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.

Autumn 2017  seminar

Fridays at 12:30-1:30pm in FSH 203 

Join the seminar remotely.


Maia Kapur

Fisheries Assessment Specialist, Pacific Islands Fisheries Science Center (NOAA)

Modeling the effects of selective harvesting on Kona crab (Ranina ranina) in the Main Hawaiian Islands


The Kona crab (Ranina ranina) is a widely dispersed crustacean harvested for commercial and recreational consumption throughout the tropical Pacific. It is one of the principal commercially harvested crab in the Hawaiian islands. Restrictions on the Hawaii Kona crab fishery began in 1938 with a minimum 4-inch carapace size limit for selling of crabs, a no-take of berried female crabs and a closed season from June through August. The most recent regulation prohibiting the taking of any female crabs was implemented in September of 2006, with the aim to protect large, fecund female crabs. This study provides demographic and risk analysis to examine the effects of varied harvest scenarios, wherein females undergo 0-90% post-release mortality under a suite of minimum capture sizes, to identify trigger points of population decline in a stochastic framework. The results indicate that, when selectivity includes crabs less than legal size, a post-release mortality value greater than 62% has a significant negative impact on r for this population. Although this study sourced multiple modern biological methods to model the growth, reproduction and mortality of crustaceans, it makes many assumptions about their population dynamics and ability to respond to fishing pressure. We look forward to audience feedback regarding the simulation approach and best representations of crustacean biology.


Grant Adams

PhD Student in SAFS – Punt Lab

Spatial variability in the individual growth of Sheepshead (Archosargus probatocephalus) in the Southeast US: Implications for assessment and management


Understanding geographic variation in individual growth dynamics is essential for the management of exploited fish populations because such variations are used to define stock structure and influence perceptions of stock productivity. Sheepshead (Archosargus probatocephalus) is a species targeted by both commercial and recreational fisheries and is distributed throughout the Gulf of Mexico and Atlantic Ocean. To investigate the spatially-dynamic individual growth of Sheepshead we analyzed fishery-dependent and –independent length-at-age and weight-at-length data from Texas, Louisiana, Mississippi, Alabama, Florida, South Carolina, North Carolina, and Virginia. We constructed a hierarchical von Bertalanffy growth function (VBGF) and power equation in the Bayesian framework that included sex and state effects and terms to limit biases from errors in observation. Median posterior VBGF parameter estimates of asymptotic length (Linf) ranged from 579 mm fork length in the Virginia Chesapeake Bay to 539 mm in Texas, while growth coefficient (k) ranged from 0.43 yr-1 in Mississippi to 0.14 yr-1 in the Virginia Chesapeake Bay. Predicted length-at-age and weight-at-length varied considerably among states. For age-1 and -5 individuals, predicted length-at-age was greater in the Gulf of Mexico than the Atlantic. However, for older age classes, predicted length-at-age was greater in the Atlantic. Predicted weight-at-length decreased along latitudinal gradients in the Atlantic and the lowest values were found in Alabama and Mississippi. Given the impact of individual growth on fisheries reference points, spatially-dynamic growth illustrated in the present study can inform the development of assessment efforts for Sheepshead in the Gulf of Mexico and Atlantic.


Andre Punt

Director of School of Aquatic and Fishery Sciences, University of Washington

Evaluating the US approach for Managing Human-Caused Mortality of Marine Mammals: Beyond the PBR Formula


The US system for managing the human-caused mortality of marine mammals is one of the most sophisticated in the world, with a limit on such mortality computed using the Potential Biological Removal, PBR, formula. Fisheries are categorized according to their impact relative to PBR, and Take Reduction Teams established to develop Take Reduction Plans when bycatch exceeds PBR. The default values of the parameters of the PBR formula were selected using Management Strategy Evaluation, but the entire system has yet to be evaluated in its entirety. A MSE framework is developed that includes the PBR formula as well as the processes for evaluating whether a stock is ‘strategic’, assigning fisheries to categories, and implementing a Take Reduction Plan. Ignoring the latter two components of management (i.e. fisheries classification and implementation of TRPs) was found not to impact the predictions related to the ability to achieve the conservation objective established for a stock under the US Marine Mammal Protection Act [i.e. recover (or maintain) the stock to (at) its optimum sustainable population level]. However, this ability is highly dependent on the life history and absolute size of the species being managed. The probability of correctly classifying fisheries depends on both the CV of the estimates of bycatch as well as the CV of the survey estimates of the marine mammal stock’s abundance because classification depends on the ratio of the estimate of bycatch by fishery-type to the PBR, and the precision of the former depends on the bycatch CV and the latter on the abundance estimate CV.

Brian Stock PhD Student in Semmens Lab, Scripps Institution of Oceanography, UCSD
What spatial model is best for predicting fisheries bycatch risk?
Bycatch (i.e. catch of at least some non-targeted species) is an omnipresent problem in commercial and recreational fisheries. High bycatch rates can reduce the efficiency and sustainability of fisheries, but even extremely low bycatch rates can be a problem for protected or rebuilding species. Given these economic and environmental concerns, the fishing community would be well served by tools that predict, and ultimately help avoid, bycatch. I will demonstrate the ability of a new, computationally efficient spatial statistics method, Gaussian Markov Random Fields (GMRFs) implemented in R-INLA software, to produce bycatch risk maps using two large U.S. fisheries observer datasets. I compare the GMRF approach with two other species distribution model frameworks, generalized additive models (GAMs) and random forests (RF), and show how the models’ performance differs for species with a broad range of bycatch rates, from leatherback sea turtles (0.7%) to blue sharks (96%) in the Hawaii longline fishery, and yelloweye rockfish (0.3%) to Pacific halibut (29%) in the West Coast groundfish trawl fishery.
Jacqueline Padillo-Gamiño Assistant Professor, School of Aquatic and Fisheries Sciences, University of Washington
Coral reproduction, parental effects and physiological mechanisms involved in the allocation of energy under thermal stress. Currently coral reefs, which are one of the most diverse ecosystems in the world, are being critically impacted by thermal stress due to global warming. Consecutive bleaching events in the last three years have led to some of the most widespread mortality on reefs around the world. To date, most studies have focused on the potential of adult colonies to recover and acclimatize from stress. However, the persistence of future reefs will not only require the survival of adult coral but will also be dependent upon a coral’s ability to continue sexual reproduction under the influence of thermal stress. To date, little is known about the mechanisms corals use to tolerate and successfully reproduce in stressful environments. In this talk, I will focus on an important and dominant reef builder in Hawaii that has the capacity to reproduce sexually despite bleaching due to thermal stress. I will share results of reproductive assessments in the field and ecophysiological investigations to understand how the coral offspring is affected by the health state of the parental colony. I will also discuss a current NSF-funded project that explores the role of nutrition in coral health using proteomics and tracking the contribution of carbon and nitrogen acquired from parental photosynthesis and heterotrophy to gamete development in bleached and unbleached colonies. I look forward to audience feedback on how to integrate coral reproductive and physiological data to develop models to predict population dynamics under different global change scenarios.
Eiren Jacobson
Postdoctoral Research Associate, NOAA AFSC
Developing a passive acoustic monitoring network for harbor porpoise in California
Researchers are increasingly interested in incorporating non-visual and remote observations to improve cetacean population assessments. Passive acoustic monitoring (PAM) can complement or replace visual surveys for cetaceans that produce echolocation clicks, whistles, and other vocalizations. For my doctoral dissertation, I used the Monterey Bay population of harbor porpoise as a case study to develop methods for long-term monitoring of harbor porpoise using PAM. Two major aspects of this project were 1) using paired visual and passive acoustic surveys to estimate the effective detection area of the passive acoustic sensors and 2) using historical aerial survey and passive acoustic data in a simulation framework to investigate the statistical power of different passive acoustic network designs to detect hypothetical changes in harbor porpoise abundance. I found that it is possible to estimate the abundance of harbor porpoise using passive acoustic data and that these data may have greater power to detect trends in abundance than traditional visual surveys. This dissertation used an applied approach to methods development to demonstrate the potential use of PAM for long-term monitoring of cetaceans.


Dr. Rosana Ouréns

Fisheries Scientist, Centre for Environment, Fisheries and Aquaculture Science (CEFAS)

The common fisheries policy in Europe and its implications for small-scale fisheries

Fisheries are complex and dynamic systems difficult to be governed. The reasons are multiple: large diversity of stakeholders, fishing resources, ecosystems, and their interactions; high levels of uncertainty relating to the ecosystems and fisher behaviour; the high vulnerability of fishing communities to climate change; growing competition with other economic sectors; mismatches between ecological and political boundaries; etc. In the European Union, the Common Fisheries Policy (CFP) is the main instrument to manage EU fishing activities and face these complexities. Rosana Ourens will talk in the seminar about the last reform of the CFP implemented in 2014, its successes and failures, as well as the challenges and new opportunities for small-scale fisheries.



Thanksgiving Holiday – No Quantitative Seminar



Lee Cronin-Fine

PhD Student in SAFS – Punt Lab

A numerical method for allowing individual variation in both growth parameters (k and L∞) in size-structured models


Stock assessment methods for many invertebrate stocks, include stocks of crabs in the Bering Sea and

Aleutian Islands region of Alaska, are based on size-structured population dynamics models. A key component of these models is the size-transition matrix, which specifies the probability of growing from one size-class to another after a certain period of time. Size-transition matrices can be defined using three parameters, the growth rate (k), the asymptotic height (L∞), and the variability in the size increment. Stock assessments can either set the size-transition matrix by analyzing mark-recapture data prior to conducting the stock assessment or the estimation of the size-transition matrix can be integrated into the stock assessment. The latter approach will better allow uncertainty in model outputs to be characterized, but can substantially increase the complexity of the assessment. Consequently, most assessments that integrate mark-recapture data into stock assessments, assume that all individuals followed the same growth curve. However, not accounting for individual variation in growth can result in biased estimators of growth parameters and it is unrealistic to assume that every individual has the same k or L∞. Unfortunately, to date, the only way to compute the size-transition matrix when allowance is made for individual variation in growth is using simulation, which is both computationally very intensive and non-differentiable. This presentation outlines an approach that uses a numerical integration technique that allows k and L∞ to vary among individuals, and evaluates it by comparing the results with a simulation-based estimation scheme.



Jon Reum

Research ecologist, NOAA Alaska Marine Fisheries Science Center/UW

Species-specific ontogenetic diet shifts lengthen food chains and attenuate trophic cascades in exploited ecosystems


Ontogenetic shifts in diet are pervasive in marine and freshwater predators and indicate a relationship between population size structure and the functional roles occupied by a species. Yet food web models often represent species or functional groups as single nodes in trophic networks and ontogenetic shifts in diet are rarely addressed. Multispecies size spectrum models (MSSMs) are a recently developed class of models that explicitly represent the size structure of species composing food webs. Predation interactions are described mechanistically using only a few assumptions regarding the prey size- and species-preferences of predators and predator-prey interactions and ontogenetic diet shifts are emergent in the model. However, their ability to adequately represent species-specific ontogenetic shifts in diet remain untested. We developed a novel extension to MSSMs that enables species-specific ontogenetic shifts in the prey-preference of predators and demonstrate an approach for incorporating diet information into a model calibrated for the Eastern Bering Sea (EBS), a highly productive fished ecosystem. We tested whether the extended model predicted predator diets better than previous model versions and if the inclusion of species-specific ontogenetic shifts in diet influenced the potential for fishing-induced trophic cascades in a simulation experiment. The extended MSSMs substantially outperformed the other models when confronted with diet data outside the calibration time period and was able to capture complex ontogenetic dietary shifts. Further, the diet-informed models resulted in longer food chains and exhibited lower predation mortality rates, particularly for small individuals (less than 1 g) which, in turn, reduced the intensity and reach of fishing-induced trophic cascades up the size spectrum. If the level and size dependency of piscivory observed in EBS predators is typical of other systems, the potential for fishing-induced trophic cascades may be over-stated in MSSMs as they are currently formulated and parameterized. Representation of species-specific ontogenetic shifts in diet can strongly influence system responses to perturbations, and the extension we propose should accelerate adoption of MSSMs as frameworks for exploring size-based food web theory and developing modeling tools to support strategic management decisions.

Recent seminar topics and abstracts

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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