cover next page > title: Molecular Evolution : A Phylogenetic Approach author: Page, Roderic D. M.; Holmes, Edward C. publisher: Blackwell Publishing Ltd. isbn10 | asin: print isbn13: 9780865428898 ebook isbn13: 9780632061488 language: English subject Molecular evolution, Evolutionary genetics. publication date: 1998 lcc: QH390.P34 1998eb ddc: 572.8/38 subject: Molecular evolution, Evolutionary genetics. cover next page > < previous page page_i next page > Page i Molecular Evolution A Phylogenetic Approach Roderic D.M. Page University of Glasgow Edward C. Holmes University of Oxford < previous page page_i next page > cover next page > title: Molecular Evolution : A Phylogenetic Approach author: Page, Roderic D. M.; Holmes, Edward C. publisher: Blackwell Publishing Ltd. isbn10 | asin: print isbn13: 9780865428898 ebook isbn13: 9780632061488 language: English subject Molecular evolution, Evolutionary genetics. publication date: 1998 lcc: QH390.P34 1998eb ddc: 572.8/38 subject: Molecular evolution, Evolutionary genetics. cover next page > < previous page page_ii next page > Page ii © 1998 by Blackwell Science Ltd Editorial Offices: Osney Mead, Oxford OX2 0EL 25 John Street, London WC1N 2BL 23 Ainslie Place, Edinburgh EH3 6AJ 350 Main Street, Malden MA 02148 5018, USA 54 University Street, Carlton Victoria 3053, Australia 10, rue Casimir Delavigne 75006 Paris, France Other Editorial Offices: Blackwell Wissenschafts-Verlag GmbH Kurfürstendamm 57 10707 Berlin, Germany Blackwell Science KK MG Kodenmacho Building 710 Kodenmacho Nihombashi Chuo-ku, Tokyo 104, Japan The right of the Authors to be identified as the Authors of this Work has been asserted in accordance with the Copyright, Designs and Patents Act, 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the copyright owner. First published 1998 Reprinted 1999, 2000 (twice) Set by Setrite Typesetters Ltd, Hong Kong Printed and bound in the United Kingdom at the University Press, Cambridge The Blackwell Science logo is a trade mark of Blackwell Science Ltd, registered at the United Kingdom Trade Marks Registry For further information on Blackwell Science, visit our website: www.blackwell-science.com DISTRIBUTORS Marston Book Services Ltd PO Box 269 Abingdon, Oxon OX14 4YN (Orders: Tel: 01235 465500 Fax: 01235 465555) USA Blackwell Science, Inc. Commerce Place 350 Main Street Malden, MA 02148 5018 (Orders: Tel: 800 759 6102 781 388 8250 Fax: 781 388 8255) Canada Login Brothers Book Company 324 Saulteaux Cresent Winnipeg, Manitoba R3J 3T2 (Orders: Tel: 204 837-2987) Australia Blackwell Science Pty Ltd 54 University Street Carlton, Victoria 3053 (Orders: Tel: 3 9347 0300 Fax: 3 9347 5001) A catalogue record for this title is available from the British Library ISBN 0-86542-889-1 Library of Congress Cataloging-in-publication Data Page, Roderic D.M. Molecular evolution: a phylogenetic approach/Roderic D.M. Page, Edward C. Holmes. p. cm. Includes bibliographical references and index. ISBN 0-86542-889-1 1. Molecular evolution. 2. Evolutionary genetics. I. Holmes, Edward C. II. Title. QH390. P34 1998 572.8'38dc21 98-4696 CIP < previous page page_ii next page > < previous page page_iii next page > Page iii Contents Acknowledgements v 1 The Archaeology of the Genome 1 2 Trees 11 3 Genes: Organisation, Function and Evolution 37 4 Genes in Populations 89 5 Measuring Genetic Change 135 6 Inferring Molecular Phylogeny 172 7 Models of Molecular Evolution 228 8 Applications of Molecular Phylogenetics 280 References and Bibliography 315 Index 335 < previous page page_iii next page > < previous page page_v next page > Page v Acknowledgements We thank Simon Rallison for commissioning the book, and for negotiating the contract at the same time that R.D.M.P.'s wife, Antje, was working in Blackwell's royalties department. This, of course, was merely a fortuitous coincidence. In any event, Antje's gentle prodding helped speed the completion of one half of the book. Ian Sherman shepherded the book to its conclusion with great patience in the face of our ludicrously optimistic assessments of when we would be finished. Several anonymous referees provided very helpful comments while Tim Anderson, John Brookfield, Mike Charleston, Nick Grassly, Rosalind Harding, Peter Holland, Mark Ridley and Vince Smith read chunks of the manuscript (some very large) for which we are extremely grateful. Jake Baum's input into part of Chapter 4 was also much appreciated. Finally we thank Paul Harvey, Wyl Lewis, Mark Ridley and Rachel Urwin for encouragement and inspiration. RODERIC D.M. PAGE GLASGOW EDWARD C. HOLMES OXFORD < previous page page_v next page > < previous page page_1 next page > Page 1 Chapter 1 The Archaeology of the Genome 1.1 The Nature of Molecular Evolution 1.2 What This Book Will Cover 1.3 Further Reading 1.1 The Nature of Molecular Evolution Although a sometimes unpleasant occupant of our respiratory tracts, Haemophilus influenzae, a small Gram- negative bacterium, was an unlikely candidate to symbolise a revolution in molecular biology. But this is exactly what happened in July 1995 when the entire 1830137 DNA base pairs of its genome was publishedthe first of a free-living organism. A new era in biological science had begun. Soon after Haemophilus influenzae came the first complete genome from a eukaryotethat of the yeast Saccharomyces cerevisiae, followed by Methanococcus jannaschii, the first representative of the third domain of cellular life, the Archaea. In the next few years molecular biology will claim its biggest prizethe 3.3 billion bases that make up the genome of Homo sapiens. DNA sequences are valuable because they provide the most detailed anatomy possible for any organismthe instructions for how each working part should be assembled and operate. Much of modern biology now relies on unravelling the information stored within gene sequences and this is true of evolutionary studies, where gene sequences are now recognised as an invaluable document of the history of life on earth. It is the aim of this book to show what evolutionary information is written into gene sequences and how this information might be recovered. This is the science of molecular evolution. Take, for example, Haemophilus influenzae, Saccharomyces cerevisiae and Methanococcus jannaschii. Until recently, most textbooks divided cellular organisms into the eukaryotes, which possess a cell nucleus, and the prokaryotes, which do not. This tidy world was upturned in the 1970s when Carl Woese and colleagues, using the highly conserved 16S ribosomal RNA (rRNA) gene, showed that there were in fact two very different groups of prokaryotesthe Eubacteria like Haemophilus influenzae, now simply referred to as the Bacteria, and the Archaebacteria whose members include Methanococcus jannaschii, now known as the Archaea (Fig. 1.1). Until the rise of molecular biology in the 1970s, this third great branch of life was lost from us but with molecular phylogenies we have learned that the Archaea are in fact probably more < previous page page_1 next page > < previous page page_2 next page > Page 2 Fig. 1.1 Phylogenetic relationships between members of the three domains of cellular life the Archaea, Bacteria and Eukarya, based on rRNA. The Archaea can be further divided into the Crenarchaeota (also known as the eocytes) and the Euryarchaeota (methanogens and halophiles). Although popular, this tree is by no means universally accepted. For example, there is still some debate as to whether the Crenarcheota are in fact more closely related to the eukaryotes than they are to the other Archaea. From Morell (1996) and originally Olsen and Woese (1993), with permission. closely related to the eukaryotes than they are to the Bacteria, even though they lack a cell nucleus and represent some of the most extreme forms of life on earth. Methanococcus jannaschii, for example, lives on deep-sea hydrothermal chimneys ('white smokers'), at pressures of 200 atmospheres and temperatures of 85ºC! Gene sequences clearly contain a unique and important archaeological record of life's tentative steps. The importance of 16S rRNA for those interested in the early evolution of life lies in its slow evolution, which allows the historical record preserved in its gene sequences to be kept relatively intact. Other genes evolve a good deal more rapidly and so allow us to reconstruct historical pathways that have been trodden only recently. One such example of evolution in the fast lane are the genes which make up the human immunodeficiency virus (HIV), the cause of the disease AIDS. HIV evolves about a million times faster than human genes, which is why developing effective drugs and vaccines is such a problem. This super-fast rate of evolutionary change also means that sequences from this virus can be used to retrace its spread through populations. Studies of this sort have had some dramatic results. For example, in 1990 the Centers for Disease Control (CDC) in Atlanta received reports of AIDS in a young woman in Florida whose only risk of HIV infection was seemingly that she had previously been treated by a dentist suffering from AIDS. A subsequent investigation then uncovered a number of the dentist's other former patients < previous page page_2 next page > < previous page page_3 next page > Page 3 who were also HIV infected. Could it be that these people were somehow infected by their dentist? A phylogenetic tree reconstructed on part of the envelope (env) gene of the virus revealed that those patients with no other risk factors for HIV infection had sequences closely related to those of the dentist, strongly suggesting that he had infected them, whilst the sequences from two patients who could have been infected in other ways were separated from the dentist on the tree (Fig. 1.2). The HIV genome had therefore stored evolutionary information, in the form of the mutations which had accumulated between transmission events, which could recount the very recent history of its spread.