Estimates of migration are important for understanding and managing natural populations. A statistic known as FST is often used as a measure of the amount of genetic difference expected for a given population size and migration rate. Equations that translate FST into estimates of migration exist but the underlying ideal assumptions often do not apply. Now a new model has been used to test which factors affect FST in a real life example based on Atlantic cod. Results showed that knowledge of the effective population size and biology of the population of interest is sufficient to use theoretical equations to translate FST into a starting point for estimates of migration. The research was authored by Ingrid Spies of the QERM program at the University of Washington, and among the coauthors were SAFS professors Lorenz Hauser and Andre Punt. It was published in the Proceedings of the National Academy of Sciences, USA
Seabirds like hanging out in river plumes
When large rivers discharge their water into the sea, this creates a plume of freshwater that is highly variable. A new study that attached tiny satellite tags to seabirds now shows that both shearwaters and murres prefer to forage in plumes created by the massive Columbia River. In particular, they prefer the boundary areas between freshwater and sea water, since this area is where zooplankton and prey fish species are most concentrated. The seabirds shift where they forage as the plume area expands and contracts in size, and moves north and south of the mouth of the Columbia River. The new paper by SAFS PhD student Elizabeth Phillips, SAFS professor John Horne, and their coauthors, appears in Marine Ecology Progress Series.
Massive new map of genetic variation in rainbow trout and steelhead
Genetic techniques are capable of finding the entire sequence (“genome”) of DNA letters (“base pairs”), and have recently been applied to completely sequence 61 unrelated rainbow trout and steelhead individuals. The study found that one in every 64 letters varied across the rainbow trout examined (with variability in more than 30 million locations), and that there were more than 4 million locations where the individual DNA letters differ substantially. These places of variability are known as single nucleotide polymorphisms (SNPs) to can be used to allocate individual fish to their birth populations, identify genetic variation underlying fitness traits, and characterize genes. The vast new SNP database will be a key resource for future genetic analyses, and was authored by a collaboration between US and Norwegian scientists including SAFS professor Kerry Naish. The paper was published in Frontiers in Genetics.
Inherited growth rates and reproductive traits in oysters
Native oysters on the Pacific coast were devastated by commercial overfishing in the 20th century and their recovery has been prevented by water pollution, habitat loss, and possibly ocean acidification. Efforts underway to restore these Olympia oysters rely on harnessing genetic variation among populations to pick the best suited oysters for restoration. Now a new study shows that, even when reared for two generations under the same laboratory conditions, differences among populations persist. Populations differed substantially in how many viable larvae they produced, when they decided to start spawning, and in larval and juvenile growth rates, with faster growth being traded for lower reproductive output. The research was published in Scientific Reports, and was authored by Katherine Silliman and Tynan Bowyer of the University of Chicago, and SAFS professor Steven Roberts.
Serious impacts of coal mining on stream dwellers
Coal mining is well known to have negative impacts on the quality of water in streams, and now new findings show that fish, invertebrates, and salamanders are badly affected by the resulting pollution. A synthesis demonstrated that animal numbers declined by more than half (53%), and species numbers declined by one third, in streams affected by coal mines. These impacts happened in spite of current federal statutes (the 1972 Clean Water Act and 1977 Surface Mining Control and Reclamation Act), and persisted even after cleanup efforts post-mining. More stringent regulations are needed to keep streams clean and healthy in the presence of coal mining. The new research was conducted by Zingli Giam, SAFS professor Julian Olden, and Daniel Simberloff, and is published in the journal Nature Sustainability.
Chelsea Wood receives UW Distinguished Teaching Award
SAFS professor Chelsea Wood has been awarded the University of Washington’s Distinguished Teaching Award, given annually to seven recipients for mastery of the subject matter; enthusiasm and innovation in the teaching and learning process; ability to engage students both within and outside the classroom; ability to inspire independent and original thinking in students and to stimulate students to do creative work; and innovations in course and curriculum design.
SAFS includes a disproportionately large number of recipients of the Distinguished Teaching Award, which is a recognition of the outstanding teaching in the School. Past SAFS recipients of the award are Andre Punt, Julia Parrish, Ted Pietsch, Thomas Quinn, and Loveday Conquest.
New tool for the safe passage of fish through hydroelectric dams
More than 80% of the world’s renewable electricity comes from hydropower generated from dams, but these dams impede upriver passage of fish, and potentially damage fish migrating downstream that pass through turbines or over slipways. A new toolset has now been developed that can better estimate injury and death rates from fish passing downstream, using the data from artificial “sensor fish” that mimic the passage of fish through turbines and slipways while collecting high-resolution data. The new tool allows users to design new studies and analyse the data from sensor fish using statistically rigorous methods, and will help future design and current operation of hydropower dams so that their impacts on fish can be reduced. A paper describing the new tool, by Hongfei Hou and coauthors including SAFS professor John Skalski and SAFS research consultant Richard Townsend, appears in a recent issue of the journal Energies.
Timing of sea-ice retreat affects where birds are found
The Bering Sea has highly variable sea ice extent in winter, which can be used to tease out the effects of future climate change on marine animals such as seabirds. In a new study, SAFS professor George Hunt and coauthors examined how seabirds change location in years when sea ice melts earlier in the year. In these years, seabirds that feed far from land tend to come closer inshore, while seabirds that feed closer to shore move further offshore. Furthermore, in warm years, small zooplankton experience changes in their growth and reproduction, which brings more young, abundant, pollock into surface waters where they can be eaten by seabirds. In the future holding warmer waters, seabirds may rely more heavily on young pollock, which has less nutritional value than other prey items. The work was published in the journal Marine Ecology Progress Series.
Centennial Story 9: Jeffrey Olsen (BS, 1981; PhD, 1999)
I received a BS degree from the College of Fisheries in 1981. At that time, rather than attempt graduate school, I pursued employment. I wanted to experience hands-on fish biology, so I spent a couple years on the seasonal circuit doing all kinds of field work from Washington State to Alaska. It was great! I got to work for fish biologists in field camps, sample and count juvenile and adult salmon, survey fishermen, and do remote eggtakes. I eventually landed a permanent job as a fish culturist with the Prince William Sound Aquaculture Corporation (PWSAC) where I spent 12 years.
The years in Prince William Sound showed me the importance of applied science in fishery management. Some of the most influential individuals in my early career included UW alumni Brian Allele, Ted Cooney, and Jim Seeb. Brian was executive director of PWSAC, Ted was an oceanographer at the University of Alaska, Fairbanks, and Jim was the lead geneticist with the Alaska Department of Fish and Game (ADF&G). I started thinking about graduate school after conversations with Brian and Ted. However, it was conversations with Jim about population genetics and hatchery and wild salmon interactions that really piqued my interest. Jim would continue to give me good advice as a member of my graduate committee and supervisor at ADF&G.
I started graduate school at the UW School of Fisheries (SOF, now SAFS) in 1994. I was very fortunate that Paul Bentzen agreed to be my advisor. Paul had recently joined the SOF and was building a molecular genetics lab with Ginger Armbrust from the School of Oceanography. It was an exciting time to be part of a new lab, using state-of-the-art (at the time) technology and molecular genetic methods to do research addressing real conservation and management questions. I shared the bench with some outstanding grad students who have since had impressive careers, including Rolf Ream (PhD, 2002), Adrian Spidle, Pam Jensen (MS, 1994), Carol Ann Woody (PhD, 1998), John Wenburg (PhD, 1998), Andres Lopez (MS, 1998), Kristina Ramstad (MS, 1998), Andy Shedlock (MS, 1992; PhD, 1997), and Mike Canino (PhD, 2003). I wasn’t the only one that benefitted from Paul’s tutelage.
I had the privilege of having Fred Utter on my graduate committee. I benefitted, as many have, from Fred’s insights and knowledge of fisheries genetics. However, it was Fred’s passion for research and positive attitude that gave me the proper perspective I needed early in grad school. Fred also gave me some very practical advice—publish as much of my dissertation as possible before graduating. Later, Fred authored a short perspectives paper on publishing in the journal Fisheries. He shared a personal mandate that I also try to adhere to that “All research projects must end with publication in an appropriate peer-reviewed outlet.” This is particularly relevant for agency scientists where the emphasis is not always on publishing, but unpublished work may ultimately be repeated at great cost to the public.
I moved back to Alaska after receiving my PhD in 1999. I wanted to work at an agency so I could be close to conservation implementation and management. I joined Jim and Lisa Seeb (now SAFS professors) at ADF&G in Anchorage. They had created a high functioning lab that, in my opinion, was (and still is) the model for fisheries genetics labs. Today, I work for the US Fish and Wildlife Service, also in Anchorage, with fellow SAFS grad John Wenburg. I stay in touch with SAFS mainly through Jim and Lisa, Lorenz Hauser, and their impressive students.
Centennial Story 8: Bernie May (MS, 1975)
Returning to the UW after two years in the army, I completed my BS in the newly created major in Molecular Biology. During my last year, I attended a class in Fish Genetics taught by Bill Hershberger. Fred Allendorf (then an MS student) gave a guest lecture on the use of genetic data from allozyme electrophoresis to address questions in fisheries management. Figuratively “a lightbulb went off in my brain” during that lecture. I knew instantly I wanted to spend the rest of my career doing just that. Fred invited any of us who were interested to meet his mentor Fred Utter across the bridge at the National Marine Fisheries Service (NMFS).
After walking the halls in trepidation at NMFS, I poked my head in to say hello to Allendorf and suddenly this guy burst out from behind a file cabinet, stuck out his hand, and introduced himself as Fred Utter. I joined the two Freds and spent two intense years studying allozyme variation in Pacific salmon. Utter treated all new students as full professionals when they walked in the door. You had his full respect from day 1. I was barely there when he took Allendorf and me on a road trip to California to attend a conference where I met a host of other giants using genetic data derived from allozyme electrophoresis.
Utter and I taught several short courses in allozymes to graduate students from a variety of disciplines during the second year of my MS. Some of those students joined Utter (including Jim Seeb [PhD, 1987] and Stew Grant [PhD, 1981]), and others took that knowledge into careers in many other disciplines. Funding for my research came from the Washington Department of Fisheries; partnerships between state and federal management agencies and university geneticists became a pattern. I appealed and was granted permission to have Utter be chair of my MS committee, with Joe Felsenstein and Bill Hershberger as committee members. Utter had simplified how allozyme electrophoresis could be done. My MS thesis included a manual for his methods and was copied hundreds of times.
I spent two years as a technician at the University of Maine after which I joined Jim Wright at Penn State for my PhD, completing the circle from whence Hershberger had done his PhD and Allendorf had been an undergraduate. Following a 14-year stint at Cornell running an interdepartmental allozyme laboratory, I spent 20 wonderful years at UC Davis training dozens of graduate students using genetic data to answer many questions posed by state, federal, provincial, and tribal fisheries management agencies, primarily in California. My 40-plus professional years have witnessed genetic data becoming a standard tool in fisheries research and management, following the pioneering work of Dr. Fred Madison Utter and the many students he influenced over his career at NMFS and SAFS.