Automated Taxon ID in Systematics - Theory, Approaches and Applns - N. MacLeod (CRC, 2008) WW

370 Pages·2008·18.53 MB·English

Half Title Page

The Systematics Association Special Volume Series 74
Automated Taxon
Identification in
Systematics

Theory, Approaches
and Applications

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Title Page

The Systematics Association Special Volume Series 74

Edited by
Norman MacLeod

Natural History Museum

London, UK

Automated Taxon
Identification in
Systematics

Theory, Approaches
and Applications

CRC Press is an imprint of the
Taylor & Francis Group, an informa business

Boca Raton London New York

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CRC Press
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© 2008 by Systematics Association with the exception of chapters 1 and 10, the Department of Palaeontology, the Natu-
ral History Museum, London.
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Library of Congress Cataloging-in-Publication Data

Automated taxon identification in systematics : theory, approaches and applications / editor, Norman
MacLeod.
p. cm. -- (Systematics Association special volumes)
ISBN-13: 978-0-8493-8205-5 (alk. paper)
ISBN-10: 0-8493-8205-X (alk. paper)
1. Biology--Classification--Data processing. I. MacLeod, Norman, 1953- II. Systematics
Association. III. Title. IV. Series.

QH83.A93 2007
570.1’2--dc22
2007006206

Visit the Taylor & Francis Web site at
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Table of Contents

Chapter 1
Introduction...................................................................................................................1

Norman MacLeod

Chapter 2
Digital Innovation and Taxonomy's Finest Hour.........................................................9

Quentin D. Wheeler

Chapter 3
Natural Object Categorization: Man versus Machine ...............................................25

Philip F. Culverhouse

Chapter 4
Neural Networks in Brief...........................................................................................47

Robert Lang

Chapter 5
Morphometrics and Computed Homology: An Old Theme Revisited......................69

Fred L. Bookstein

Chapter 6
The Automated Identification of Taxa: Concepts and Applications..........................83

David Chesmore

Chapter 7
DAISY: A Practical Computer-Based Tool for Semi-Automated Species
Identification.............................................................................................................101

Mark A. O'Neill

Chapter 8
Automated Extraction and Analysis of Morphological Features for Species
Identification.............................................................................................................115

Volker Steinhage, Stefan Schröder, Karl-Heinz Lampe and Armin B. Cremers

Chapter 9
Introducing SPIDA-Web: Wavelets, Neural Networks and Internet Accessibility
in an Image-Based Automated Identification System .............................................131

Kimberly N. Russell, Martin T. Do, Jeremy C. Huff and Norman I. Platnick

Chapter 10 Automated Tools for the Identification of Taxa from Morphological Data:
Face Recognition in Wasps ......................................................................................153

Norman MacLeod, Mark A. O'Neill and Stig A. Walsh

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Automated Taxon Identification in Systematics

Chapter 11 Pattern Recognition for Ecological Science and Environmental Monitoring:
An Initial Report.......................................................................................................189

Eric N. Mortensen, Enrique L. Delgado, Hongli Deng, David Lytle, Andrew Moldenke,
Robert Paasch, Linda Shapiro, Pengcheng Wu, Wei Zhang and Thomas G. Dietterich

Chapter 12 Plant Identification from Characters and Measurements Using Artificial
Neural Networks.......................................................................................................207

Jonathan Y. Clark

Chapter 13 Spot the Penguin: Can Reliable Taxonomic Identifications Be Made Using
Isolated Foot Bones?................................................................................................225

Stig A. Walsh, Norman MacLeod and Mark A. O'Neill

Chapter 14 A New Semi-Automatic Morphometric Protocol for Conodonts and a
Preliminary Taxonomic Application ........................................................................239

David Jones and Mark Purnell

Chapter 15 Decision Trees: A Machine-Learning Method for Characterizing
Morphological Patterns Resulting from Ecological Adaptation..............................261

Manuel Mendoza

Chapter 16 Data Integration and Multifactorial Analyses: The Yeasts and the
BioloMICS Software as a Case Study.....................................................................277

Robert Vincent

Chapter 17 Automatic Measurement of Honeybee Wings.........................................................289

Adam Tofilski

Chapter 18 Good Performers Know Their Audience! Identification and Characterization
of Pitch Contours in Infant- and Foreigner-Directed Speech..................................299

Monja A. Knoll, Stig A. Walsh, Norman MacLeod, Mark A. O'Neill and Maria Uther

Appendix .......................................................................................................................................311

Subject Index................................................................................................................................329

Taxon Index ..................................................................................................................................337

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vii

The Systematics Association Special Volume Series

Series Editor

Alan Warren
Department of Zoology, The Natural History Museum
Cromwell Road, London SW7 5BD, UK

The Systematics Association promotes all aspects of systematic biology by organizing conferences
and workshops on key themes in systematics, publishing books and awarding modest grants in
support of systematics research. Membership of the Association is open to internationally based
professionals and amateurs with an interest in any branch of biology including palaeobiology.
Members are entitled to attend conferences at discounted rates, to apply for grants and to
receive the newsletters and mailed information; they also receive a generous discount on the
purchase of all volumes produced by the Association.

The first of the Systematics Association’s publications The New Systematics (1940) was a classic
work edited by its then-president Sir Julian Huxley, that set out the problems facing general
biologists in deciding which kinds of data would most effectively progress systematics. Since
then, more than 70 volumes have been published, often in rapidly expanding areas of science
where a modern synthesis is required.

The modus operandi of the Association is to encourage leading researchers to organize symposia
that result in a multi-authored volume. In 1997 the Association organized the first of its international
Biennial Conferences.This and subsequent Biennial Conferences, which are designed to provide
for systematists of all kinds, included themed symposia that resulted in further publications. The
Association also publishes volumes that are not specifically linked to meetings and encourages new
publications in a broad range of systematics topics.

Anyone wishing to learn more about the Systematics Association and its publications should
refer to our website at http://www.systass.org

Other Systematics Association publications are listed after the index for this volume.

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ix

Foreword

The desire to classify objects is one of the most fundamental properties of the human being. The
manifestation of this is reflected in everyday life in the form of the energy devoted to the classification
and labelling of the population for taxation purposes, military conscription, political aspirations and
marketing. A less aggressive aspect occurs in the field of hobbies – stamp collecting is perhaps the
most widely spread of these, but there are many who, arising from a biological interest, make
collections of various groups of insects, birds and the like. There is also a sinister side to the trait
– for example, the clandestine collection of pillaged archaeological objects. This antisocial type of
behaviour is much in evidence today – for example, the organized looting from the shattered
museums of Iraq and, less dramatically but nonetheless equally destructive to the cultural heritage
of all mankind, the seemingly uncontrollable theft of invaluable artefacts from China.
Leaving such dismal thoughts behind, let us consider the scale and scope of the topics in the
present volume. Firstly, be it noted that the timing is perfect. The year 2007 is being devoted to
the 300 year-jubilee of the father of classical taxonomy, the genius of Carl von Linné. Notwith-
standing that the wish to stabilize the description, identification and classification was afoot in
many quarters in Europe, it is to the credit of Linné that an organized, logical system for the
description and recognition of plants and animals was developed and, moreover, quickly caught
on. For more than a century and a half, taxonomists were largely satisfied with the Linnaean
doctrine. The frequently rather boring anatomical exercise attaching to the correct identification
and location of new categories seemed, for most, a small price to pay for maintaining order in the
scheme of plants and animals.
An alternative (unwittingly so?) was proposed by a contemporary of von Linné, Michel Adan-
son, a French botanist. Adanson's ideas were more a modus operandi, so phrased as to incite the
taxonomist to assemble as much data as reasonably possible on the organism of interest. This
admirable approach was not always observed by the binomial nomenclaturists – least of all within
the sphere of palaeontology. Notwithstanding von Linné's achievements with respect to the naming
of species, he became, even during his lifetime, outmoded. The French biologist Count Georges
Louis Leclerc de Buffon, a contemporary of von Linné, was critical of the scientific basis of what
was in essence a man-made attempt at putting life forms into slots and did not reflect the results
of divine creation. In the Official Jubilee Book of the Linnean Year, Professor Nils Uddenberg has
pointed out that it was the work of Buffon that opened the way for Darwin's evolutionary theories
and not the work of von Linné.
Dissatisfaction with the descriptive techniques of 'Linnaean taxonomy' led to the formation of
a mechanically oriented discipline, Numerical taxonomy (NT), with Adanson as patron saint, as it
were. This eventually computer-oriented approach was strongly promoted by Robert Sokal and
Peter Sneath during the 1960s and 1970s. Numerical taxonomy quickly acquired a dedicated
following and a jargon of its own – for example, OTU (operational taxonomic unit). This 'new
taxonomy' brought to the fore the need for a way of defining species that was as unbiased as
possible. It is still stimulating to consult many of the treatises that were spawned by the period of
ascendancy of NT for the closely reasoned and admirably logical presentation of theses. It had,
however, a negative aspect: to wit, a tendency towards degrading the skills necessary for actually
studying the functional biological properties of organisms. More than a few numerical taxonomists
felt this tiresome pursuit could be best left to computerized treatment. Classical taxonomy ceased

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