Analysis of Phylogenetics and Evolution with R
The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adapt
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Use R! Paradis: Analysis of Phylogenetics and Evolution with R Pfaff: Analysis of Integrated and Cointegrated Time Series with R
Emmanuel Paradis
Analysis of Phylogenetics and Evolution with R
Emmanuel Paradis Institut de Recherche pour le Développement UR 175 Caviar GAMET-BP 5095 361 rue Jean François Breton F-34196 Montpellier c´edex 5 France [email protected] Series Editors: Robert Gentleman Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 Seattle, Washington, 981029-1024 USA
Kurt Hornik Department für Statistik und Mathematik Wirtschaftsuniversität Wien Augasse 2-6 A-1090 Wien Austria
Giovanni Parmigiani The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University 550 North Broadway Baltimore, MD, 21205-2011 USA
Library of Congress Control Number: 2006923823 ISBN-0-387-32914-5 ISBN-978-0387-32914-7 Printed on acid-free paper. © 2006 Springer Science+Business Media, LLC All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed in the United States of America. 9 8 7 6 5 4 3 2 1 springer.com
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Preface
As a result, the inference of phylogenies often seems divorced from any connection to other methods of analysis of scientific data. Felsenstein Once calculation became easy, the statistician’s energies could be devoted to understanding his or her dataset. Venables & Ripley The study of the evolution of life on Earth stands as one of the most complex fields in science. It involves observations from very different sources, and has implications far beyond the domain of basic science. It is concerned with processes occurring on very long time spans, and we now know that it is also important for our daily lives as shown by the rapid evolution of many pathogens. As a field ecologist, for a long time I was remotely interested in phylogenetics and other approaches to evolution. Most of the work I accomplished during my doctoral studies involved field studies of small mammals and estimation of demographic parameters. Things changed in 1996 when my interest was attracted by the question of the effect of demographic parameters on bird diversification. This was a new issue for me, so I searched for relevant data analysis methods, but I failed to find exactly what I needed. I started to conduct my own research on this problem to propos
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