Table Of ContentMolecular 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
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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
