol/g for untreated (n=27) and thiamine treated (n=33) females, respectively. Mortality rate of offspring from untreated females averaged 32.97 ± 0.33 %, with rates ranging from 0 to 100%, while offspring from thiamine treated females had a mean mortality rate of less than 1%. Using a binomial logistic regression model, we predicted that a mean total egg thiamine concentration of ~5 nmol/g supports 95% survival within a family (EC95). There were no statistically significant effects of maternal treatment on any of the physiological or behavioral metrics assessed in this study. Overall, we recommend the administration of supplemental thiamine to increase thiamine concentrations past the threshold at which TDC symptoms are commonly observed; however, additional research should be conducted to further examine potential latent effects of thiamine deficiency in Pacific salmonids.

Parent-offspring conflict arises because of the unequal patterns of relatedness among parents, offspring, and siblings. From an evolutionary perspective, parents optimize investment in each offspring to maximize their lifetime reproductive success. Females are equally related to all their offspring, so natural selection favors them allocating resources equally to each offspring. In contrast, natural selection will favor those offspring that acquire more resources, even at the expense of their mother and siblings. Recent thinking expands the potential influence of parent-offspring conflict from post-natal familial interactions to other facets of the organism’s biology. The evolution of a livebearing reproductive mode, particularly involving a placenta, for example, is predicted to cause pre-natal mother-offspring conflict. In the livebearing fish family Poeciliidae, a placenta-like organ has evolved independently at least nine times. In my dissertation, I examine the potential for reproductive barriers in placental (Heterandria formosa and Poeciliopsis prolifica) and non-placental (P. infans) poeciliid species. I perform both natural and artificial insemination crosses between populations within three separate species of fish in the family Poeciliidae. In my first chapter, I find that both placental and non-placental species exhibit reproductive incompatibility, but the location of the incompatibility is different. In my second and third chapters, I use artificial insemination to further investigate the effects of inter-population crosses on offspring size and number in two placental species, H. formosa and P. prolifica. In these species, natural differences in offspring size between populations of H. formosa are the source of conflict in offspring size. However, when females are mated to both their own and nonresident males, they produce intermediate offspring, discriminating against nonresident male’s embryos. In P. prolifica, while there are no natural offspring size differences in the two populations, we find a similar pattern of incompatibility present in crosses that is mitigated when females are provided with sperm from her own, and a genetically distinct population. These results provide a new path for studying reproductive incompatibility and conflict in placental species, as well as evidence for cryptic female choice and discrimination against genetically different males.

Temperature and body size are two fundamental factors shaping physiological and ecological processes across all levels of biological organization. Understanding the relationship between these two factors is therefore essential to our ability to understand how species are responding to climate change, especially as one response of ectotherms to warming is a decline in body size. Declining body size in fishes can consequently lead to declining economic and recreational fisheries value, declining population productivity, declining food security, and altered size-structure function of communities. My thesis explored the physiological mechanisms and the ecological consequences of body size and life-stage specific vulnerability to warming. First, I used a meta-analysis approach to determine species- and group-specific vulnerability to warming in fishes. I evaluated how aerobic metabolism scales with body mass in fishes across temperature and how these changes in scaling may differ with species ecology and morphology. Further, to better understand the mechanisms behind temperature-modulated scaling of aerobic metabolism, I tested how metabolism and maximum heart rates change with acute temperature change and body size in a model species, barred surfperch (Amphistichus argenteus). I then reviewed aerobic swim performance in adult salmon to determine the potential ecological consequences of shifting body sizes. By combining work both across and within species, and examining ecologically relevant physiological performances and contexts, my thesis demonstrates that relationships between body size and performance can provide a mechanistic platform to identify climate change vulnerability in fishes.