SAFS hosts weekly lunch-time seminars where students and faculty share findings from their current research. Read through our past seminars to get an idea of topics covered and be sure to check out our events calendar to download upcoming seminars on your calendar.

Spring 2018  seminar

Fridays at 12:30-1:30pm in FSH 203 

Join the seminar remotely.


Dr. Timothy Essington (Professor and Associate Director, UW SAFS & Director of UW QERM)

Title: When do species interactions matter?  A bioeconomic model of multi species fisheries.


People like me have been calling for greater inclusions of ecological principles into fisheries management decisions and the models used to inform those decisions.  Yet there has been little attempt to quantify the economic benefits of considering ecological interactions in fisheries management.  Here I detail the development of a generalized ecological model of a piscivore – prey fishery system, and use that model to reveal when and where ecosystem considerations provide economic benefits.  Our model is a minimal model of predator – prey interactions that retains the ability to realistically account for a wide range of species interactions: top -down predation, predator-dependent predation; egg predation by prey.  We show that the optimal harvest trajectory is highly dependent on species interactions.  However, the economic cost of assuming the wrong interaction was generally small.  We find that the largest benefit of ecosystem considerations are two fold – more equitably distributing risk, and defining management safe zones where uncertainty leads to large trade-offs in risk.



Robert Emmet (Graduate Student, UW QERM)

Title: Developing occupancy models for wide-ranging species


Wolverines are recolonizing Washington’s Cascade Mountains, but their reliance on spring snow cover makes them vulnerable to climate change, making an effective monitoring framework crucial. The species’ low population density makes monitoring occupancy via remote cameras more realistic than monitoring abundance. However, wolverine distribution is difficult to assess using standard occupancy models, because wolverines’ low density and high mobility may lead to biased estimates of occupancy and detection probabilities. In this talk, I introduce a novel continuous-time, dynamic occupancy model for monitoring wide-ranging species such as wolverines. I compare this model to competing models using both simulation and analysis of an existing dataset from a large-scale wolverine survey. Finally, I discuss a new method to account for the effect of using perishable bait on detection probability.



Dr. Robin Waples (Senior Scientist, NOAA Fisheries, Northwest Fisheries Science Center)

Title: Consequences of sex reversal for effective population size


Sex reversal (sequential hermaphroditism) is common in plants, some invertebrates, and several marine fish families. Protandrous species start life as males and later change to females, while protogynous species do the opposite. Evolutionary theory indicates that sex change can be favored when fecundity increases with age faster in one sex than the other, in which case the sex with the faster rate of increase becomes the terminal sex. Conversely, the adult sex ratio is skewed toward the initial sex—sometimes very highly so. For a given set of vital rates (age-specific survival and fecundity for both sexes), there exists an optimal age for sex change (ESS age) that is evolutionarily stable. These ESS analyses, however, do not account for indirect effects on another key evolutionary parameter, effective population size (Ne), which is reduced when sex ratios are skewed.   Wright’s famous sex-ratio adjustment for Ne is not directly applicable to sequential hermaphrodites, because it is necessary to consider lifetime variance in reproductive success by the same individuals operating as both males and females. This raises the following question: Do species that exhibit sex change incur an evolutionary cost in terms of reduced Ne caused by skewed sex ratios? If so, evolutionary tradeoffs must be involved, at least at the population level. I evaluated this issue using both hypothetical vital rates and empirical data for 8 marine fish species that are sequential hermaphrodites. Results: 1) In all cases, Ne at the ESS age at sex change was as high or higher than for a gonochoristic (fixed sex) population with a 1:1 sex ratio. This occurred in spite of the skewed adult sex ratio in the sex-changing population, which indicates that the ability of individuals to operate as both male and female allows the population to avoid some of the evolutionary constraints imposed by fixed sexes (i.e., that half the genes for the next generation must come from each sex). 2) However, Ne at the ESS age at sex change was always lower than it could have been if sex change had occurred at an earlier age. This implies an opportunity cost for the population in terms of a missed chance to further reduce effects of genetic drift. 3) Using a simple transformation of vital rates, I develop a novel method to quantify the strength of selection for sex reversal in a population.



Dr. Sean Brennan (Research Associate, UW SAFS)

Title: Shifting habitat mosaics and fish production across river basins


The generation and maintenance of biological complexity over ecological and evolutionary timescales ultimately depends on processes that generate habitat heterogeneity across landscapes. Such heterogeneity is produced from interactions between local geomorphic features (e.g., topography) and overriding environmental forcing (e.g., regional climate). Habitat can be described as a mosaic of environmental conditions arranged across landscapes but, importantly, the spatial configuration of productive habitat patches can shift through time as prevailing environmental conditions interact with geomorphic conditions, successional processes, and the biological responses of locally adapted populations. This concept – the shifting habitat mosaic (SHM) – has been empirically tested at small scales, but no quantification of how these dynamics playout across a range of spatial scales exists, and specifically in terms of how they influence the reliability of crucial ecosystem services (e.g., fisheries). We present the first quantitative assessment of how SHMs are expressed across a range of spatial scales within a large (35,000km2), free-flowing river to ensure the reliable production of two species of salmon that support fisheries essential to the livelihood, nutrition, and culture of local communities. Analyses of the strontium isotope records of salmon ear stones (otoliths) show that the productivity of components of the river network, as both natal and juvenile rearing habitat, fluctuate widely among years, and that this variability is expressed across a wide range of spatial scales. Conservation should focus on protecting and restoring such habitat complexity, and the processes that generate it, to ensure reliable flows of resources to humans, particularly in river basins which are coming under unprecedented pressure from climate change and expanding urban and industrial growth.



Yeuan (Allen) Chen (Graduate Student, UW Department of Economics)

Title: Constructing catch expectations in fisheries discrete choice models


In order to compare expectations of catch at different locations in discrete choice models of fisher behavior, researchers typically construct proxies using fishery-dependent data. However, economic principles from a standard random utility model (RUM) suggest that catch data observed by the researcher and chosen by the fisher are non-randomly sampled. In this paper we illustrate how selection by the fisher biases catch expectation proxies constructed using fishery-dependent data and how this results in incorrect econometric inference. By using a flexible correction function approach (Dahl 2002), we can test if bias exists and correct for selection. We find that full information maximum likelihood estimation can completely correct the bias in the discrete choice parameters, where expected catches are overestimated and welfare losses from spatial closures are underestimated when selection is ignored. As an application, we apply the model to the Bering Sea catcher vessel fishery.



Nissa Ferm (Fisheries Biologist, NOAA Alaska Fisheries Science Center)

Title: Guts to Bits: Fish Diet Data, Its Limitations, and Establishing Knowledgeable Priors: As Told Through a Juvenile Pollock Predictive Model.


What did the fish eat? On the surface this seems to be a relatively simple question. However, when diet data are incorporated into models, there are both logistical and ecological limitations. Understanding the methodologies of how diet data are generated, combined with an understanding of the underlying predator-prey ecology, can help generate more informed models with robust priors. I will present an overview of diet data methodologies used to investigate feeding of young of the year Walleye Pollock (Gadus chalcogrammus). Based on this knowledge, I will describe a Random Forest model, built upon the scaffold of zooplankton ecology that was designed to predict Walleye Pollock condition. The model I developed predicts fish length from consumed prey taxa weight and composition. Length is related to known ontogentic shifts in diet that are important milestones for juvenile Pollock survival and ability to overwinter. When modeled fish size was smaller than observed, I concluded that fish were not consuming their optimal prey in order to meet energetic demands. One possible mechanism for not meeting these thresholds, under prediction, was a spatial mismatch between the fish and optimal prey.



Keita Abe (Graduate Student, UW Department of Economics)

Title: A Dynamic Model of Fishing Cruise Duration


Production function, or harvest function in natural resource economics, is often estimated with temporally aggregated data. However, such estimations can be misleading if variable inputs are dynamically determined within a time period of the data, because the variation within a period is not taken into account. In this study, using a data from a longline fishery, I demonstrate a case that cruise-level production is determined not only by use of quasi-fixed inputs, but rather by dynamic consideration of the rate of daily harvest, balancing the quantity and quality of harvest to maximize their cruise level revenue. This response is modeled as a daily optimal stopping problem, with the state variables representing the decreasing freshness of fish caught on each previous day of the cruise. I estimate trip duration decisions based on unusually detailed daily logbook data on a Japanese longline fleet. The dynamic discrete choice problem is modeled with a conditional choice probability (CCP) estimator, which estimates the reduced form of CCP and transition probabilities in the first step to calculate the continuation value, and estimate the structural parameter using the calculated continuation value in the second step. The predictability is improved avoiding over-fitting in flexible logit to estimate CCP in the first step with elastic-net logit, a machine learning method. The results show harvesters are particularly sensitive to freshness deterioration after 20 days, and are more likely to terminate their fishing cruise when more fish is caught 20 or more days ago. This suggests that catching power defined by quasi-fixed inputs is not fully utilized due to a dynamic consideration of fish quality, and that a management strategy based solely on technical efficiency will systematically over-predict actual catches.



Elizabeth Ng (Graduate Student, UW QERM)

Title: Assessing trends in historical abundance of Puget Sound groundfish


Groundfish are an important component of the Puget Sound ecosystem and have historically supported important commercial and recreational fisheries. However, many populations have declined over the past century, necessitating sharp reductions in fishing effort. A number of factors, including pollution, water quality, and climate change have been implicated in this decline. Long-term historical data sets provide a unique opportunity to characterize groundfish abundance and distribution, as well as elucidate potential drivers of change. We used two long-term data sets to evaluate relative abundance and occurrence of groundfish in Puget Sound from 1948 to 2016. By combining insight from multiple surveys and using quantitative standardization methods, we characterize changes in the ecosystem baseline and correlate them to environmental drivers. This work seeks to inform ongoing food-web and ecosystem modeling efforts in the Puget Sound region.



Dr. Christopher Anderson (Associate Professor, SAFS)

Title: So, You Want an Academic Job? Selling Yourself on the Assistant Professor Market


You have already done the great science! Now, you have to package yourself so that academic search committees will notice you. What should you expect as you prepare an application, move to a Skype interview, a campus interview, and finally an offer of the coveted title of “Assistant Professor”? As a veteran of too many search committees, I will walk you through what search committees are—and are not—looking for at each step of the process. How do you use a research statement to tailor your papers to a job ad? What makes a strong diversity statement? How can you convey your maximum awesomeness in a seven-minute Skype presentation? How do you explain your teaching interests? What are the differences among a teaching demonstration, a chalk talk, and a seminar? What do you even have to say to a Dean, anyhow? I will prepare advice for each section of the application and stage of interviews, along with suggestions for things you can do while still in school/postdoc to strengthen your package. There will be lots of time for discussion and questions.



Kristin Privitera-Johnson (Graduate Student, SAFS)

Title: Quantifying uncertainty in projections of overfishing limits


Many of us in the fisheries community spend significant amounts of time and energy refining our collective understanding of the inherent uncertainties that accompany data collection, using data and assessment models to determine stock biomass, and the efficacy of management measures to achieve desired goals. This talk will focus on a retrospective analysis of fisheries stock assessments completed in Stock Synthesis to identify and quantify the influence of uncertainty on the outcomes of these assessments. The context for this work is the U.S. west coast groundfish stocks and the buffer between the overfishing limit and the acceptable biological catch, i.e., a proportion based on a measure of between-assessment variance in historical biomass estimates from a previously conducted retrospective analysis. But the current method for quantifying between-assessment variation ignores uncertainty in productivity and target fishing mortality rates and this uncertainty can be substantial for some assessments. Therefore, I am pursuing a revised retrospective approach to quantify the total uncertainty associated with projecting overfishing limits using assessment outputs for U.S. west coast groundfish stocks. This uncertainty could be used to inform management decisions about the process of setting acceptable biological catches for U.S. west coast fisheries.



Archived seminar schedules

Year Coordinator links to archives
2014–2015 Hilborn Lab fall/winter/spring
2013–2014 Branch Lab fall/winter/spring
2012–2013 Punt Lab fall/winter/spring
2011–2012 Anderson Lab fall/winter/spring
2010–2011 Kotaro Ono fall/winter/spring
2009–2010 Chantel Wetzel fall/winter/spring
2008–2009 Dawn Dougherty fall/winter/spring
2007–2008 Essington Lab fall/winter/spring<
2006–2007 Ian Taylor fall/winter/spring
2005–2006 Eric Ward all quarters
2004–2005 Jason Cope fall/winter/spring
2003–2004 Lucy Flynn fall/winter/spring
2002–2003 Gavin Fay fall/winter/spring
2001–2002 Carolina Minte-Vera fall/winter/spring
2000–2001 Juan Valero fall/winter/spring
1999–2000 Arni Magnusson fall/winter/spring
1998–1999 Ivonne Ortiz fall/winter /spring
1997–1998 Carlos Alvarez-Flores fall/winter/spring
1996–1997 Billy Ernst fall/winter/spring

Spring 2015 Seminars

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