Beyond Cladistics: The Branching of a Paradigm

by David M. Williams (Editor), Sandra Knapp (Editor)

Overview

Cladistics, or phylogenetic systematics—an approach to discovering, unraveling, and testing hypotheses of evolutionary history—took hold during a turbulent and acrimonious time in the history of systematics. During this period—the 1960s and 1970s—much of the foundation of modern systematic methodology was established as cladistic approaches became widely accepted. Virtually complete by the end of the 1980s, the wide perception has been that little has changed. This volume vividly illustrates that cladistic methodologies have continued to be developed, improved upon, and effectively used in ever widening analytically imaginative ways.

Product Details

ISBN-13:	9780520947993
Publisher:	University of California Press
Publication date:	10/28/2010
Series:	Species and Systematics , #3
Sold by:	Barnes & Noble
Format:	eBook
Pages:	352
File size:	7 MB

About the Author

David M. Williams and Sandra Knapp are both in the Botany Department at the Natural History Museum of London.

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Beyond Cladistics

The Branching of a Paradigm

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By David M. Williams, Sandra Knapp

UNIVERSITY OF CALIFORNIA PRESS

Copyright © 2010 The Regents of the University of California
All rights reserved.
ISBN: 978-0-520-94799-3

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CHAPTER 1

David M. Williams, Kåre Bremer, and Sandra Knapp

CHRIS HUMPHRIES, CLADISTICS, AND CONNECTIONS

INTRODUCTION

By way of introduction, we offer this short piece describing a few subjects that attracted Chris Humphries's attention during his thirty-plus years as botanist and systematist. While it is impossible to cover all the subjects with which Chris was involved, we have selected a few that seem representative of his breadth: botanical cladistics, cladistics and daisies, and biogeographic cladistics (the conservation studies are ably summarized by Vane-Wright; see Chapter 3, this volume).

A SHORT BIOGRAPHY

Chris joined the Department of Botany of the Natural History Museum in 1972 replacing Alexsandr Melderis (1909–1986), then head of the European Herbarium, "whose substantial frame belied his most kindly and benign personality" (Cannon 2001: 128). Chris was hired as assistant curator, a nearly finished PhD student, coming directly from Vernon Heywood's Department of Botany in Reading University. Flora Europaea (FE) was being brought to a conclusion, and Chris was to help put the project to bed (for a summary of FE achievements, see Walters 1995). But his first task was to finish his thesis and obtain his PhD degree, which he did in 1973. His study was on species of Argyranthemum, a genus of daisy in the family Asteraceae, and is a fine example of a morphological investigation (with a little phytochemistry) and anatomical interpretation, with comments on their relationships and geographic distribution. Most of the morphological part was published as a monograph in the museum's now-defunct Bulletin series, covering "22 species, grouped into five sections ... all of which occur in the North Atlantic insular archipelagos of Madeira, the Salvage Islands and the Canary Islands" (Humphries 1976: 147, abstract). Chris would return to the subject of Madeira and the geographic relations of its plants (Carine et al. 2009).

Chris—one of the first of Vernon Heywood's students (David Bramwell [see Chapter 6, this volume] was another)—by moving to the museum began the invasion of what became known as the "Reading Mafia." Others followed and are represented within the pages of this book: Stephen Blackmore (see Chapter 2) and Charlie Jarvis (see Chapter 8) (see also Leadlay and Jury 2006). With the exception of three sabbaticals—two of them at the University of Melbourne, the first in 1979–1980 and the second in 1986, and a six-month stay at the Wissenschaftskolleg zu Berlin (Institute for Advanced Study Berlin) in 1994—Chris worked in the Department of Botany at the museum.

Chris's studies on Asteraceae to one side (see later), the next period in his career focused almost exclusively on biogeography, and in 1979 he published his first considered paper on the subject, "Endemism and Evolution in Macaronesia" (Humphries 1979a). Between times he published a number of revisions and smaller accounts of other flowering plant families such as Poaceae, but of greater significance were his papers on the southern beeches (Nothofagus) and their relevance to Southern Hemisphere biogeography (Humphries 1981a, 1981b, 1983); a series of papers on Eucalyptus and their geographic dimension (Ladiges and Humphries 1983, 1986; Ladiges et al. 1983, 1987, 1989; see also Ladiges et al., Chapter 14, this volume); an intellectual justification for documenting the Central American flora (Humphries 1983), which blossomed into Flora Mesoamericana (Knapp and Press, Chapter 5, this volume); some early angiosperm molecular papers (Mishler et al. 1988; Humphries 1989); and a textbook summary of cladistic biogeography (Humphries and Parenti 1986, 1999; see also Parenti and Humphries 2004; Parenti and Ebach, Chapter 15, this volume). Most of these topics find biogeography as the unifying theme.

Around 1990, Chris, Dick Vane-Wright, and Paul Williams put biogeographic matters to a more practical application, addressing what they called the conservationist's "Agony of Choice" (Vane-Wright et al. 1991) with their "WORLDMAP" approach to conservation biology. As Dick Vane-Wright relates in his chapter in this book (Chapter 3), Chris's interest in conservation biology goes back to his early days, publishing on the subject with respect to Argyranthemum in 1974 (Humphries 1974). Remarkably, this was only his third publication, his first as a sole author. When asked how he came to write such a paper so early in his career, Chris offered the following: "[T]he paper you asked about was because as a reviewer I didn't like the original entry—so I rewrote it for them" (C.J. Humphries, pers. comm., March 9, 2009). Chris explored the scientific and policy aspects of biological conservation for nearly a decade until, encouraged by the enthusiasm of Malte Ebach (see Chapters 10 and 15, this volume), he returned to the more fundamental matters of biogeographic investigation (e.g., Ebach and Humphries 2002; Humphries and Ebach 2004; see also the bibliography in this book).

Chris received a number of honors: He was awarded the Linnean Society's Bicentenary Medal in 1980 (Biological Journal of the Linnean Society 2001;14: 456–457); twenty-one years later, in 2001, he received the Linnean Society's most prestigious award, its Gold Medal (Linnean Society Annual Report 2001: 36–37, with photograph); and in 2002 he became an honorary fellow of the American Association for the Advancement of Science. He has been president of the Systematics Association (2001–2003) and its treasurer (1996–1999), president of the Willi Hennig Society (1989–1991), being elected fellow honoris causa in 1998, and vice president and botanical secretary of the Linnean Society (1994–1998).

BOTANICAL CLADISTICS

Reading Chris's doctoral thesis today, thirty-six years after it was printed, one gets little direct sense of the future, what was to come, except for the odd sentence here and there, such as this one:

The most fruitful systematic evidence for speculation on evolutionary sequence in Argyranthemum stems from the relationship between distribution and eco-geographical specialization.

(Humphries 1973, p. 217)

There were no cladograms, no schemes of relationships, but there was geography—and discussions of its relevance and interpretation, in the sense that "evolutionary sequence[s] ... stem[s] from the relationship between distribution and eco-geographical specialisation." Here we take a short digression to consider the beginnings of botanical cladistics, a subject difficult to pin down, largely because cladistics, even in its botanical guise, was—and probably still is—interpreted in a myriad of different ways.

For botany, it is generally acknowledged that Warren "Herb" Wagner (1920–2000; see Farrar 2003) and his ground plan divergence method spawned many early contributions to a "cladistic" approach from the mid-1950s through to the late 1960s (see the bibliography published by Funk and Wagner 1982). Wagner's ground plan divergence method was developed as part of his thesis work on ferns (Wagner 1952; see also Wagner 1980), which was derived from Benedictus Danser (1891–1943; Jansen and Wachter 1943) and his notion of ground plans and their relevance rather than from the works of Willi Hennig (Danser 1950; see also Wagner 1969; for a recent incarnation, see Kukalová-Peck 2008; for commentary, see Béthoux et al. 2008). Wagner's name did eventually become inextricably linked to one of the earliest and most commonly used parsimony algorithms (Farris 1970), an approach that was later associated with some of Willi Hennig's ideas (Farris et al. 1970).

A more direct connection to Willi Hennig can be found in the work of bryologist Timo Koponen and his study on Mniaceae, which included possibly the first botanical Hennigian argumentation plan (Koponen 1968: 136, Fig. 107). With respect to British botanical cladistics, the first argumentation plan (and probably the first paper in Taxon to use Hennig's ideas—a few earlier papers mention Hennig but only in passing) was published by Chris in a multiauthored piece entitled "Chromosome banding and synthetic systematics in Anacyclus" (Ehrendorfer et al. 1977: 390, Fig. 4). Much was captured by that title. Chromosome banding and related matters might have sounded like the future in the 1970s, but Chris was to home in on "synthetic systematics"—it was a subtle beginning. We mentioned briefly above Chris's first biogeography paper, "Endemism and Evolution in Macaronesia" (Humphries 1979a). Although betraying a sense of its time with subheadings such as "Gradual Speciation," "Morphology and Adaptive Radiation," and "Abrupt Speciation: Apoendemism," the discussion treads cautiously over new ground, without mentioning Hennig, but using Hennigian terminology:

The retention of plesiomorphic features, i.e. ancestral morphological attributes and the same chromosome numbers as sisters groups, together with the fact that many are taxonomically isolated are rather dubious lines of evidence on which to estimate the age of species ... the fact that many [taxa] possess synapomorphic features (uniquely derived attributes) shared by sister groups is indicative of a monophyletic origin from a single island ancestor.

(Humphries 1979a: 194)

Such coded and oblique references may have been difficult for many to comprehend, even if plesiomorphic features and synapomorphic features were both defined ("ancestral morphological attributes" and "uniquely derived attributes," respectively). Matters were different when Chris published his Anacyclus monograph (Humphries 1979b). By that time, Bremer and Wanntorp had published their summary and review of Hennig's phylogenetic systematics, boldly stating that they "deplore that phylogenetic systematics has not been introduced into botany and we considered it high time that botanists in general should become aware of this taxonomic approach" (Bremer and Wanntorp 1978: 317–318). Responses to this call were quick and often negative, bordering on the hostile (Burger 1979; F[aegri], 1979; Guédès 1981; Meeuse 1981; further comment and clarification came from Wanntorp 1980, 1983). Such was the climate that Chris could provide a three-page summary of phylogenetic systematics, adding, with some poignancy "... the construction of 'phylogenetic trees' based on ill-defined principles and the elaboration of nominalistic methods has created considerable disillusionment and disregard of sound phylogenetic discussion" (Humphries 1979b: 102). The relationships among the species of Anacyclus were portrayed in a Hennigian argumentation plan, characters determined by the assessment of relative apomorphy rather than by any computer-aided assistance (Humphries 1979b: 107, Fig. 10). Humphries and Richardson (1980) provided a further overview of phylogenetic systematics in botany in the context of phytochemistry, and, later, Humphries and Funk (1984) wrote a more general piece. Things were not easy: "The adoption of cladistic methodology did not happen without a degree of dogged persistence: Chris Humphries' paper with Vicki Funk ... at a subsequent international symposium also held at Reading, Current Concepts in Plant Taxonomy, received a hostile reception from members of the audience" (Blackmore and Wortley, Chapter 2, this volume). Thus, promotion of botanical cladistics, in its Hennigian form, truly began with Chris, Hans-Erik Wanntorp, and Kåre Bremer, and that beginning, like the reform of paleontology (Patterson 1981b), may be traced back to the enthusiasms of Lars Brundin (Wanntorp 1993; Brundin 1993, 1995).

At a more fundamental level, the more direct impact of phylogenetic systematics on green plant classification was ignited and stimulated by two papers,"A Phylogenetic Analysis of the Land Plants" by Lynne Parenti, an ichthyologist from the American Museum of Natural History (Parenti 1980; a response came from Smoot et al. 1981, with replies from Parenti 1981; Young and Richardson 1982), and "A Cladistic Classification of Green Plants" by Bremer and Wanntorp (Bremer and Wanntorp 1981a, 1981b), along with further commentary from zoologists (Farris and Kluge 1979; Wiley 1980; Mitter 1981). Both the empirical papers (Parenti 1980; Bremer and Wanntorp 1981a, 1981b) inspired further research into green plant relationships. In July 1984, Chris organized a symposium, held at the Natural History Museum, sponsored by the Linnean Society, the Systematics Association, and the Willi Hennig Society. This resulted in a series of papers published in the first volume of the journal Cladistics, a new journal to a large extent established thanks to the efforts of Chris; he was also one of the two first editors.

By 1982, Funk and Wagner published a "botanical cladistics" bibliography with 123 items (Funk and Wagner 1982), and, two years later, Baum et al. published a bibliography of "numerical phenetic studies" numbering some 426 items (Baum et al. 1984). These two compilations are of general interest, as the Funk and Wagner bibliography included numerical studies generated by various computer programs alongside noncomputer Hennigian analyses. Thus, one might have imagined at the time it would have been difficult to determine just exactly what cladistics ("phylogenetic systematics") was—or at least how it was done. If one was to examine the various methodology papers published in Taxon from its beginning (1951) through to the 1970s, most were exploring the various strands of numerical taxonomy, in its broadest interpretation, as understood in Sneath and Sokal (1973) and in Sneath (1995). It might be just to consider that "phylogenetic systematics" (sensu Willi Hennig) progressed almost as if invisible to the desires of numerical taxonomy. That changed, of course, after the debate in Taxon between proponents of parsimony and compatibility (a debate starting with Churchill et al. 1984). That debate is too complex to deal with here, save to note of the combatants early in the botanical discussion, Farris and Kluge suggested that "All authors evidently deemed it desirable to be termed 'Hennigian' ..." (Farris and Kluge 1979: 411). It is important to note that, at least in terms of popularity of use, if not soundness of justification, parsimony triumphed for a while (Farris and Kluge 1986). Part of that triumph was assisted by the Forey et al. (1992) book, another publication eased into existence by Chris, the Systematics Association, and the Natural History Museum (a short history can be found in Williams and Ebach 2009).

CLADISTICS AND DAISIES

In 1975 (July 14–18), Vernon Heywood, Jeffrey Harborne, and Billie Turner arranged a symposium on the biology and chemistry of the Compositae (= Asteraceae), held at the University of Reading (Heywood et al. 1977; reviewed by Humphries 1979c). There was no mention of phylogenetic systematics, even though both Chris and Kåre Bremer were present and both aware of the subject. Both were working on genera in the tribe Anthemideae. Bremer was studying the South African genus Osmitopsis (Bremer 1972), and Chris was working on Argyranthemum (Humphries 1976).

The Reading symposium focused on the tribal classification and phytochemistry of the Asteraceae, which with some 25,000 species is one of the largest of flowering plant groups. The classification of Asteraceae in use at that time was essentially George Bentham's nineteenth century division of the family into about a dozen tribes defined by a variety of morphological characters (Bentham 1873). Much of the discussion at the symposium centered on the delimitation of tribes and the tribal position of various odd genera. Among the "problem" genera discussed at the Reading symposium were Osmitopsis, Cotula, and Ursinia, relative to whether they were or were not part of the Anthemideae (the reason for those discussions are evident today, as the three genera are now placed close to the root of the Anthemideae phylogenetic tree; Osmitopsis may even be sister to all other Anthemideae).

(Continues...)

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Table of Contents

Contributors vii
Preface xi

PART ONE: ON CHRIS
Bibliography of Works by Chris Humphries 1

1 Chris Humphries, Cladistics, and Connections 19
David M. Williams, Kåre Bremer, and Sandra Knapp

2 Ontogeny and Systematics Revisited: Developmental
Models and Model Organisms 35
Stephen Blackmore and Alexandra H. Wortley

3 Rooted in Cladistics: Chris Humphries,
Conservation—and Beyond? 47
Richard I. Vane-Wright

4 Do We Need to Describe, Name, and Classify All Species? 67
Quentin D. Wheeler

5 Floras to Phylogenies: Why Descriptive Taxonomy Matters 77
Sandra Knapp and J. Robert Press

PART TWO: BOTANY
6 Island Hot Spots: The Challenge of Climate Change 91
David Bramwell

7 Endemism and Evolution of the Macaronesian Flora 101
Mark A. Carine, Arnoldo Santos Guerra, I. Rosana Guma,
and J. Alfredo Reyes-Betancort

8 Early British Collectors and Observers of the
Macaronesian Flora: From Sloane to Darwin 125
Javier Francisco-Ortega, Arnoldo Santos-Guerra, Charlie E. Jarvis,
Mark A. Carine, Miguel Menezes de Sequeira, and Michael Maunder

PART THREE: CLADISTICS
9 Monophyly and the Two Hierarchies 147
Olivier Rieppel

10 Beyond Belief: The Steady Resurrection of Phenetics 169
David M. Williams, Malte C. Ebach, and Quentin D. Wheeler

11 Monographic Effects on the Stratigraphic Distribution
of Brachiopods 197
Gordon B. Curry

12 The Eukaryote Tree of Life 219
Diana Lipscomb

PART FOUR: BIOGEOGRAPHY
13 Tethys and Teleosts 243
Peter L. Forey

14 East–West Continental Vicariance in Eucalyptus
Subgenus Eucalyptus 267
Pauline Y. Ladiges, Michael J. Bayly, and Gareth J. Nelson

15 Wallacea Deconstructed 305
Lynne R. Parenti and Malte C. Ebach

Index 321
About the Editors 335