Dynamic Homology and Phylogenetic Systematics: A Unified Approach Using POY Ward Wheeler Lone Aagesen Division of Invertebrate Zoology Division of Invertebrate Zoology American Museum of Natural History American Museum of Natural History Claudia P. Arango Julián Faivovich Division of Invertebrate Zoology Division of Vertebrate Zoology American Museum of Natural History American Museum of Natural History Taran Grant Cyrille D’Haese Division of Vertebrate Zoology Département Systématique et Evolution American Museum of Natural History Museum National d'Histoire Naturelle Daniel Janies William Leo Smith Department of Biomedical Informatics Division of Vertebrate Zoology The Ohio State University American Museum of Natural History Andrés Varón Gonzalo Giribet Department of Computer Science Museum of Comparative Zoology City University of New York Department of Organismic & Evolutionary Biology Harvard University Published in cooperation with NASA Fundamental Space Biology, the U.S. Army Research Laboratory, and the U.S. Army Research Office Copyright 2006 by the American Museum of Natural History All rights reserved Printed in the United States of America Library of Congress Cataloging-in-Publication Data Dynamic homology and phylogenetic systematics : a unified approach using POY / Ward Wheeler ... [et al.]. p. cm. "Published in cooperation with NASA Fundamental Space Biology." Includes bibliographical references. ISBN 0-913424-58-7 (alk. paper) 1. Homology (Biology) 2. Animals--Classification. 3. Phylogeny. 4. POY. I. Wheeler, Ward. QH367.5.D96 2006 578.01'2--dc22 2006028134 Contents An Approach to Phylogenetics....................................................... 1 Part I Phylogenetics 1 Data..................................................................................7 Evidence................................................................................................................ 7 Value of Evidence................................................................................................ 8 Sources of Evidence............................................................................................ 8 Phenotypic and genotypic data...................................................................... 9 Homology...........................................................................................................10 Suggested Reading.............................................................................................11 2 Cladograms .................................................................... 13 Cladograms, Trees, and Tree-Shaped Objects...............................................13 Terms and Notation..........................................................................................16 Suggested Reading.............................................................................................18 3 Analysis .......................................................................... 19 Cladograms and Data........................................................................................19 Implications of Coding Methods ....................................................................20 Additive ...........................................................................................................20 Nonadditive ....................................................................................................21 Matrix or Sankoff...........................................................................................21 Sequence..........................................................................................................22 Chromosomal.................................................................................................23 Computational Issues........................................................................................23 P, NP, and NPC..............................................................................................24 Techniques..........................................................................................................25 Exact methods ...............................................................................................25 i ii Heuristic methods .....................................................................................25 Parallel Computation.....................................................................................26 Integration of Heuristic Analysis ................................................................26 Suggested Reading.........................................................................................26 Part II POY 4 Overcoming Limitations in Phylogenetics................. 29 Alignment .......................................................................................................30 Manual alignment ......................................................................................30 Automated multiple sequence alignment...............................................32 Exclusion of Data..........................................................................................32 Alignment problems..................................................................................32 Noise and saturation .................................................................................33 Taxon exclusion .........................................................................................33 POY .................................................................................................................34 Optimality criteria and epistemological background............................34 Suggested Reading.........................................................................................36 5 Character Optimization.............................................. 37 Notation and Definitions .............................................................................38 Notation......................................................................................................38 Definitions..................................................................................................38 Qualitative Character Optimization Algorithms ......................................40 Down pass ..................................................................................................40 Up pass........................................................................................................41 Additive characters ....................................................................................42 Nonadditive characters .............................................................................43 Sankoff Algorithm.....................................................................................44 Sequence Optimization Algorithms ...........................................................45 Direct optimization ...................................................................................47 Extending direct optimization: chromosome data...............................52 Fixed states and search-based optimization ..........................................55 Iterative pass optimization .......................................................................56 Likelihood.......................................................................................................57 Likelihood as an optimality criterion......................................................57 Comparison with other likelihood methods..........................................58 Pairwise comparison..................................................................................58 Models.........................................................................................................59 Dynamic homology...................................................................................60 Implied alignment......................................................................................61 Combined analysis.....................................................................................61 Support measures ......................................................................................61 Suggested Reading........................................................................................62 Contents iii 6 Cladogram Searching..................................................... 63 Definitions..........................................................................................................64 Branch and Bound.............................................................................................64 Wagner Trees......................................................................................................65 Branch Swapping...............................................................................................67 Subtree pruning and regrafting (SPR) ........................................................67 Tree bisection and reconnection (TBR).....................................................71 Ratcheting...........................................................................................................72 Tree Drifting.......................................................................................................72 Tree Fusing.........................................................................................................74 Static Approximation........................................................................................74 Parallel Cladogram Searching ..........................................................................75