Many scientific fields require long-term monitoring of regions using sensors that are fixed in place, such as weather stations or acoustic stations that monitor fish abundance. These sensors produce high-quality streams of data in time, but typically over a small proportion of the study area. A long-standing sampling design problem is calculating how many sensors should be deployed to accurately estimate amounts of monitored variables such as rainfall. After a review of methods to scale point measurements to area, a new decision tree has been developed to help users decide which techniques should be used to scale time to space, and how many sensors to deploy to monitor an area of interest. The work by SAFS professor John Horne and SAFS Master’s graduate Dale Jacques, appears in the journal Environmental Monitoring and Assessment.
Deep secrets of even-year and odd-year pink salmon unveiled by genetics
A new analysis of DNA differences between populations of pink salmon in the North Pacific reveals some fascinating insights into how these populations first arose and how they are related. Pink salmon all come back to spawn exactly two years after their parents spawned, which means that pink salmon coming back in even years (2014, 2016, 2018, etc.) are distinct from those coming back in odd years (2013, 2015, 2017, etc.). The new analysis is the latest confirmation of the surprising result that even year salmon all across the North Pacific are more closely related to each other, than to odd year pink salmon spawning in the same rivers. In every region examined, the odd-year pink salmon were more genetically variable than the even-year salmon. The results suggest that the last glacial maximum separated pink salmon populations, with one group surviving in Asia and North Alaska, and another group extending from southcentral Alaska to Washington. The new paper was authored by SAFS MS student Carolyn Tarpey, SAFS postdoc Garrett McKinney, and SAFS professors James Seeb and Lisa Seeb, as part of an international collaboration, and was published in the Canadian Journal of Fisheries and Aquatic Sciences.
Fishing reduces the abundance of fish parasites with complex life cycles
Fishing removes parasite species that rely on multiple hosts, according to a comparison of fish parasites on three fished islands and three unfished islands in the central Pacific. The new research also finds that the positive relationship between parasite diversity and fish diversity is eliminated on fished islands. However, it remains an open question whether the impacts of fishing on parasite species increase or decrease disease in host fish. The new research was led by SAFS professor Chelsea Wood and is published in the journal Global Change Biology.
With warming, polar bears spend less time in their maternal dens
In recent years (2009-2015) polar bears in Baffin Bay come on to land about one month earlier than they did in the 1990s, largely owing to early sea ice breakup. This has reduced the duration of maternity denning by approximately 27 days. Maternity dens are now at higher elevations than they were in the 1990s as pregnant bears seek places with deep snow. In Kane Basin sample sizes were too few to make similar assessments of changes, but the impact of climate warming in Baffin Bay leaves little doubt of its effect on polar bears. The research was conducted by SAFS student Erica Escajeda and SAFS professor Kristin Laidre and appears in the journal Polar Biology.
Faster method of dealing with uncertainty in fisheries assessments
Complex computer models are used to estimate sustainable catches in fisheries, by finding the best values for dozens or hundreds of variables so that the models explain data such as trends in abundance and the number of fish at each age and length. Traditionally, software packages are used for this kind of model fitting, most commonly a package called AD Model Builder (ADMB), but more recently a package called Template Model Builder (TMB). These models work well when trying to find the very best values for model fitting, but may take days or weeks to estimate uncertainty using what are called Bayesian methods. Recently, a new Bayesian algorithm was developed that is much faster at solving the uncertainty problem, called the No-U-Turn-Sampler (NUTS), which is implemented in a third software package called Stan. In a new paper, the NUTS algorithm is adapted for use in ADMB and TMB, allowing all of the models already written in these packages to make full use of this faster method for assessing uncertainty. The paper finds that the speed can be comparable to Stan, and is likely to allow widespread usage of Bayesian methods in fisheries stock assessments, so that catch setting can be more precautionary when the models are more uncertain. The paper, by SAFS research scientist Cole Monnahan, and Kasper Kristensen of the Technical University of Denmark, appears in the journal PLoS One.
Centennial Story 15: Chang-Ik Zhang (PhD, 1987)
Chang-Ik Zhang started his studies at the University of Washington in 1981 and received a PhD in fisheries under Donald Gunderson in 1987. During his UW graduate studies, he received the Ellis Memorial Scholarship and the Anderson Memorial Scholarship. He was on the Dean’s List for 1985–1986 due to his academic achievements at UW. While a graduate student, he worked with classmates, Patrick Sullivan, now a professor at Cornell University, and Anne Hollowed, now at NOAA/Fisheries, writing scientific papers for publication and discussing scientific issues.
Dr. Zhang has been a professor at Pukyong National University (PKNU) since 1995 and has been director of the Institute of Fisheries Science at PKNU. He has also taught at several other universities as a special lecturer. Dr. Zhang has served the Korean government as a member of The Presidential Commission on Agriculture, Fishery and Rural Policy and also as a member of The Presidential Commission on Policy Planning.
Since 2005, Dr. Zhang has served as a member of the Marine Stewardship Council’s Technical Advisory Board. He was elected as Fellow of the Korea Academy of Science and Technology in 2005 and as Chair of Fisheries Science Section since 2012. He served as chairman of the Commission for the Conservation of Southern Bluefin Tuna (CCSBT) during 2008 and 2009
Dr. Zhang’s fields of interest are fisheries ecology, population and ecosystem dynamics, and fishery assessment and management. He is the author of nine books (1991, 1994, 1998, 1999, 2002, 2005 and 2010) on fisheries ecology and management, including a recent book, Marine Fisheries Resource Ecology. He has published more than 160 scientific papers and given numerous presentations at scientific conferences, many of them as keynote addresses. He has served on the editorial boards of international journals, including Fisheries Oceanography. He has been editor-in-chief of the Journal of the Korean Society of Fisheries Resources.
Dr. Zhang was the 1991 winner of the Most Significant Paper Award from the American Fisheries Society and the Best Paper Award from both the Korean Cooperation of Science and Technology in 1993 and the Korean Fisheries Society in 1994. He has received the Service Merit Medal of Honor (2010) of the Republic of Korea. He has also received the Marine Science and Technology Award (2010) from the Korean Corporation of Marine Industry Development.
Dr. Zhang has been deeply involved in the work of the North Pacific Marine Science Organization (PICES), and since 1996 as chairman of the Fishery Science Committee. He has also served as a member of the Executive Committee of the Climate Change and Carrying Capacity Program Implementation Panel; the SCOR (Scientific Committee on Oceanic Research) Working Group 105 on The Impact of World Fisheries Harvests on the Stability and Diversity of Marine Ecosystems; the Living Marine Resources Panel of Global Ocean Observing System of the Intergovernmental Oceanographic Commission (IOC) of UNESCO; and the Joint CAgM-JCOMM (Commission for Agricultural Meteorology- Commission for Oceanography and Marine Meteorology) Task Team on Weather, Climate and Fisheries of the World Meteorological Organization (WMO) and IOC.
Dr. Zhang is planning to retire from PKNU this summer and pursue his “second life”, sometimes visiting his daughter (Haeyoung Zhang, 2008 UW School of Pharmacy graduate, now in PhD program for Pharmacy at UW) in Seattle.
Centennial Story 14: Suam Kim (PhD, 1987)
Suam Kim received his B.Sc (1976) and M.Sc. (1979) in the Department of Oceanography from the Seoul National University (Republic of Korea) and his PhD in fisheries oceanography in the School of Fisheries (now SAFS) in 1987. His main research interest at the UW, conducted in collaboration with scientists at the Alaska Fisheries Science Center, was the recruitment process for walleye pollock in the Gulf of Alaska. In 1992, he became the team leader of the Antarctic King Sejong Station, where he managed research operations and studied Antarctic resources. Dr. Kim served as director of the Polar Research Center of the Korea Ocean Research and Development Institute and developed an international program with members of the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) on Antarctic Ocean
Ecosystems, especially Antarctic krill (Euphausia superba), in the 1990s. He moved to Pukyong National University (PKNU) in 2000, and focused on environmental/climatic variability leading to fluctuations in fishery catches in North Pacific and Korean waters. He devoted considerable energy to fostering the next generation of marine and fishery scientists. As a member and then chairman of the Korean Committee of Global Ocean Ecosystem Dynamics (GLOBEC), he convinced an anonymous benefactor to provide funds that would enable young Korean scientists to attend and present their studies in international venues. This support has enabled more than 50 young Korean scientists to share their research results at various venues, including the North Pacific Marine Science Organization (PICES) and GLOBEC. Many of his students received best presentation awards at PICES annual meetings.
Dr. Kim has represented Korea on committees of several international organizations and scientific programs, including: PICES (co-chairman for the Implementation Panel on the Climate Change and Carrying Capacity Program), GLOBEC (Scientific Steering Committee member), CCAMLR (vice-chair of the Scientific Committee), and the North Pacific Anadromous Fish Commission (president). He has published over 100 peer-reviewed articles on topics related to climate change, trends in fishery resources, ecosystem change, forecasting of fish stocks, and marine policy. He has published six books in Korean, and contributed chapters to 28 books domestically and globally. He has also served on the editorial boards of several international journals, including CCAMLR Science, Fisheries Oceanography, Estuaries and Coasts, and Marine and Coastal Fisheries.
In September 2017, Dr. Kim received the PICES’ Wooster Award, which is given annually to an individual who has made significant scientific contributions to North Pacific marine science.
Dr. Kim retired from PKNU in February 2018, and is now an Emeritus Professor.
Some differences between sexes in coho salmon are not linked to sex-determining DNA
A section of DNA in each species determines sex, and it is usually assumed that the many differences between sexes are due to DNA variability in this section. However, fresh evidence suggests that other parts of the genome also contribute to differences between sexes in many species from humans to fruit flies. A new study examines what parts of the DNA result in males and females reaching sexual maturity at different ages in coho salmon, and what influences their growth rates at young ages, finding that indeed there is some sex-specific control over these traits that comes from DNA outside of the sex-determining section of DNA. The research by former SAFS PhD student Miyako Kodama, NOAA researcher Jeffrey Hard, and SAFS professor Kerry Naish appears in the journal Marine Genomics.
Centennial Story 13: Martin Hall (PhD, 1983)
After graduating in Marine Biology from the University of Buenos Aires, I went to Patagonia to conduct research. My main interests were the management of the natural resources of the area, and I became involved in several projects. I realized that my training was not the right one to produce solid scientific answers to the questions of how much could be harvested sustainably and other issues relevant to most developing countries. I decided to improve my training, and after reviewing many options, I applied for and got a Fulbright Fellowship. They offered me a choice of schools, and after going over many catalogues and chatting with my friend Lobo Orensanz (another UW School of Fisheries [SOF] alum), I picked SOF. The program had a very broad curriculum, with emphasis on the quantitative subjects that I felt I needed to reinforce.
It was an incredible opportunity—with a specialized, comprehensive library and an open system where you could take classes in different departments and really put together your individual program with the help of your advisor and supervisory committee. This gave me a sense of freedom, coming as I did from the very regimented systems of Latin American universities. You could follow your curiosity, connect disciplines, and explore scientific tools.
But the most important change for me was the interactions with faculty and students. I had good professors in my country, many trained within the European system. However, education was quite “vertical.” You had to learn what the professors taught and follow their lead. The professors seldom said, “I don’t know.” At the UW, I met many people who helped forge my future, but I will just give two examples. My advisor was Doug Chapman. He was a very famous researcher who never showed off, was very solid, and emphasized the quality of the science, and not “running outside your data.” When I came with a question he had no answer for, he would say “let’s explore that,” and go to the books and search for the answer. Never arrogant, always patient. I had total access to him anytime I needed it, even though he was active in many projects and had many responsibilities (he was the Dean of SOF at the time). Both he and his wife made a point of getting foreign students to feel at home, organizing picnics, where I saw him taking his first steps on a soccer field because the Latin contingent was into soccer. No fear of ridicule, just being friendly. We also learned what Thanksgiving was, and shared many with them.
I took a class of Ecology at the Department of Zoology with Gordon Orians. There was a revolution in the making with the introduction of evolutionary ecology, understanding the adaptive reasons for ecological and behavioral observations, and he was a leader in the field. He emphasized the application of critical thinking and avoiding repeating concepts that were in the books, but had never been fully tested. Professor Orians was another wonderful human being, with strong ties to Latin America and supportive of many foreign students. Loved and admired by everyone, but again very approachable. He was generous with his time and challenged you to grow.
I am very proud of my degree, and in the field of Fisheries Science I don’t think there is anything comparable. I have traveled all over the world, and I know many excellent universities, but still haven’t found a match to SOF at the UW.
Centennial Story 12: Ximing Guo (MS, 1987; PhD, 1991)
I began graduate school at the School of Fisheries in 1985, after receiving a BS degree from Shandong College of Oceanography (now Ocean University of China). My decision to join UW was influenced by Lauren “Doc” Donaldson, whom I had the fortune to meet in Qingdao. Donaldson, a legendary fish geneticist who developed the famous “Donaldson Trout,” introduced UW to me and encouraged me to come. Dr. Donaldson would become a mentor and a friend who influenced me greatly. Donaldson and I worked together helping Professor Guochang Ge to introduce rainbow trout to China. His super Donaldson Trout should be thriving in many places in China, carrying his legacy and the legacy of UW Fisheries.
Bill Hershberger was my major professor for my MS and PhD. I studied triploidy in rainbow trout for my MS. Jim Myers (PhD, 1990), who was also one of Bill’s PhD students at the time, introduced me to polyploid induction. I was fascinated by the fact that fish can tolerate polyploidy so well. Bill was great in giving his students the freedom to explore. UW was a wonderland to me, coming from China where science in the 1980s was decades behind the west. I benefited greatly from the interdisciplinary training that included courses such as cell biology, developmental biology, molecular genetics, population genetics, and statistics taught by renowned professors from other departments. I also had the opportunity to work in Fred Utter’s lab at the National Marine Fisheries Service, learning about allozymes and their applications in population genetics.
For my PhD, I turned to oyster genetics with a focus on tetraploids. At that time, Stan Allen (PhD, 1987) and Sarah Downing (MS, 1987; PhD, 1993) were working on producing triploid oysters using chemical induction, a process that is complex and rarely totally effective, while Jim Myers produced tetraploid rainbow trout for triploid production. I spent four years testing different ways of making tetraploid oysters. I conducted most of the experiments in Coast Seafood’s hatchery in Quilcence, and I still remember the occasional joy of just getting on the last ferry back. Tetraploid embryos were readily produced, but none would develop normally. Looking at the embryonic cells with abnormally large tetraploid nuclei, it occurred to me that the eggs might not have enough cytoplasm to support the large tetraploid nuclei, and viable tetraploids might be developed using large eggs from triploids. After my PhD, I joined Stan’s lab at Rutgers University as a postdoc, and we tested my hypothesis, which was correct and led to the production of viable tetraploids. Tetraploid oysters would soon be commercialized for triploid production and had a major impact on oyster farming worldwide. Although tetraploid oysters were first produced at Rutgers, the idea of making viable tetraploids from triploids was conceived by me at UW.
My committee members included Ken Chew, Marsha Landolt, Aimee Bakken (Zoology), and Ralph Elston (Battelle). Ken gave me a strong sense of the importance of working closely with the industry. Aimee shared her insights in developmental biology, and Ralph’s research led to an interest in oyster diseases that continues today. Marsha’s qualifying exam for me was to write a grant proposal (on genetic toxicology of an oil spill) in five hours, a skill that I had to improve throughout my career
I moved to Rutgers University in 1992 as a postdoc, joined the faculty of Marine Sciences in 1995, and have been directing the shellfish genetics and breeding program at Rutgers since 1998. Rutgers has probably the longest oyster breeding program in the world. It developed disease-resistant diploid and triploid oysters for the oyster farming industry. I later ventured into genomics and co-directed the International Oyster Genome Project, trying to introduce genome-based approaches to oyster breeding. It has been a wonderful ride, and I owe much of it to my education at UW Fisheries. I have maintained some connections with SAFS faculty and former students through the years. It is great to see the global impact that SAFS has made and continues to make.