The Center for Stock Assessment Research (CSTAR) is a partnership started in 2001 between the NMFS laboratories in Santa Cruz and La Jolla, with the objective of undergraduate, graduate and post-graduate training in the basic science associated with the problems of assessing the numerical abundance, spatial distribution, size distribution and reproductive status of commercially important fish species. A broad and deep understanding of population processes is critical to the development and management of sustainable fisheries.

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 CSTAR grant provides level of core support which is then leveraged by teaching assistantships and graduate research assistantships or post-doctoral scholar support from other grants or contracts .This enables us to create a relatively large and interactively group of quantitative scientists working on a wide range of problems in fishery management.

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.

CSTAR Activities and Accomplishments, April 2013-March 2014

CSTAR continued its work of training students and post-docs in quantitative population biology relevant to the mission of NOAA Fisheries and placing them in positions in NOAA Fisheries and beyond.

During this period, CSTAR Representation in the Fisheries Ecology Division Teams included:

-- Groundfish Analysis (CSTAR Alum EJ Dick, CSTAR Post-doc Melissa Monk)

-- Salmon Assessment (CSTAR Alum Will Satterthwaite)

-- Landscape Ecology (CSTAR student Juan Lopez, CSTAR Alum Valerie Brown, CSTAR Researcher Jarrod Santora)

-- Fisheries Economics (CSTAR student Duran Fiack)

-- Early Life History (CSTAR Alum Steve Munch, CSTAR Post-doc Carl Boettiger, Valerie Poynor, Santiago Salinas)

-- Molecular Ecology (CSTAR Alum and Visiting EU Marie Curie Fellow Simone Vincenzi)

and in La Jolla

-- US AMLR (CSTAR Student Kate Richerson)

During the review period, CSTAR students and post-docs continued to do novel and important work in quantitative population biology as it pertains to sustainable fisheries. Some highlights include:

CSTAR sponsored a month-long visit by colleagues Mark Bravington and Marinelle Basson, from the CSIRO lab in Hobart, to work with CSTAR member Eric Andersen and visitor Hans Skaug on close-kin methods for estimating population size. Bravington gave two seminars and Basson one. CSTAR also sponsored seminars (that complemented the regular weekly seminar at NOAA Fisheries) by Dr. Matt Bouro (UC Berkeley), Dr. Andrew Hein (Princeton University), and Dr. Anieke van Leeuwen (University of Amsterdam).

CSTAR sponsored a two week visit by colleague Chris Wilcox, from the CSIRO lab in Hobart, to discuss state space models for animal movement, and application to IUU fishing.

CSTAR PhD student Kate Richerson participated in the AMLR winter cruise. Richerson also co-authored a PLoS biology editorial on interdisciplinary graduate education.

CSTAR PhD student Duran Fiack worked as science adviser to the Watsonville Area Teens Conserving Habitat and began collaborations with the members of the economics team on the effects of fracking on salmon habitat.

CSTAR students Juan Lopez and Daniel Ladd completed MS. Degrees in Statistics and Applied Mathematics.

CSTAR post-doc Melissa Monk developed new methodologies to analyze the recreational fisheries catch data from California and Oregon. The resulting indices of abundance were used for the first time to inform stock assessments in 2013. Monk also participated in the stock assessments of eight data-moderate fish stocks. In addition, Monk, working with Director Mangel and USGS colleague Tim Tinker is developing a population dynamics model for southeast Alaskan sea otters. The U.S. Fish and Wildlife Service will use the model for management of the population and to predict future population sizes.

CSTAR post-doc Carl Boettiger was offered the position of Assistant Professor of Ecoinformatics at UC Berkeley.

CSTAR post-doc Santiago Salinas participated in an invitation only meeting on transgenerational plasticity, in Amsterdam.

CSTAR post-doc Vanessa Labrada Martagon completed her year-long UCMEXUS-CONACyT fellowship, developing models for the life history of green sea turtles, and is lead author on a major review of non-lethal methods for determining reproductive status in marine vertebrates.

Dr. Jarrod Santora joined CSTAR as Assistant Research Applied Mathematician at UCSC. Santora published 11 peer-reviewed papers, received an NSF award from the Office of Polar Programs to conduct 3 research cruises to the Antarctic Peninsula, participated on the second U.S. Antarctic Marine Living Resources winter survey of sea ice conditions and predator-prey interactions, and presented papers at the annual North Pacific Marine Science Organization (PICES) meeting and at the CalCOFI conference.

Dr. Valerie Poynor joined CSTAR as a post-doc, to work with NOAA Fisheries colleague Stephan Munch on Bayesian non-parametric descriptions of population dynamics and fishery management.

CSTAR EU International Outgoing Marie Curie Fellow Simone Vincenzi was invited to present his research on the consequences of extreme events on population dynamics at the EURAEXESS event at Columbia University in March 2014.

CSTAR Director Marc Mangel served as the independent scientific expert witness in the case in the International Court of Justice “Whaling in the Antarctic: Australia v. Japan. New Zealand Intervening” and received the degree of DSc. honoris causa from the University of Guelph.

Current Members of CSTAR

Eric Anderson (Staff Member, NMFS Santa Cruz Laboratory)

Carl Boettiger (NSF Postdoctoral Fellow)

Mariah Boyle (Staff Member, FishWise)

Valerie Brown (Assistant Specialist, UCSC)

Ryan Dricoll (PhD Student, Ocean Sciences, UCSC)

Edward (EJ) Dick (Staff member, NMFS Santa Cruz Laboratory)

Chris Edwards (Faculty, UCSC)

John Field (Staff Member, NMFS Santa Cruz Laboratory; Co-Director)

Xi He (Staff member, NMFS Santa Cruz Laboratory)

Thanassis Kottas (Faculty, UCSC)

Who-Seung Lee (Post-doctoral scholar)

Juan Lopez (PhD student, Applied Mathematics)

Marc Mangel (Faculty UCSC, Co-director)

Melissa Hedges Monk (Staff member, NMFS Santa Cruz Laboratory)

Steve Munch (Staff member, NMFS Santa Cruz Laboratory)

Valerie Poynor (Post-doctoral Scholar)

Steve Ralston (Emeritus Staff member, NMFS Santa Cruz Laboratory)

Kate Richerson (PhD student, Ecology and Evolutionary Biology)

Jarrod Santora (Assistant Research Applied Mathematician, UCSC )

Will Satterthwaite (Staff member, NMFS Santa Cruz Laboratory)

Simone Vincenzi (EU Marie Curie Fellow)

Brian Wells (Staff member, NMFS Santa Cruz Laboratory)

 

Long-term Visitors to CSTAR

Michael Bonsall (Royal Society Research Fellow, Imperial College, January-May 2003; currently Professor of Mathematical Biology, University of Oxford)

Nadiezhda Cantu (Graduate Student, CiBNor, La Paz, Mexico; Spring 2008)

Sigrun Elliasen (Graduate Student, University of Bergen, March-July 2003) Return visit academic year 2011-12 as a Researcher at the University of Bergen

Katja Engberg (Post-doctoral resesearcher, University of Bergen, Fall 2008, 2011)

Jarl Giske (Professor, University of Bergen, Summer and Fall 2010; Summer 2011)

Hiroshi Hakoyama (Research Visitor from the Stock Assessment Division, National Research Institute of Fisheries Science, Japan, February-March 2005)

Christian Jorgensen (Post-doctoral resesearcher, University of Bergen, Fall 2008, 2011)

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

Who Seung Lee (Graduate Student, University of Glasgow, Winter 2009)

Ricardo Lemos (Graduate Student, University of Lisbon, Fall 2004, Winter 2009)

Hans Skaug (PRofessor, University of Bergen, Academic year 2012-13)

Simone Vincenzi (Post-doctoral researcher, University of Parma, Spring 2009; Summer and Fall 2010; Calendar years 2013 and 2014 as EU Marie Curie International Outgoing Fellow)

 

Former members of CSTAR (their CSTAR position) and current positions

Suzanne Alonzo (Post-doc): Professor, Departent of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA

Valerie Brown (MS, Statistics and Applied Mathematics): Research staff, NMFS Santa Cruz Laboratory

Christie Boone (PhD, Anthropology): Principal, Ichthyofaunal Analysis, Seattle, WA

Jacqueline Campos (Assistant to Marc Mangel): Biotech industry

Stephane Carlson (NSF Bioinformatics post-doc): Assistant Professor UC Berkeley

Kate Cresswell (Post-doctoral scholar): Personal leave

Robert Curzon (MS, Statistics and Applied Mathematics): Staff member, McGraw Hill

Katy Doctor (Assistant to Marc Mangel): Staff Member, Washington Department of Fisheries

Daniel Hively (MS, Statistics and Applied Mathematics): Research Staff, School of Fisheries and Aquatic Sciences, University of Washington

Kristen Honey (MA, Enviornmental Studies): NMFS Silver Spring Office

Leah Johnson (PhD Physics): Post-doctoral scholar, University of Chicago

Teresa Ish (MSc, Marine Sciences): Staff Member, Walton Family Foundation

Cynthia Kern (Post-doctoral scholar): Staff Member, NMFS Santa Cruz Laboratory

Holly Kindsvater (Senior Thesis Student): NSF Postdoctoral Fellow in Biology and Mathematics

Taal Levi (PhD, Environmental Studies): Assistant Professor, Department of Wildlife and Fisheries, Oregon State University

Yasmin Lucero (PhD student, Ocean Sciences and NMFS/Sea Grant Fellow): Senior Statistician, Gravity.com

Melissa Monk (Post-doctoral scholar): Staff member, NMFS Santa Cruz Laboratory

Steve Munch (Post-doctoral scholar): Staff member, NMFS Santa Cruz Laboratory

Anand Patil (PhD student, Statistics and Stochastic Modeling): High tech industry

Roxanna Pourzand (Administrative and Scientific Assistant): Oracle Corporation

Santiago Salinas (Post-doctoral scholar): Visiting Assistant Professor, Department of Biology, University of the Pacific

Will Satterthwaite (Post-doc): Staff Member, NMFS Santa Cruz Laboratory

Ole Shelton (Post-doctoral scholar): Staff Member, Northwest Fisheries Science Center

Kate Siegfried (PhD, Environmental Studies): Research Fishery Biologist NMFS Beaufort, NC Laboratory

Chris Simon (Assistant to Marc Mangel): 1010 Data Corp, New York City

Melissa Snover (National Research Council Post-doctoral fellow): Staff Member, Fish and Wildlife Service, Corvallis, OR

David Swank (Post-doctoral scholar): Staff member, NMFS Regional Office, Sacramento

Andi Stephens (PhD, Ocean Sciences): Fishery Biologist, Northwest Fisheries Science Center, Newport, OR

Matt Taddy (PhD, Statistics and Stochastic Modeling): Associate Professor, Graduate School of Business, University of Chicag

John Wiedenmann (PhD, Ocean Sciences): Research Scientist, Rutgers University

Chris Wilcox (PhD, Environmental Studies): Staff Member, CSIRO, Hobart

Nick Wolf (Doctor Philosoph, University of Bergen, supervised by Marc Mangel): Instructor, Cascadia Community College, Seattle , WA

Justin Yeakel (PhD, Ecology and Evolutionary Biology) Postdoctoral Fellow, Santa Fe Institute

 

CSTAR Theses and Technical Reports

T. Ish. 2003. Conceptual Tools for Managing Two Monterey Bay Fisheries. MSc. Thesis, Marine Sciences, UCSC.

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, 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 Consequences of Age-Dependent Maternal Effects in Rockfish (Sebastes spp.). PhD dissertation, Ocean Sciences

M. Taddy. 2008 Bayesian Nonparametric Analysis of Conditional Distributions and Inference for Poisson Point Processes PhD dissertation, Statistics and Stochastic Modeling

E.J. Dick 2009 Modeling The Reproductive Potential of Rockfishes (Sebastes spp.) PhD dissertation, Ocean Sciences

J.R. Wiedenmann 2010 Implications of Climate Change for Antarctic Krill and Their Cetecean Predators PhD dissertation, Ocean Sciences

V. Brown 2011 Implementing State-dependent Models to Investigate Complex Life History Stages and Their Influence on Population Dynamics MS Thesis, Statistics and Applied Mathematics

R.Curzon 2011 Estimating Rates of Natural Mortality for Fish Using Bayesian Linear Regression Methods: A Comprehensive Approach MS Thesis, Statistics and Applied Mathematics

D. Hively 2011 Biological Monitoring in Data Poor Scenarios MS Thesis, Statistics and Applied Mathematics

D.Ladd 2013 Mathematical and Econometric Modelling of Farm Labor Demand and Financial Risk Management MS Thesis, Statistics and Applied Mathematics

J. Lopez Arriaza The Use of Mathematical Models for Informing Management Strategies: An Application in Steelhead Trout and Fleet Dynamics MS Thesis, Statistics and Applied Mathematics

Monk, M., Dick, E.J., Buell, T., ZumBrunnen, L., Dauble, A., and D. Pearson Documentation of a Relational Database for the Oregon Sport Groundfish Onboard Sampling Program NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-519

Monk, M., Dick, E.J. and D. Pearson Documentation of a Relational Database for the California Recreational Fisheries Survey Onboard Observer Sampling Program 1999-2011 NOAA Technical Memorandum NOAA-™-NMFS-SWFSC-529