Finding means to conserve fish populations and to achieve sustainable fisheries requires understanding the effects of fishing on behavior, life history and population biology of exploited fishes. The work at CSTAR focuses on using mathematical, statistical and computer models to solve important environmental and ecological problems. The work is grounded in data, and also seeks to expand the base of basic knowledge that supports rigorous application of science to real-world problems. Furthermore, research on marine fisheries conducted in CSTAR allows testing theoretical predictions via natural and human experiments on a scale that is appropriate for understanding the dynamics of ecosystems. Such large scale experiments are rarely available to the scientific community.
The foci of research at CSTAR are
Spatially explicit population dynamics
This area of research includes studies of variation in population processes in space and time, including variability in demographic processes, movement of individuals and populations, and the genetic structure and dynamics of spatially structured populations, with applications to marine protected areas and understanding the causes and consequences of spatial pattern of fishing effort.
Environmental variability and population processes
This area of research includes studies of the relationship between environment, population dynamics, and life history parameters such as growth rates, asymptotic size and age at first reproduction, with application to understanding the relationship between climate variability and sustainable fisheries.
Risk analysis
This area of research includes studies of decision-making and investment under uncertainty, particularly within a Bayesian framework, and ecological detection, with application to adaptive management.
Fish population and community ecology
This area of research includes studies of the population dynamics of fish, particularly when population size is depressed and multispecies interactions, with application towards recovery of overfished stocks and development of ecosystem-based approaches to understanding natural and human impacts on marine systems.
Scientists at CSTAR are also involved in ecoinformatics, that sub-field of bioinformatics involving the application of mathematics, statistics and information technologies to the analysis of the large ecological data sets which arise naturally in the study of fisheries.
To achieve its goals, CSTAR supports graduate student research and undergraduate internships and senior theses when those students work in partnership with NMFS scientists and UCSC faculty advisors. Graduate students can participate as members of a stock assessment team in their second or third years of graduate school.
The research and training of first class fishery scientists at CSTAR is science done in the national interest and moves in the direction outlined by the National Research Council in its report Recruiting Fihsery Scientists: Workshop on Stock Assessment and Social Science Careers.
Current members of CSTAR
Stephanie Carlson (NSF Bioinformatics Postdoctoral Fellow)
Kate Cresswell (Post-doctoral scholar)
Edward (EJ) Dick (Staff member, NMFS Santa Cruz Laboratory and PhD student, Ocean Sciences)
Xi He (Staff member, NMFS Santa Cruz Laboratory)
Meisha Key (Staff member, California Department of Fish and Game)
Thanassis Kottas (Faculty, UCSC)
Alec MacCall (Staff member, NMFS Santa Cruz Laboratory, Co-director)
Marc Mangel (Faculty UCSC, Co-director)
Steve Ralston (Staff member, NMFS Santa Cruz Laboratory)
Lucinda Robledo (PhD student, Statistics and Stochastic Modeling)
Bruno Sanso (Faculty, UCSC)
David Swank (Post-doctoral scholar)
Matt Taddy (PhD student, Statistics and Stochastic Modeling)
George Watters (Staff member, Pacific Fisheries Environmental Laboratory)
John Wiedenmann (PhD student, Ocean Sciences, UCSC)
Will Satterthwaite (Post-doctoral scholar)
Long-term Visitors to CSTAR
Michael Bonsall (Royal Society Research Fellow, Imperial College, January-May 2003; currently Lecturer at the University of Oxford)
Sigrun Elliasen (Graduate Student, University of Bergen, March-July 2003; currently post-doctoral scholar University of Bergen)
Kai Lorenzen (Sabbatical Visitor from Imperial College of Science and Technology; Fall 2003). While at CSTAR, Lorenzen began work on a software package for fish stock enhancement. This can be found at http://www.aquaticresources.org/enhancefish.htm
Ricardo Lemos (Graduate Student, University of Lisbon, Fall 2004)
Hiroshi Hakoyama (Research Visitor from the Stock Assessment Division, National Research Institute of Fisheries Science, Japan, February-March 2005)
Former members of CSTAR (their CSTAR position) and current positions
Suzanne Alonzo (Post-doc), Assistant Professor, Yale University
Jacqueline Campos (Assistant to Marc Mangel), Biotech industry
Katy Doctor (Assistant to Marc Mangel), PhD student, University of Washington
Kristen Honey (MA, Enviornmental Studies), PhD student, Stanford University
Leah Johnson (PhD Physics), Post-doctoral scholar, University of Cambridge
Teresa Ish (MSc, Marine Sciences), Staff Member, Environmental Defense
Holly Kindsvater (Senior Thesis Student), PhD student, Yale University
Yasmin Lucero (PhD student, Ocean Sciences and NMFS/Sea Grant Fellow), NRC Postdoctoral Fellow, Northwest Fisheries Science Center
Steve Munch (Post-doc), Assistant Professor, SUNY Stonybrook
Anand Patil (PhD student, Statistics and Stochastic Modeling), Postdoctoral Scientist, The Malaria Atlast
Kate Siegfried (PhD, Environmental Studies), Research Fishery Biologist NMFS Panama City Laboratory
Chris Simon (Assistant to Marc Mangel) PhD student, Statistics and Stochastic Modeling UCSC
Melissa Snover (National Research Council Post-doctoral fellow), Staff member, Stock Assessment Division, Protected Species Group, NMFS Pacific Islands Center, Honolulu, HI
Andi Stephens (PhD, Ocean Sciences), Fishery Biologist, Southeast Fishery Management Council
Chris Wilcox (PhD, Environmental Studies) Staff member at CSIRO, Hobart
Nick Wolf (Doctor Philosoph, University of Bergen, supervised by Marc Mangel), Installation Engineer, Akeena Solar, Los Gatos, CA
CSTAR Presentations and Publications
Presentations by CSTAR students, post-docs and faculty
Publications by CSTAR students, post-docs and faculty
Press Releases About CSTAR
General informationArticle from the New Scientist (22March 2003) on Bayesian approaches to stock assessment
Article from the Monterey Herald (2June 2003) on CSTAR
CSTAR Theses and Technical Reports
S. Alonzo, M. Key, T. Ish and A. MacCall. 2004. Status of California Sheephead (Semicossyphus pulcher) Stock (2004). This is the first ever stock assessment for California sheephead.. As part of that work, we also examined sources of data for potential assessments of other species in the Nearshore Management plan:
T. Ish. 2003. Conceptual Tools for Managing Two Monterey Bay Fisheries. MSc. Thesis, Marine Sciences, UCSC.
T. Ish, M. Key and Y. Lucero. 2005. Summary of Data Sources for Stock Assessments for the Species in the Nearshore Fisheries Management Plan (NFMP).
N. Wolf, K. Shea and M. Mangel. 2005. A review of the evidence for density dependence or independence in the life history of Coho (Oncorhynchus kisutch) and other salmonids from the west coast of North America.
Stephens, A. 2005. Assessment in Salmon and Groundfish Fisheries. PhD dissertation, Ocean Sciences
Siegfried, Kate I.2006 Fishery Management in Data-Limited Situations: Application to stock assessment, marine reserve design, and fish by-catch policy. PhD dissertation, Environmental Studies
Johnson, L. 2006. Mathematical Modeling of Cholera: From Bacterial Life Histories to Human Epidemics. PhD dissertation, Physics
N. Wolf 2006. Understanding the Decline of The Western Alaskan Steller Sea Lion: Assessing the Evidence Concerning Multiple Hypothesis. Dr. Philosoph dissertation University of Bergen
A. Patil. 2007. Bayesian Nonparametrics for Inference of Ecological Dynamics. PhD Dissertation, Statistics and Stochastic Modeling
Y. Lucero. 2007. Population Consequneces of Age-Dependent Maternal Effects in Rockfish (Sebastes spp.). PhD dissertation, Ocean Sciences
CSTAR/AMS Lecture Series in Applied Theoretical Ecology 2002-03*
January 13: Per Lundberg, Lund University : Of birds and benthos: on environmental variability, monitoring and community composition
February 10: Larry Crowder, Duke University: Quantitative approaches to sea turtle bycatch: Protecting animals with ocean-sized habitats
February 28: Sarah Newkirk, Stanford University: Property Righs in EEZ Fisheries.
March 10: Russ Lande, UCSD: Accounting for stochasticity and uncertainty in sustainable harvesting strategies
March 14 Daniel Promislow, University of Georgia: Thinking About Longevity; New evolutionary perspectives on an old age problem
April 8: Gunnar Steffanson, Univ. of Iceland and Marine Research Institute, Reykjavik: A statistical approach to multispecies models of the marine ecosystem
April 14: Colette St. Mary, University of Florida.Estimating: Population Demography. Considering Its Implications For Management
May 12: Elizabeth Marschall, Ohio State University, Using optimality models to investigate patterns of energy allocation in fish
CSTAR/AMS Lecture Series in Applied Theoretical Ecology 2003-04*
20 October: Jon Brodziak, NMFS Northeast Fisheries Science Center: What are appropriate rebuilding targets for overfished stocks?
27 October: Katriona Shea, Pennsylvania State University: Management of Populations Under Uncertainty
17 November: Jim Kitchell, University of Wisconsin: Food Webs and Fisheries
24 November: Ron Lee, University of California Berkeley: Rethinking the evolutionary theory of aging: Transfers, not births, shape senescence in social species
10 December: Kai Lorenzen, Imperial College: Population dynamics and potential of fisheries stock enhancement: practical theory for assessment and policy analysis
12 January: Simon Levin, Princeton University: Resiliency and the management of complex adaptive systems.
2 February: Robert Francis, University of Washington: Marine fishery management from an ecosystem prespective:Searching for a path.
23 February: James Brown, University of New Mexico: Towards a Metabolic Theory of Ecology (jointly sponsored by CSTAR and Environmental Studies)
8 March: Enric Cortes, Southeast Fisheries Science Center: Assessment of coastal shark stocks off the U.S. east coast: recent
12 April: Mercedes Pascaul, University of Michigan, Disease-climate couplings: a nonlinear time series model of cholera
17 May: Paul Dayton, Scripps Institution of Oceanography, The loss of nature and the nature of the loss: impacts of specialization
24 May: Caleb Finch, University of Southern California, The nexus of diet and inflammation in the evolution of human longevity
CSTAR/AMS Lecture Series in Applied Theoretical Ecology 2004-05
27 September Ricardo Lemos, Instituto de Oceanografia - Faculdade de Ciencias da Universidade de Lisboa: Climate Change and Coastal Upwelling Ecosystems
4 October Colin Clark, University of British Columbia: Fisheries Management -- The Problem of Overcapacity
18 October Ray Hilborn, University of Washington: Biocomplexity and fisheries sustainability
22 November Nadav Nur, Quantitative Ecology Program, PRBO Conservation Science: Population responses of Cassin's Auklets to changes in oceanographic condition: proximate and ultimate factors
10 January Pat Livingston, NOAA Fisheries, Alaska Fisheries Science Center: The role of multispecies and ecosystem models in a framework for assessing ecosystem impacts of fishing
24 January Lillian Hoddeson, Department of History, University of Illinois: John Bardeen's approach to problem solving
7 February Claudia Neuhauser, Department of Ecology, Evolution and Behavior, University of Minnesota: The role of space in trophic interactions
28 February Hiroshi Hakoyama, National Research Institute of Fisheries Science, Yokohama, Japan: Extinction risk of a population: estimation, aggregration and model selection
7 March Carlos Castilla-Chavez, Arizona State University: Dispersal, disease and life history evolution
5 May Sir John Krebs FRS, Department of Zoology, University of Oxford: Risk: food fact and fantasy
6 May Sir John Krebs FRS, Department of Zoology, University of Oxford: Science and policy -- handling uncertainty
16 May Dan Goodman, University of Montana: A theoretician looks at salmon supplementation
CSTAR/AMS Lecture Series in Applied Theoretical Ecology 2005-06
October 10 Leonid and Natalia Garrilov, University of Chicago (local host: Leah Johnson). Two talks:
Testing Biological Ideas on Evolution, Aging and Longevity with Demographic and Genealogical Data (Natalia Gavrilova, Leonid Gavrilov); http://longevity-science.org/Evolution-Chicago-2005.pptReliability Theory of Aging and Longevity (Leonid Gavrilov, Natalia Gavrilova) http://longevity-science.org/Reliability-Chicago-2005.ppt
November 21 Derek Roff, Univesity of California Riverside, Growth or mortality costs: which determines the evolution of the optimal life history?
January 9 Jason Link, Northeast Fisheries Science Center, Marine Fish, People, and the Ecosystems They Share
March 6 Paul Rago, Northeast Fisheries Science Center, Complex population dynamics and stock dynamics
March 13 John Vucetich, Michigan Technological Univesity, Population dynamics of wolf and moose on Isle Royale
April 10 Roger Nisbet, University of California Santa Barbara, Population dynamics in advective systems
April 21 Laura Richards, Pacific Biological Station, Managing fisheries in the context of environmental change
April 24 Jon Schnute, Pacific Biological Station, Reference points and management strategies: lessons from quantum mechanics
*The CSTAR/AMS Seminar Series in Applied Theoretical Ecology 2002-03 and 2003-04 was sponsored by the California Sea Grant and the Center for Stock Assessment Research
Course in WinBUGS for Fisheries Scientists
In May 2006, CSTAR offered a three-day course to introduce fisheries scientists to Bayesian estimation using WinBUGs software. It was led by Dr. Murdoch McAllister (Imperial College) . The following topics were covered.
Day 1: 9AM-5PM
Morning Session: Introduction to Bayesian methodology
Exercise: Linear regression analysis
- Introduction to the problem and traditional regression analysis
- Bayesian and Frequentist linear regression analysis using Excel
- Bayesian and Frequentist hypothesis testing using Excel
- Interpretation of the results
Afternoon Session: Introduction to WinBUGS
- Model syntax
- Compiling the model
- Initial values
- Updating and monitoring
Exercise: Linear regression analysis in WinBUGS
- Parameter estimation
- Hypothesis testing
- Model prediction
Day 2: 9AM-5PM0
Morning Session: Markov chain Monte Carlo for sampling from the posterior distribution: dangers, diagnostics and dealing with model uncertainty
Exercise: Model diagnostics, DIC, Bayes’ Factors in linear regression analysis
Exercise: Developing growth model in WinBUGS e.g. von Bertalanffy growth model
Afternoon Session:
Exercise:Using different probability distributions
Exercise: Setting up WinBUGS programs using participant's own data
Day 3: 9AM-5PM
Morning Session: Hierarchical models: advantages, exchangeability, hyperpriors
Exercise: Estimating stock-recruitment parameters in a hierarchical meta analysis
Exercise: The Schaefer surplus production model
Afternoon Session
Exercise: Using tagging data in WinBUGS
Marc Mangel and Alec MacCall (Alec.MacCall@noaa.gov, NMFS-SCL) are co-PIs of the CSTAR grant. Either one can be contacted for further information.
CSTAR/AMS Lecture Series in Applied Theoretical Ecology 2007-08
Oct 22: Marc Mangel: How To Do SDP in Biology. 1) The Crisis of the Common Currency and Patch Choice
Oct 29: Marc Mangel: How To Do SDP in Biology.2) Numerical Implementation of the Patch Choice Algorithm
Nov 5: Barney Luttbeg (UC Davis): Predator and prey movement rules shaped by game dynamics
Nov 19: Marc Mangel: How To Do SDP in Biology 3) Allocation Problems
All talks start promptly at 12:30 in Baskin Engineering 330.