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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Emmanuel Paradis
Analysis of Phylogenetics and Evolution with R Second Edition
Emmanuel Paradis Institut de Recherche pour le Développement (IRD) Institut des Sciences de l’Évolution (ISEM) – UMR 226 IRD/CNRS/UM2 Jl. Taman Kemang 32B Jakarta 12730 Indonesia [email protected]
ISBN 978-1-4614-1742-2 e-ISBN 978-1-4614-1743-9 DOI 10.1007/978-1-4614-1743-9 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2011940221 © Springer Science+Business Media, LLC 2012 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.
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to Laure
Preface to the Second Edition
Some kinds of problems may yield to sophisticated statistical technique; others will not. The goal of empirical research is—or should be—to increase our understanding of the phenomena, rather than displaying our mastery of technique. —Freedman [91] The first edition of APER was published five years ago. The subject of the book has grown in importance and audience during this time, so this second edition is certainly timely. Moreover, the changes in ape and several related packages have been so important in the last few years, that, for some time, I have felt this new edition was required. Though I acknowledge that the first edition of APER was quite appreciated by researchers, lecturers and students, it was not out of criticism. With this second edition, I have tried to improve on all possible points and issues as much as I was able to do. At the same time, I had to think over on the progress of the approach I presented five years ago. A difficult task was to review the development of the many new packages contributing to phylogenetics and evolutionary biology. It was my choice to focus on some of these packages with the aim to provide to the reader a consistent set of “techniques” to address a wide range of issues in phylogenetics and macroevolution. Even restricting our interest to these two fields, a number of packages are not considered in this book: this is a choice I fully assume. Besides, I decided to not tackle two related fields: population genetics and paleobiology. Both have seen critical developments in the form of several packages. A useful treatment of these would require two new books, so I have limited m
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