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PRINCIPLES AND METHODSOF

PHYLOGENETIC SYSTEMATICS:

A CLADISTICS WORKBOOK

DANIEL R. BROOKSJANINE N. CAIRATHOMAS R. PLATT

riARY R. PRITCHARD

The University of KansasMuseum of Natural History


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HARVARD UNIVERSITY

LIBRARY

GRAY HERBARIUM


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UNIVERSITY OF KANSASMuseum of Natural History

Special Publication No. 121984

PRINCIPLES AND METHODS OF PHYLOGENETIC SYSTEMATICS:A CLADISTICS WORKBOOK

By

Daniel R^, BrooksDepartment of ZoologyUniversity of British Columbia2075 Wesbrook MallVancouver, British Columbia V6T 2A9CanadaJanine N^. CairaSchool of Life Sciences andHarold W. Manter LaboratoryDivision of ParasitologyUniversity of Nebraska State MuseumUniversity of NebraskaLincoln, Nebraska 68488 USAThomas R. PiattDepartment of BiologyUniversity of RichmondRichmond, Virginia 23173 USAMary H. PritchardHarold W. Manter LaboratoryDivision of ParasitologyUniversity of Nebraska State MuseumUniversity of NebraskaLincoln, Nebraska 68488 USA

The University of KansasLawrence

1984


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1 ^x

UNIVERSITY OF KANSAS PUBLICATIONSMUSEUM OF NATURAL HISTORY

Editor: Joseph T. Collins

Special Publication No. 12Pp. V + 1-92; 37 figures

Published 20 April 1984

ISBN 0-89338-022-.9

Copyrighted 1984By

Museum of Natural HistoryUniversity of Kansas

Lawrence, Kansas 66045USA

n


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PREFACE

This booklet is designed as a practical introduction tothe principles and methods of CLADISTIC ANALYSIS. Cladisticshas emerged as a powerful analytical tool in comparative Biology.Developed by Hennig (1966) as an aid to reconstructingPHYLOGENIES and subsequently refined by recent workers (seePertinent Literature) , cladistics provides the most informativesummation of any set of biological observations. The resultsare displayed in a consistent, testable and reproducibleframework. Use of the techniques by systematists and extensionof the principles to other comparative areas of Biology hasbeen hampered by the lack of an easily-understood account ofthe procedures involved. This workbook represents an attempt toacquaint interested biologists with the mechanics ofnon-quantitative and quantitative approaches in cladistics,provide a representative sampling of literature concerningthe principles and techniques, and supply a summary of the mainprinciples involved. It was first compiled as a teachingaid for a workshop on cladistic methods sponsored by theAmerican Society of Parasitologists. Thus, the hypotheticaltaxa have been deemed parasites, but the methods and principlesare generally applicable.

There are five main sections in this workbook. Thefirst section contains an essay delimiting the goals andprinciples of cladistic analysis. The second section containsa simple example demonstrating the use of cladistics inexamining the relationships among three natural taxa: a CaliforniaQuail, a Ruffed Grouse, and a Sharp-Tailed Grouse. The nextsection deals with the actual mechanics of cladistics, itcomprises a) descriptions and explanations of CHARACTERS foreight hypothetical taxa, seven to be classified and one to serveas the OUT-GROUP, b) a step-by-step cladistic analysis of thetaxa using a non-quantitative technique and c) a step-by-stepquantitative analysis using the Wagner algorithm developed byDr. James S. Farris, State University of New York, StonyBrook. Section four contains a glossary of the terms capitalizedin this workbook. And finally, we have included a representativelist of recent literature concerning cladistics, including asummary of all pertinent literature published in SystematicZoology from 1959 to 1981. For a more in-depth study, werecommend Phylogenetics- The Theory and Practice of PhylogeneticSystematics by E.O. Wiley (see literature section).

m


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CONTENTS

PART 1. CLADISTICS - A BRIEF REVIEW 1PART 2. A SIMPLE PRACTICAL EXAMPLE 15PART 3. THE MECHANICS OF CLADISTICS

A. Taxa and Characters 19B. Non-quantitative Approach (Hennig's

Argumentation Scheme) 25C. Quantitative Approach (Farris'

(Wagner Analysis) 49PART 4. GLOSSARY OF TERMS 79PART 5. PERTINENT LITERATURE 83EVALUATION SHEET 92


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PART 1: CLADISTICS- A BRIEF REVIEW*

This essay will be an attempt to present a brief reviewof the assumptions of phylogenetic systematics, and examine theconstruction of classifications based on cladistic analyses.There is little original information in this presentation. Ihave relied heavily on material published in Systematic Zoologyduring the past decade, and particularly the work of Dr. E. 0.Wiley of the University of Kansas. Errors of interpretation,however, rest soley with me.The past decade has seen a revolution in BiologicalSystematics. This is generally regarded as a highly conservativediscipline, hardly fraught with controversy (at least regardingmethodology) since the publication of Darwin's (1859) Originof the Species , some 120 years ago. The publication of the

Origin represented a major shift in systematic thought, fromthe cataloguing of the plan of the Creator to the realizationthat all life is related on the basis of genealogical descentfrom a common ancestor.The philosopher-historian Thomas Kuhn, in his book TheStructure of Scientific Revolutions , established four criteriafor detecting revolutions in science, which are outlined below:

1. An accumulation of observations that cannot beexplained on the basis of existing theories orparadigms2. Expression of discontent by individuals working inthe area.3. A proliferation of competing hypotheses.4. A recourse to philosophical examinations ofthe fundamental nature of the discipline.

These are all symptoms of a transition from what Kuhn termed"normal" to "extrodinary" research. A brief review of thepapers included in the bibliography of this volume will

Revised from a presentation by T.R. Piatt as part of thesymposium, "Shoring Up the Foundations of ComparativeBiology - Systematics" at the 55th Annual Meeting of theAmerican Society of Parasitologists, 4-8 August, 1980.Berkeley, California.1


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provide ample evidence to support the existence of a revolutionin systematics. The transition was prompted, in my opinion, bya perceived lack of objectivity in systematics. Descriptionsof the discipline as a combination of "art and science" bysuch luminaries as G.G. Simpson and E. Mayr have led to thedesire for a more objective approach to systematics and theestablishment of an objective science of comparative biology.The revolution has encompassed several competing approachesto systematics. It is not, however, my intention to reviewthem here. The remainder of this presentation will be devotedto phylogenetic systematics, or cladistics.

The assumptions of phylogenetic systematics, as outlinedby Wiley (1975) are as follows:1. Evolution occurs.2. There exists a single phylogeny of life and itis the result of genealogical descent.3. Characters are passed from generation to genera-tion, modified or unmodified, during genealogicaldescent.

The emphasis encompassed by these assumptions is clearly ongenealogical descent. This is considered the only necessaryand sufficient criterion for the establishment of a naturaltaxon. Genealogical relationships, however, cannot beobserved. They must be inferred. Characters (morphological,biochemical, behavioral, etc.) can be observed and can beused to infer genealogical relationships.Characters can be divided into two categories: 1) thosethat infer genealogical relationships, i.e., homologies; and

2) those that do not infer genealogical relationships, i.e.,non-homologies (convergences and parallelisms) . Bridgeprinciples, in the sense of Hempel (1965) , are required inorder to use observable characters to infer genealogicalrelationships. The following bridge principles were proposedby Wiley (1979)

1. The hypothesized .... set characters of a proposedtaxon may be used as justification for the natural-ness of that taxon if it is also hypothesized thatthese characters indicate that the members of thetaxon are genealogically more closely related toeach other than to any other organism outside thetaxon.

2. The hypothesized .... set characters of a hypoth-esized natural taxon may be present only in certainstages of ontogeny or modified during subsequentevolution in members of subsets of the taxon.


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Therefore, characters hypothesized to be homologous aresufficient to infer a natural taxon.In a phylogenetic system, all taxa must be monophyletic.Monophyly, as defined by Hennig (1966) , indicates that allmembers of a taxon are descended from a single stem species,which includes all members of the stem. In the figure below,

taxa A, B and C are contained in taxon X and constitute amonophyletic group (on the left) . In the figure on theright, taxa A and B are contained in taxon X, while C isplaced in Y. As all descendents of the stem (0) are notcontained in a single taxon, both groups are paraphyleticand do not constitute natural taxa.

Only monophyletic taxa are considered natural and the goalof phylogenetic systematics is the identification of suchtaxaTwo types of homologies are recognized in cladisticanalysis. Plesiomorphies are the general or more primitivestate of a character. The subsequent modification of theplesiomorphic state is regarded as derived and termedapomorphic . An apomorphic character shared by two or moretaxa is termed a synapomorphy . Monophyletic taxa can only


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be identified on the basis of synapomorphies, which areassumed to have been inherited from a most recent commonancestor.Hennig (1966) proposed four methods for analyzing thedirection of change in a series of homologous characters,termed a transformation series. These are outlined below:

1. Holomorphological analysis via out-group comparison.2. Ontogenetic analysis.3. Geological precedence.4. Chorological (biogeographic) analysis.

Out-group comparison consists of comparing character statesin members of a proposed monophyletic taxon with species notincluded in that taxon. Ideally, the comparison is made withthe sister-group, if known. However, all species not includedin the proposed taxon comprise the out-group. A character-state present in the proposed monophyletic taxon that is notpresent in the out-group is considered derived or apomorphicA character-state that is present in both the proposed mono-phyletic taxon and the out-group is considered plesiomorphicFor example, in the hypothetical taxa used in Part 3 of thismanual, all the organisms under consideration possess anchoringdevices. A comparison with the out-group, represented by X,reveals that the out-group lacks anchors. Therefore, thepresence of these structures is considered apomorphic at thelevel of the group in question.

Ontogenetic analysis is based on the Biogenetic Law ofvon Baer. More general characters appear earlier in ontogenythan more specialized characters (see Nelson, 1978, for adetailed review of this topic) . Geological precedence statesthat characters found in organisms in older fossil strata areplesiomorphic compared to those found in more recent strata.The chorological method involves the implied progression oforganisms in space as a criterion for determining the directionof evolution. The latter two methods are not widely acceptedat the present time.Once character analysis is complete, a data matrix isconstructed. The constructions and evaluation of datamatrices will be thoroughly discussed inpart 3 ofthis manual and will not be dealt with further at this time.The resulting cladogram (e.g., see figure opposite Step 13in part 2) is an unambiguous hypothesis of the relationshipsof the members of a monophyletic taxon. This hypothesiscan be tested by the discovery of new members hypothesizedto belong to that taxon and/or the identification of newcharacters. This rigorous testing of phylogenetic hypotheses

is a primary function of the hypothetico-deductive method.


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In many cases more than one possible hypothesis may beproduced. In situations where more than one cladogram results(see the figure opposite step 8 in part 2) the most parsimo-nious set of relationships (i.e., requiring the fewest con-vergences) is chosen.

The methods that have been described to this pointresult in the relative ranking of taxa. Note that thebranch angles and branch lengths of the cladograms inPart 3 do not impart subjective information regarding thedegree of divergence or "adaptiogenesis" of the taxa.Classification is the process of assigning absoluterank to monophyletic groups inferred from the cladogram.A requirement of phylogenetic systematics is that all taxaare monophyletic and that there is direct correspondencebetween the cladogram and the classification derived from

it. The result is a classification that consists of mono-phyletic taxa based on genealogical relationships. Anagenesisor adaptiogenesis of evolutionary systematics are consideredsubjective and result in paraphyletic taxa (grades) ratherthan monophyletic taxa (clades) and are not considered. Suchdecisions are based on opinion or authoritarianism, notobjective criteria.

Absolute ranking in a phylogenetic system was originallybased on the time of origin of the group. Hennig (1966) pro-posed the following time scale for the establishment of supra-specific taxa:Geological Age Category

Pre-Cambrian Phylum or Sub-PhylumCambrian-Devonian ClassCarboniferous OrderTriassic-Early Cretaceous FamilyLate Cretaceous-Oligocene TribeMiocene GenusThe timing of geological events, the chorological method,can also be used to determine the minimum age for mono-phyletic taxa. Absolute ranking is considered by manyindividuals to be the weakest part of Hennig ' s theory.It does, however, have the advantage of separating theranking process from attempts to determine the degree ofdivergence which, as mentioned earlier, is a subjectiveprocess.

Wiley (1979) has set forth a formal framework for thepresentation of phylogenetic classifications utilizing the


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Linnaean Hierarchy. He formalized the following criteria:1. Taxa classified without restriction are mono-phyletic groups (sensu Hennig, 1966).2. The relationships of sister-taxa within theclassification must be expressed exactly.

Cladistic classifications have often been criticized asbeing too complex to be useful as a general reference systemin biology. Wiley (1979) has proposed a series of conventionsto be applied to the Linnaean System aimed at economy inclassification, integration of fossil and recent classifi-cations and the expression of reticulate evolution in aphylogenetic system. I will discuss only those conventionsthat directly affect the classification of parasitic organisms.

The first convention states that, "The Linnaean Hierarchywill be used, with certain other conventions, to classifyorganisms." The second convention advocates the use of mini-mum-length classifications. Only the five mandatory cate-gories (genus, family, order, class and phylum) may be re-dundant. In addition, where possible and when consistentwith phylogenetic relationships, taxa of "essential impor-tance" will be retained at the traditional rank.

The third convention, the sequencing convention, is apowerful tool in reducing the number of redundant categoriesand names of taxa. This convention permits the placementof taxa forming an asymmetrical part of a cladogram at thesame categorical rank and sequenced in the classificationin order of origin. In the example on the facing page, thecladogram illustrates the relationships between taxa A-ETaxa C-E form an asyiraiietrical branch of the cladogram. Thenon-sequenced classification includes two additional taxa(Taxon C and D+E) , erected to contain C-E and retain thesister-group relationships demonstrated in the cladogram.The sequenced classification eliminates tv/o category- namesand the arrangement of C, D and E, in order of theirbranching pattern represents a minimum classification,while retaining the sister-group relationships.


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NOT SEQUENCED SEQUENCEDTAXON A+B+C+D+E

TAXON A+BAB

TAXON C+D+ETAXON C

CTAXON D+E

DE

TAXON A+B+C+D+ETAXON A+B

AB

TAXON C+D+ECDE


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The fourth convention is the use of the term i,(idl^matabtZA (L. - of changeable position) (Wiley, 1979)This term is used in classifying trichotomous or poly-otomous relationships within monophyletic group. In theexample below taxon A+B+C has been erected to accomodatetaxa A, B and C. Using this convention

TAXON A+B+CABC

each is given equivalent rank and identified as iec/X^muitCLbt-l^ , clearly acknowledging the unresolved natureof the relationship.

The remaining conventions proposed by Wiley (1979)fall into three categories: 1) the placement of mono-phyletic as well as para- and polyphyletic groups ofuncertain origin in phylogenetic classifications, 2) theintegration of fossil and recent classifications and, 3)the classification of reticulate evolution. Althoughthese conventions will undoubtedly prove useful in con-structing parasite classifications, their general use-fulness at the present time is limited and they will notbe discussed further.

I have chosen an analysis of the cestode orderProteocephalata proposed by Brooks (1978) as an exampleof a parasite classification using the conventionsdescribed above. Rather than presenting the completecladogram for discussion, I will concentrate on thesuperfamily Monticelloidea (see the facing page)


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