Who’s who? Using identification tools to tell freshwater sculpin apart

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Scanning through the rows and rows of preserved fish housed in the UW Fish Collection, it’s easy to get lost trying to figure out what each fish is, especially to the untrained eye. Fish identification is a necessary step when preserving specimens from the wild, which deliver key insights for researchers delving into the untold secrets of fish. What fish is it? Male or female? What age? Where was it collected from? These are just some questions answered before they’re put in jars to preserve for the future. 

For Liam Aston, an undergraduate in his final year at SAFS, his capstone research involves Cottus, a group of freshwater sculpin found throughout the Northern Hemisphere. Although sculpin are found in both marine and freshwater environments, Liam is specifically focusing on the clade of Cottus found in Washington and two freshwater sculpins: Cottus gulosus (inland riffle sculpin) and Cottus perplexus (Reticulate sculpin). “These species are often confused in identification due to the overlap in identifying characters, leaving it to be decided by a coinflip most times,” Liam shared. “Determining which dichotomous keys – also known as identification tools – lack characters will further help identify sculpin in the future.”

A man sits at a table with green gloves on, with a tray in front of him holding 3 fish specimens. Also on the table is a jar with clear liquid, holding more fish specimens.
Niamh Owen-McLaughlin
Liam Aston sits in the UW Fish Collection with freshwater sculpin specimens.

Some of the characters found in keys used to identify sculpin are standard length (snout to the hypural plate), depth of fins, height of the dorsal connection, and mouth width. Part of Liam’s analysis of keys will also help to determine at what step identification error happens and therefore improve the process as a result. “I have been taking measurements of all the sculpins that are on the phylogenetic tree – also known as the family tree – completed by Álvaro Cortés, Vertebrate Collections Manager at Oregon State University. Using these measurements in combination with the tree, I will be able to create models to determine if there are any characters separating the species,” Liam said.

At SAFS, the capstone research project is the culmination of the undergraduate experience, an exciting opportunity to put classroom learning into practice and allow students to make a lasting contribution to aquatic and fishery science. For Liam, he chose to work with the UW Fish Collection’s Curator of Fishes, Luke Tornabene. “I had been interested in the work of the Fish Collection since I took FISH 311 with Luke in sophomore year, so this was a great opportunity to finish off my SAFS degree,” Liam said.

When asked what his favorite part of his capstone research has been so far, Liam had a couple of things to share: “Going up to Friday Harbor Labs to use their modern CT scanner was pretty awesome because, for one, you get to visit the San Juan Islands, and two, using a CT scanner to scan a fish is cool.” A modern CT scanner takes roughly 30 minutes to scan a fish, when in the past, it would take 4-5 hours per fish! “It’s also been fun to learn from Katherine Maslenikov (Collections Manager) and Luke to gain a better understanding of taxonomy and the Fish Collection as a whole,” Liam added. Taxonomy is the scientific study of classifying, describing, and naming organisms.

If you’ve paid close attention to CT images or photos of fish specimens, they’re usually lying on their right sides, with their left sides featured in the image. Ever wondered why? This is because the standard in museum specimens is to cut material or take genetic samples from the right side of a fish, leaving the left side intact. So when you see the photos or scans of fish, they’re usually facing all the same way!

A man stands in a room surrounded on two sides by tall shelves filled with jars. The jars contain various fish specimens. The man is holding a jar of fish specimens and pointing to it with one hand.
Niamh Owen-McLaughlin
Liam browses the UW Fish Collection, which holds over 12 million preserved fish specimens from around the world.

CT scanning is a very important tool when it comes to fish specimens. “One key identifying characteristic of freshwater sculpin is the internal presence of palatine teeth. The standard method to determine the presence of palatine teeth requires the jaw of the fish to be pried open, which can damage the specimen and still leaves uncertainty in the determination of palatine teeth presence,” Liam said. “Using the CT Scanner maintains the fish collection specimens held by the University of Washington and Oregon State University, and allows for the determination of palatine teeth to be certain. For the project I’m working on, many external counts and measurements need to be taken, but existing damage on collection specimens prevents accurate data from being collected. The CT Scanner circumnavigates the issue allowing accurate counts and measurements to be taken, plus these models can also show internal features that wouldn’t have been recognized just visually looking at fish specimens.”

One of the ways in which undergraduates conduct research for their capstone project is by working on research questions posed by faculty members. In Liam’s case, this happened to be freshwater sculpin. “I was most interested in freshwater fish, but I also wanted to do something involving speciation and phylogenetics. I wasn’t expecting to be separating species using morphometrics (for example, shape, form or size), but it has definitely grown my interest in taxonomy as a result,” Liam said. 

As a culminating requirement of the SAFS degree, a key aim of a capstone is to put into practice the teaching and learning occurring over an undergraduate’s journey through SAFS classes. “A number of the classes I’ve taken while at SAFS have helped me with my research. FISH 311 introduced me to taxonomy and gave me a really strong understanding of phylogenetic trees and actually working through taxonomic keys, which has been a big part of this research to understand where the differences in species identification comes from,” Liam said. “FISH 290 helped me learn to read and understand scientific literature which has proved useful when going through literature for this project.”

Interested in other SAFS undergraduate research stories?

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SAFS undergrad conducts research in Hawai’i during HPP internship

Hurricane hunting with NOAA: Hollings Scholarship internship set for 2025

Evolution and elongation in deep dwelling anglerfishes

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Many of us are familiar with anglerfishes, though we may not be aware that that’s what they are called, or that more than one type exists. Frequently depicted in popular culture with giant heads, large mouths, sharp teeth and a lightbulb appendage on top, this is indeed a real type of anglerfish that occupies the deep sea (think Finding Nemo), but it’s just one of more than 200 species of anglerfish.

Working with specimens from the Burke Museum and NOAA, Elizabeth Miller, a former National Science Foundation Postdoctoral Fellow at the University of Washington School of Aquatic and Fishery Sciences (SAFS), was captivated by the great diversity of shapes of anglers, which was at odds with how the species is often depicted. Inspired by the world-renowned anglerfish research that has taken place at SAFS and the Burke Museum under Curator Emeritus Ted Pietsch – who wrote the book on the diversity of anglerfishes – Elizabeth set out to build a family tree of anglerfishes and delve into the evolution of new shapes, such as body elongation.

A picture showing five different types of anglerfish, with captions including their names.
Elizabeth Miller
From blobby to elongated: the shape diversity of anglerfishes.

In a new study published in Nature Ecology & Evolution in November 2024, Elizabeth (now a postdoctoral scholar at University of California, Irvine) worked with SAFS Associate Professor and Curator of Fishes, Luke Tornabene, and a multinational team including scientists from Scripps Institution of Oceanography, The University of Oklahoma, and Rice University, to combine genetic material that has been collected and stored from anglerfishes over many years by agencies such as NOAA and museums like the Burke. Much like humans build their family trees by sending in DNA and tracing their lineage online, anglerfish phylogeny is also based on genetic similarity, but over a much longer timescale. “Think millions of years instead of a few hundred,” Elizabeth said. 

A woman smiles into the camera while holding a footballfish specimen
Elizabeth Miller
Elizabeth Miller holds a footballfish that had washed up in Southern California.

The team then paired this family tree with measurements of body and skull shape to ask how the diversity of anglerfishes evolved over time. This is where specimen collections such as those housed in The UW Fish Collection are so important, because they preserve fish species as a snapshot in time to when they were collected from often very hard to reach places, such as the deep ocean. The measurements were taken from over 400 anglerfish specimens, with a quarter of these also CT scanned at Friday Harbor Labs (FHL). CT scans provide three-dimensional images of the skeleton and skull of preserved specimens without damaging them, an important tool for preserving very rare museum specimens. These images were used to quantify the shape of anglerfishes, which the team then used to infer how shape evolved using phylogenetic approaches.

What they learned was that the evolution of new shapes is very fast in deep-sea anglerfishes, especially in association with body elongation. “In evolutionary biology, we call a lineage like this an adaptive radiation, meaning a lineage that evolves a lot of different shapes associated with different ecological niches or ways of living,” Elizabeth said. “Adaptive radiations are well known on land and shallow water, but I had never heard of an adaptive radiation in the deep-sea. I was excited to see if anglerfish fit that mold.” Which they did. The researchers found that the deviation away from the archetypical globose shape is especially associated with rapid evolution. 

A CT scan image showing the skeleton of a fish against a black background, with a smaller photo of the fish in real life located on the bottom right.
Elizabeth Miller
A micro CT scan of a Burke Museum specimen. This is Lophodolos – or Whalehead dreamer – which appears in the elongation graphic above.

How exactly do they know this? This is where the family tree comes in handy. It showed that elongated anglers, such as the wolftrap angler, are closely related to “blobby” ones such as the footballfish. As they share a recent common ancestor, that means there was a short amount of time in between the blobby ancestor and that elongated shape they have today. “A high evolutionary rate implies a lot of change in a short amount of time,” Elizabeth said.

“This study is a great example of how new technology is allowing us to look at museum specimens in ways no one imagined when they were collected decades ago,” said Katherine Maslenikov, Ichthyology Collections Manager at UW. “Anglerfishes are rare and delicate so there has historically not been a lot of research into their anatomy. Genetics has allowed us to build powerful data sets that help us construct the family trees of organisms, but it is the museum specimens that then let us examine their anatomy to try to understand the ecology and behavior in evolutionary terms. Micro CT scanning allows for non-destructive imaging of the specimens, so we are now able to see the delicate skeletons of these rare species and be inspired to ask new questions.” 

The name anglerfish applies to all members of the order Lophiiformes, which has five groups: frogfishes, batfishes, monkfishes, sea toads, and the bathypelagic anglers. Most picture the bathypelagic group when they hear the word anglerfish (suborder Ceratioidei). There are 350 species in Lophiiformes, with roughly half in the bathypelagic ceratioid lineage, the group that this paper is focused on. 

“As to why rapid evolution over a quick time frame happens in the deep sea? It is hard to know, but we have some hypotheses,” Elizabeth added. “Anglerfish don’t really swim – they just float and wait for prey to come to them, drawn by their lures. This means the body can take on different forms and not negatively impact the fish, such as a blobby shape increasing drag in the water.” Some elongated shapes may have evolved as an increased surface area in a dark environment enhances sensation. “But all of these are just hypotheses right now – fruit for future research!” Elizabeth said.

read the paper published in Nature Ecology & Evolution

Giant fish keep washing up in Oregon

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In a new video created by the Burke Museum, Fish Collections Manager Katherine Maslenikov takes us behind the scenes to answer questions about the giant bizarre Sunfish washing up on the shores of Oregon. Where are these fish coming from? What do they eat to get so large? Why are they the “pinnacle of fish evolution”?

Visit the Burke Museum YouTube channel

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