Stock Identification Methods

Applications in Fishery Science

Steven X. Cadrin, Lisa A. Kerr, Stefano Mariani

• Publisher: Academic Press
• Year: 2013
• ISBN:
  9780123972583
• Edition: 2
• Topic: Technology & Engineering
• Subtopic: Fisheries & Aquaculture
• Index: Technology & Engineering

Stock Identification Methods, 2e, continues to provide a comprehensive review of the various disciplines used to study the population structure of fishery resources. It represents the worldwide experience and perspectives of experts on each method, assembled through a working group of the International Council for the Exploration of the Sea. The book is organized to foster interdisciplinary analyses and conclusions about stock structure, a crucial topic for fishery science and management.

Technological advances have promoted the development of stock identification methods in many directions, resulting in a confusing variety of approaches. Based on central tenets of population biology and management needs, this valuable resource offers a unified framework for understanding stock structure by promoting an understanding of the relative merits and sensitivities of each approach.

• Describes 18 distinct approaches to stock identification grouped into sections on life history traits, environmental signals, genetic analyses, and applied marks
• Features experts' reviews of benchmark case studies, general protocols, and the strengths and weaknesses of each identification method
• Reviews statistical techniques for exploring stock patterns, testing for differences among putative stocks, stock discrimination, and stock composition analysis
• Focuses on the challenges of interpreting data and managing mixed-stock fisheries

Chapter One

Stock Identification Methods

An Overview

Steven X. Cadrin¹, Lisa A. Karr^1,2 and Stefano Mariani³, ¹University of Massachusetts, School for Marine Science and Technology, New Bedford, MA, USA, ²Gulf of Maine Research Institute, Portland, ME, USA, ³School of Environment and Life Sciences, University of Salford, Manchester, United Kingdom

Abstract

Stock identification involves delineation of population structure of fishery resources—a central theme in fisheries science and management. Developments in molecular biology and chemistry and advances in image analysis and tagging technologies have prompted revolutionary changes in many stock identification approaches. Stock identification is developing as an increasingly interdisciplinary field and has become a requisite component of fishery science and management programs performed worldwide by research institutions and government agencies.

Continued sophistication of technological aspects across disciplines (from genomics to modeling) and improved understanding of biological and environmental processes in the oceans have led to a dramatically reappraised second edition of Stock Identification Methods. This book provides a new outlook on recently developed techniques, and continues to provide guidance on how to integrate information from multiple stock identification approaches and draw holistic and robust conclusions that have practical implications for fisheries management and conservation biology.

Keywords

Glossary; Methods; Stock Identification

Chapter Outline

Glossary

Acknowledgments

References

Acknowledgments

We thank the chapter authors for their dedication of time, energy, and expertise to this initiative. We also thank Kevin Friedland and John Waldman for their leadership in producing the first edition. The ICES Stock Identification Working Group and other collaborators have been an active influence on our thoughts and the organization of this book. We thank ICES for their continued support and the staff at Elsevier for their help.

Stock identification is a central theme in fisheries science that involves the recognition of self-sustaining components within natural populations. Stock identification is a prerequisite for the tasks of stock assessment and fishery management because most applied population models assume that the group of individuals has homogeneous vital rates (e.g., growth, maturity, mortality) and a closed life cycle, in which young fish in the group were produced by previous generations within the same group.

Secondary roles for stock identification in fishery science are also important but less obvious. Any study that wishes to represent a living resource through field sampling, or even laboratory studies, should consider the species' population structure in the sampling and analytical design. Whether the research concerns general life history, growth, physiology, or diet, the population of inference and its stock components should be identified. Therefore, stock identification can be viewed as a prerequisite for any fishery analysis, just as population structure is considered a basic element of conservation biology (Crandall et al., 2000; Thorpe et al., 1995).

Despite its importance in the development of fishery advice and management, stock identification continues to be an afterthought. The fishery science community has a habit of building assessments from back to front, often only giving cursory treatment to stock identification, and in the name of being expeditious, population vital rates are estimated without regard to lingering questions about stock structure. We hope that this volume will not only provide source material to improve the quality of stock identification research but also may stimulate new research on stocks being assessed without the benefit of reliable stock identification.

One reason for the reluctance to prioritize stock identification is that it remains one of the most confusing subjects in fisheries science, with a wide variety of approaches, rapidly advancing methodologies, challenges in sampling, as well as conflicting terminologies and interpretations. There have been some excellent reviews of stock identification research, including concise overviews (Simon and Larkin, 1972; Templeman, 1982; Pawson and Jennings, 1996; Waldman, 1999) and conference proceedings that include various case studies (Ihssen et al., 1981; Kumpf et al., 1987; Begg et al., 1999). However, many of the case studies on stock identification are result oriented and narrowly focused, and overview perspectives lack the detail needed to guide researchers.

In 1992 the International Council for the Exploration of the Sea (ICES) established a “Study Group on Stock Identification Protocols for Finfish and Shellfish Stocks” to review methodologies of stock identification and develop a protocol for the application of stock identification results. The support of this work by the ICES community reflects the continuing leadership of ICES in oceanographic and fishery research. Coincidentally, it was an ICES committee that first promoted stock identification as an important consideration for fishery science in the early 1900s (Smith, 1994). The ICES Study Group was organized in an open format to invite a wide participation of experts on stock identification to summarize the various approaches. Over the following decade, the group expanded to the “Study Group on Stock Identification Methodology” and developed a volume of contributions to review each existing method, with emphasis on recent advances, review of benchmark case studies, critique of strengths and weaknesses, and guidance for effective protocols. The compilation provided the basis for the first edition of this book (Cadrin et al., 2005). The compendium of methodological reviews was designed to serve as a resource for researchers interested in comparative studies in stock identification as well as a general introduction for all scientists and managers of natural resources. Methodological chapters were not necessarily comprehensive reviews but focused more on historical development, benchmark case studies, critique of current issues, and prescriptions for the most effective protocols for stock identification.

One theme that emerged throughout the development of this volume was the strength of interdisciplinary analyses. Over the history of stock identification, new methods were developed and promoted as better ways to approach stock identification, often leading to equivocal information from competing methodological camps. However, when results from each approach are viewed in the context of what precise aspect of stock structure they reveal (defined in this volume), a more holistic view with multiple perspectives is possible, providing more reliable information for resource management. As new methods continue to emerge, their results should be considered along with those from traditional approaches to improve our ability to study stock structure.

After publication of the first edition, the “Working Group on Stock Identification Methods” continued to serve ICES. Each year the working group summarized advances in the field and formed recommendations on specific stock identification issues related to ICES advice. The second edition was developed to update the information on advancing technologies and interdisciplinary approaches to fish stock identification. Developments in molecular biology, electronic tags, chemical methods, and image analysis have prompted revolutionary changes in many stock identification approaches. In the foreword of the 2005 edition, Mike Sissenwine stated that “Although this volume will be a valuable reference for years to come, I think that we should all be excited by the prospect of innovative advances in the near future that surely will render some of the conclusions in the book out of date. The scientists responsible for the volume, and ICES as the sponsor of the Working Group, do not want to rest on their laurels. Advances in biochemistry, analytical chemistry, and electronics (including microtechnology with nanotechnology on the horizon) foretell a very productive era unfolding when it comes to stock information in support of better science and better resource management. Speaking as both the President of ICES and the Chief Science Advisor for the US National Marine Fisheries Service, I look forward to important and exciting discoveries in the future.”

The general goals of the second edition were to: (1) update each chapter with information on the technological and methodological advances in the last decade and (2) address a shortfall of the first edition by providing guidance on how to integrate information from multiple stock identification approaches to draw interdisciplinary conclusions. More specifically, several new genetic techniques have been developed and refined, while others have been so rapidly superseded that they no longer find space in the stock identification methods tool kit. Electronic tagging technology has also rapidly advanced in the last decade with technological developments in acoustic, archival, and satellite tags. Additionally, simulation studies have emerged as a useful tool for integrative analyses and understanding the practical implications of stock structure for fishery management and conservation biology. The revised final section of the book describes applications of stock identification for fishery management and conservation biology through interdisciplinary analysis and synthesis.

This book provides guidance on best practices for stock identification so scientists and managers can confront the complex issues and management challenges that they are faced with. This new edition also offers a glossary at the end of this chapter to standardize terminology and promote consistent use of terms. We hope that the ideas in this volume can be developed and applied in a wide range of scenarios so management units can be practical reflections of biological population structure.

Glossary

Adaptive genetic markers Genetic markers whose variation depends on the action of natural selection.

Biological population A self-sustaining group of ind...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• List of Contributors
• Foreword
• Introduction
• Chapter One. Stock Identification Methods: An Overview
• Chapter Two. The Unit Stock Concept: Bounded Fish and Fisheries
• Chapter Three. Fishery Management Strategies for Addressing Complex Spatial Structure in Marine Fish Stocks
• Chapter Four. Quantitative Traits
• Chapter Five. The Continuing Role of Life History Parameters to Identify Stock Structure
• Chapter Six. Morphometric Landmarks
• Chapter Seven. Morphometric Outlines
• Chapter Eight. Analysis of Growth Marks in Calcified Structures: Insights into Stock Structure and Migration Pathways
• Chapter Nine. Meristics
• Chapter Ten. Parasites as Biological Tags
• Chapter Eleven. Chemical Composition of Fish Hard Parts as a Natural Marker of Fish Stocks
• Chapter Twelve. Fatty Acid Profiles as Natural Marks for Stock Identification
• Chapter Thirteen. Application of Mitochondrial DNA in Stock Identification
• Chapter Fourteen. The Nuclear Genome: Neutral and Adaptive Markers in Fisheries Science
• Chapter Fifteen. The Use of Early Life Stages in Stock Identification Studies
• Chapter Sixteen. Conventional and Radio Frequency Identification (RFID) Tags
• Chapter Seventeen. Acoustic and Radio Telemetry
• Chapter Eighteen. Estimation of Movement from Tagging Data
• Chapter Nineteen. Telemetry Analysis of Highly Migratory Species
• Chapter Twenty. Sampling for Interdisciplinary Analysis
• Chapter Twenty One. Simulation Modeling as a Tool for Synthesis of Stock Identification Information
• Chapter Twenty Two. Interdisciplinary Evaluation of Spatial Population Structure for Definition of Fishery Management Units
• Index