Sonar fish counts on the Chignik River

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Myra Scholze steering ADFG’s skiff in Chignik, Alaska. Photo courtesy of Myra Scholze.

Field work is often seen as the glamorous part of science, where researchers get to experience the outdoors and be close to the subjects that they study. The sad reality is though that most scientists spend their time analyzing and processing data on computer screens at office desks. For Myra Scholze, a Fish and Wildlife Technician, for the Alaska Department of Fish and Game (ADFG), this is no unfamiliar territory.

Scholze began working for the ADFG seven years ago in the sport fisheries division in Kodiak. Two years ago, she began doing research for ADFG near Chignik, Alaska on the Alaskan Peninsula. The community of Chignik is primarily a fishing village that relies on the commercial and subsistence fisheries there.

Scholze’s work with ADFG helps manage those fisheries to maintain their sustainability. Her work is to count the salmon that swim up river between May and September.

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Myra Scholze on the Chignik River. Photo courtesy of Myra Scholze.

“Counting the fish is what tells fish and game when to open and close commercial fisheries,” Scholze said. “For each day of the month, in June and July, there’s escapement goals you’re supposed to meet that indicate that you’re going to meet your total number of fish that’s needed to maintain a sustainable run. We count the fish up and meet those goals then the manager at Chignik decides when and what areas to open and for how long.”

Specifically, Scholze is funded through a grant that is comparing and trying to find the correlation between fish counts made on a weir or on a sonar. The two fish counting methods generate a massive amount of data that must be processed.

Weir measurements are made by forcing salmon through a bottleneck in the river, the weir itself, and recording video of the salmon as they pass by. Researchers then go back and count how many individual salmon pass the camera lens.

Sonar doesn’t record video in a traditional sense, but rather records how sound moves through water. Sonar data is collected on both banks of the river and then a researcher must sit and watch back each of the videos and count how many fish blips they see on screen.

“We have two sonars and every ten minutes they create a file that looks kind of like a fish finder on a boat. That’s what you’re counting,” said Scholze. “Every bank creates 144 files per day, we have a sonar on each bank of the river, so we are creating 288 files a day. Over a month you’re creating about 10,000 files and that’s why we have such a back log and why I count files.”

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Myra Scholze adjusts the sonar in Chignik. Photo courtesy of Myra Scholze.

The massive amount of data and the nearly real-time nature (the videos can be sped up slightly when only a few fish are moving by) of watching back the files and counting fish makes for long work hours. Scholze has spent months outside of Chignik in the Kodiak ADFG office, in addition to long evenings at the bunkhouse in Chignik, just counting back fish on videos, so finding a correlation between weir and sonar counts may take years to come. The preliminary conclusions about correlation can’t even be made yet.

“They’ve looked at it [the correlation], but we don’t have enough done from 2016 yet.” Scholze said.

The work may be grueling to some, but to Scholze she loves being able to collect the data that helps inform management decisions for Alaskan fisheries. She intends to continue working for ADFG in Chignik for as long as they have files for her to count. She’s currently in Dutch Harbor, Alaska working for ADFG as a Fish and Wildlife Technician for the crab fishery there. Myra will return to Kodiak in the spring to restart her sonar counts before heading back to the field in Chignik as a Fishery Biologist.

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Myra Scholze collecting samples in Alitak, Alaska for a job she held with ADFG before working for ADFG in Chignik, Alaska. Photo courtesy of Myra Scholze.


Stickleback – The super fish

Darting through Cheney Lake in Anchorage, Alaska are thousands of small fish, about three inches in length, with three spiny projections that jut off the top of their bodies, pricking anything that dares touch them. The color of their scales varying in color depending on the season, sex, or population from which they descend. They gleam shiny silver, blue, or a dull brown, sometimes with a greenish hue. They’re named threespine stickleback, and they’ve become a powerhouse organism for study.  Found in nearly all Alaskan lakes and across most of the northern hemisphere, scientists have taken keen interest in these fish for the practical uses they hold for studying evolution and conducting research.

Threespine stickleback from Cheney Lake in Anchorage, Alaska during their reproductive stage of life. The fish with blue eyes is a reproductive male.

        At the University of Alaska Anchorage, Kat Milligan-Myhre, heads a laboratory of undergraduates, graduates, lab techs, and post docs who are all using threespine stickleback as a model organism for a variety of projects on host gut microbe interactions. The lab is able to study how the microbes within the gut of threespine stickleback, the host, affect a variety of things like development, physiology, behavior, and more. Milligan-Myhre developed a procedure that allows the lab to fertilize eggs of the fish and then make them free of all microbes. They can then add back in select microbes or none at all to study how the microbes are actually affecting the fish.

A 7-day-old transparent juvenile threespine stickleback. Milligan-Myhre has developed a protocol to rear threespine stickleback free of microbes until 14 days after the eggs they’ve hatched from have been fertilized.

        “Stickleback have a number of really cool qualities. One is that they are transparent so we can actually watch fluorescent microbes move around in the gut of a live stickleback,” said Milligan-Myhre, “We can make large amounts of genetically similar eggs from a single cross or a couple of crosses… with fish you can get 100 to up to 200, if you’re lucky, of genetically related fish. That allows us to have a lot of power so we can do some really good statistical analysis on these changes that we’re seeing when we treat these animals.”

Kelly Ireland and Kat Milligan-Myhre set traps for threespine stickleback in Cheney Lake in Anchorage, Alaska in May of 2017. The lab uses minnow traps that have a funnel and hole on either end of the trap that threespine stickleback then swim into and get trapped.

        They are studying a variety of populations from varying lakes across Alaska, but by far their most frequented lake of interest is Cheney Lake. The lake had threespine stickleback introduced to it in 2009 from a parental population found in Rabbit Slough, Alaska, by Frank Von Hippel, a former professor at UAA, who like Milligan-Myhre used them as a model organism. Von Hippel’s lab was interested primarily in the evolution of the fish, however.

Ryan Lucas, Emily Lescak, and Kelly Ireland of Kat Milligan-Myhre’s lab pull traps from Y Lake of the Talkeetna Lakes chain in Talkeetna, Alaska. The lab then does in field gut dissections to assess gut microbe composition within the threespine stickleback.

        “What really sets stickleback apart from zebrafish, which are the traditional go to fish model, is that we can take stickleback that have evolved in different environments and we can relate the environments in which they evolved to their physiological and genetic variation,” said Emily Lescak, former doctoral student of Von Hippel’s, currently working as a post-doctoral fellow in Milligan-Myhre’s lab, “Basically we can understand what selection pressures in the environment cause a fish to evolve in certain ways, so we can understand what sort of ecological pressures there are on fish populations.”

Threespine stickleback fish from Rabbit Slough, near Wasilla, Alaska. The Rabbit Slough population is anadromous meaning they’re born in freshwater, then travel to oceanic environments for most of their life, and then return to freshwater to mate.


       Incidentally there’s already evidence that the threespine stickleback Von Hippel introduced into Cheney Lake are already undergoing evolution from their anadromous (meaning the fish, like salmon, are born in freshwater, travel to the ocean, and then come back to the freshwater to mate) ancestral form, to freshwater forms. The threespine stickleback in Cheney Lake were introduced in 2009 after the Alaska Department of Fish and Game applied a Rotenone treatment in October, 2008, to the lake. Rotenone was used to eliminate northern pike that were introduced illegally. The Rotenone treatment wiped out all fish populations in the lake and allowed Fish and Game to restock Cheney Lake with rainbow trout, and Von Hippel to introduce threespine stickleback from a known population, Rabbit Slough. Milligan-Myhre’s lab has been collecting data on Cheney Lake and threespine stickleback from the lake monthly to assess the changes of the threespine stickleback population over time.


        “We can follow evolution in real time. That’s exciting,” said Milligan-Myhre.

        The lab is collaborating with a lab at Stony Brook University in New York to look at genetic differences as the population evolves. Milligan-Myhre’s lab hopes to also take a look at how as the population changes over time into their freshwater form the microbiota and threespine stickleback’s immune response to microbes also change.

Rachael Kramp an undergraduate student of Kat Milligan-Myhre’s lab, works with microbes from the guts of threespine stickleback from Cheney Lake in the anaerobic chamber of Milligan-Myhre’s lab at the University of Alaska Anchorage.

        The tools these fish offer are nearly limitless from using them as a model for biomedical research, as they have similar physiology to humans, to studying evolution, these fish also make great models for studying ecotoxicology, as well as, host microbe interactions, just to touch on a few of their benefits. The threespine stickleback came to be a model organism in the 1900s with the work of Nobel Prize laureates, Niko Tinbergen, Konrad Lorenz, and Karl von Frisch, because of the ease to which they could be manipulated in the lab, now in 2017 the threespine stickleback shows no signs of slowing down as being the model organism of many scientist’s dreams. In 2018, hundreds of researchers will even gather together for the 9th International Conference on Stickleback Behavior and Evolution in Kyoto, Japan. These prickly little fish may not seem like much to the majority of people, but to many scientists they are the crux of their entire careers.


Written by Kelly Ireland. Kelly Ireland is an undergraduate student doing research in Kat Milligan-Myhre’s lab.