Surf smelt (Hypomesus pretiosus) are ecologically and culturally important forage fishes that rely on intertidal beach habitat for spawning. However, the combined effects of rising sea level and human modification (e.g. seawalls, bulkheads, riprap) have put this habitat at risk of coastal squeezing, which could reduce available spawning areas along Puget Sound. This research aims to assess the vulnerability of surf smelt spawning beaches to climate change by combining field data collection with quantitative analysis. We evaluated existing risk assessment methods, such as the Coastal Vulnerability Index (CVI) to determine its applicability to Puget Sound. Additionally, we conducted beach surveys at productive spawning beaches to characterize the beach morphology. Our morphodynamic analysis included measurements of beach slope, sediment composition, pH, and water table depth from the high tide line to the waterline. Our hypothesis suggests that spawning beaches with a lower slope, smaller sediments, and a shallow water table will be more resilient to climate change impacts. Findings from this study will improve our understanding of climate-driven and anthropogenic threats to intertidal ecosystems and provide insight into habitat resilience, supporting conservation efforts for surf smelt populations.

Aquacultures are an environmentally responsible way of breeding and harvesting a variety of marine organisms. Challenges to aquacultures include the introduction of nonnative pathogens and parasites to wild fish as well as intense changes to the physical environment. Monitoring the environment for impacts of aquaculture is costly and time-consuming, so finding a cost-effective rapid monitoring solution is important. This project tests the feasibility of monitoring the diversity of meiofauna species present in the sediment via DNA sequencing. Meiofauna species are marine organisms between 0.06 mm and 1 mm in size that live in marine sediment. DNA sequencing is quicker and cheaper than current monitoring practices, and since changes to the physical environment affect meiofauna species diversity, observing the change in species diversity is a potential alternative to monitoring aquaculture health. Through samples taken before and after the introduction of a sablefish net pen aquaculture, analysis of both physical sediment samples and meiofauna samples will determine the feasibility of implementation. By looking at the total organic carbon content and grain size distribution of the sediment samples, we can determine the physical changes to the environment caused by aquaculture. Suppose the DNA sequencing results show shifts in species diversity that match the physical changes. In that case, we can confirm there is evidence supporting the feasibility of implementing monitoring via meiofauna DNA sequencing. 

Viral evolution theory hypothesizes that specialist strategies increase fitness by reducing interspecific competition, while generalist viruses increase fitness by accessing multiple hosts. However, specialism may come at the cost of infecting few hosts, while generalism may reduce fitness in any single host. These tradeoffs have been demonstrated in Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus infecting multiple salmonid species. High rates of viral replication have been observed for specialized subgroups in their respective hosts, while lower rates of replication across multiple hosts have been observed for the generalist subgroup. However, the host-virus mechanisms underlying these replicative differences are unknown. Here, I aim to characterize the early innate immune response of sockeye salmon, the ancestral host of IHNV, to specialist and generalist subgroups at target tissues. Specifically, I seek to test whether sockeye salmon display distinct transcriptomic responses to IHNV specialist and generalist subgroups in the kidney 2 days post-exposure (dpe). To accomplish this goal, RNA was extracted and sequenced from kidney tissue of individuals 2-dpe following exposure to specialist (n=9), generalist (n=9), or control (n=4) IHNV treatments. Overexpressed and underexpressed genes will be identified between each subgroup and control samples. These genes will then be used for pathway enrichment to compare differences in transcriptomic response. Replicative rates have shown a difference between specialist and generalist subgroups of IHNV 2-dpe in the kidney; therefore, we expect to observe differences in the number and magnitude of over- or underexpressed genes and enriched pathways between hosts exposed to specialist and generalist subgroups. Results from this study will aid in characterizing evolutionary mechanisms underlying viral specialism and generalism, understanding host innate immune response and evasion strategies, and identifying biological markers associated with response to viral exposure. This knowledge will be critical in predicting future disease outbreak and informing disease mitigation strategies.

Surf smelt (Hypomesus pretiosus) are an ecologically and economically significant forage fish species that spawn in the intertidal zone of beaches throughout the Salish Sea. Despite their importance to marine food webs, the environmental factors influencing their spawning site selection and seasonal distribution remain poorly understood. This project aims to investigate the morphological characteristics of beaches used for surf smelt spawning during different times of the year, comparing morphological and spatiotemporal variables that influence spawning. In order to study these characteristics, we will record sediment grain size, slope, wave energy, beach temperature and the water chemistry at verified winter as well as summer spawning sites identified by the Washington Department of Fish and Wildlife (WDFW). We will also sample non-productive sites in order to identify key differences between them and further establish parameters that enhance spawning success. Preliminary research suggests that these key characteristics strongly influence surf smelt spawning distribution​​​. Optimal surf smelt spawning beaches appear to consist of mixed sand and gravel substrates, low levels of wave action, high amounts of shading, moderate slopes and moderate temperatures. Habitat alterations such as shoreline armoring along with sea-level rise in response to global warming could lead to a drastic decrease in the upper inner tidal ranges where surf smelt usually spawn. Consequently, we expect beaches heavily influenced by these factors to be poor spawning sites​​. The results of this study will contribute to a deeper understanding of the environmental variables driving spawning site selection, egg survival, and seasonal spawning peaks. This research will be instrumental in informing conservation projects and supporting policy initiatives aimed at preserving surf smelt populations and their critical spawning habitats in the Salish Sea.

We analyzed the effects of marine heatwaves on primary production in the Northern California Current from 1997 to 2023, a productive ecosystem that has been impacted by intense and long-lasting heatwaves, most notably the 'Blob' (2014-2016) and the 'Blob 2.0' (2019). Using Copernicus Marine Service's Global Ocean Colour and NOAA's Optimum Interpolation Sea Surface Temperature (SST) products, we analyzed chlorophyll and temperature bounded by the Columbia River and the Strait of Juan de Fuca. Heatwave metrics were compared to chlorophyll concentrations before and after events, and dynamic linear models (DLMs) were used to determine the changing regression slopes between temperature and primary production for six areas on and off the continental coast. We then used self-organizing maps (SOMs) to analyze spatiotemporal variation in phytoplankton blooms during heatwave years. Chlorophyll decreased during heatwaves for all six locations (p<0.05) and DLMs showed increasingly negative correlations between SST and chlorophyll during heatwaves for the two locations closest to the Strait of Juan de Fuca. Phenological analysis showed that the spring blooms occurred significantly earlier and with lower peaks (p<0.05) during most heatwave years. We conclude that marine heatwaves negatively affect primary production in this region, especially near the Strait of Juan de Fuca. Heatwaves also shifted the timing of spring blooms, indicating possible ecosystem impacts from mismatched phenology. Further analysis is needed to determine the mechanisms of these effects through covariates such as nutrient availability and mixed layer depth.

 Marine debris, classified as solid, man-made litter and material that has been lost or discarded in the ocean, is a persistent pollution issue in coastal regions around the world, and Puget Sound is not an exception. This research investigates the distribution and abundance of marine debris across various regions of Puget Sound and how they are changing over time. Since 1987, the Washington Department of Fish and Wildlife (WDFW) has conducted annual trawls to assess bottom fish populations in Puget Sound. The contents of these trawls provide valuable representation of the soft-bottom habitat, including the organisms and debris inhabiting the seafloor. The WDFW’s extensive records of these surveys include the location, depth, type, and abundance of debris collected in each trawl. With this dataset, I explore spatial patterns in different types of debris, examine trends in abundance over the last two decades, and identify hotspots for debris accumulation in Puget Sound. The results of this study contribute to a deeper understanding of the dispersal of aluminum, plastic, glass, fishing gear, and other debris that lie at the bottom of Puget Sound. Insights on these patterns are vital to informing effective clean up and guiding prevention efforts to create cleaner and safer waters for both humans and marine life. 

Recent technological breakthroughs have allowed important advances in the description of deep reefs (below 30 m). However most research has been restricted to the upper section of deep reefs (down to 80 m) and has primarily focused on fish and coral communities. By contrast, the composition of the lower portion of deep reefs, and of non-coral habitat-forming communities remains limited. This work focuses on how the composition and structure of habitat-forming communities change across the entire depth range of a tropical reef-dominated ecosystem, from 5 to 300 m. Using a combination of SCUBA and manned submersible diving, benthic transects were performed in  Curaçao , an island in the Southern Caribbean Sea. Using a combination of morphology, taxonomy, and trait ecology, I will evaluate the faunal breaks of habitat-forming communities with depth. In addition to providing one of the first descriptions of the diversity and community structure of habitat-forming communities across the entire range of a reef’s slope, this work will contextualize over a decade of deep-reef fish observations conducted at this study site. This study will also provide insights into the vertical reef connectivity and resilience, informing future management efforts of deep Caribbean reefs. 

Understanding the structure and habitat preferences of deep-reef fishes is crucial for effective conservation management. Mesophotic ecosystems, occurring between 40 and 150 m, are understudied ecosystems with limited biodiversity assessments, although their importance in supporting species of commercial interest is established.  In particular, very few studies have described mesophotic fish assemblages in the Mediterranean, where essential fish ecosystems face increasing pressures from human activities. This study investigates fish species composition, abundance, and depth distribution at two sites in the Aegean Sea (Eastern Mediterranean).  Fish observations were collected by technical rebreather divers from the surface to 90 meters depth, along with information on habitat and fishing pressure. I will complement this dataset with information collected from the IUCN to identify patterns in species distribution, vulnerability, and habitat associations. This study will provide valuable insights into the community structure and habitat associations of mesophotic fish assemblages, ultimately contributing to conservation strategies that protect vulnerable marine ecosystems in the Mediterranean.

The aim of this study is to identify possible differences in Anisakis spp., or “sushi worm”, infection intensities between three different species of wild Alaskan salmon, O. keta (chum), O. nerka (sockeye), and O. gorbuscha (pink), by examining canned salmon samples from three different canning regions from the 2024 season. Species were selected from three different canning regions: Kodiak, Prince William Sound, and Southeast Alaska. Distribution of these parasites among species and location have marine ecology (pinniped health and distribution), salmon biology (physiological and biochemical parasite defense, dietary preferences), and seafood safety implications (marketing, establishing safe food handling protocols) that make it important to establish a baseline dataset.

Pacific Oysters (Magallana gigas, previously named Crassostrea gigas) are marine bivalves that are widely cultivated in the US Pacific Northwest. A widespread range combined with high commercial interest makes the Pacific Oyster a very crucial species to study for both environmental and human health. Shellfish farms often experience major summer mortality due to multiple interacting factors that heavily impacts production and profitability. Two current key concerns are 1) the increasing severity and frequency of marine heat waves and 2) impacts of diseases (e.g., OsHV-1) that cause oyster mortality. Under current environmental stress scenarios, shellfish require capacity to withstand interacting stressors through their sophisticated innate immunity and cellular stress responses. In the face of multiple environmental stressors, it is of great interest in the aquaculture community to increase oyster stock resilience. However, it remains unclear how temperature influences survival of early life stages of oysters and whether strengthened immune system responses offer protection to thermal stress. To address this need, we conducted an immune challenge using PolyI:C (i.e., an RNA analog that mimics viral DNA to activate the oyster’s immune system) in oyster broodstock and reared their offspring until the spat stage. Oyster spat were then exposed to thermal challenges and we characterized metabolism, survival, and growth. Offspring from immune-challenged parents had higher survival under thermal stress and differences in their metabolic response to elevated temperature. This work raises additional questions about how the biological responses between thermal stress and immune response are connected and the potential to apply immune priming in oyster aquaculture. Further, it is important to understand if there are growth trade-offs associated with improved stress tolerance. Improving the general understanding of temperature affects in oysters and their interacting stressors as climate change amplifies is important and applicable to other farmed invertebrates.

Developing and validating new methods of enumerating species of concern is important for many conservation and management goals. Environmental DNA (eDNA) has shown potential to be a viable tool for obtaining non-invasive and cost-effective estimates of many organisms, including fishes in streams such as salmon. However, before eDNA can be used beyond an experimental basis, we need to understand how eDNA flows through small streams where salmon may spawn. This study aims to examine how sockeye salmon (Oncorhynchus nerka) eDNA is transported in small streams by collecting samples while ascending two morphologically unique streams. eDNA within each reach was analyzed against two measures: the abundance of salmon within each reach and cumulative abundance salmon above of the reach. Preliminary analysis suggests that eDNA is effectively transported to stream mouths when salmon are in high abundance. Moreover, eDNA does not accurately predict the abundance of salmon within individual reaches but corresponds more closely with the cumulative abundance of salmon above each reach, particularly when salmon are highly abundant. This closer alignment with cumulative salmon abundance is likely due to the cumulative nature of eDNA within streams.

The conservation of global marine mammal abundance has been considered largely successful as the widespread ban of the industrial harvest of pinnipeds and large cetaceans has led to their strong recovery in abundance. However, it remains unknown whether the story of their conservation applies to marine mammals that were not heavily harvested such as oceanic dolphins. Here, I plan to fill this knowledge gap by presenting a meta-analysis of global abundance trends of oceanic dolphins by conducting a systematic literature review of government reports, journal articles, and marine biodiversity data sets to gather abundance trend data. I expect to find data for roughly 25% of all 38 oceanic dolphin species, mostly represented by line-transect surveys and mark-recapture evidence in coastal waters. Using a Bayesian multi-population state-space model, I intend to estimate abundance trends for each dolphin population, in addition to the uncertainty in population changes and varying survey methods. I seek to summarize abundance trends of populations by species and regions to identify which of these have declining or highly unknown abundance trends. I expect dolphins with restricted geographic ranges, especially coastal species, to have the strongest declines, and dolphins that occupy high seas to have the least known trends. I aim to highlight which taxa and areas need further conservation and monitoring attention. These findings represent a crucial first step in gaining insight from rising dolphin populations, which can be used to help reverse the decline of other populations.  

Invasive Red lionfish (Pterois volitans) are responsible for the heavy destruction of reefs, resulting in a decline in biodiversity and negative impacts on commercial fishing. Their success in their non-native range is attributed to their lack of predators in their invasive range. Parasites are often overlooked as predators, but low parasitic loads make for a more biologically fit individual, allowing for higher invasion success. For this reason, it is hypothesized that lionfish carry a lower parasitic load in their invasive range. This project aims to assess the parasite abundance in lionfish collected from along the entire reef slope in Curaçao in 2019 and 2022 by the Tornabene Lab. Using these fish I am conducting dissections examining various parts of the fish under a dissection microscope and carefully looking for parasites. The parts that are examined are the skin, body cavity, buccal cavity, fins, gonad, liver, spleen, eye, heart, intestine, filet, and gills. Using data collected from dissections, I am performing descriptive analyses to summarize parasite presence and quantity by species and body site where they were found. It is most likely that there is a low abundance of parasites within these lionfish, suggesting that parasites could play a major role in regulating populations. Understanding the role that predation plays in invasive species can help us develop strategies to control their spread and prevent ecological damage.

In 1972, Washington State implemented the Marine Mammal Protection Act (MMPA), following which there was a drastic spatial expansion of pinniped populations throughout the region. Harbor seals, specifically, had been impacted prior to this act, with a reduction in population due, in part, to state-financed population control. Since 1970, there has been a 7 to 10-fold increase in population sizes. Predation from pinnipeds can decrease salmon population sizes, leading to negative impacts on Pacific salmon as pinniped populations grow. This is especially concerning for endangered species of salmonids, such as ESA-listed Chinook salmon, which show little recovery since federal protections have been placed on them. I reviewed historical and modern literature to find available harbor seal population data from years before and after the implementation of the MMPA. I used documentation regarding injury and human-caused death of marine mammals, including reports from the National Oceanic and Atmospheric Administration (NOAA), to relate encounter frequency with species abundance. I used R to generate maps showing the distribution of pinnipeds throughout Puget Sound to illustrate the spatial expansion of this species. I expect to find an increase in pinniped populations, particularly an accumulation of harbor seals in areas of abundant food resources and areas less impacted by human development. This study, compiled with further research, will be helpful for the future conservation of impacted salmonids and understanding the ecological responses to the management of pinniped populations.

Fishes are the most species-rich and ecologically diverse group of vertebrates, and display a broad array of sensory adaptations that are essential for survival. Included in this evolutionary toolkit are appendages on or around their heads that may act as additional sensory organs. Such attachments, which are often referred to as cirri, occur in dozens of lineages across the fish phylogeny, and are present in species such as decorated warbonnets (Chirolophis decoratus) in the Stichaeidae family, roughhead blennies (Acanthemblemaaria aspera), in the Chaenopsidae family, and kelp greenlings (Hexagrammos decagrammus), in the Hexagrammidae family. While there is limited research on the purpose of cirri, I hypothesize that they serve a role in chemoreception or some other sensory behavior, due to their location on the body, their structure, and their appearance. With the use of electron microscopy, clearing and staining, and histological sectioning to observe cirri morphology, I analyze the types of cells, physical support systems, and signals cirri may receive from the surrounding environment. These methods help determine possible roles of cirri in chemoreception, mechanoreception, camouflage, or mating, although predicted results lean towards chemoreception for gustation or olfaction. These result can help fill gaps in the fish phylogeny, shed light on fish morphology, and indicate possible signs of convergent evolution across diverse lineages of fishes.