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Primate-Science / PrimateLit

CLADISTICS: A PRACTICAL PRIMER ON CD-ROM

CLADISTICS: A PRACTICAL PRIMER ON CD-ROM

 By Peter Skelton and Andrew Smith
 Accompanying booklet by Neale Monks

 Cambridge University Press, 2002


 FROM THE BACK COVER

 Cladistics and phylogenetic reconstruction are subjects which biology 
 students find quite difficult to grasp when taught from conventional 
 textbooks. This CD provides students with a complete self-study 
 introductory course in phylogenetic reconstruction using cladistic 
 analysis. The CD is fully interactive and includes animated sequences, 
 questions at the end of each section, and practical exercises. It is 
 the first exclusively pedagogical CD-ROM devoted to this topic. By the 
 end of the course students should have a basic understanding of 
 cladistics and be ready to reconstruct phylogenetic relationships from 
 morphological and molecular data

 The CD-ROM is accompanied by a short textbook. The book is meant to be 
 used in conjunction with the CD-ROM but can act as a stand-alone aid 
 to learning when the reader is away from the computer.

 Peter Skelton is based in the Department of Earth sciences in The open 
 University, Milton Keynes, UK.

 Andrew Smith is a palaeontologist in The Natural History Museum, 
 London and is a Fellow of the Royal Society.

 Neale Monks is a science writer and biology teacher based in London.

 SYSTEM REQUIREMENTS: PC with Pentium 200 MHz processor or Mac PowerPC 
 and above. Windows 9S or Mac OS 7.6 and above. CD-ROM drive, 32 
 megabytes of RAM.


 TABLE OF CONTENTS

 Preface,    vii
 About the CD-ROM and the booklet,    ix
 Instructions for installing and running the CD-ROM,    x

 1.  FIRST PRINCIPLES

 1.1 Reconstructing evolutionary history from observed differences,    1
 1.2 Parsimony and tree reconstruction,    16

 2. CHARACTERS AND HOMOLOGY

 2.1 Homology and homoplasy,    26
 2.2 Homology in molecular data,    29
 2.3 Character definition,    33
 2.4 Weighting,    39

 3. CLADOGRAMS AND TREES

 3.1 Rooting procedures and character polarity,    40
 3.2 Cladograms, phylograms and phylogenetic trees,    45
 3.3 Monophyly, paraphyly and polyphyly,    48
 3.4 Consensus trees,    50

 4. FIT AND ROBUSTNESS

 4.1 Measuring goodness of fit,    55
 4.2 Tests of robustness,    64

 5.  PRACTICAL

 5.1 Phylogenetic analysis of eight species of sea-urchins,    66
 5.2 Cladistic analysis of morphological characters,    67
 5.3 Cladistic analysis of molecular characters,    75
 5.4 Comparison of results and conclusions,    78

 Appendix: Cladistics software,    79


 PREFACE

 The last few decades have seen a revolution in the reconstruction of 
 evolutionary relationships. Eclectic models based on ad hoc arguments, 
 and hence liable to subjectivity, have been replaced by a consistent 
 methodology - cladistics - that is open to objective evaluation.  Two 
 technological innovations have helped to foment this revolution. 
 First, computing, especially the rise of personal computers, has made 
 easy the previously unthinkable task of sifting through myriads of 
 alternative trees of shared ancestry, as required by the method. 
 Second, molecular sequencing of genes and their products has provided 
 a rich new source of evidence that is also amenable to cladistic 
 analysis, in addition to conventional morphological data. Where these 
 two discrete sources of data yield the same phylogenetic conclusion, a 
 high degree of confidence can be placed on it.  Thus what before was 
 virtually a priestly art practiced by taxonomic specialists has become 
 a robust science.

 Consequently, discussion of cladistics forms a necessary component of 
 any modern course on evolution. However, many students have 
 difficulties getting to grips with the strict logic of the method, not 
 to mention its somewhat daunting technical vocabulary. Accordingly, 
 the Evolution Course Team at the Open University decided in 1998 that 
 treatment of the topic could especially benefit from the lively and 
 colourful medium of an interactive CD-ROM, and thus the present 
 project was born. A proposal for the structure and content of the 
 CD-ROM was commissioned from Andrew Smith at the Natural History 
 Museum, and this was realised in detail by Peter Skelton at the Open 
 University, working with a technical design team from BBC Factual & 
 Learning (MK). Co-publication was agreed with Cambridge University 
 Press, who commissioned the present
 booklet from Neale Monks - an inspired choice - to accompany the 
 CDROM. We, the authors of the latter, are indeed most grateful to 
 Neale for the elegant but down-to-earth guidance notes and backup 
 information that he has provided here for users of the CD-ROM.

 Peter Skelton
 Open University, Milton Keynes
 Andrew Smith
 Natural History Museum, London


 WHERE TO ORDER

 Cambridge University Press
 110 Midland Avenue
 Port Chester, NY 10573-4930

 phone:  (914) 937-9600
 toll free:  800-872-7423
 Fax:  (914) 937-4712

 http://us.cambridge.org

 ISBN: 0-521-52341-9  $55.00

Posted Date: 5/8/2003