Cataloging the canaries of the sea: studying vocal behavior, kinship and microbial transfer in Cook Inlet beluga whales

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Known as the canaries of the sea for their highly vocal nature, beluga whales are found across the Arctic and sub-Arctic. There are 21 beluga populations worldwide, with five populations found in Alaska. Of these, the Cook Inlet beluga population is the most endangered, with current estimates hovering around the 300 mark. A highly diverged population, the Cook Inlet belugas are geographically and genetically isolated, remaining in Cook Inlet year-round.

Arial Brewer, a PhD student in the Complex Ecological Systems Lab led by Andrew Berdahl and the Whale and Dolphin Ecology Lab led by Amy Van Vise at SAFS, has been working on this population since pre-grad school at NOAA. “There is still so much unknown about this population, particularly how their social nature affects the transfer of information and the transfer of disease” said Arial.

It has been hypothesized that belugas may have a fission-fusion type of social structure, rather than matrilineal like we see in killer whales. Interested in how information is shared among group members, Arial wanted to explore how sociality affects the vocal behavior and microbial transfer in this endangered population.

Arial Brewer
A group of beluga whales in Cook Inlet, Alaska. NOAA Permit No. 25563.

In the first two chapters of her PhD, she is diving into acoustics and exploring the vocal repertoire and calling behavior of Cook Inlet belugas. Moving a step beyond this, she has also investigated the impact of anthropogenic noise on the population. Cook Inlet has a large commercial shipping presence, and similarly to how a human conversation would be masked in a loud rock concert, Arial found that beluga whale vocalizations are masked by ship noise.

Arial Brewer
Beluga whales are dark grey as calves. Their skin lightens with age, becoming white. NOAA Permit No. 25563.

While exploring the seven most commonly used call types of Cook Inlet belugas, analysis revealed that all of them were completely masked by shipping noise at close distances, and partially masked at further distances. This is a critical issue for a population which heavily relies on acoustic communication for group cohesion and safety in a number of ways, such as communicating movement decisions, mother/calf contact, and information regarding feeding locations and predator presence. Another key issue around anthropogenic noise is that these beluga whales do not migrate and are therefore subjected to this noise year-round. Arial hopes that by opening up conversations around the masking of calls and how impactful it is on the beluga population, it can lead to further research and mitigation efforts for this population.

Arial Brewer
It is hypothesized that belugas may have a fission-fusion type of social structure. NOAA Permit No. 25563

Now that Arial has described the vocal repertoire and how noise affects these calls, she is moving on to the behavioral aspect. Arial is currently working on a project studying how behavior, calf presence, group size and tidal state are affecting vocal behavior. She hopes that this will lead to more efficient efforts in passive acoustic monitoring. “Currently, we are only able to describe where and when the belugas are with passive acoustic monitoring”, Arial said. “Understanding how various factors shape calling behavior can help us better describe habitat use and more effectively monitor this population”. 

This is only the tip of the iceberg in Arial’s work in the Cook Inlet. With her upcoming research focusing on population structure, kinship and epidermal microbiomes, she aims to investigate how sociality and kinship may be affecting disease transfer in Cook Inlet beluga whales.

New job opening for aquatic food system data scientist

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Position now closed

A new position is opening for an Aquatic Food System Data Scientist in incoming Professor Jessica Gephart’s lab.

The Aquatic Food System Data Scientist will join an interdisciplinary team focused on aquatic food production and trade. Aquatic food plays an important role in global food security, providing nearly 20% of global animal protein and supplying essential fatty acids and micronutrients. Aquatic foods are also among the most highly traded foods and the sector is rapidly evolving with the growth in aquaculture, geographical shifts in trade, and increasing commoditization and vertical integration.

This research team brings together global trade data, local consumption data, and environmental pressure data to understand the opportunities and risks of seafood globalization for sustainable production and food security.This position is based at the University of Washington in the School of Aquatic and Fishery Sciences and will interact with a broad network of interdisciplinary and international collaborators. The Aquatic Food System Data Scientist is a two-year grant-funded position with the possibility of extension dependent on funding availability. The desired start date is January 2024.

For full details and application, click here.

“Someday I’ll fly away”: monitoring hatchling to fledgling timescales on Protection Island

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Liam Pendleton

Nesting season on Protection Island is a busy time for SAFS Masters student, Liam Pendleton. Home to tens of thousands of pigeon guillemots and rhinoceros auklets, Liam travels to Protection Island in the Strait of Juan de Fuca every week from May to September to conduct research and monitoring of these seabirds.

Working in the Quantitative Conservation Lab, led by Sarah Converse, Liam is studying the link between breeding success, and marine environmental conditions. Existing as a natural wildlife refuge for 40 years, Protection Island offers an untouched habitat for researchers to explore questions to do with seabirds, with the island being closed off to the public.

Researchers measure the bill length of a pigeon guillemot.

The pigeon guillemot is a seabird which forages solely in nearshore marine habitats, diving into the sea to feed on small fish and marine invertebrates. Their breeding sites are on steep bluffs or cliffs where they can burrow, or on beaches where driftwood provides cover for their nests. Building on a dataset which has been running since 1996, Liam is part of a project which lays nest boxes along the beach on Protection Island, and these are then used by pigeon guillemots to hatch their chicks.

A nest box used by pigeon guillemots on Protection Island.

Starting in May 2023, just before the breeding season began, Liam placed 45 nest boxes at different sites around the island and began his monitoring. Visiting weekly, he records what is happening in the nests – are they occupied? Have eggs been laid and how many? The truly exciting part comes when chicks are born. Liam measures their wing length, beak length and weight on each visit, and this growth is recorded throughout their early life until they become fledglings and leave the nest.

A pigeon guillemot egg nestled inside a nest box.

One of the big questions during Liam’s work is how to assess whether a nest is a success or a failure? Some methods have focused on an index of body condition, i.e., weight and wing length, but Liam is also looking at length of time a chick spends in the nest box. How many days does it take for each nest from hatching to fledging? The number can range from as early as 29 days up to 54 days. This time span is dependent on factors such as the quality of food and the amount of feeding provided by the parents.

Researchers measure the wing chord of a pigeon guillemot.

He’s also relating oceanographic trends with nesting success. How do regional marine conditions such as sea surface temperature and indices of upwelling influence this success? And looking more broadly, how do factors such as the Pacific Decadal Oscillation, El Nino or oceanic productivity play a role? Seabird population dynamics are tightly linked with conditions in the habitats they forage in, and marine environmental conditions directly influence the quantity and quality of the resources they need to survive and reproduce. Understanding the role these factors play in determining nesting success is key to understanding long-term seabird population dynamics on Protection Island.

Liam Pendleton on Protection Island. The island is a National Wildlife Refuge and is closed to the public.

This is just one part of Liam’s work. Check back in soon to hear about his GPS tagging and monitoring of one of the largest populations of rhinoceros auklet in the world, located on Protection Island.

Apply to be a postdoctoral scholar to conduct coastal drone research at SAFS

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Dr. Corey Garza’s lab at the University of Washington (the Marine Landscape Ecology Lab), seeks to hire a Postdoctoral Scholar in the School of Aquatic and Fishery Sciences (SAFS). The position is supported by internal funding from the School of Aquatic and Fishery Sciences. The candidate hired into this position will have the opportunity to engage in research that utilizes aerial drones to map coastal habitats ranging from the rocky intertidal to kelp forests and statistical modeling to understand the drivers of spatial variation in coastal habitats.

The Marine Landscape Ecology Lab is dedicated to advancing the use of autonomous technologies and spatial analysis to understand the environmental drivers that shape the composition of coastal habitats across multiple scales of organization. Training the next generation of scientists is also a critical focus area of the lab. In particular, reaching out to and providing opportunities to groups that have historically been underrepresented in the sciences is a central activity of the lab. The Marine Landscape Ecology Lab is committed to these goals and supports active participation in broadening participation activities by all members of the lab.

Click for more details about the position and how to apply

Ecosystem modeling of the Gulf of Alaska for fisheries management

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In a post-doc focused on modeling climate change effects in the Gulf of Alaska (GOA), Alberto Rovellini is part of the Punt Lab at SAFS. Beginning in 2020, Alberto’s work is on this area of Alaska which is facing big implications as a result of climate change, from negative economic implications for important fisheries to adverse ecological impacts on plankton, fish, mammals, and seabirds. It’s also one of the most productive marine ecosystems in the North Pacific, and this productivity supports high species diversity and valuable fisheries managed under state and federal jurisdictions.

Alberto Rovellini works on the Gulf of Alaska Climate Integrated Modelling Project (GOA-CLIM) using the Atlantis framework.

The GOA ecosystem supports valuable and diverse marine fisheries, annually producing $1.3-2.1 billion dollars first wholesale value as well as supporting valuable recreational and subsistence fisheries. The majority of Alaska’s population resides in the GOA region, many living in isolated fishing-dependent communities.

The Punt Lab is focused on modeling and management. How can models of climate, ecosystems and fisheries help managers make decisions in these areas? Climate projections in the Gulf of Alaska point to continued future warming, and a high probability of repeated events such as ‘the blob’ in 2013-2017, a heatwave that dealt a huge blow to fisheries, with some not fully recovering for years.

Climate projections suggest events such as these will happen more frequently as temperatures continue to rise, and so Alberto’s work is to figure out what this entails for fisheries management in terms of adapting management frameworks, anticipate changes that are coming, and how this will translate for the communities that rely on commercial fisheries.

Topography and bathymetry of the Gulf of Alaska region included in the Atlantis GOA model domain.

Extensive modeling research has already been conducted in Alaska, but a lot of focus has been on the Bering Sea region. Never before has this particular research using the Atlantis modeling framework been used in Alaska, or specifically for the Gulf of Alaska. This is where the Gulf of Alaska Climate Integrated Modeling Project (GOA-CLIM) comes in.

Alberto has been working on this project with partners, including NOAA Alaska Fisheries Science Center, to develop an ecosystem model for the Gulf of Alaska, and to use the model as a simulation tool aiming to capture all components of the ecosystem, from the physical properties to the food web and the fisheries, in a dynamic way. He describes the beauty of the model as one that allows them to explore how climate events can propagate through the ecosystem and affect the species that inhabit it, their interactions, and their availability to commercial fisheries. Being able to model various scenarios with different temperatures and a focus on different species, can generate information on climate impacts on different ecosystem components, and how these translate to impacts on human uses.

Spatial domain of the Atlantis GOA model (top), and a visual representation of the coupling of the physical, biological, and socioeconomic submodels.

So where is the data-driven model at right now? Work to this point has focused on building the model and conducting technical validation. The team have used the model to run a theoretical scenario where the Gulf continues to heat up. In this scenario, food becomes limited from primary producers, i.e., those at the bottom of the food web, which would have important effects on fish species, including the commercial groundfish.

The next step is to apply the model to simulate real-world past and future climate scenarios. From simulating climate change and warmer water, and how fish species respond and how populations can adapt, this is part of the exciting work that brought Alberto to the Punt Lab and to research on the Gulf of Alaska.

Near or far: how is fish abundance affected by shoreline armoring?

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Emily Bishop holds a herring

Conducting fieldwork as part of a project funded by Washington Sea Grant, Emily Bishop, a masters student in the Marine Conservation and Ecology Group at SAFS, is exploring the effects of shoreline armoring on nearshore fish abundance.

Shoreline armoring is the term for structures that landowners install on their beaches to prevent erosion and preserve property extent. These structures change the physical characteristics of the beach, potentially making the habitat lower quality for fish that use shallow water to avoid predators, or to feed on terrestrial insects.

A chinook salmon is measured during fieldwork.

With lead researchers including scientists from NOAA Northwest Fisheries Science Center and SAFS affiliate professor, Tessa Francis from the Puget Sound Institute at UW Tacoma, the team wanted to find out whether fish were avoiding these potentially low-quality areas in nearshore waters around Puget Sound adjacent to armored shorelines.

This project involved four years of field sampling, and Emily has been a part of the project for the last two years. The research team used a lampara net (a modified beach seine) to catch fish at different depths offshore from armored, restored, and reference shoreline segments at 12 different sites around the Southern Salish Sea. The sites ranged from Olympia to the San Juan Islands, and they went out once a month to net fish and count and measure them.

The team cast a net during field sampling in Puget Sound.

Emily is using the data collected to relate abundance of fish to extent of shoreline armoring at different spatial scales to see if she can find which scale matters most to fish. Would a small-scale restoration project benefit nearshore fish, or is the removal of greater amounts of armoring throughout a region needed to see a positive effect? That’s the question they’re hoping to answer!

A sculpin caught during fieldwork is measured by the team.

 

Mutation rate and mentorship: undergrad summer research with dolphins

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Spending the summer working on a mutation rate project with SAFS Professor Amy Van Cise, Sophie Garrote is using bioinformatics to delve into different dolphin species.

Part of a mentorship program through UW LSAMP which focuses on enhancing minority participation in STEM, Sophie has been picking up valuable skills such as programming, knowledge of cetacean species, and getting hands-on experience with research.

She started working with her mentor Amy Van Cise, head of the Whale and Dolphin Ecology Lab at SAFS, when the application matched them based on research interests. Kicking off the summer with an in-depth introduction to dolphin species and their ecology, Sophie is now using Linux and R programming to understand how genomic mutation rates differ among species. Through her internship she has also learned to work with Hyak, UW’s high-performance computing cluster, which she’s been using for the intensive computational power that it takes to align and analyze whole genome sequence data.

Sophie has been working on both Linux/bash and in R to process the data.

Mutation rate is an important number in evolutionary biology. It’s used in many ways such as to construct ancestries of different animals, trace back where they came from, and calculate ancestral population sizes. These estimates all play a vital role in the conservation of these species, and getting them right depends on having a precise understanding of the fundamental rate at which genomes mutate in each species.

For marine mammal populations, a lot remains unknown about their life history and interactions as it is difficult to study them in the wild, so mutation rate is a helpful piece of information even for those species not considered endangered. Sophie shares that it’s interesting work because it offers the opportunity to learn much more about marine mammals, as well as potentially assisting in conservation efforts.

Using programming for the first time, Sophie has been working with genomic datasets for species that already have this data available, i.e., the genome has been sequenced by another lab and shared publicly in our national genomic archive, NCBI GenBank.

With the project due to finish up at the end of summer, Sophie will present her work during a poster session at the Summer Undergraduate Research Symposium, building more critical skills for her future academic journey and career.

The LSAMP program plays a key role for minority participation in STEM by focusing on building resources, networks and experience for underrepresented students who don’t have research experience and want to get involved in this type of work with professors. Sophie shared that it’s valuable in helping students to build confidence and knowledge in a variety of ways from reaching out to professors for potential research experiences, writing cover letters and CVs, and connecting students with valuable resources throughout their studies.

About to begin her second year at UW as an Environmental Science and Resource Management Major, Sophie’s tips for others wanting to get involved in research is to always use the resources available to you as a student, and don’t be afraid to reach out to new connections to pursue research opportunities.

Birds, beaches and boat rides: conducting research in Tetiaroa

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Almost 5,000 miles away from the University of Washington lies Tetiaroa, an atoll in French Polynesia surrounded by a ring of coral reefs.

Researchers from UW and University of French Polynesia heading into a seabird colony to start sampling.

A team of UW scientists have visted Tetiaroa each year since 2018 to study seabird populations, which play a vital role in marine environments and the islands that lie within them. A variety of factors negatively impact Tetiaroa’s seabird population, including invasive species and climate change.

Brown Booby checking out UW researchers in Tetiaroa.

Some of the seabird species that call Tetiaroa home are Red-footed and Brown Booby, Great Crested Tern, and Brown Noddy. Using a variety of tools such as acoustic monitoring, nest monitoring, banding, and point counts, the team comprised of SAFS and SEFS scientists – led by Beth Gardner and Sarah Converse – are at the forefront of efforts to support a sustainable future for Tetiaroa’s seabird population.

UW researchers banding and taking morphometric measurements of Brown Boobies. (L to R -Chapin Czarnecki, Beth Gardner, Eve Hallock, and Lisanne Petracca)

The team will return to Tetiaroa later this year to conduct more research so stay tuned for updates from across the ocean!

Read about the team’s work on their 2021 trip

Red-footed booby chick sitting in its nest.

Marine heat waves caused mass seabird die-offs, beach surveys show

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New research led by the University of Washington uses data collected by coastal residents along beaches from central California to Alaska to understand how seabirds have fared in recent decades. The paper, published July 6 in the journal Marine Ecology Progress Series, shows that persistent marine heat waves lead to massive seabird die-offs months later.

Shoreline restoration: community science to monitor effectiveness

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Jason Toft from the UW Wetland Ecosystem Team has been monitoring shoreline armor restoration in Puget Sound for over a decade at sites where artificial armor on beaches has been removed to facilitate the restoration of intertidal areas.

Jason Toft surveying for beach wrack.

Shoreline armor, also known as seawalls and bulkheads, occurs on over 25% of Puget Sound’s shorelines and was historically installed along homes and infrastructure to address erosion risk. We now know that in many cases armor does not prevent erosion and actually disrupts natural processes that replenish sand and gravel to beaches that provide habitat for fish and wildlife. As more and more sites are being restored, efforts to understand the effectiveness of restoration techniques are critical to developing future best practices and design for armor alternatives.

Partnering with community science groups, Washington Sea Grant, Washington Department of Fish and Wildlife, Vashon Nature Center, Northwest Straits Foundation, Friday Harbor Laboratories, and Sound Data, the collaborative project begun with developing publicly accessible, standardized protocols to allow for widespread shoreline monitoring and training. The team was funded by EPA Puget Sound Geographic Program Funds through the Washington Department of Fish and Wildlife and Department of Natural Resources Habitat Strategic Initiative Lead.

Jason Toft
UW research scientists Julia Kobelt and Kerry Accola survey for logs at the Bowman Bay restored site.

Now existing as the Shoreline Monitoring Database, this tool allows monitoring data to be uploaded and downloaded, and then analyzed. This analysis is the basis for a new publication in Frontiers, with the goal of assessing restoration effectiveness. Restoration projects in Puget Sound usually have the overarching aim of restoring habitat for juvenile salmon and other wildlife.

The paper also brings in other components useful for shoreline managers to be aware of when involved with restoration projects such as the impact of shore type, and wind and wave exposure.

Jason Toft
UW research scientist Julia Kobelt surveying beach wrack at the Lowman Beach Park restored site.

So, what’s the outcome? Often, the sites monitored have proved to have been effectively restored when compared with natural sites that did not have artificial armor installed. There are factors that cause variability in restoration, such as bluffs against a beach or a shallow beach present all the way, and length of time – for example, some sites have only been undergoing restoration for a year, others for many years.

As new funding through the Habitat Strategic Initiative Lead becomes available and the project expands, the collaborative team will add additional years, locations, and types of monitoring at fish and wildlife habitat sites to the existing database. This will ensure improved implementation of future habitat protection and restoration, and address knowledge gaps.

Phoenix Moore
Vashon Nature Center high school marine science intern Phoenix Moore takes a selfie before starting his snorkel survey to measure fish use of the Dockton Park beach restoration site on Vashon Island.

Excitingly, additional funding will also mean a SAFS graduate student will be included in the team starting in Autumn 2024.

Bringing the theme of community science to life, the Vashon Nature Center has been conducting beach surveys on Vashon Island this summer with a group of high school marine science interns and community volunteers. High School internships are supported by a King County Stewardship, Engagement and Learning grant.

Caroline Barnes
Vashon Nature Center volunteer and UW student Gibson Silagi suits up for a snorkel survey at Piner Point restoration site on Vashon Island as part of a mixed team of community volunteers and highschool marine science interns. On this particular night a pod of Biggs orca whales swam by just as the survey finished!

Read the paper ‘Coastal Landforms and Fetch influence Shoreline Restoration Effectiveness’ in the Frontiers journal