Molecular Techniques in Taxonomy PDF
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Molecular Techniques in Taxonomy NATO ASI Series Advanced Science Institutes Series A series presenting the results of activities sponsored by the NATO Science Committee, which aims at the dissemination of advanced scientific and technological knowledge, with a view to strengthening links between scientific communities. The Series is published by an international board of publishers in conjunction with the NATO Scientific Affairs Division A Life Sciences Plenum Publishing Corporation B Physics London and New York C Mathematical and Kluwer Academic Publishers Physical Sciences Dordrecht, Boston and London o Behavioural and Social Sciences E Applied Sciences F Computer and Springer-Verlag Systems Sciences Berlin Heidelberg New York G Ecological Sciences London Paris Tokyo Hong Kong H Cell Biology Barcelona Budapest I Global Environmental Change NATo-pea DATABASE The electronic index to the NATO ASI Series provides full bibliographical references (with keywords and/or abstracts) to more than 30000 contributions from international scientists published in all sections of the NATO ASI Series. Access to the NATO-PCO DATABASE is possible in two ways: - via online FILE 128 (NATO-PCO DATABASE) hosted by ESRIN, Via Galileo Galilei, 1-00044 Frascati, Italy. - via CD-ROM "NATO-PCO DATABASE" with user-friendly retrieval software in English, French and German (© WTV GmbH and DATAWARE Technologies Inc. 1989). The CD-ROM can be ordered through any member of the Board of Publishers or through NATO-peO, Overijse, Belgium. Molecular Techniques in Taxonomy Edited by Godfrey M. Hewitt Andrew W. B. Johnston University of East Anglia School of Biological Sciences Norwich, NR4 7TY United Kingdom and J. Peter W. Young John Innes Institute Colney Lane Norwich NR4 7UH United Kingdom Springer-Verlag Berlin Heidelberg New York London Paris Tokyo Hong Kong Barcelona Budapest Proceedings of the NATO Advanced Study Institute on Molecular Techniques in Taxonomy held in Norwich (England), July 9-20, 1990. ISBN-13:978-3-642-83964-1 e-ISBN-13:978-3-642-83962-7 001: 10.1007/978-3-642-83962-7 Library of Congress Cata[oging-in-Pub[ication Data NATO Advanced Study Institute on Mo[ecu[ar Techniques in Taxonomy (1990 : Norwich, Eng[and) Mo[ecu[ar techniques in taxonomy I edited by Godfrey M. Hewitt, Andrew Johnston, and J. Peter W. Young. (NATO AS[ series. Series H, Cell bio[ogy; vol. 57) "Proceedings of the NATO Advanced Study Institute on Mo[ecu[ar Tech niques in Taxonomy held in Norwich (Eng[and), Ju[y 9-20, 1990"-Tp. verso. [SBN-13978-3-642-83964-1 (U.S.) 1. Bio[ogy-C[assification-Mo[ecu[ar aspects-Congresses. I. Hewitt, Godfrey M. [I. Johnston, A. III. Young, J. Peter W. [V. Tit[e. V. Series. QH83.N321990 574'.012-dc20 91-17381 This work is subject to copyright. A[[ rights are reserved, whether the whole or part of the material is concerned, specifically the rights oftrans[ation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microfilms or in other ways, and storage in data banks. Dup[ication ofthis publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9, 1965, in its current version, and a copyright fee must always be paid. Violations fall under the prosecution act of the German Copyright Law. © Springer-Verlag Berlin Heide[berg 1991 Softcover reprint of the hardcover 1st edition 1991 Preface The NATO Advanced Study Institute on Molecular Techniques in Taxonomy was held on 9-20 July 1990 at the University of East Anglia, Norwich, England. In recent years, molecular techniques have begun to have a major impact in taxonomic and evolutionary studies, and we felt that many scientists were now ready to apply the new techniques and would appreciate the chance to learn more about them at first hand. We were clearly right, because the meeting was heavily oversubscribed and we had to tum away many worthy applicants while attempting to maintain a balance of interests and experience. The result was that about a hundred very diverse, very talented, and very enthusiastic people gathered in Norwich; they were so full of ideas and newly discovered mutual interests that the success of the meeting was ensured from that point on. As organizers, however, we felt obliged to impose some structure on these interactions, so we had asked our invited lectures to give overviews of major areas, or presentations of their own work as case histories, or practical demonstrations of the critical stages of common laboratory techniques, or in some cases all three of the above! These formed the. essential backbone of the course (and of this book), but a still wider range of approaches was represented at the meeting because every participant brought a poster describing their recent work, and some also gave short oral presentations in convivial evening workshops. This display of diverse talents was essential to the success of the "hands-on" phase of the meeting, in which we aimed to facilitate ("organize" is too strong a word!) a free market in laboratory techniques. After hearing the lectures, each participant was asked which techniques they would most like to try out. Then we matched them in small groups with a suitable tutor, and tried to provide the necessary materials and laboratory facilities. This approach was astonishingly successful, considering that the tutors were operating in a foreign environment with untested materials, and in some cases without prior warning. Under expert supervision, our group8 of VI novices successfully prepared DNA from everything from grass to grasshoppers, and demonstrated RFLPs using digoxigenin-Iabelled probes. Others experienced at first hand the frustrations, and occasionally the joys, of PCR, and everyone had the opportunity to discuss· their future plans with others interested in the same techniques. Indeed, one of the great delights of the meeting was the free flow of ideas and expertise among all the participants. We invited "teachers" and we offered places to "learners", but many participants of both kinds were world-class experts in their field, and in practice everyone found they had something to learn, and almost everyone had something to teach. For practical reasons, though, this book has to be limited to the contributions of the "official" lecturers. We have arranged them in three main sections: overviews of important topics in molecular taxonomy, case studies of the successful application of molecular methods to taxonomic and evolutionary questions, and protocols for a range of generally applicable methods. It would be artificial to keep these categories entirely isolated and pure, though, and the reader will certainly find some interesting examples among the overviews, some useful methods in the case histories, and even some general reviews enhancing the protocols. There is one important element missing from this book, and that is the computational analysis of taxonomic data and the reconstruction of phylogenetic trees. This was very ably covered at the meeting by Dave Swofford and Gary Olsen, who provided us with a two-day minicourse in the principles, as well as hands-on computer tuition. However, Dave and Gary had just written a major review of the subject, and felt that they could not better it just yet. Accordingly, we recommend very strongly their chapter on phylogeny reconstruction in Mol e cui a r Systematics (edited by D.M. Hillis & C. Moritz, published by Sinauer, 1990), and that book is also a very valuable and comprehensive source of protocols and practical advice on all the main laboratory techniques. Our task as organizers would have been impossible without the help of many others. Our impromptu approach to laboratory practicals VII would certainly have degenerated into chaos but for the exceptional professional skill and dedication of the technicians of the School of Biological Sciences, in particular Alan Cavill, Derek Fulton and Ian Twaite. Deborah Clemitshaw provided a level of secretarial support normally reserved for top executives and helped smooth the paths of many participants. The participants were invited to a civic reception in Norwich Castle by the Lord Mayor, and the Vice-Chancellor of the University gave a reception before the "NQJ"folk Dinner" in the Sainsbury Centre on the last night. Several companies assisted with displays and products. To these and all the others - our sincere thanks. Most of all we thank the lecturers and participants for following the example of Chaucer's Scholar of Oxford "and gladly wolde he Ierne, and gladly teche". We believe that the Advanced Study Institute was a success, and fulfilled a real need. Indeed, some of the participants asked, as they left, to be invited to the next meeting! There will not be another one, at least not in exactly the same format, but we hope that this book will be helpful to all those who were not able to come, as well as a a reminder for those who were here. Godfrey Hewitt, Andy Johnston, Peter Young, NORWICH Acknowledgements In addition to the major financial support from NATO for this ASI, we are also grateful to Natural Environmental Research Council UK, Aldrich Chemical Co. Ltd, Anachem, Applied Biosystems Ltd, Boehringer Corp Ltd, BDH Chemicals, BIO-Rad Laboratories Ltd, Denley Instruments, Fisons, Genetic Research Instrumentation Ltd, Gihco, LEEC Ltd, Lahsystems, Laser Labsystems Ltd, Kodak Ltd, Mailbox. International Ltd, Milligen Biosearch, Sigma, Stratec Scientific Ltd, UVP, Whatman and finally the City of Norwich and University of East Anglia for their assistance and support. Contents A Prologue Past and Future of Taxonomy J .R. David ............................................................................................... 1 Overviews Taxonomy: an Essential Key to Evolutionary Biology R.I. Berry ............................................................................................... 5 Variation at the DNA Level: Something for Everyone M. Kreitman ............................................................................................ 15 Molecular Systematics at the Species Boundary: Exploiting Conserved and Variable Regions of the Mitochondrial Genome of Animals via Direct Sequencing from Amplified DNA C. Simon ................................................................................................ 33 Ribosomal RNA Phylogenies M. Solignac, M. Pelandakis, F. Rousset and A. Chenuil.. ....................................... 73 Evaluating Gene Versus Genome Evolution R. Cedegren, Y. Abel and D. Sankoff. .............................................................. 87 DNA and Higher Plant Systematics: Some Examples From the Legumes J.J. Doyle and J.L. Doyle. ............................................................................ 101 DNA-DNA Hybridization: Principles and Results J.R. Powell and A. Caccone .......................................................................... 117 Satellite DNA L. Bachmann, M. Raab, J. Schibel and D. Sperlich ............................................... 13 3 DNA Fingerprinting D.T. Parkin and J.H. Wetton ......................................................................... 145 The Statistical Interpretation of Hypervariable DNAs J.F.Y. Brookfield ...................................................................................... 159 Case Studies A Multidimensional Approach to the Evolution and Systematics of Dolichopoda Cave Crickets V. Sbordoni, G. Allegrucci and D. Cesaroni ....................................................... 171 Sperm and Evolution in Drosophila: Morphological and Molecular Aspects D. Lachaise and D. Joly ............................................................................... 201 Episodic Evolutionary Change in Local Populations H.L. Carson ............................................................................................ 2 1 7 x Searching for Speciation Genes in the Species Pair Drosophila Mojavensis and D. Arizonae E. Zouros ................................................................................................ 233 Colonizing Species of Drosophila A. Fontdevila ........................................................................................... 249 Molecular Taxonomy in the Control of West African Onchocerciasis R.J. Post, K.A. Murray, P. Flook and A.L. Millest.. ............................................ 271 Protocols DNA Protocols for Plants J. Doyle .................................................................................................. 283 Prepartion and Visualization of Mitochondrial DNA for RFLP Analysis M. Solignac ............................................................................................. 295 Hybridization of DNA Probes to Filterbound DNA Using the "DIG-DNA Labeling and Detection System Nonradioactive" (Boehringer Mannheim) L. Bachmann and D. Sperlich ........................................................................ 321 DNA Fingerprinting R.E. Carter .............................................................................................. 3 2 3 The Polymerase Chain Reaction: DNA Extraction and Amplification C. Simon, A. Franke and A. Martin ................................................................. 329 Protocols for 4-Cutter Blots and PCR Sequencing M. Kreitman ............................................................................................ 3 5 7 Ribosomal RNA Sequencing M. Solignac ............................................................................................. 369 Quantitative DNA:DNA Hybridization and Hydroxyapatite Elution B.D.W. Jarvis, G. Ionas and J.C. Clarke .......................................................... 379 A Protocol for the TEACL Method of DNA-DNA Hybridization A. CacconeandJ.R. Powell. ......................................................................... 385 List of Participants ................................................................................ 409
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