A 3D view of ocean conservation and fishing activities

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In recent years, there has been a global push to expand marine conservation efforts, but the quality of the implemented conservation network has often been neglected in favor of quantity. In a new paper published in Nature Communications, Juliette Jacquemont tackles one of the limitations of marine spatial planning by conducting the first global assessment of the 3D distribution of fishing activities and conservation coverage. As with many other marine features, such as species distribution, this information has until now only been assessed in two-dimensions, overlooking the vertical dimension inherent to the ocean, which reaches an average depth of 3,800 m. This simplistic representation of the ocean has remained unchallenged in part because until recently, most human activities and impacts were limited to coastal and shallow areas where the vertical dimension is more limited.

Juliette Jacquemont
Juliette entering the submersible Curasub in Curaçao in the Caribbean to survey deep-reef ecosystems down to 300 m.

This representation shift is particularly important given the current context of marine conservation. With the ratification of the United Nations (UN) Convention on Biological Diversity (CBD)’s Kunming-Montreal Global Biodiversity Framework (GBF), a commitment to protect 30% of Earth’s oceans, coastal areas and inland waters by 2030, and the ‘High Seas’ treaty, which now provides legal instruments to implement marine protected areas in the High Seas, an increasing amount of protection coverage will be targeting deep, vertically complex areas. The High Seas are areas beyond national boundaries, covering two thirds of the planet’s oceans, and where much of the deepest zones of the ocean are found. These advances in marine conservation are paralleled with increasing human activities targeting deep marine ecosystems, with fisheries pursuing deeper stocks as shallow ones deplete, and prospects for deep-sea mining multiply.

Hoping to better inform the next wave of conservation, Juliette’s PhD work at SAFS aims to augment existing 2D spatial planning tools of the ocean by adding a third dimension: depth. How are ecosystems at different depths captured by global conservation efforts, and how does this contrast with the depth distribution of fishing activities? These were a couple of the questions driving Juliette’s work with her co-authors, including her advisor, SAFS Professor Luke Tornabene.

Using a global fisheries dataset (the Global Fishing Watch), which captures 60% of all large-scale, industrial fishing effort in the world, Juliette overlaid spatial information on fishing activities, gear types, and ocean bathymetry maps (which provide the depth of ocean floors). This allowed her to identify the depth at which fisheries are occurring, in comparison to the depth covered by marine protected areas, which she obtained using the World Database on Protected Areas.

What she discovered was an uneven distribution of conservation coverage across depths, with the shallowest ecosystems, down to 30 m, receiving the most protection. In contrast, mesophotic (60-300 m) and abyssal (3500-6000 m) depths were woefully behind global conservation targets, a result of being “out of sight, out of mind”, but also because of the lack of legal instruments to implement conservation beyond national jurisdictions. Furthermore, Juliette found that a surprising large proportion (over a third) of fishing activities occurred in deep-sea (deeper than 300 m) areas. Additionally, an important part of epipelagic and mesopelagic fishing occurs in areas overlying abyssal depths, which might be impacting the fragile abyssal benthic communities which depend on pelagic biomass.

Figure from Jacquemont et al., 2024.
Different fishing gears target different depth ranges, but the information available on the specific depth range targeted across fisheries and oceanic regions remain very scarce. This data gap represents a barrier to sustainable ocean management.

Another concerning result from Juliette’s work is that many of the areas that have received the most conservation effort correspond to areas where the least fishing occurs, a phenomenon called “residual conservation”. Residual conservation is often motivated by ease of implementation, as no interference with human activities arises from the newly implemented conservation unit. However, the ecological additionality of these conservation actions is limited, as these areas were already protected ‘de facto’. This common mechanism has led to the incidental representation of some deep marine ecosystems at the limits of territorial waters, which are usually under less human uses than shallow, coastal ones. Unfortunately, the associated levels of protection of these areas are often weak, providing little protection from potential future uses.

While the remoteness of deep ocean ecosystems has also resulted in them not being very well-described by science, the development of new surveying tools, for example rebreather diving and remotely operated vehicles, is unveiling a staggering amount of diversity, often extremely sensitive to extractive activities because of slow growth and low productivity. As such, deep ecosystems appear as priority areas to actively conserve and avoid irreversible impacts from “boom and bust” fisheries and multiplying mining prospects.

Franck Gazzola / Under The Pole
Biodiversity thrives on deep reefs, documented here by technical divers in French Polynesia between 100 and 150 m depth. Unfortunately, these reefs remain largely unprotected.

Many things aligned at the same time as Juliette began her research in this area. She always had an interest in global conservation targets and in weaknesses limiting the efficiency of the global conservation network. Being a member of the Fish Systematics and Biodiversity Lab at SAFS, which has a focus on deeper ecosystems, solidified the idea of looking at representation across the depth dimension. With the High Seas treaty and the updated Global Biodiversity Framework being ratified while working on her paper, it makes her findings even more relevant as nations will have to expand their conservation network to cover 30% of their territorial waters, requiring the inclusion of deep-sea areas.

This study revealed important knowledge and management gaps that Juliette intends to investigate in future research. In particular, the lack of information on the depths targeted by fishing gear types and targeted species, and the absence of discrimination between pelagic and benthic activities in the Global Fishing Watch dataset, constitute major limitations in understanding the 3D footprint of fisheries and the 3D space they impact. In parallel, developing follow-up studies at the regional scale would better account for small-scale fisheries (commonly under-represented in global datasets), local fishing practices, specificities of area-based management plans, and of ecosystem distribution. This, in turn, would provide actionable recommendations at the regional scale for policy- and decision-makers to account for the vertical stratification of marine life and human uses, as well as the multiple connectivity processes through which impacts might trickle between pelagic and benthic systems. While working on this area of study, Juliette is also participating in research efforts to better describe understudied and under-protected marine ecosystems, such as mesophotic reefs.

Read the paper: 3D ocean assessments reveal that fisheries reach deep but marine protection remains shallow

Are wild salmon following hatchery salmon? Testing the Pied Piper hypothesis

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Maria Kuruvilla

Ever heard of the Pied Piper? What about in the context of fisheries research? Taking the concept embodied by the Pied Piper story of strong but delusive enticement, Maria Kuruvilla applied it to hatchery fish and wild salmon in three Washington State rivers during their migratory journey downriver. Maria conducted her research as a PhD student in Professor Andrew Berdahl’s lab at SAFS.

Each year, salmon species in the Skagit, Dungeness, and Puyallup Rivers begin their migration downriver, spawning in the upper reaches of the river, then making their way to the marine environment of the Puget Sound. In these same rivers, hatcheries managed by State and Tribal governments exist to supplement salmon as part of conservation efforts, especially in the face of declining populations.

Maria’s Pied Piper hypothesis is based on the idea that hatchery fish – which are released in large numbers each year and migrate downriver immediately – are playing the role of the Piper. The children? The wild salmon encouraged to follow. This could be a problematic scenario if wild fish migrate at a time that they wouldn’t normally and enter the marine environment at sub-optimal conditions. Such conditions include the size and weight of fish, or oceanographic conditions not as favorable to juveniles.

Maria Kuruvilla
A wild (top) and a hatchery (bottom) yearling Coho salmon caught in the Dungeness River trap.

Testing this hypothesis in the three rivers with two species of salmon – coho and Chinook – Maria found results consistent with the hypothesis in four out of the six populations tested. So how do you tell the difference between wild salmon and hatchery salmon? “Hatchery salmon are usually bigger, plus they have a tag or a clip on the fin that allows tracking and distinguishes them from wild salmon,” Maria shared.

The typical migration period for wild juvenile Chinook salmon is from March to July and the typical migration period for wild juvenile coho salmon is from April to June in Washington’s Skagit, Dungeness, and Puyallup Rivers.

Using smolt traps located near the mouth of the rivers, fish present in these traps are usually at the final stages of their downriver migration, and so it’s a good location to collect data on which fish are present: hatchery, wild, or both. Using this data, provided by the Washington Department of Fish and Wildlife and the Puyallup Tribe of Indians, Maria plotted the migrations of hatchery and wild salmon, then did a deeper dive on the data to figure out if hatchery salmon are influencing wild salmon migration.

When released, hatchery salmon usually complete their migration downriver and enter the marine environment within one to two days. Wild salmon, however, are typically on a more protracted migration timeline. By collecting data on environmental stimuli, such as water temperature and flow, which is also known to affect wild salmon migration, Maria can rule this out as a possibility in the influence data.

“Looking at the whole peak and duration of migration, my data shows that as the number of hatchery salmon increases in a river, the duration of wild salmon migration decreases. This is consistent with the Pied Piper hypothesis and suggests that wild salmon are being influenced by the migrating hatchery salmon”, Maria said. “Generally, a population all migrating over the space of a day or two is not beneficial, as ocean conditions may be unfavorable or there could be a lot of hungry seals waiting, things like that.” There is also an important possibility to consider in Maria’s work, which she shared: “There might also be advantages of hatchery salmon influence on wild salmon migration. Moving with a big group of hatchery salmon could provide an increased level of protection from predation when entering marine environments.”

Hatcheries have a lot of control on how and when they release fish into rivers, and this is where Maria hopes her research will be particularly useful. “Managers of hatcheries can take the results of my paper and edit their release timing if needed, to more closely align with wild salmon migration patterns, or even marine conditions when it’s most favorable for fish to transition from freshwater to marine environments,” Maria said.

Maria Kuruvilla
The rotary screw trap on the Dungeness River. The trap consists of big cone that, when lowered into the water, collects some salmon as they swim downstream, which are then passed into a tank.

There were two salmon populations part of Maria’s study that didn’t correspond to the Pied Piper hypothesis, which Maria explained could be a result of hatchery release decisions. “The theory is that the Skagit River hatchery released their Chinook salmon quite late in the migration season, and a lot of wild Chinook had already left the river, or this particular part of the river, by that point in time.” For the Dungeness River coho, the wild salmon are usually in the headwaters, whereas the release of hatchery salmon is more downstream. “And so, it’s possible that the wild coho are not being influenced as much in this situation,” Maria shared.

This study not only looks at how hatchery salmon affect the migration timing of wild salmon, but also supports the idea that salmon rely on social cues to decide when to migrate. Just like in other animal populations, social behavior can influence these timing decisions and it’s becoming more recognized that considering social behavior is important for understanding migration timing. If salmon and other species use social information to make better decisions during critical events like migration, a decrease in population size could impair their decision-making. This, in turn, could lead to further population declines.

Recently defending her PhD at SAFS, Maria is now a post-doctoral fellow at the University of Victoria. The manuscript is currently under peer review by the Movement Ecology Journal; however, the preprint is available for reading below.

Social influences complement environmental cues to stimulate migrating juvenile salmon | bioRxiv

Canines for conservation: Southern Resident killer whale research

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Alongside two student researchers from her lab, SAFS Assistant Professor Amy Van Cise has been out on the Puget Sound for a few days conducting killer whale research. Working with a team comprised of UW students, Wild Orca, and San Diego Zoo Wildlife Alliance, they’re assisted in locating fecal samples from the whales by Wild Orca’s poop-sniffing dog, Eba.

Eba, the poop-sniffing Wild Orca dog.

Amy Van Cise, with student researchers Sofia Kaiaua and Mollie Ball, were aboard the Wild Orca boat with Research Director Dr. Deborah Giles, who is also a Resident Scientist at Friday Harbor Laboratories, where she teaches Marine Mammals of the Salish Sea in the Spring. Recent UW Marine Biology and Oceanography graduate, Aisha Rashid, was also present, now working for Wild Orca. They were joined by Hendrik Nollens from the San Diego Zoo Wildlife Alliance, and Eba’s handler, Jim Rappold.

NOAA research permit #26288 (Wild Orca)
The research team is collecting fecal samples from Southern Resident killer whales.

To collect samples, Wild Orca drives slowly about 500-1000m downwind of the killer whales (preferably behind them), waiting for Eba to catch a scent. Once she does, one of her trainers (either Giles or Jim Rappold) works with Eba to have her direct the boat to the sample location, where the team then scoops it out of the water and carefully spins it down, pours off the excess sea water, and stores it in a conical tube on ice until they can get it in a freezer.

Hendrik Nollens (San Diego Zoo Wildlife Alliance) holds one of the samples collected during the trip.

From a single sample, the collaborative research team can get hormones (to tell things like pregnancy, stress, or nutritional stress), genetics (to ID the whale, determine diet composition, and/or look a gut microbiome and parasites), and also look at toxins/contaminants.

NOAA Research Permit #26288 (Wild Orca)
A single fecal sample can reveal a wealth of information about a killer whale.

The trip has also been used to collect content to develop an outreach video based on the diet research underway at the WADE lab and how it fits into the broader conservation goals for Southern Resident killer whales. For the video, Mollie and Sofia interviewed Dr. Michael Weiss, who is the Research Director of the Center for Whale Research, and Jay Julius, the former Chairman of the Lummi Nation, full time fisherman and father, and the Founder and President of Se’Si’Le.

All photos of killer whales are taken under NOAA research permit #26288 to Wild Orca

Examining the gap between ecological science and environmental management

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Working for more than 15 years in Alaska’s Bristol Bay region, Sarah O’Neal is part of the SAFS PhD program. Recently publishing a new paper in BioScience examining the gap between ecological science and environmental management, Sarah’s article focuses on indirect ecological effects and how these are often defined differently in regulatory decisions. Indirect ecological effects are those in which the interactions of two species are modified by another species or abiotic factor (for example, valuable metals like copper, physical habitat alteration, and other factors).

Sarah O'Neal
Sarah measuring fish in the field.

Part of a larger effort involving her PhD research, advised by SAFS Professor Daniel Schindler, Sarah led a team that reviewed more than 20 National Environmental Policy Act (NEPA) documents for proposed mining projects across the US, to compare the treatment of indirect effects in regulatory versus ecological literature.

What she found was a clear dichotomy between regulatory and academic definitions of indirect effects, which in turn has far-reaching consequences when being used to make environmental management decisions. Where does this disconnect come from? “In part, some of this comes down to the terminology used in science, by scientists,” Sarah shared. “Especially when evaluating indirect ecological effects – which are by nature a bit harder to define and assess than direct ecological effects – the terminology used can be confusing. The ecological literature often uses overly complicated and redundant language, and is limited in its utility by regulators as a result.”

Sarah O'Neal
In Alaska, Sarah works with a fellow researcher on data collection.

In some of her other PhD work, Sarah is using GIS and statistical tools to consider spatial correlation within stream networks, as opposed to the more common method of Euclidean (straight) line-to-line distance. Doing this in concert with environmental DNA (eDNA), Sarah collected data from a small watershed in Bristol Bay, only accessible via helicopter. These eDNA methods were particularly useful for covering more ground in this remote part of the world with difficult access. “What’s cool about this research is that it’s one of very few watersheds in the area that doesn’t support a ton of salmon,” Sarah shared. “The assumption was that it didn’t support any salmon at all, but we found evidence to the contrary. Now we can plug this into the spatial stream network and predict salmon distribution throughout that watershed.”

Why is work like this important? Because it ties directly into the work behind NEPA documents when considering proposed mining and other development projects. “The importance of headwater streams to fish as well as their contributions to downstream habitat are often overlooked, so developers often assume alteration of headwater habitats will have minimal effects to aquatic life. Our work shows that this isn’t the case,” Sarah added.

Copper is one of the most toxic elements to aquatic life, even at levels far below regulatory criteria. It impacts the ability of salmon to find their way home, find food, detect predators, find mates, and even find other family members. “The known impacts of copper on fish behavior—even at concentrations well below legal limits—is a clear example of indirect effects being overlooked in a regulatory context,” Sarah shared. Improving this situation, according to Sarah, would require regulators and scientists to work together to come to an ecologically relevant and legally applicable definition of indirect effects to ensure they are considered in environmental assessments. To bolster the ability to regulate indirect effects of development, ecosystem-wide experiments before, during, and after the development of a project are critical. In regard to more comprehensively incorporating indirect effects into regulation, Sarah added, “We have a job to do as scientists to simplify our language and make it more understandable. We showed that in a quantitative way in this new paper.”

Sarah O'Neal
Sarah’s new paper examines the gap between ecological science and environmental management.

Another area of Sarah’s work, funded by the US Environmental Protection Agency (EPA) and others, is to evaluate sculpin, a bottom-dwelling small fish, as a bio-indicator species of contamination. “Sculpin are a good fit for this because they don’t have swim bladders and therefore generally don’t move very far over their lifetime. They’re easy to catch, sensitive to many contaminants, and ubiquitous,” Sarah shared. “Right now, we’re comparing the utility of sculpin relative to other species in the watersheds we’re studying in relation to the effects of copper.”

Over the course of her research, Sarah has worked with numerous partners including Trout Unlimited, the University of Alaska Anchorage, EPA, Bristol Bay Native Corporation, the National Park Service, the Center for Science in Public Participation, United Tribes of Bristol Bay, the Bristol Bay Native Association, the Nature Conservancy, Nondalton Tribal Council, and the Gordon and Betty Moore Foundation.

Sarah O'Neal
Much of Sarah’s work was conducted in very remote areas, only accessible via helicopter.

SAFS hosts 20th working meeting of the Polar Bear Specialist Group, co-chaired by Kristin Laidre

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A meeting of the IUCN/SSC Polar Bear Specialist Group (PBSG) was held at SAFS on 10-14 June 2024, co-chaired by Professor Kristin Laidre, together with Nick Lunn from Canada. Some of the key outcomes of the 20th working meeting of this group were:

  • Recognition of a new subpopulation of polar bears – the Southeast Greenland subpopulation – which has been recently identified as the most isolated and genetically distinct in the world.
  • Updating of the status of four other subpopulations based on new information. The listing of polar bears as Vulnerable under the IUCN Red List will be reviewed in 2025.
  • Discussion about the new harvest management system in Nunavut, Canada, which affects two-thirds of the global population of polar bears, and is a potentially unsustainable management practice.
  • Discussion of the impact of loss of sea ice on polar bears, which is their primary threat, and the scientific need for polar bear location data, only attainable by capture and deployment of tracking devices, to support conservation efforts.

You can read the full press release from the working meeting of the IUCN/SSC Polar Bear Specialist Group, published on June 18, 2024, on their website.

Kristin Laidre
The loss of sea ice is the primary threat to polar bears.

Best practices in marine mammal research: developing a toolkit for sample collection and preservation

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Over the last two decades, there has been huge growth in the availability of different ‘omics methods used to study marine mammals. From elusive beaked whales and near extinct vaquitas to more common dolphins and sea lions, understanding the ecology, evolution, and health of marine mammal populations around the globe is critical for conservation efforts. A new paper published in Marine Mammal Science, involving 19 scientists from around the globe, has laid out best practices for collecting and preserving marine mammal biological samples in the ‘omics era.

The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. 

Marine mammal scientists are working on different species, in different locations, and asking different questions, using tissue samples collected from wild marine mammals. Those tissue samples give scientists access to vast amounts of information, allowing them to answer questions ranging from a population’s recent foraging habits, health status, or contaminant load to its deeper evolutionary history or its resilience in the face of climate change. They provide scientists, and us, a window into the secret lives of these elusive animals and hints about how we can be better stewards of their ecosystems, but they come at a price – literally.

A group of people on a small boat watch orcas in the water, with four dorsal fins visible in front and to the left of the boat. Seagulls can be seen flying and swooping close to the water.
NOAA (permit # 21348)
NOAA scientists collect data near a pod of Bigg’s killer whales.

Most marine mammals live far from shore, and spend the majority of their lives underwater. To collect tissue samples from these animals, large teams of scientists will venture out onto the ocean for months at a time. Many marine mammal species have huge home ranges, such as the 9,000 mile migration range of humpback whales; simply finding them is a monumental task. Adding to the challenge, collecting samples from marine mammals is inherently invasive and scientists work under strict permits to minimize both the number of times samples need to be taken, and the impact on the animal during collection.

Jeff holds a fecal sample from a killer whale in a clear tube with a blue lid, wearing blue globes and wearing an orange jacket with a lifejacket on top.
Arial Brewer (permit # 21348)
Jeff Hogan (Killer Whale Tales/NOAA) presents a freshly collected fecal sample from a Southern Resident killer whale.

Phillip Morin from NOAA Southwest Fisheries Science Center, who has been working in genetics for over 35 years, understands all too well the difficulty in getting quality samples for genomics. “A good illustration is the sample used for the vaquita reference genome, which is one of only two live-cell samples ever obtained from this species. The vaquita, a member of the porpoise family, is the most endangered marine mammal in the world,” he shared. “A conservation project in 2017 took two years of extensive planning with over 90 experts from nine countries, and 11 days at sea, to try to capture vaquita for captive management. As part of that project, we worked to get the appropriate samples collected, transported quickly to the cell culture lab across the international border, and cultured to preserve live cells for DNA and RNA extraction.”

Because of all of these challenges, each tissue sample could represent an investment of tens of thousands of dollars. Caring for those samples and preserving them in a way that will allow them to be used by many generations of future scientists, and with many generations of emerging techniques, is a priority that is always at the forefront of a marine mammal scientists’ mind. “For some populations or species, decades of sampling effort have resulted in only 10s of samples, highlighting how critical it is to figure out the best collection and preservation techniques,” says Amy Van Cise, Assistant Professor at the University of Washington School of Aquatic and Fishery Sciences (SAFS). 

A group of people on a boat on the water, with one at the front holding a long blue net reaching towards the water, while a seagull flies overhead.
NOAA (permit # 21348)
NOAA scientists collect a fecal sample from the water using a pole net.

What are some of the best practices for collecting and preserving marine mammal samples that research teams have gone through such effort to collect? This is the overarching question bringing together a team spanning 11 different institutions, including Van Cise, with the goal of creating a unifying set of guidelines that will ensure these samples can be shared among labs, analyzed with a variety of new and emerging technologies, and used for years to come. “What’s  impressive about this study is that it brings together scientists examining different types of questions,” shared Amy Apprill from Woods Hole Oceanographic Institution (WHOI). Apprill’s particular focus is on microbiome analysis, which sheds insight into the health of marine mammals as a result of changing oceans and human impact.

Microbiome analysis is a great example of an emerging technology that’s revolutionizing how we study marine mammal health. Unlike humans, it’s difficult to assess the health of wild animals, and nearly impossible when those animals live in the ocean. “Wherever you are in the world, a doctor can sample and test your blood and those results are understandable and comparable around the globe,” Apprill said. Marine mammals don’t schedule regular doctor’s appointments, but emerging ‘omics technologies are making it possible to determine whether an individual is sick or healthy using tissue samples. Apprill is one of the scientists at the forefront of the effort to characterize the microbiomes of healthy and diseased individuals. “As we obtain  samples from different animal health states, we’re gaining valuable data that builds a type of health metric,” Apprill said. This type of work can only be successful if researchers can examine samples collected by many scientists around the world. Similar to the way hospitals have standardized the way they test for diseases and assess human health, Apprill said that, “as scientists in marine mammal research, we need a similar system of guidelines, best practices, and protocols to follow, so that our samples have the maximum use.”

The gold standard for sample preservation is collecting it quickly from the animal, either when alive or recently dead before the cells start degrading, and freezing it to -80°C  or colder immediately. However if this isn’t possible in the field, then what is the best alternative? The answer depends on the anticipated research needs, availability and transportability of preservatives, and time until samples reach a permanent storage site. While there is no single solution for all situations, some methods provide broader preservation characteristics, allow international transport, and/or greater stability prior to freezing. 

“In science, there are a thousand ways you could conduct each step,” Apprill shared. “But you don’t want to spend valuable time, effort, and resources figuring out those steps if someone else already has the best method and protocol laid out.”

Four killer whales are visible in the water in front a boat. One person stands at the front of the boat holding a large black pole, with two others visible sitting down behind.
Arial Brewer (permit # 21348)
NOAA scientists approach a pod of Southern Resident killer whales for data collection.

The ways we can use ‘omics techniques are rapidly expanding every year, adding another layer of importance to the need for high-quality, well-preserved samples. “Just like forensics held on to human samples from crime scenes while the world was waiting for DNA capabilities to expand, marine mammal science works the same way. As technological advancement expands really quickly, it’s imperative to preserve samples in a way that the wealth of information contained in them can be uncovered in the future,” Morin said.

The institutions involved in the best practices effort are: NOAA Northwest Fisheries Science Center, Stanford University, Woods Hole Oceanographic Institution, University of Washington, McGill University – Mila-Québec AI Institute, NOAA Southwest Fisheries Science Center, University of Exeter, and Mystic Aquarium.

A trip to DC for the NOAA Hollings Scholarship orientation

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Each year, hundreds of students apply for the competitive NOAA Ernest F. Hollings Undergraduate Scholarship. This scholarship recognizes outstanding students studying in NOAA mission fields, such as aquatic and marine science, with scholars receiving funds to support their studies, as well as paid summer internship opportunities at NOAA facilities across the US. We caught up with Michael Han, a SAFS undergrad, who along with three other students from the UW College of the Environment, was chosen as 2024 Hollings Scholars. Check out our Q&A with him to find out more about his orientation experience at NOAA’s headquarters near Washington DC in May.

What did orientation for NOAA Hollings Scholars involve?

Michael Han
A trip to DC for NOAA Hollings orientation

Orientation involved a three-day session at NOAA headquarters near Washington DC, with the Monday and Friday of that week spent traveling, with all these expenses covered as part of the scholarship award.

On Tuesday, all the scholars for this year gathered for the first time outside the NOAA auditorium. We had introductions from various members of the NOAA administration and senior leadership, where they talked about their hopes for us and gave general advice and motivation for succeeding in the Hollings program.

In the afternoon, presentations from the line offices (departments) began. These offices included NMFS (fisheries), NWS (weather), and NOS (ocean). Each line office had one or two representatives who explained the purpose of their work, several current projects currently being undertaken, and afterward a period for questions. After the official program concluded on Tuesday, there was a networking dinner session at a nearby theater which allowed us to meet, talk, and network with other scholars.

Wednesday started similarly, with presentations from NESDIS (satellites), and OMAO (aviation and NOAA corp). this was followed by a career internship fair, where all the presenters we had previously heard from, plus additional NOAA employees, were there at individual tables separated by office. This gave us the opportunity to ask them specific questions and career advice for succeeding in our chosen paths. At the fisheries table, I was able to ask about NOAA’s work with anadromous fishes and learn more about the pathway to becoming a fisheries biologist.

On Friday, tours were conducted to destinations that we had chosen earlier, including NESDIS, the National Aquarium, and wetlands kayaking.

What was a particular highlight for you in attending the orientation?

The tour I decided to take was the NMFS National Systematics Laboratory, and it was definitely the highlight of my trip. The Systematics Lab is located inside the Smithsonian’s Museum Support Center, a small grouping of buildings around half an hour from the Natural History Museum. The director, Dr. Collins, gave us a quick presentation on the importance of systematics and taxonomy before leading us through hallways, which were filled with working spaces and labs. Inside the labs there were many complicated machines that I don’t remember the names of, but the cryogenic freezers were probably the coolest. There were around 8-10 of these massive 10ft tall aluminum tanks filled with nitrogen, and inside these animal matter can be kept indefinitely allowing scientists in the future to work on the same samples as they are now.

We then walked through the collections, which included massive tortoises, crocodiles, antlers, horns, and even an entire giraffe that Teddy Roosevelt shot. The invertebrate and fish collections had also amassed huge numbers of specimens in jars. Looking at the rows and rows of preserved organisms, and then realizing it’s just a tiny proportion of all the creatures on the planet, makes you wonder what’s still out there undiscovered.

Top tip for other students applying for NOAA Hollings Scholarship?

Michael Han
Presentations during orientation

The best advice I could give is to participate in activities that align with NOAA’s mission of learning more about the ocean and atmosphere and to show that in your essays as well. This could mean explaining what your career goals are, how you’re currently working towards them, how Hollings can help you achieve them, and what you’d get out of your internship. I’d also say that a strong letter of recommendation is really important, so make sure to find someone who can write a good, knowledgeable letter.

Finally, I’d recommend checking out the Hollings Prep Program, which is an opportunity designed for freshmen to later become more competitive in Hollings, plus it’s a great chance to make professional connections. It also comes with a stipend and an internship at a NOAA location!

What are next steps for you in this journey as a NOAA Hollings Scholar?

On October 1, the internship database will open which lists all the possible projects an intern can apply for. It should come with a general project description and working location for each project. I’m able to apply for multiple projects, and each one has different requirements, but they may require interviews like applying for a job.

Once the mentor has settled on an intern and both are in agreement, a 3-day site visit will be arranged before next summer. This allows us to visit the location we’ll be working on, learn more about the project, and meet the people doing the science. All travel and housing costs are covered by NOAA. A 10-week internship will then be conducted over the summer of 2025, and at the end we’ll return to DC for a symposium to present our findings and learn about what other scholars have been working on!

UW College of the Environment 2024 NOAA Hollings Scholars: Michael Han (SAFS), Minda Chen (Environmental Engineering), Megan Cosand (Marine Biology), Hannah Tucker (Marine Biology)

Congratulations to the 2024 SAFS Faculty Merit Award winners

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We’re happy to announce this year’s Faculty Merit Award winners, given annually to graduating students at all ranks in recognition of exceptional achievement and contributions to the School of Aquatic and Fishery Sciences. This is by far the most prestigious of the many awards conferred by the School to students, where the nominations come directly from SAFS faculty.

Bachelor of Science

Kat Rogers

Working on their capstone project involving the systematics and taxonomy of a genus of damselfishes from the Caribbean, Kat Rogers also spends a lot of time working in the UW Fish Collection. From data entry and specimen organization to participating in outreach events with the Burke Museum, Kat Rogers has been described by their award nominator as a “one-of-a-kind student, an academic superstar, and an absolute gem to have around SAFS”. We look forward to hearing all about their experience as a Fisheries Observer with NOAA this summer.

Master’s Program

Nicole Doran

Defending her master’s thesis in March 2024, Nicole Doran’s work was a novel avenue for graduate research in SAFS. Described as a rising leader and a creative, independent researcher, Nicole is also active in the wider SAFS community, authoring an Indigenous Terminology Guide and organizing a community building event for grads and undergrads to discuss research opportunities and mentoring relationships. Active in both the DEIJ space and the IBIS program, we’re excited to have Nicole continue her academic journey at SAFS with the start of her PhD studies this summer.

Jezella Peraza

Recognized as a contributor to the field of marine renewable energy, and having presented her project results at international conferences, Jezella Peraza has a strong quantitative background that continues to develop through her master’s work at SAFS. Active in the SAFS community, Jezella has been a representative on the Equity and Inclusion Committee, lead initiatives to provide peer mentoring for undergrads and grads and is an active participant in the CESL and Environmental BIPOC Affinity groups. We recognize Jezella’s academic growth and her efforts to advocate for greater STEM access for underrepresented groups at SAFS.

PhD Program

Jeremy Axworthy

Described as an exceptional student and researcher, Jeremy Axworthy has presented his research on microplastics and corals at national and international conferences, including winning Best Presentation award at the SAFS graduate symposium. Beyond research, he actively works in community building and outreach initiatives, from collaborating with schoolteachers on K-12 curriculum activities to inspiring underserved high school students to pursue marine conservation.

Marta Gomez-Buckley

Returning to academia after raising her daughter and working as a high school teacher, Marta Gomez-Buckley earned her master’s from SAFS and is now conducting her PhD research on the diversity and evolution of cryptobenthic fishes. Through this work, Marta has contributed to the UW Fish Collection with thousands of specimens that will be foundational for systematic research in the future. A vital member of the SAFS community, Marta is active in FINS, the Grad Student Symposium, DEI Committee, outreach events at SAFS and the Burke Museum, plus mentoring undergrads and leading the PAC-ISLEs America Samoa Study Abroad program.

Marie Zahn

Highly collaborative and involved in many interagency projects during her time at SAFS, Marie Zahn’s work is focused on oceanography, climate change, and ecology in high-latitude polar regions. Writing four peer-reviewed manuscripts with colleagues during four years of graduate school, Marie has been described by her mentor as having intellectual curiosity, productivity, perseverance and research aptitude. As well as her academic pursuits, Marie actively supports women and minority group in STEM initiatives, including through her work with SEAS.

We congratulate these outstanding scholars and members of the SAFS community, and we look forward to supporting their future endeavors.

Small but mighty: studying cryptobenthic fishes on Tonga’s reefs

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Swimming around tropical coral reefs in a colorful array are an ever-changing multitude of fishes, some in schools of hundreds, others in pairs, and ones that prefer their own company. These are the fishes divers see on a heathy coral reef, but they are often only half of the diversity found in the reef’s fishes. The “hidden half” are the cryptobenthic fishes. So-called for their habit of camouflaging and hiding away in reefs and on the seafloor, cryptobenthic fishes, such as gobies, blennies, and cardinalfishes, are a fundamental part of thriving coral reef ecosystems around the globe. The gobies in this group are the focus of Marta Gómez-Buckley’s PhD research at SAFS.

A person wearing scuba diving gear is pictured underwater holding a clear jar with a white lid, close to the seabed, with corals visible in the background.
Ray Buckley
Cryptobenthic fishes collected from Afo Island, in Vava’u, Tonga. The number on the jar helps keep track of the specific sampling station where the specimens were collected.

“Cryptobenthic fishes are very small and are normally overlooked whenever surveys are done on coral reefs,” Marta shared. And most are so small that you could fit hundreds in your hands. “These fishes are often only as big as 2cm when adults, so they’re extremely tiny compared to most fishes, but they play a big role as a prey resource. In the first chapter of my dissertation, I investigated new techniques to collect such small specimens.” Marta is conducting her work in the Vava’u Archipelago, Kingdom of Tonga, a collection 41 islands in the more than 170 islands in the Tongan Group in Polynesia. Marta studied and collected cryptobenthic reef fishes in several areas around Vava’u which is the northern-most island group in Tonga.

Working with her advisor, Luke Tornabene in the Fish Systematics and Biodiversity Lab, Marta collects her samples – both fishes and water for environmental DNA (eDNA) – from the seafloor and coral heads when on her research trips. Marta has now visited Tonga four times, building on work she started in the region prior to joining SAFS. Re-entering academia after being a high school teacher for eight years, Marta completed her master’s at SAFS in 2000.

Part of the impetus for Marta’s work in Tonga is collecting specimens for the UW/Burke Museum’s Fish Collection, one of the largest collections of its kind in the world. “I saw so many fishes when diving in these coral reef areas. I have made now four trips to Tonga, and one to American Samoa. While on these trips, I was able to collect a lot of fish species never housed in the Fish Collection.” Home to more than 12 million preserved fish specimens from around the globe, the Fish Collection is a critical resource for some of the research of SAFS scientists, students and other researchers in the broader community in the fields of genetics, fish biology, taxonomy, and parasite ecology, to name a few. It is also a very popular destination for outreach education, with Fish Collection tours being hosted throughout the year for UW students and members of the wider community.

During the 2019 fieldwork in Tonga, which was partially supported by the Hall Conservation Genetics Research Fund from the College of the Environment, Marta collected samples underwater using two different techniques. “I wanted to see if I could detect the same number species (or maybe more) from water samples (eDNA) collected within the interstices of live coral or coral rubble and compare the results with the physically collected specimens in those same habitats.” The result was that physically collecting the fishes is by far the best method, as documented by Marta in a publication in Coral Reefs in 2023.  “One of the unexpected things I noticed is that even in and around a dead coral rock full of crevices, there is so much life hiding away, especially cryptobenthic fishes. From one of these ‘dead coral’ rocks the size of a football, I collected 100 ’cryptos’ of several different species!” Marta shared.

How many species comprise the populations of a specific cryptobenthic reef fish that is found around Tonga’s coral reefs and other Indo-Pacific locations? “This is the main question in Chapter 2 of my dissertation,” Marta shared. “We know in the specific genus I’m looking at – the Eviota – there are 132 described species so far. This is a highly diverse genus.” Marta looked specifically into the shortest-lived fish (and vertebrate), the Eviota sigillata, also known as the adorned dwarfgoby, which has a lifespan of 59 days. “They are reproducing fast and evolving rapidly because of this short lifespan. These fishes spend about half of their lives or more in the planktonic stage before recruiting back to their settling reef and starting to reproduce. To me, this is an incredible ‘life circus’ act!” Marta added.

After doing in depth morphological and genetic analyses of the specimens available at the Burke Museum from previous collections, specimens borrowed from other museums around the world, and her own collections in Tonga, the conclusion of her Chapter 2 is that there are at least seven undescribed species within the adorned dwarfgobies clade. The other approximately 20 clades within the genus have many species waiting to be formally confirmed using similar genome-wide techniques as Marta has pioneered in her Chapter 2. “We suspect that the number of species for this genus may double the ones described so far. We are going to need a lot of new taxonomists to work on these descriptions!”

A woman takes a photo of tiny fishes set up in front of her on a small brown table.
Luke Tornabene
Photographing cryptos after a dive. Using a macro-lens and fish photo-box.

In her Chapter 3, Marta is taking this work a step further to look at the whole Eviota phylogenetic tree. “The easy part of my research is the field work, even with the exhausting long hours spent underwater and then the processing and photographing of each specimen collected each day. The hardest, longest part is the time spent back at the lab using a microscope and a camera to measure and record morphological features, preparing genetic material for DNA sequencing, and the complex bioinformatic analysis of the data that requires the use of the UW high performance computer system. One of the main questions I answer in my third chapter using genome-wide data is to determine if all the Eviota species groups share a close common ancestor, or if they must be split into different genera. To answer this question, I must look for genetic clues in about 200 specimens that are part of the described Eviota, and include other related species that are also gobies, to use as a frame of reference,” Marta shared.

Using specific genome-wide techniques and comparing specific morphological features across these 200 tiny specimens, Marta hopes to answer this question. “I get asked many times why it is important to know how many and what species are part of a particular ecosystem, and why unveiling the hidden diversity of cryptobenthic reef fishes is important. My answer is, how can you study relevant ecological questions about coral reef ecosystems if you don’t know about half of the fish species that inhabit them?”

Marta is finishing her PhD this summer and she is the proud recipient of a 2024 SAFS Faculty Merit Award for the SAFS PhD program. Marta plans to continue working on cryptobenthic reef fishes after her PhD completion. She wants to complete taxonomic descriptions of new undescribed species she collected from Tonga. In 2025, Marta plans to return to Tonga where she will again be diving alongside her husband, SAFS Affiliate Faculty Ray Buckley, collecting more ‘cryptos’, and working with local community groups and NGOs.

What is another student in Luke Tornabene’s lab working on? Find out