School of Aquatic and Fishery Sciences

Fishery-independent survey data represents essential information for stock assessment, ecosystem-based fishery management initiatives, and applied ecological research. These data refers to information collected over space and time about populations of marine organisms, such as population abundance and biomass. The data can be used to fit statistical models to obtain multiple products for the assessment and management of marine populations. and can provide a comprehensive and standardized picture of marine populations when collected consistently over time, particularly with respect to gear selectivity and sampling design. However, fluctuations in resources for sampling effort, climate change, and limited spatial-temporal coverage can affect the consistency, precision, and accuracy of fishery-independent survey data. Therefore, it is critical to determine how to design surveys that can provide accurate and precise estimates to inform effective fishery management in the face of all these challenges.

Daniel Vilas, a researcher at SAFS, has been working on a project called “Adapting monitoring to a changing seascape: increasing the efficiency, flexibility, and continuity of bottom trawl surveys in the Bering Sea and beyond” led by Lewis Barnett from the NOAA Alaska Fisheries Science Center (AFSC). His work involves developing a framework for designing efficient and flexible fishery-independent survey sampling design, to effectively monitor ecosystems given limited resources and shifting species distributions.

Environmental factors can influence the physiology, metabolism, growth, reproduction, survival, and behavior of marine fishes and invertebrates, consequently impacting their distribution and phenology. For example, increasing sea temperatures due to climate change can cause shifts in species distributions and drive marine populations to colder and deeper regions. Variation in species distributions over time can also impact the spatial availability of species to sampling by surveys, with consequences for consistency and precision of abundance estimates over time.

The Bering Sea is undergoing major environmental changes, such as warming and high variation among years in seasonal sea ice cover and cold pool extent (the area of the seafloor with bottom temperatures below 2°C). The cold pool extent is a key factor contributing to the redistribution of the Arctic and subarctic demersal communities in the Bering Sea. Genetic analyses and bottom-trawl survey data revealed changes in the distribution of several commercially important species associated with such temperature fluctuation. Given that changing environmental conditions are likely to continue or become more novel in the following years, it is critical to evaluate the abundance of marine populations under feasible future environmental conditions.

The quantitative framework that Daniel is working on consists of building delta-generalized linear mixed models conditioned on historical fishery-independent bottom trawl data and observed sea bottom temperature in the Eastern Bering Sea and Northern Bering Sea for several species such as Pacific cod, halibut, and red king crab. These spatiotemporal operating models are used to simulate observations to evaluate several stratified sampling designs informed by environmental variables. This work aims to facilitate the precise and accurate estimation of abundance under current and future climates to maintain the quality of survey data products for managing marine populations.

The use of eDNA methods is a new and exciting area of research. Tania Valdivia, a post-doctoral student in the Whale and Dolphin Ecology Lab, is working on a large marine project under the guidance of Amy Van Cise from SAFS, and Ryan Kelly from the School of Marine and Environmental Affairs (SMEA).

The project focuses on the application of eDNA methods to detect and identify the spatial distribution of marine mammals and their prey in the California Current. Moving southward along the West Coast of North America, the California Current is a cold water Pacific Ocean current. The goal of the project is to advance eDNA methods for use in a variety of ecological and conservation questions that are relevant now and in the future.

Found in environmental samples, different aspects of eDNA can be investigated, each with complex behavior depending on the environment and the study scale. Tania’s interest is in using marine eDNA for the study of marine biodiversity and applying its potential in conservation studies.

Using eDNA to detect different species across the California Current system, she is working on samples from hake surveys from 2019, 2021 and 2023. This marine monitoring project takes place along the West Coast of the US at depths up to 500m. For several years, scientists have been collecting seawater samples during these oceanographic campaigns to extract eDNA. These samples are used to assess the presence of marine mammals throughout the US West Coast, covering a wide geographical and temporal range.

Detecting marine mammals can be a challenging task using acoustic, visual, or eDNA methods. Therefore, the project also focuses on identifying potential prey such as fish and cephalopods, as they play a crucial role in predicting the distribution of marine mammals. After the identification of the presence of marine mammals, Tania’s research combines marine mammal and prey detections with statistical models and environmental variables, with which she can gain valuable insights into marine mammal distribution. One unique contribution of incorporating eDNA methods is its ability to detect both marine mammals and their prey simultaneously at various depths, which is difficult to achieve using traditional methods alone.

How is the eDNA data used in projects like this collected? By deploying an array of Niskin water sampling bottles from a vessel, which go to different depths to retrieve samples. The water samples are then filtered and stored to prevent eDNA degradation, until eDNA extraction takes place back at the NOAA Northwest Fisheries Science Center (NWFSC) laboratory. Processing involves extracting and quantifying the eDNA obtained per sample. These samples are precious and must be stored correctly, as each sample takes a lot of effort and funding to collect and can be used for other research.

After obtaining eDNA in good enough concentration, polymerase chain reactions (PCRs) are conducted with specific primers. Different primers are selected depending on the taxonomical feature you want to focus on in the eDNA mixture. In this research, primers have been chosen specifically for cetaceans, fishes, and cephalopods.

After the PCR reaction, numerous copies of eDNA molecules are produced, sequenced, and analyzed using bioinformatics. Part of Tania’s research concentrates on analyzing millions of sequences using various pipelines to obtain a catalog of sequences that can be identified taxonomically using genetic reference databases. This data enables researchers to indirectly determine the species presence and abundance in the area where the samples were collected.

At this moment in time, many different species such as the Pacific white-sided dolphin, the Northern right whale dolphin, Risso’s dolphin, Dall’s porpoise, humpback whale, orca and the Baird’s beaked whale have been detected using eDNA collected from the Washington Coast above the Columbia River – the Northern portion of the California Current. These detections will then be used to create distribution models of marine mammal species at different depths. This project is particularly notable as it may be one of the first attempts to 3D map the distribution of marine mammals across such a vast area.

One of the end goals of collecting and working with eDNA is to transform this information and its complexities in different ways, into informative ecological data. This can be then used in conservation assessments and applied to real-world management of species of interest. For Tania, one of the highlights of this work is despite not physically being out in the field and on the vessels collecting eDNA data, she is a crucial part of detection efforts through working with complex code to detect marine mammals through eDNA.

Spending the summer at Friday Harbor Labs (FHL), SAFS grad student Chris Mantegna mentored four students – two as part of the NSF-funded Research Experience for Undergrads-Blinks (REU) program and two as part of the Doris Duke Conservation Scholars Program (DDCSP). During the program, students get to collaborate on a research project with their scientist-mentor to build marine research skills.

Chris Mantegna

Specifically geared towards enhancing diversity within the marine sciences, the program welcomes students from underrepresented groups. This year, Chris’ students came from institutions across the US, including Kentucky, Massachusetts, Vermont and North Carolina, to work with her on an intertidal monitoring survey on Yellow Island in the Salish Sea.

Chris Mantegna

The REU-Blinks program based out of FHL takes advantage of the pristine environment, remarkable biodiversity, and the scientific and technical resources available at the marine science research facility. The DDCSP program aims to increase diversity in conservation work and allows students from all over the US a chance to participate in a two-year program where second year scholars participate in an onsite internship of their choosing.

Chris Mantegna

Yellow Island is a nature preserve that The Nature Conservancy purchased in 1980, that also doubles up as a marine reserve, with no boating or fishing allowed within 300 yards of the island. The island is being used by Chris and the research team as a proxy for health in the wider Salish Sea due to the lack of human disturbance.

As part of a wider program sponsored by Black In Marine Science (BIMS) and The Nature Conservancy, Chris restarted a monitoring project to get a better idea of the biodiversity on the island, and this kicked off last year in 2022 with a pilot program nailing down methods for collecting data. This year, with her mentees, the team collected a full season of data, complemented with eDNA work.

Carley Bishop

There are other benefits to conducting research in this area. Chris shared that it is a fantastic place to teach marine literacy skills for underrepresented students, in a place where they can be free to ask questions, conduct research, and be present in the space without fear of being harassed or threatened while working. Framing it as a learning ecosystem, the idea is also to teach students how to get the information they need for their research in the least invasive way. The primary drivers of this research are supporting the needs of community partners as part of the Yellow Island Program, with the overarching objective to provide useful information and science to local Salish Sea communities.

Chris Mantegna

One partner, the Lopez Island Family Resource Center (LIFRC), led by Quaniqua Williams, DEI Consultant for LIFRC, came out with a group of families to celebrate Juneteenth and learn about the island and a little bit of intertidal ecology. Throughout their time on the island, Chris and the team supported other REU and DDCSP members coming out to learn about what their work, as well as sharing the research with the the greater Friday Harbor community via a workbook created by Carley Bishop and Kamryn You Mak, the DDCSP scholars on the island.

Logan Evans

After a summer of fieldwork, both DDCSP and REU students were able to present their work, methods, findings, and how they grew in their skills to external audiences.

Intending to bring projects such as these to a wider group of students, Chris worked with a team at UW to design a program to couple environmental literacy skills with art, to create a way to teach intertidal ecology in a more inclusive and intuitive way. The creativity and joy of art has many similar applications in science – touching cool stuff, drawing things seen in the field, going out to beautiful locations, listening to the sounds of nature. 

Carley Bishop

Awarded the Innovation Grant by UW EarthLab in April 2023, the Yellow Island work inspired this proposal, which aims to empower students from underserved communities, who have historically been excluded from environmental science, to engage with the intertidal ecosystem as equal partners students. The program building kicked off in August 2023 and will include different aspects like teaching using art and experiential tools, and applying this in the field with real, hands-on experience. It is bringing together experts in art, pedagogy, and marine science to really bring to life art and science for students, with a true run with students in late Spring 2024.

Read the full list of partners on the ‘Increasing Environmental Connection, Literacy and Engagement through an Art + Science Collaborative Education Practice’ project here.

Carley Bishop

Claire Vaage, a masters student in the Freshwater Ecology and Conservation Lab advised by Julian Olden, spoke with us about her summer field season in Central Oregon.

Spending 5 weeks during this summer in Oregon, I led a research team of two to four people at a time. Each day we conducted snorkel surveys and collected samples of freshwater macroinvertebrates and vegetation.

Taking place on the South Fork of the John Day River, I led a team of two technicians in a collaborative project with support from the Oregon Department of Fish and Wildlife (ODFW) and the Confederated Tribes of the Warm Springs Reservation.

One of our key focuses was steelhead, with the goal of understanding potential threats to this ESA-listed population of less than one thousand individuals. Using snorkel surveys, we also monitored Chinook fry and parr that migrate to rear in South Fork. Across various field sites, we collected density estimates, and confirmed presence-absence of both steelhead fry and rusty crayfish. Due to high water flow, both our team and ODFW were unfortunately unable to conduct redd surveys which would have allowed us to investigate competition for space. Field work is never perfect!

Another facet of the field season was macroinvertebrate sampling and habitat surveys. This involved kick-seining for rusty crayfish, a rapidly spreading invasive species in the river basin, and signal crayfish which are native to the waters. We observed densities of >40 rusty crayfish in a square meter area—a jarring and concerning number. An important part of freshwater work is community composition estimates of bugs which will be leveraged to understand how the invasion may impact steelhead through competition for food.

A third area of the work was collecting samples of bugs, algae, crayfish and steelhead to be used for stable isotope analysis. This allows us to reconstruct the food web and estimate diet sources using mixing models. Furthermore, we’ll look at how invasion may impact steelhead through predation on steelhead eggs, alevins, and fry. We can do this through the identification of a marine-derived signature through bulk stable isotope and fatty acid analyses, using muscle tissue and hepatopancreas taken from the crayfish.

Invasive crayfish have become a target of concern due to their high densities and notable polytrophic feeding habits. Research investigating the potentially detrimental impacts to salmonids, here in the West in particular, has been slow to accumulate. To best guide federal, state, and tribal management of the threatened population of steelhead, we first need to understand what harm the rusty crayfish may be causing and how the threats may vary across the invasion gradient.

In the world of fisheries management systems, many do not account for predator-prey interactions that scientists know can have big impacts on the dynamics and available biomass of commercially targeted species.

For his dissertation work as part of the Gulf Of Alaska Climate Integrated Modeling Project (GOA-CLIM), Grant Adams from the Punt Lab at SAFS, has been developing multi-species population dynamics models for the Gulf of Alaska. Focusing on four species of commercially important fish in this region – cod, pollock, arrowtooth flounder and pacific halibut – Grant has been examining their predator-prey interactions in the Gulf of Alaska.

The model is in the similar sphere to the Atlantis model worked on by Alberto Rovellini but is relatively more simple in terms of being able to use observed data from NOAA and the International Pacific Halibut Commission (IPHC) in the region to inform the model.

So which species are prey, and which are predators? Pollock has been observed as the main prey species among the four, and researchers are interested about the impacts of predation on this very important fishery and how the different species interact with each other. The Alaska pollock fishery is one of the most valuable in the world, worth $383 million in 2021.

The first half of Grant’s work was geared towards developing the model for the Gulf of Alaska and understanding predator-prey interactions more deeply, including the implications on future dynamics of pollock, as their population is heavily impacted by how many predators are in the system. The model used is called CEATTLE (Climate-Enhanced, Age-based model with Temperature-specific Trophic Linkages and Energetics), first developed for the Bering Sea by Kirstin Holsman at the NOAA Alaska Fisheries Science Center.

The second part of his work focused on fisheries management and how these models can be used to evaluate how robust the current management system is to predator-prey dynamics and how management advice from multi-species models compares.

Using a simulation approach called Management Strategy Evaluation, this involves simulating data from multi-species models accounting for predator-prey interactions, applying the current management system used, which in this case, does not consider predator-prey relationships, and then evaluating management performance.

This sheds insight into how biased the perception and management of fisheries are. How many fish do we think are in the system, is it productive or less productive, is over or under-harvesting in the fishery taking place as a result?

The next step in the process is to incorporate external factors such as climate change into these models, and see what projections are made for the future for fish abundance. One of the key aims of developing multi-species models that include interactions like predator-prey relationships is to evaluate if such models can better achieve management objectives under climate change. Leaving enough fish in the system for other animals, sustaining fisheries, ensuring reliable catches without too much variability, and securing enough catch to maintain local communities, are all things at stake.

Previously working in Peru with the Peace Corps, Grant was inspired to work in fisheries management when he observed the big impacts of El Nino and other climate factors on fisheries in that region. Enjoying working with the quantitative side and the use of data and statistics, his journey brought him to SAFS where he it’s exciting to work in a field that combines fisheries and climate, and is likely to have an important impact in the future.