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Numerical Taxonomy NATO ASI Series Advanced Science Institutes Series A series presenting the results of activities sponsored by the NA TO Science Committee, which aims at the dissemination of advanced scientific and technological knowledge, with a view to strengthening links between scientific communities. The Series is published by an international board of publishers in conjunction with the NATO Scientific Affairs Division A Life Sciences Plenum Publishing Corporation B Physics London and New York C Mathematical and D. Reidel Publishing Company Physical Sciences Dordrecht, Boston and Lancaster o Behavioural and Martinus Nijhoff Publishers Social Sciences Boston, The Hague, Dordrecht and Lancaster E Applied Sciences F Computer and Springer-Verlag Systems Sciences Berlin Heidelberg New York Tokyo G Ecological Sciences Series G: Ecological Sciences No.1 Numerical Taxonomy Edited by Joseph Felsenstein Springer-Verlag Berlin Heidelberg New York Tokyo 1983 Proceedings of the NATO Advanced Study Institute on Numerical Taxonomy held at Bad Windsheim, Germany, July 4-16, 1982 Joseph Felsenstein Department of Genetics, University of Washington, Seattle, Washington 98195, USA Published in cooperation with NATO Scientific Affairs Division ISBN-13978-3-642-69026-6 e-ISBN-13978-3-642-69024-2 DOl 101007/978-3-642-69024-2 Library of Congress Cataloging in Publication Data. NATO Advanced Study Institute on Numerical Taxonomy. Numerical taxonomy. (NATO ASI series. Series G, Ecological sciences; no. 1) Includes index. 1. Numerical taxonomy - Congresses. I. Felsenstein, Joseph. II. Title. III. Series. QH83.N33 1983 574'.012 83-6571 This work is subiect to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically those of translating, reprinting, re-use of illustrations, broadcastings, reproduction by photocopying machine or similar means, and storage in data banks. Under § 54 of the German Copyright Law where copies are rnade for other than private use, a fee is payable to "Verwertungsgesellschaft Wort", Munich. © Springer-Verlag Berlin Heidelberg 1983 Softcover reprint of the hardcover 1st edition 1983 2145/3140-543210 PREFACE The NATO Advanced Study Institute on Numerical Taxonomy took place on the 4th - 16th of July, 1982, at the Kur- und Kongresshotel Residenz in Bad Windsheim, Federal Republic of Germany. This volume is the proceedings of that meeting, and contains papers by over two-thirds of the participants in the Institute. Numerical taxonomy has been attracting increased attention from systematists and evolutionary biologists. It is an area which has been marked by debate and conflict, sometimes bitter. Happily, this meeting took place in an atmosphere of "GemUtlichkeit", though scarcely of unanimity. I believe that these papers will show that there is an increased understanding by each taxonomic school of each others' positions. This augurs a period in which the debates become more concrete and specific. Let us hope that they take place in a scientific atmosphere which has occasionally been lacking in the past. Since the order of presentation of papers in the meeting was affected by time constraints, I have taken the liberty of rearranging them into a more coherent subject ordering. The first group of papers, taken from the opening and closing days of the meeting, debate philosophies of classification. The next two sections have papers on congruence, clustering and ordination. A notable concern of these participants is the comparison and testing of classifications. This has been missing from many previous discussions of numerical classification. The next section moves from the subject of classification to that of reconstructing the course of evolution. It is followed by a number of papers on numerical methods for analyzing morphology. Although the meeting did not have a separate session on this topic, the papers form a natural group. The next two sections have applications papers: I have separated the biochemical applications. The general applications include not only studies of morphological characters, but also applications of numerical-taxonomic methods to ecology and oenology. The volume concludes with several papers on use of computers in taxonomy. Limitations of space prevent the reader getting more than a taste of many of the presentations, particularly the contributed papers, most of which were limited to five pages in length. For example, it is impossible to get the full flavor of Lima's presentation without having the opportunity, as the participants did, of an organoleptic assessment of a large sample of his taxa. The invited presentations were limited to twenty pages each, which may allow a fuller picture of their contents. As editor, I have intervened as little as possible: these papers are as the authors wanted them to be. The index was compiled from keywords supplied by the authors: the page references in the index a.re to the first page of the relevant paper. VI The organizing committee for this Institute was: Robert R. Sokal (Director) F. James Rohlf (Program Chairman) Joseph Felsenstein (Editor) George F. Estabrook Walter M. Fitch Pierre Legendre Manuel B. Lima Gary D. Schnell Peter H. A. Sneath This meeting was sponsored and funded by the Advanced Study Institutes Program of the North Atlantic Treaty Organization. We received additional support from the London section of the U. S. Office of Naval Research. I am sure that the participants would want me to express their particular thanks to the staff of the Kur und Kongresshotel, to the Director of the ASI, Dr. Robert R. SOkal, and to the members of the steering committee of the Institute. I must also express my personal thanks to Ms. J. Bogie, who did most of the typographical corrections, and to the members of the Department of Genetics, University of Edinburgh, for their hospitality during the period in which this volume was compiled. Joseph Felsenstein Department of Genetics University of Washington Seattle, Washington U. S. A. TABLE OF CONTENTS APPROACHES TO CLASSIFICA'l'ION Joel Cracraft The significance of phylogenetic classifications for systematic and evolutionary biology. 1 V. A. Funk The value of natural classification. • • 18 P. H. A. Sneath Philosophy and method in biological classification. 22 Robert R. Soka1 The phenetics-c1adistics controversy: a personal view. 38 Daniel P. Faith Parsimony and paraphy1y •••••• 42 John McNeill The future of numerical methods in plant systematics: . . a personal prospect. • • • • • • • 47 Richard J. Jensen A practical view of numerical taxonomy or should I be a pheneticist or a c1adist? •• 53 Wayne Moss Taxa, taxonomists, and taxonomy. 72 TAXONOMIC CONGRUENCE Robert R. Soka1 Taxonomic congruence in the Camina1cu1es. 76 F. James Rohlf, Donald H. Co11ess, and Gene Hart Taxonomic congruence - a reanalysis •••• 82 Kent L. Fiala A simulation model for numerical taxonomic methods. 87 Jorge V. Crisci Taxonomic congruence: a brief discussion. 92 Roger I. C. Hansell and Peter H. A. Sneath Algorithms optimizing the taxonomic information of classifications. 97 James W. Archie Prediction = Parsimony or Partitions? 102 Daniel P. Faith Information content and most parsimonious trees. 107 Sue Gardner Numerical taxonomic evaluation of the taxonomic value of character suites in Ti11andsia L. • • • • • • • • • 112 M. Adey, I. C. Prentice, F. A. Bisby, and J. A. Harris Instability and incongruence in the brooms and gorses (Leguminosae subtribe Genistinae) ••••• 117 F. R. McMorris, D. B. Meronk, and D. A. Neumann A view of some consensus methods for trees. 122 William H. E. Day Distributions of distances between pairs of classifications. 127 K. Shao and F. J. Rohlf Sampling distribution of consensus indices when all bifurcating trees are equally likely. 132 VIII CLUSTERING AND ORDINATION J. C. Gower Comparing classifications. 137 David W. Matula Cluster validity by concurrent chaining. 156 Glenn W. Milligan Characteristics of four external criterion measures. 167 Jocelyne Ferraris Comparison of classifications with the data from which they are derived •.• 174 I. C. Lerman Sur la signification des classes issues d'une classification automatique de donnees .••••••••••• 179 Christophe Perruchet Significance tests for clusters: overview and comments. • •••••••••• 199 Lawrence J. Hubert Inference procedures for the evaluation and comparison of proximity matrices. 209 J. Douglas Carroll and Sandra Pruzansky Representing proximities data by discrete, continuous, or "hybrid" models. • •••••••• 229 PaulO. Degens Hierarchical cluster methods as maximum likelihood estimators. 249 Gene Hart The occurrence of multiple UPGMA phenograms. 254 RECONSTRUCTING PHYLOGENIES Donald H. Colless Wagner trees in theory and practice. . • 259 George F. Estabrook The causes of character incompatibility. 279 Walter J. Le Quesne The uniquely derived concept as a basis . . . . for character compatibility analyses ••• 296 Christopher A. Meacham Theoretical and computational considerations of the . . . compatibility of qualitative taxonomic characters. • 304 Joseph Felsenstein Methods for inferring phylogenies: a statistical view. • • . • • • • • • • • • • • . • • • • • • 315 Daniel P. Faith A divisive algorithm for estimating parsimonious trees. . • • • • • • • . . . • 335 Bernard R. Baum Relationships between transformation series and some numerical cladistic methods at the infraspecific level, when genealogies are known. • •••••••••••• 340 ANALYZING MORPHOLOGICAL VARIATION William R. Atchley Some genetic aspects of morphometric variation. . • • • 346 Jean-Marie Hubac Choice of descriptors in numerical taxonomy for static and dynamic shape analysis and recognition in biology. 364 Chris Simon A new coding procedure for morphometric data with an example from periodical cicada wing veins. • 378 M. T. Almeida and F~ A. Bisby A quick method for making multistate characters out of continuous measurements. • • • • . • . • • • • • • •• 383 IX GEOGRAPHIC VARIATION Robert R. Sokal Analyzing character variation in geographic space. 384 R. S. Thorpe A review of the numerical methods for recognising and analysing racial differentiation. • • . • • • 404 John A. Endler Testing causal hypotheses of geographical variation. 424 A. Piazza and P. Menozzi Geographic variation in human gene frequencies. 444 A. Piazza and L. L. Cavalli-Sforza Treeness tests and the problem of variable evolutionary rates ••••••••••••• 451 R. S. Thorpe Phylogenetic analysis of range expansion in the grass snake: reticulate evolution: primary and secondary contact zones. ••••••••. 464 Kani Isik Correspondence between geographic proximity and phenetic similarity among pinus brutia Ten. populations in southern Turkey •••••• 469 Robert Gorenflot, Jean-Marie Hubac, Maurice Jay, and Paul Lalande Geographic distribution, polyploidy and pattern of flavonoids in Phragmites australis (Cav.) Trin. ex Steud. . ••••• 474 BIOCHEMICAL APPLICATIONS J. J. Beintema Molecular evolution of mammalian pancreatic ribonucleases. 479 Georg E. Schulz Quantitative comparison of protein chain folds. 484 B. Suetterlin, G. E. Schulz, R. H. Schirmer, A. Jung, W. Hupe, and R. Frank An approach to the taxonomy of malaria parasites on the basis of protein structures: adenyl ate kinase and glutathione reductase as examples. .••• 489 Mireille Bruschi Evolutionary relations of sulfate reducers. 490 P. Mick Richardson Methods of flavonoid data analysis. • • 495 Paul G. Mahlberg and Joanna Pleszczynska Phylogeny of Euphorbia interpreted from sterol composition of latex. • • • • • • • • • • • • • • • • • • • • 500 x GENERAL APPLICATIONS Pierre Legendre Numerical ecology: developments and recent trends. 505 A. J. Gilmartin Evolutionary trees and numerical taxonomy in studies of Tillandsia (Bromeliaceae) •••• 524 Chris Simon Application of numerical techniques to the systematics of Toxorhynchites (Diptera: Culicidae). • ••••• 527 Lajos Hajdu A chromosome inversion pathway for some Chironomus species and two new techniques for analyzing similarity functions ••.•.•...••.•• 532 K. Daly and D. A. Kuhn Multivariate analysis of variability associated with source of origin in the bacterium Simonsiella. 536 G. David E. Povel Reflections on the classifications of Yponomeuta (Yponomeutidae, Lepidoptera) and numerical taxonomic procedure. .••• • ••••••.•••. 538 Rubens A. da Cunha A phenetic study of the genus XYlocopa (Hym.-Apoidea). 543 Hari K. Seth Numerical taxonomy of the genus Chaetomium Kze •• 547 I. Togan, N. ~dem, and A. Kence A numerical taxonomic study on Carthamus L. taxa in Turkey. • .•••••••••••••• 552 Walter Titz Multivariate analysis of the polyploid complex Valeriana officinal is (preliminary report) •• 557 Gary D. Schnell and Barbara L. Woods Application of numerical taxonomic techniques to the study of behavior ..•..•••••• 562 Manuel B. Lima Numerical taxonomy of some Portuguese wines. 582 COMPUTERS IN SYSTEMATICS F. James Rohlf and Scott Ferson Image analysis ••.•.• 583 Joseph Felsenstein Computers in systematics: one perspective. 600 Leslie Marcus Automated measurement with portable microcomputers. 620 F. A. Bisby, R. J. White, T. D. Macfarlane, and M. T. Babac The Vicieae database project: experimental uses of a monographic taxonomic database for species of vetch and pea. . ••• 625 LIST OF PARTICIPANTS. 630 INDEX.
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