Molecular Genetics in Fisheries PDF
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Molecular Genetics in Fisheries Molecular Genetics in Fisheries Edited by Gary R. Carvalho Marine and Fisheries Genetics Laboratory University ofWales, Swansea, UK and Tony J. Pitcher Fisheries Centre University of British Columbia, Canada lal'l SPRINGER-SCIENCE+BUSINESS MEDIA, B.V. First edition 1995 © 1995 Springer Science+Business Media Dordrecht Originally published by Chapman & HalI in 1995 ISBN 978-0-412-62950-1 ISBN 978-94-011-1218-5 (eBook) DOI 10.1007/978-94-011-1218-5 Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the UK Copyright Designs and Patents Act, 1988, this publication may not be reproduced, stored, or transmitted, in any form or by any means, without the prior permission in writing of the publishers, or in the case of reprographic reproduction only in accordance with the terms of the licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of licences issued by the appropriate Reproduction Rights Organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to the publishers at the London address printed on this page. The publisher makes no representation, express or implied, with regard to the accuracy ofthe information contained in this book and cannot accept any legal responsibility or liability for any errors or omissions that may be made. A catalogue record for this book is available from the British Library 8 Printed on permanent acid-free text paper, manufactured in accordance with ANSIINISO Z39.48-1992 and ANSIINISO Z39.48-1984 (Permanence ofPaper). Contents Preface vii 1 Developments in molecular genetic techniques in fisheries 1 Linda K. Park and Paul Moran 2 Appraisal of molecular genetic techniques in fisheries 29 Robert D. Ward and Peter M. Grewe 3 Molecular genetics and the stock concept in fisheries 55 G. R. Carvalho and L. Hauser 4 The role of molecular genetic markers in the management of cultured fishes 81 M.Ferguson 5 Perspectives of molecular genetics and fisheries into the 21st century 105 Fred M. Utter 6 Molecular genetics in fisheries: current and future perspectives 111 Andrew Ferguson 7 Microsatellites: genetic markers for the future 117 Jonathan M. Wright and Paul Bentzen 8 Molecular genetics applications in fisheries: snake oil or restorative? 123 Rich Lincoln Glossary of terms 127 Index 135 Preface The basic principle of all molecular genetic methods is to employ inherited, discrete and stable markers to identify genotypes that characterize individuals, populations or species. Such genetic data can provide information ori the levels and distribution of genetic variability in relation to mating patterns, life history, population size, migration and environment. Although molecular tools have long been employed to address various questions in fisheries biology and management, their contributions to the field are sometimes unclear, and often controversial. Much of the initial impetus for the deployment of molecular markers arose from the desire to assess fish stock structure based on various interpretations of the stock concept. Although such studies have met with varying success, they continue to provide an impetus for the development of increasingly sensitive population discriminators, yielding information that can be valuable for both sustainable exploitation and the conservation of fish populations. In the last major synthesis of the subject, Ryman and Utter (1987) summarized progress and applications, though this was prior to the wide-scale adoption of DNA methodology. New sources of genetic markers and protocols are now available, in particular those that exploit the widely distributed and highly variable repeat sequences of DNA, and the amplification technique of the polymerase chain reaction. The innate desire of many geneticists to disclose ever increasing levels of genetic diversity has, however, produced a daunting variety of tools to choose from, and it is often unclear how to match the technique to the question under study. Indeed, the advances in technology sometimes appear to have developed with little recourse to how and why they may help. The time therefore appears ripe to review the range of approaches available, their relative strengths and weaknesses, and the diversity of applications to which they are best suited. An important aim of this book is to make it accessible to the non specialist: we include an introductory chapter on basic principles of gene and protein structure in relation to the current methodologies, and a glossary of terms to provide guidance through complex terminology. Our overall aim is to provide an objective appraisal of the criteria required to plan a molecular genetics fishery project, including information on sampling logistics, information content, costs and appropriate data analysis of the various approaches. This fundamental information is illustrated throughout by informative examples of its various applications. In this book, we have invited four main review chapters. Linda Park and Paul Moran provide an introductory chapter which reviews the fundamental nature of genetic variation detectable at the protein and nucleic acid levels, and they explain the range of techniques available to measure it. Bob Ward and Peter Grewe consider the relative strengths and limitations of the alternative approaches, and the type of data they provide. Illustrative examples include studies in stock structure analysis, aquaculture and species discrimination. Gary Carvalho and viii Preface Lorenz Hauser discuss the contribution of molecular genetics to the stock concept by considering critically the meaning of the term 'stock', and how such information can be employed to manage a fishery. Both short-term (persistence of self sustaining entities) and long-term (conservation of genetic resources) management objectives are considered in relation to molecular genetic data. Moira Ferguson reviews the application of molecular genetics to the management of cultured fishes, including its contribution to the use of stocks in culture facilities, and the detection of interactions between cultured and wild fish. The four Points of View authors cover several historical and practical perspectives, with particular emphasis on the most promising ways forward. Fred Utter provides an historical perspective on the application of molecular genetics to fishery management, summarizing the diversity of questions currently tackled. Andrew Ferguson presents a critical review of fundamental concepts, and identifies some common misunderstandings of data analysis and interpretation. Jonathan Wright and Paul Bentzen advocate the benefits of using microsatellite analysis coupled with the polymerase chain reaction, and summarize some recent promising results. Richard Lincoln discusses the value of molecular genetics data from the viewpoint of a practising fishery manager. The diversity of opinions expressed exemplify the continuing vitality of debate, though four common themes emerge: first, the continuing value of allozyme electrophoresis for many routine population studies; secondly, the importance of a sound understanding of population genetics to fully analyse and interpret the data generated; thirdly, the need to link genetic markers to measures of fish performance (e.g. reproductive success) and finally, the demand for improved communication between molecular geneticists and fishery managers. It is indeed the frequent inability of molecular geneticists and managers to communicate in mutually understandable terms that has generated obstacles to cooperation and led to missed opportunities. It is critical that fishery managers provide clear questions of priority, and that molecular geneticists respond by employing realistic and appropriate methodologies, but only if such approaches are going to help: unrealistic claims by either side will foster mistrust and the persistence of prejudiced views. We hope that this book will provide a balanced review of the current field, and in so doing, encourage collaboration between fishery managers and molecular geneticists, and serve to stimulate further debate and applications. Molecular Genetics in Fisheries was also published as a Special Issue of the journal Reviews in Fish Biology and Fisheries, edited by Tony J. Pitcher and published by Chapman & Hall. The editors would like to thank Dr Gavin Gatehouse (Bangor, UK) for providing facilities (GRC) during the final stages of editing, Professor John Beardmore (Swansea, UK) for supporting the provision of study leave (GRC) to facilitate editorial duties, Dr Chris Gliddon (Bangor, UK) for his helpful comments on the glossary, Dr A. R. Child (MAFF, Conwy, UK), Dr M. G. Pawson (MAFF, Lowestoft, UK) and eight anonymous referees for their valuable comments on the manuscripts, and all authors for following a tight and demanding schedule. Preface ix Reference Ryman, N. and Utter, F. (1987) Population Genetics and Fishery Management. Seattle and London: Washington Sea Grant Program, Univ. Washington Press. Gary R. Carvalho and Tony J. Pitcher Swansea, UK and Vancouver, Canada 1 Developments in molecular genetic techniques in fisheries LINDA K. PARK* and PAUL MORAN National Marine Fisheries Service, Northwest Fisheries Science Center, Coastal Zone and Estuarine Studies Division, 2725 Montlake Boulevard East, Seattle, WA, 98112, USA Contents Introduction page 1 Molecular genetic markers 2 Isozymes DNA Coding and non-coding DNA Non-repetitive and repetitive DNA Mitochondrial DNA Nuclear DNA DNA-level variation Hybridization of DNA molecules Molecular genetic techniques 9 Gel electrophoresis Restriction enzymes Polymerases PCR Sequencing Ligases Comparison of various molecular methods for fisheries applications 16 The future of molecular genetics in fisheries 21 Acknowledgements 22 References 22 Introduction The use of molecular genetic techniques in fisheries research has increased dramatically over the past several years, largely due to the increased availability of techniques and an increased awareness of the value of genetic data. Today, the boundaries of fisheries related molecular genetic research encompass topics from the identification of markers for stock discrimination (Park et al., 1993) to the genetics of pathogenic organisms of commercially important species (Meyers et al., 1992) to the expression of growth factors during maturation (Duguay et al., 1992). We cannot hope to cover all of these appli- *A uthor to whom correspondence should be addressed. Molecular Genetics in Fisheries. Edited by Gary R. Carvalho and Tony 1. Pitcher. Published in 1995 by Chapman & Hall, London. ISBN 0 412 62950 X 2 Park and Moran cations in the space of this review but we would like to at least acknowledge the breadth of research that is being conducted. With that said, we shall focus primarily on molecular methods as they relate to population genetic/evolutionary questions, because most data (in terms of volume and diversity) exist for these applications, and this is our area of research. Research in this area generally involves the characterization of molecular genetic variants that can be used as genetic markers. The goals of this review are first, to familiarize the reader with the basis of molecular genetic research, and second, to introduce some of the most widely used techniques now being applied to popUlation genetic research, particularly in fish species. The research in our own group has been on the population genetics of Pacific salmon species (Oncorhyn chus spp.), and the examples we describe tend to reflect that; however, this type of research is being conducted with many different fishes to address a wide range of ques tions. Our aim is not to make the reader an expert in molecular techniques; rather, we hope to impart a basic understanding of the potentials and limitations of molecular genetic analysis that will enable the reader to better evaluate this type of research. We focus here on the most widely used techniques to date, but we will also speculate on the direction molecular genetic research will take in the next few years. To further narrow the scope of this review, the molecular techniques covered in this review will be mostly concerned with DNA-level research, which has experienced a sharp growth in recent years. This is not to imply that more traditional, protein-level (isozyme) analyses are obsolete: on the contrary, they are, and will continue to be, the mainstay of fisheries genetics for years to come. But reviews on the application of isozymes in fish eries genetics have been published (Shaklee, 1983; Seeb and Miller, 1990; Utter 1991; Utter and Ryman, 1993), as have detailed descriptions of the practical aspects of this technique (Aebersold et al., 1987; Buth, 1990; Hillis and Moritz, 1990), and we feel there is little need to repeat that information here. Instead, we have tried to focus on techniques that have only recently attained widespread application in fisheries research and we will limit our discussion of isozymes to what is essential to evaluation in the context of the other techniques described. Molecular genetic markers ISOZYMES Isozymes are functionally similar but separable forms of enzymes, encoded by one or more loci (Markert and Moller, 1959). Isozymes that are the products of different alleles at the same locus are termed allozymes. For the past 20 years, fish geneticists have been using protein (isozyme) electrophoresis as their primary tool to characterize population level genetic variation in various fish species (Avise and Smith, 1974; Allendorf et al., 1976; Winans, 1980; Waples, 1990). The technique was first used to examine blood groups in humans (Smithies, 1955) but was later adopted for use in other species (Sick, 1961; Lewontin and Hubby, 1966; Sartore et al., 1969; Utter et aL, 1976). This tech nique is ideally suited to popUlation studies: it is relatively inexpensive and requires little in the way of specialized equipment, it is a fairly rapid procedure to perform on a large scale, and a large number of unlinked loci that are dispersed throughout the genome (Pasdar et al., 1984) can be screened simultaneously. Protein electrophoresis can be useful for defining genetic markers for stock identification in fishes, especially anadro mous species, as evidenced by numerous studies that document differences in protein
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