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

Harbor seals and fish parasites: How two undergrads contributed to major discoveries in cryptic diversity

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Almost 25 years ago, an undergraduate took the SAFS “Aquatic Ecological Research in Alaska (AERA)” summer field class, as part of the Alaska Salmon Program (ASP). Always interested in marine mammals, Donna Hauser, a biology student who ended up double majoring in Biology and Aquatic and Fishery Sciences, started a study of the resident harbor seals in Iliamna Lake for her independent research project. Alaska’s largest lake and 7th largest in the US, students from the University of Washington have been conducting research on Iliamna Lake since the early 1960s, and these harbor seals are well-known to people living around the lake, but formal research on the seals was very limited prior to Donna’s work.

Donna Hauser
An Iliamna Lake harbor seal. Research conducted under NOAA scientific research permit 15126-03.

Combined with data collected by a subsequent student in the class, Donna published her findings in the Aquatic Mammals scientific journal in 2008, looking into the summer diet and consumption patterns of Iliamna Lake’s resident harbor seals. Going on to complete her MS and PhD at SAFS on killer whales and belugas, respectively, Donna is now a Research Associate Professor working for the University of Alaska Fairbanks. “Interest in these seals increased and after sampling for genetic tissue by Donna and others, a new paper has now been published by Biology Letters”, shared Tom Quinn, SAFS Professor and advisor to Donna for her undergraduate project at SAFS. “The essence of the paper is that these seals, which are easily capable of swimming to and from Bristol Bay and thus integrating with seals there, are highly different from them genetically.”

Peter Westley
FRI crew surveying for seal scats. Research conducted under NOAA scientific research permit 15126-03.

In comparison with other harbor seals, it has been revealed that there is more genetic similarity between harbor seals along their whole Pacific Rim range (e.g., based on samples from California to Japan, including Bristol Bay) than there is between Bristol Bay and Iliamna Lake. “This is a very cool discovery. While geneticists have done the bulk of the work to show how genetically different these seals are from other harbor seals, it was Donna’s opening, back in 2001, that got us thinking about them,” Tom said.

Donna Hauser
Iliamna Lake harbor seals. Research conducted under NOAA scientific research permit 15126-03.

Fast forward to 2012, when another undergraduate, Brian Harmon, headed up to Iliamna Lake for the same AERA class. “Brian’s serendipitous observation of parasites in sculpins initiated a study on the genetic status of the parasites, in comparison to the similar ones commonly seen in 3-spine and 9-spine sticklebacks”, Tom shared. Sticklebacks are a family of ray-finned fishes, and are found in freshwater, brackish, and marine environments and consume zooplankton, including copepods which are the source of infection. Sculpins are a primarily benthic species and generally do not appear to consume copepods in these environments, leading researchers to wonder what the mechanism is for widespread infection by the parasites.

“The study was expanded from Iliamna Lake to Lake Aleknagik, another Alaska Salmon Program site, and included parasites from two sculpin species as well as both stickleback species, and involved collaboration with parasitologists and geneticists,” Tom said. “This study, recently published in Parasitology in May 2024, shows that the parasites in the sculpins are highly different from those in the sticklebacks, and probably should be a distinct species”. After obtaining his BS in 2012, Brian completed his MS in Natural Resource Sciences at the University of Nebraska in 2017, and now works in the sustainability space as a Principal Technical Advisor for LMI.

Brian Harmon
Brian Harmon’s observation of parasites in sculpins initiated a study on the genetic status of the parasites, in comparison to the similar ones commonly seen in 3-spine and 9-spine sticklebacks.

The so-called “cryptic diversity” of both these species – Iliamna’s harbor seals and parasites found in fish in Alaska’s lakes – means that although they are superficially similar, their genetics are very different. “I credit the terrific opportunities of the AERA class and the creativity and hard work by these two students for a couple of major discoveries,” Tom said. “I am very proud of both Donna and Brian, for their insights and eagerness to see the projects through, and the wonderful collaborators inside and outside of the University of Washington, without whom these projects would have died on the vine.”

Puget Sound Salmon on Drugs

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The Seattle Times Reports “Puget Sound salmon are on drugs — Prozac, Advil, Benadryl, Lipitor, even cocaine. Those drugs and dozens of others are showing up in the tissues of juvenile chinook, researchers have found, thanks to tainted wastewater discharge.”

A research team of NOAA and UW scientists, including SAFS’ professor Dr. Graham Young, have documented levels of over 80 “chemicals of emerging concern”, pharmaceuticals and personal care products in estuarine waters and in juvenile chinook salmon and Pacific staghorn sculpin at sites in south Puget Sound impacted by discharge from wastewater treatment plants. The levels of some of these chemicals are amongst the highest detected in the US.

See the full research paper here: Contaminants of emerging concern in a large temperate estuary.