Mathematics of Evolution and Phylogeny Library of Congress Cataloging in Publication Data (data Available)

Mathematics of Evolution and Phylogeny Oliv: " fm " — 2004/11/16 — 22:56 — page ii — #2 Oliv: " fm " — 2004/11/16 — 22:56 — page iii — #3 1 Oliv: " fm " — 2004/11/16 — 22:56 — page iv — #4 3 Great Clarendon Street, Oxford ox2 6dp Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York The moral rights of the author have been asserted Database right Oxford University Press (maker) First published 2005 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, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose this same condition on any acquirer British Library Cataloguing in Publication Data (Data available) Oliv: " fm " — 2004/11/16 — 22:56 — page v — #5 ACKNOWLEDGEMENTS thanks to: All the contributors, who have spent time, energy, and patience in writing and writing again their chapters, and have cross-reviewed other chapters with much care: A number of distinguished " anonymous " referees, whose suggestions, recommendations and corrections greatly helped to improve the content of this volume: the Latex specialists who have given this volume its final form, which was a real challenge regarding the extreme diversity of original manuscripts. The people from Institut Henri Poincaré and elsewhere, who helped in organizing the " Mathematics of Evolution and Phylogeny " conference in June 2003: v Oliv: " fm " — 2004/11/16 — 22:56 — page vi — #6 INTRODUCTION Olivier Gascuel The subject of this volume is evolution, which is considered at different scales: sequences, genes, gene families, organelles, genomes, and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations and, inevitably, give them orientation. Recent years have witnessed rapid progress in this area, with models and methods becoming more realistic, powerful, and complex. This expansion …