SAFS hosts weekly lunch-time seminars where students and faculty share findings from their current research. Read through our past seminars to get an idea of topics covered and be sure to check out our events calendar to download upcoming seminars on your calendar.
Cody Szuwalski (Research Fish Biologist, Alaska Fishery Science Center)
Title: Global fishery reform and climate change impacts: what details can we ignore?
Climate change and management reform are socially and ecologically important questions in fishery science. Our ability to protect marine ecosystems and keep fish on the menu may depend on our ability to address these questions. Fishery scientists use models to project the impacts of management reform and identify relationships between climate and stock productivity. However, model choice can influence the outcome of these analyses and the presentation of results can influence the message conveyed from the same analysis. In this seminar, I will describe a series of recent papers on the influence of environmental factors on the productivity of global marine fisheries, with particular attention on the methods used to identify these influences. Time willing, I will describe a series of papers aimed at understanding the impacts of global fishery reform. The relative merits of surplus production models, age-structured models, and ecosystem models will be explored in the context of these questions.
Christine Stawitz (Stock Assessment Modeler, ECS Federal in support of NOAA Fisheries)
Title: The life-changing magic of tidying…your code
In this seminar, I will argue that quantitative fisheries scientists often end up re-using and sharing code. For this reason, writing replicable, high-quality scientific code has the potential to reduce error, make thesis-writing and manuscript review and publication less painful, give researchers more time to focus on scientific innovation by reducing duplication, and spark joy. Drawing heavily from “Good enough practices in scientific computing” (2017) by Wilson, Bryan, Cranston, Kitzes, Nederbragt, & Teal (PLoS Computational Biology), I will talk about the most useful and easiest-to-implement programming tools and practices researchers should consider adopting to improve their code quality and reproducibility. These include code conventions and naming practices, functional programming, writing basic code documentation, and implementing simple tests. Each topic will be touched on briefly, but reference links to more in-depth tutorials and examples will be provided. Examples will be given in R, but the guidance will be applicable to any software language. This information is geared to scientists who do not have lots of experience creating software tools and may be simplistic for those who have already created and published R packages.
Shirley Leung (Graduate Student, School of Oceanography)
Title: ENSO drives near-surface oxygen and vertical habitat variability in the tropical Pacific
El Niño-Southern Oscillation (ENSO) is the leading cause of sea surface temperature variability in the tropical Pacific with known impacts on tuna geographic range, but its effects on oxygen and available oxygenated habitat space are less clear. Variations in oxygenated vertical habitat space in the upper ocean can alter interactions between predator and prey, as well as drive changes in the vulnerability of economically important tuna and other pelagic fish to surface fishing gear. Using in situ measurements, we show that ENSO is the primary driver of upper-ocean oxygen partial pressure (pO2) variability on year-to-year time scales in the tropical Pacific. Mechanistically, these pO2 variations are primarily caused by vertical shifts in thermocline depth, which alternately elevate and depress cold, hypoxic waters from the ocean interior depending on the ENSO phase and location. Transport-driven, isopycnal pO2 variations within the thermocline also play an important but secondary role. In the western tropical Pacific, waters within the exclusive economic zones of Palau, Micronesia, Nauru, and the Marshall Islands undergo the greatest variations in oxygenated tuna vertical habitat extent: approximately 19.5 m, 23.9 m, 19.4 m, and 19.3 m, respectively, between El Niño and La Niña phases. Oxygen thus plays an important role in altering available tuna vertical habitat space between different phases of ENSO.
Title: Dynamic ensemble models to predict whale distributions and anthropogenic risk exposure in near-real time
Species distribution models are key tools for describing species’ habitats and distributions across marine and terrestrial systems. However, there is frequently a mismatch between the spatiotemporal resolution of species occurrences and that of environmental data, particularly in dynamic marine environments. Such mismatches can lead to false inferences and increased uncertainty. In addition, responsive management strategies for highly mobile species often rely on up-to-date information on species’ distributions. We matched daily animal tracking data with daily environmental data from ocean circulation models to predict dynamic, near-real time distributions of blue whales (Balaenoptera musculus) along the West Coast of North America. We selected and validated candidate models using multiple cross-validation metrics and a large independent observer dataset. We evaluated the performance of multi-model ensembles and found that such ensembles outperformed single-model approaches. Our final ensemble model predicted daily blue whale distributions with high skill and accurately reproduced roundtrip migratory behavior. Given that ship strikes are a primary source of mortality for this Endangered species, we demonstrate an application for evaluating the spatiotemporal dynamics of risk exposure to vessels off the coast of California. Risk exposure varied within and among years as a function of environmental conditions (e.g., warm-water anomalies), indicating that management strategies could benefit by incorporating dynamic environmental information. This dynamic ensemble modeling approach is readily transferable to other species, systems, and management needs.
Jonathan Reum (UW)
Title: Research Scientist
Hannah Sipe (Graduate Student, QERM)
Title: Washington State Common Loons: Multi-state occupancy models using citizen science and survey data
Common Loons (Gavia immer) are a state listed Sensitive species in Washington State. However, little is known about Common Loon distribution or the factors affecting distribution within Washington state. Summer habitat for Common Loons is found in isolated and difficult to survey areas, as such there is limited biologist survey data available. Given the size of the area of interest, obtaining the data necessary for a robust analysis of state-wide Common Loon occupancy presents a challenge. Citizen science eBird data is easily available in large quantities and can be used in distribution modeling. The state survey data and citizen science data were integrated in a multi-state occupancy model, with consideration for the structure of each data type and the uncertainty inherent in the citizen science eBird data. These extensions to the traditional multi-state occupancy model will be discussed in application to Common Loons. Results of the occupancy model, significant habitat associations, and detection-effort relationships determined during modeling will be presented, as well as discussing issues relating to the use of citizen science data in the context of this application. The findings from this project will be used to create an optimized survey strategy for state biologists and will help management to make informed conservation decisions for Common Loons in Washington State.
Sean Rohan (Graduate Student, SAFS)
Title: A new model of aquatic visual foraging: Confronting theory with data
Jodi Young (Assistant Professor, School of Oceanography)
Title: Metabolism in the ice: responses of ice algae to shifts in temperature and salinity
Algae growing within the sea ice are an important food source for polar ecosystems. Over the seasonal melt and freeze of the ice, algae respond to the varying temperatures and salinities by altering their metabolism. I will present data from lab cultures and the field, analyzing how the abundances of major intracellular metabolites shift in response to changing temperature and salinity and discuss the implications of these changes on polar biogeochemical cycles.
Cole Monnahan (Postdoc, SAFS and AFSC)
Title: Combining data series within a spatio-temporal index standardization model to improve estimates and reduce uncertainty, with application to Eastern Bering Sea Pollock