De Queiroz and Gauthier, 1990 Phylogenetic Definitions of Taxon Names

7/27/2019 De Queiroz and Gauthier, 1990 Phylogenetic Definitions of Taxon Names

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Society of Systematic Biologists

Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon NamesAuthor(s): Kevin de Queiroz and Jacques GauthierReviewed work(s):Source: Systematic Zoology, Vol. 39, No. 4 (Dec., 1990), pp. 307-322Published by: Taylor & Francis, Ltd. for the Society of Systematic BiologistsStable URL: http://www.jstor.org/stable/2992353 .Accessed: 26/05/2012 12:05

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Syst.Zool., 39(4):307-322, 1990

PHYLOGENY AS ACENTRAL PRINCIPLE INTAXONOMY:PHYLOGENETIC DEFINITIONS OFTAXON NAMES

KEVIN DE QUEIROZ ANDJACQUES GAUTHIER

Department f Herpetology, alifornia cademy f Sciences,GoldenGate Park, an Francisco, alifornia 4118

Abstract.-Defining he names of taxa n terms f common ancestry, hat s, using phylogeneticdefinitions f taxon names, departs from tradition f character-based efinitions y grantingthe concept of evolution a central role in taxonomy. Phylogenetic definitions bear on othertaxonomic principles and practices, ncluding the following: 1) Names cannot be applied tononmonophyletic axa as the result of mistaken deas about relationships or characters. uchmistakes do not affect onclusions about the monophyly of taxa but about their content nd/ordiagnoses. Because nonmonophyletic axa can only be named deliberately, hey re easily avoid-ed. (2) Definitions are clearly distinguished from descriptions and diagnoses. Definitions areontological tatements bout the existence f entities hat esult from herelationships f common

ancestry mong their parts; descriptions and diagnoses are epistemological statements bouthow we recognize the parts of those entities. 3) By precisely specifying he clade (ancestor)with which a name is associated, phylogenetic definitions larify he limits of taxa, and this nturn clarifies related phenomena such as time of origin and duration. 4) Unlike the case forcharacter-based ntensional definitions nd enumerative extensional definitions, hylogeneticdefinitions provide an unambiguous criterion for synonymy f taxon names: names are syn-onymous f they refer o clades stemming from he same ancestor. 5) Because of their relevanceto synonymy, hylogenetic definitions lso are relevant o priority, f both names and authorship.In phylogenetic taxonomy, priority s based not on first se of a name at a particular rank orrank-group but on first se of a name in association with a particular ancestor. [Definition;diagnosis; nomenclature; phylogeny; priority; ynonymy; axonomy.]

Such expressions as that famous one of Linnaeus,and which we often meet with in a more or lessconcealed form, hat the characters do not makethe genus, but that the genus gives the characters,seem to imply that omething more s included inour classification, han mere resemblance. believethat omething more s included; and that propin-quity of descent .. is the bond, hidden as it is byvarious degrees of modification, which is partiallyrevealed to us by our classifications Darwin, 1859:413-414].

Despite the widespread belief that mod-ern biological taxonomy s based on ourknowledge of evolutionary history, he de-velopment of phylogenetic taxonomy re-mains ncomplete. As the principle of com-mon descent gained acceptance, t took ona superficial ather han central role in tax-onomy. Preexisting axonomies came to beinterpreted s the result of evolution, andevolutionary principles were developed tojustify ong-standing taxonomic practices,but the principle of descent did not be-come a central enet from which taxonomicprinciples and methods were derived Ste-vens, 1984; de Queiroz, 1988).

In several important respects, the con-cept of evolution retains this superficialrather han central role. The definitions fthe names of taxa is one area in which theconcept of evolution has yet to be granteda central role-a change that would haveimportant taxonomic consequences. Al-though the possibility f phylogenetic def-initions of taxon names, that s, definitionsbased on phylogenetic relationships, hasbeen suggested (e.g., Wiley, 1979, 1989;Ghiselin, 1984;Ridley, 1986; Rowe, 1987;de Queiroz, 1988; Gauthier et al., 1988a),the significance and consequences ofadopting this kind of definition have notreceived a detailed treatment. ere we ex-plore the history f the definitions f taxonnames, the fundamental role that defini-tions based on ancestry play in phyloge-netic taxonomy, and some of the conse-quences of adopting such definitions.

"Phylogenetic axonomy," s we use thisterm, s concerned with the representationof phylogenetic relationships, pecifically,with issues related directly o the naming

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308 SYSTEMATICZOOLOGY VOL. 39

of axa nd notwith hose oncerning owrelationships redetermined. onsequent-ly, we assume the goal of representingphylogenetic elationships s well as someof the basic principles f the more nclu-sive discipline alled "phylogenetic ys-tematics," or example, he principle ofsynapomorphy nd the untenability fparaphyletic axa. he ogical asesof hesepropositions ave been considered hor-oughly lsewheree.g.,Hennig, 965, 966,1975; Brundin, 966; Nelson, 1971,1974;Rosen,1974;Platnick, 978;Eldredge ndCracraft, 980; Wiley, 1981;Ax, 1987; deQueiroz,1988).Becausewe are concernedwith the naming of systems f commondescent, e avoid he erm classification,"which s best restricted othe recognitionof classes Griffiths, 974; Hennig, 1975;Ax,1987;de Queiroz,1988).

Our discussion f phylogenetic axono-my concerns the so-called higher taxa,which, n phylogenetic ystematics, renamed lades r monophyletic ntities e.g.,Hennig, 1966), hat s, biological ystemsderiving heir xistence rom he processof common escent Griffiths, 974;Hen-nig, 1975;Ax,1987;de Queiroz, 988).Therelevance f our discussion o taxa of thespecies ategory epends n whether ne'sspecies oncept efers oa subgroup f thecategory clades," n which case the ar-guments resented ere apply to species,or f t refers o the classof biological ys-tems eriving heir xistence rom hepro--cess f nterbreeding, n which ase thesearguments o not apply to species see deQueiroz nd Donoghue, 988).Finally,wediscuss he definitions f axon names. ef-initions are given to words, includingnames, not to the things hat he namesrepresent, hat s, he axa hemselves Ghi-selin, 966a).Becauseprevious uthors el-domdistinguished etween axa nd theirnames, hey ffectively reated efinitionsas if they pplied to both.

THE HISTORY OFDEFINITIONS OF

TAXON NAMESAristotelianefinitionsAccording to Hull (1965:315), .... in no

other cience s definition s important s

it is in taxonomy." n this light, t is sur-prising that the way in which the namesof taxa are defined has changed little overthe last 2,000 years. t also exemplifies hefailure of the theory of evolution to pen-etrate he core of biological taxonomy. Al-though other forms f definition ave beensuggested, raditionally, axonnames havebeen treated s if they re defined by char-acters possessed by those organisms con-sidered to be members of the taxa. Undersuch character-based efinitions, axahavebeen treated as if they are classes of or-ganisms (Ghiselin, 1969, 1974;Hull, 1976,1978;de Queiroz, 1988;for explicit exam-ples see Gregg, 1950; Beckner, 1959; Buckand Hull, 1966, 1969; Muir, 1968; Suppe,1974, 1989) in that their characters havebeen viewed as intensions, that is, thoseproperties connoted by the taxon names.Consequently, traditional definitions oftaxon names have been considered inten-sional definitions e.g., Ruse, 1973). Suchdefinitions have their roots n the Aristo-telian form of definition, which was sum-marized by Hull as follows:

In Aristotle's iew three hings an be known aboutany entity-its essence, ts definition, nd its name.The name names the essence. The definition ivesa complete and exhaustive description of the es-sence. Derivatively, he name is the name of theentity nd the definition description of it [Hull,1965:318].

Most modern taxonomists have aban-doned the notion of essences (but see Kitts,1983; Bernier, 1984), and many have re-jected the notion that taxa are classes oforganisms. Nevertheless, elements of theAristotelian form of definition have per-sisted in modern biological taxonomy nthat he names of taxa continue to be treat-ed as if they are defined by lists of organ-ismal characters see the ection titled Def-inition" in numerous recent taxonomicpapers).

Cluster oncepts: haracter-BasedDefinitionshatAccommodatedvolutionIn post-Darwinian times it has become

accepted widely that biological taxonomyis, or should be, evolutionary. However,


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1990 PHYLOGENETICDEFINITIONS 309

even disassociated from the notion of es-sences, the Aristotelian form f definitionproved to be incompatible with the prin-ciple of evolution (Hull, 1965). As Hull(1965:318)noted, "... what Aristotle wasadvocating in modern terms s definitionby properties connected conjunctivelywhich are severally necessary and jointlysufficient for membership n the taxon]."But evolutionary hange may result n lossor modification, n lineages within taxon,of the very characters hat supposedly de-fine he name of that taxon. Given that themodified ineages remain parts of the tax-on, t must be concluded that he charactersin question were not necessary and suffi-cient to define its name (Sober, 1988;seealso Beatty, 982).

Hull (1965)noted that names can be de-fined by kinds of (intensional) definitionsother than conjunctive ones, that s, defi-nitions in which each property n the en-tire set is necessary for membership e.g.,a bachelor is both unmarried and male).For example, names also can be defineddisjunctively, hat s, by sets of propertiesnot all of which are necessary, without vi-olating the spirit f Aristotelian efinition.Thus, each property n a definite disjunc-tive definition may be sufficient y itself,and only some subset of the properties snecessary for group membership (e.g., asibling is either a brother r a sister). Hull(1965:323; see also Beckner, 1959; Hull,1974) argued, however, that "... neitherof these types of definition s appropriatefor defining he names of taxa and, hence,for delineating taxa. Whether from theviewpoint of phylogenetic or numericaltaxonomy, axonnames can be defined nlyby sets of statistically ovarying ropertiesarrangedn indefinitelyongdisjunctiveefi-nitions" emphasis in original). The dis-tinction between definite conjunctivedefinitions and indefinite disjunctivedefinitions as also made by Beckner 1959)and by Sneath (1962),who used the terms"monothetic" and "polythetic" to refer othe classes of taxa based on these two class-es of definitions.

Indefinite disjunctive definitions, orcluster oncepts, voided the problem thatevolution posed for Aristotelian defini-

tions. Because no character r set of char-acters was necessary for the definition ofa taxon name, and any one of numeroussets was sufficient, volutionary changecould occur without nvalidating the def-inition. Nevertheless, luster oncepts, ikeAristotelian definitions, defined taxonnames in terms of characters. Althoughsuch definitions may have been consistentwith evolution, they were not evolution-ary, which is to say that they made no ref-erence to common descent or any otherevolutionary phenomenon.

Phylogenetic efinitions

Taxonomists ave long suspected hat hecharacters of taxa are merely manifesta-tions of a more fundamental phenomenon(see epigraph). Butdespite the fact hat mosttaxonomists subsequent to Darwin haveaccepted evolution as that underlying phe-nomenon, they are only beginning to re-alize that this concept provides the possi-bility of an entirely different kind ofdefinition.

Viewing taxa as wholes, or individuals,led Ghiselin (1966b, 1974, 1981, 1984) andHull (1976, who rejected his earlier treat-ment of taxa as classes)to conclude that henames of taxa are proper names and hencecan only be defined ostensively, hat s, bypointing out the entity owhich the nameis given. A simple enumeration of includ-ed subtaxa (pointing out the members orrepresentatives) oes not qualify s an evo-lutionary stensive definition, or t makesno reference o evolution. Furthermore, fenumeration s viewed as listing a taxon'sknown content with an implicit tatementabout common ancestry, t fails to capturethe ntended meaning of the name. Simpleenumeration makes no provision for thediscovery of previously unknown repre-sentatives of a taxon. n order to make thedefinitions of taxon names evolutionary,they must be rooted n the concept of com-mon ancestry. Thus, an evolutionary os-tensive definition, ereafter eferred o asa phylogenetic definition, consists ofpointing to a clade, that s, to an ancestorand its descendants (Ghiselin, 1984). Thiscan be accomplished, verbally or on a


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a b cFIG. 1. Three possible ways of defining axon names phylogenetically. a) Node-based definition. b) Stem-

based definition. c) Apomorphy-based definition bar indicates origin of the apomorphy). See text for ex-planations and examples.

branching diagram, in at least three dif-ferent ways:

1. By defining he name of a taxon as theclade stemming rom he most recent com-mon ancestor of two other taxa, hereafterreferred o as a node-based efinition Fig.la). For example, Gauthier et al. (1988a:34)defined Lepidosauria" as "the most recentcommon ancestor of Sphenodon nd squa-mates and all of ts descendants." For oth-er examples see de Queiroz [1987],Estes etal. [1988], Gauthier et al. [1988a, b], andRowe [1988].)

2. By defining he name of a taxon as allthose entities sharing a more recent com-mon ancestor with one recognized taxonthan with another, hereafter eferred o asa stem-based efinitionFig. lb). For example,Gauthier et al. (1988a:27) defined "Lepi-dosauromorpha" as "Sphenodon nd squa-mates Lepidosauria] and all saurians shar-ing a more recent common ancestor withthem than ... with crocodiles and birds."(For other examples see Gauthier et al.[1988a,b].)

3. By defining he name of a taxon as theclade stemming from the first ncestor topossess a particular synapomorphy, here-after eferred o as an apomorphy-basedef-inition Fig. lc). For example, "Tetrapoda"is usually defined mplicitly s the first er-tebrate to possess digits (i.e., hands andfeet rather han fins) and all of its descen-dants.

All three classes of phylogenetic defi-nitions are firmly ooted n the concept ofcommon ancestry n that this concept isfundamental to the meaning of taxonnames. Although the apomorphy-basedphylogenetic definition makes reference o

a character, t differs undamentally froma character-based ntensional definition. ncontrast with the latter, he character sedin an apomorphy-based phylogenetic def-inition s simply a means of specifying nancestor. The definition oes not mply thepresence of the character n all organismsof the taxon, for these characters may belost in some descendants of the specifiedancestor. Thus, it is neither necessary norsufficient or an organism to possess thecharacter n order to be considered part ofthe taxon; what is both necessary and suf-ficient s being descended from the spec-ified ancestor.

The use of phylogenetic definitions ib-erates biological taxonomy from a 2,000-year-old tradition f basing the definitionsof taxon names on characters. Because ofthe antiquity of this tradition nd the im-portance of definitions n taxonomy Hull,1965), one might expect the adoption ofphylogenetic definitions o have far-reach-ing consequences for other taxonomicprinciples, practices, nd conventions.

PROPERTIESOF PHYLOGENETICDEFINITIONS

Relationshipo the ConceptsfMonophyly,Paraphyly, ndPolyphyly

Traditional definitions of taxon namestake the same form, hat is, lists of char-acters, regardless of whether the taxa aremonophyletic, paraphyletic, or polyphy-letic. Although the definitions of thesethree classes of taxa are stated n terms ofcommon ancestry e.g., Hennig, 1966; Far-ris, 1974), the classes themselves are nev-ertheless haracterized by different lassesof characters: ynapomorphies n the case


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1990 PHYLOGENETIC DEFINITIONS 311

of monophyletic taxa, symplesiomorphiesin the case of paraphyletic taxa, and con-vergences in the case of polyphyletic axa(Hennig, 1965, 1966, 1975). For any giventaxon, however, both the patterns f com-mon ancestry hat would place it n one ofthe three classes of taxa and the apomor-phic, plesiomorphic, r homoplastic statusof its characters an be recognized only inthe context of an accepted phylogeny.Consequently, under character-based ef-initions of taxon names, nonmonophyletictaxa can be named accidentally. f phylo-genetic relationships are unknown (thesynapomorphic, ymplesiomorphic, r ho-moplastic status of the characters s ig-nored or uncertain) or if notions of phy-logenetic relationships are in error(symplesiomorphies or homoplasies aremistaken for ynapomorphies), hen para-phyletic r polyphyletic axa can be namedaccidentally ven by those wishing to avoidthem.

Under phylogenetic definitions, nameswill never be defined as referring o non-monophyletic taxa as the result of mis-takes; the associations must be deliberate,and this holds regardless of potential mis-takes bout phylogenetic elationships seebelow). Consequently, hevery definitionsof their names give warning of paraphylet-ic and polyphyletic taxa. The names ofparaphyletic axamust be defined s mono-phyletic taxa from which a part or partshave been removed, that s, as incompletesystems f common ancestry. or example,"Reptilia," traditionally the name of aparaphyletic taxon, might be defined as"the most recent common ancestor ofMammalia and Aves and all of its descen-dants exceptMammalia and Aves." On theother hand, the names of polyphyletic axamust be defined as sets of two or moreseparate systems f common ancestry. Forexample, "Haemothermia," the name of adiphyletic taxon, might be defined as "themost recent common ancestor of mono-tremes and therians and its descendants(=Mammalia) and the most recent ommonancestor f paleognaths and neognaths ndits descendants (=Aves)." The incompletenature of paraphyletic taxa and the com-

posite nature of polyphyletic axa are thusrevealed directly by the manner n whichtheir names are defined. n contrast, efi-nitions of the names of monophyletic axacontain no phrases excluding certain de-scendants of the specified common ances-tor from the taxon, nor do they requireconjunctions linking separate systems ofcommon ancestry.

The relevance of these considerations ophylogenetic taxonomy is that becausenames can only be associated with non-monophyletic taxa deliberately, such as-sociations re easily avoided. Furthermore,phylogenetic definitions an be worded sothat they necessarily efer nly to monophy-letic ntities. his does not mean that mis-takes cannot be made; however, such mis-takes will be seen for what they are, thatis, mistakes about phylogenetic relation-ships, diagnostic characters, or includedtaxa. They will never result n the conclu-sion that a name originally defined as re-ferring o a monophyletic taxon actuallyrefers to a paraphyletic or polyphyleticgroup.

For example, Gauthier et al. (1988a) de-fined the name "Lepidosauromorpha" asall saurians sharing more recent ommonancestor with lepidosaurs than witharchosaurs. They considered Lepidosau-romorpha to include lepidosaurs, kueh-neosaurs, Paliguana*, Saurosternon*, alae-agama , and Younginiformes, s illustratedin-Figure a (an asterisk fter taxon nameindicates that evidence for monophyly slacking). Now suppose that the true phy-logenetic relationships of Younginiformesare as illustrated n Figure 2b; this taxonis the sister group of the clade stemmingfrom he most recent common ancestor ofLepidosauria and Archosauria. Under tra-ditional definitions of taxon names, onemight conclude that Lepidosauromorphais paraphyletic, ecause it now appears thatArchosauria is descended from the mostrecent common ancestor of the taxa orig-inally considered to be lepidosauromorphs(Fig.2b).Butaccording to the phylogeneticdefinition s stated, his s not so. The def-inition of "Lepidosauromorpha" does notcontain a phrase excluding any descen-


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A Pa S P K A Pa S Pi K A Pa S Pi K L

a bCFIG.2. Phylogenetic definitions nd monophyly. a) Phylogenetic relationships within Sauria, with bubble

encircling Lepidosauromorpha as its name was defined by Gauthier et al. (1988a). (b) Hypothetical changein ideas about the relationships f Younginiformes Y),which seems to mply paraphyly f Lepidosauromorphawhen the content rather han the definition s considered. (c) The actual limits and monophyly of Lepido-sauromorpha under the revised relationships according to the definition s stated. See text for additionaldiscussion. Abbreviations: , Archosauria; Y, Younginiformes; a, Palaeagama*;S, Saurosternon*; i, Paliguana*;K, Kuehneosauridae; L, Lepidosauria.

dants of the specified common ancestors;therefore, his name must efer o a mono-phyletic taxon. And, because it is definedwith respect oArchosauria, ne must con-clude not hat Lepidosauromorpha s para-phyletic, but that Younginiformes s notpart of it (Fig. 2c).

By granting the principle of descent acentral role in biological taxonomy, phy-logenetic definitions reorient questionsaway from he monophyletic, paraphylet-ic, or polyphyletic status of taxa to theircontent and diagnoses. The concepts ofmonophyly, paraphyly, and polyphylywere formulated n an era when the evo-lutionary world view had been acceptedbut was granted herole of ittle more thanan after-the-fact nterpretation f the orderalready manifest n taxa (see de Queiroz,1988).Largely as a result of Hennig's writ-ings (e.g., 1965,1966,1975),the role of theconcept of evolution in biological taxon-

omy began to change -from hat of a su-perficial nterpretation o that of a centraltenet (de Queiroz and Donoghue, 1988,1990). But Hennig did not take this per-spective to its logical conclusion, that is,adopting phylogenetic definitions f taxonnames and stating hese definitions n sucha way that all taxa necessarily would bemonophyletic. And because taxon nameshave continued to be defined with respectto characters rather than ancestry, t was

meaningful not only for Hennig, but alsofor systematics p to the present time, toinquire about whether these names re-ferred o monophyletic ntities.

The use ofphylogenetic efinitions illeffectively nitiate new era n biologicaltaxonomy. n this ra there will be, n onesense,noexisting axanamed ntities), orthe nameshavenotyet eentied xplicitlyto the entities hrough hylogenetic efi-nitions. Once these names re tied to theentities y their definitions s completesystems f common ancestry, ll taxonnames an be worded o that hey efer omonophyletic ntities y definition.onse-quently, he concepts of paraphyly ndpolyphyly illbecome uperfluous nd n-teresting rimarily n a historical ontext.Thesignificant uestion o longer will bewhether taxon s monophyletic, araphy-letic, r polyphyletic; nstead asin the x-ample of Lepidosauromorpha, bove) thesignificant uestions bout ny taxonwillconcern ts ontent nd ts diagnostic har-acters seebelow).

As one manifestation f granting he

principle f descent he roleof a central

tenet n taxonomy, hylogenetic efini-tions cknowledge hat ommon ncestryis fundamental o the existence of thethings eingnamed.Accepting hisprop-osition provides he basis for table andunambiguous hylogenetic meanings oftaxon names n the context f changingideas about hedetails f phylogeny, othin terms f relationships nd in terms fthe precise evelat which particular har-

acters xist s synapomorphies. his sta-bility nd clarity erives rom hefact hat,for ny two organisms, ommon ncestryat some evel scertain, hereas heprecise


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content f a taxon nd its diagnostic har-acters re not.

MetataxaThe relevance of phylogenetic efini-

tions to metataxa-taxa based on plesio-morphy ut for which evidence of para-phyly, and monophyly, is lacking(Donoghue, 985;Gauthier t al., 1988a)-is similar o that oncerning araphyleticand polyphyletic axa.Although t s pos-sible to define he name of a metataxonphylogenetically, herewouldbe little ea-son for doing so. Metataxa equire ncer-tainty bout relationships f common e-scent, and, therefore, he phylogeneticdefinitions f their namesrequire mbig-uous statements bout hese relationships.Using phylogenetic efinition, henameof a metataxonmust e defined s a com-mon ncestor nd all, or maybe nly ome,of its descendants. ike the concepts fparaphyly nd polyphyly, he metataxonconcept s the product f an era n whichphylogenetic elationships ad becomeimportant onsiderations, ut characters,rather than phylogenetic elationships,continued o be granted primacy n thedefinitions f axon ames.ndeed, heveryfact hatparaphyly, olyphyly, nd meta-taxa re mportant onceptssevidence hattaxon names continue o be treated s ifthey re defined y characters ather hanby phylogenetic elationships. f the useof phylogenetic efinitions ecomespre-dominant, hen he metataxon oncept, ikethose f paraphyly nd polyphyly, ill be-come superfluous xcept n a historicalcontext.

Relationship o CharactersSome properties f phylogenetic efi-

nitions re clarified y considering heirrelationship o characters. t is sometimessaid that haracters re diagnostic or de-scriptive) f axa ather handefining e.g.,Ghiselin, 966a, , 1984, 1985;Hull, 1976;Wiley, 979; Beatty, 982; Ridley, 986; o-ber, 1988). The difference etween defi-nition nd diagnosis s that between nentity tself nd the evidence for ts exis-tence, hat s,between ntology nd epis-

temology. his distinction s obscured ytraditional efinitions f taxon names,because traditional efinitions ake thesame form s descriptions nd diagnoses,that s, ists f characters Ghiselin, 966a).From n essentialist's erspective, harac-ter-based ntensional efinitions ake n-tological as well as epistemological)tate-ments nthat hey re viewed s descriptionsof taxon's ssence, nd the ssence s thatfrom hich he axon erives ts xistence.When the essentialist nderpinnings reremoved, however, haracter-based efi-nitions onfuse ntology nd epistemolo-gy. Thetaxon eems o exist olelybecauseitsorganisms ave characters ywhichwerecognize hem s belonging othe taxon.Adopting hylogenetic efinitions lar-ifies he distinction etween efinition nddiagnosis.Here the definitions f taxonnames are ontological tatements n thatthey efer omonophyletic ntities clades),which re presumed oexist nder he en-tral enet f common escent ndependentof our ability o recognize hem.Mono-phyletic axa, hat s, named lades, re notconcepts contra L0vtrup, 986)but realthings-systems eriving heir existencefrom common ancestry relationshipsamong heir arts Griffiths, 974;Hennig,1975;de Queiroz, 988).Phylogenetic ef-initions re of little use, however, nlessthe critical relationships an be deter-mined.This s one role of characters. ndafter he relationships ave been estab-lished nd the taxonnamesdefined, har-acters also permit he determination fwhich entities fit a definition, hat is,whether given specimen s a represen-tative f the taxon n question see Hull,1976).Just s symptoms re used to diag-nose a disease which ften asan unseenunderlying ause),so characters re usedto diagnose axa Ghiselin, 984).

Thus, in the previous example, thechange n ideasabout he relationships fYounginiformes oesnot change hedef-inition of "Lepidosauromorpha" r itsmonophyletic tatus. t does, however,imply changes in ideas not only aboutincluded taxa but also about diagnosticcharacters. ne possibility s that he char-


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acters ormerly hought o support closerrelationship f Younginiformes o Lepi-dosauria han to Archosauria ctually di-agnose a more nclusive axon of whichArchosauria s a part. Perhaps derivedcharacters ormerly hought o be absentin archosaurs re determined obe presentin a modified orm. n this casethe char-acters n question urn ut to be irrelevantto determining hich entities it he def-inition f hename Lepidosauromorpha."Thisname s defined s all saurians haringa more ecent ommon ncestor ith Lepi-dosauria than with Archosauria, ven ifthe characters hought o be diagnostic fthis taxon ctually pply to a more nclu-sive clade.

Alternatively, he conclusion hat cer-tain derived characters re diagnostic fLepidosauromorpha may remain un-changed, but now it is concluded thatyounginiforms o not possessthese char-acters. ounginiforms re extinct, nd thecharacters n questionmayhave nvolvedpoorly preserved arts of the body. Per-hapsnew pecimens r further reparationhas revealed that the characters oncethought o be present re n fact bsent.

A strength f viewing haracters s di-agnostic rather han defining of taxonnames sthat t voids ertain roblems orthe traditional orm f definition ausedbyplesiomorphy nd homoplasy. ow canTetrapoda, or xample, e defined y thepresence f limbs f sometetrapods e.g.,snakes) ack hem? ne possibility s to usecluster oncepts n which none of the de-fining haracters s necessary or taxonmembership. nother ossibility s to con-sider he bsence f imbs o be a modifiedform f he haracter limbs resent" e.g.,Platnick, 979).The olution s simpler ndmore traightforward nder phylogeneticdefinitions. ere the absence of limbs nsnakes n no way compromises he nameTetrapoda, efined s the clade stemmingfrom particular imbed ncestor. ecausesnakes re among he descendants f this

ancestor, hey re tetrapods hether heyhave imbs r not. The absence f imbs nsnakesonly makes t more difficult oes-tablish heir etrapod ncestry.

RelationshipoTaxon imits ndOriginationimes

Byprecisely pecifying heclade ances-tor) o which name refers, hylogeneticdefinitions larify mbiguities bout thelimits f taxa that re perpetuated ndertraditional, haracter-based efinitions.Oneof hese oncerns hediscovery f newtaxa. Under the traditional orm f defi-nition, t was generally onsidered ref-erable o basethedefinition f taxon ameon several haracters, resumably ecausehaving more characters onstitutes ettersupport or hat axon. However, he dis-covery f organisms ossessing ome butnot ll of the defining haracters f taxonposed problems. re these organisms artof that axon?Are all of the characters e-fining, r only some of them, nd if thelatter, hich ones?Thus,for xample, hediscovery f monotremes ed to a debateabout whether hese animals were mam-mals or representatives f some separatetaxon Gould, 1985).That this debate oc-curred mplies hat the limits nd hencethe defining haracters f "Mammalia"were called into question. Similar prob-lems ontinue o the present ay, special-ly n paleontology here organisms ithnew combinations f characters re dis-covered egularly see Rowe, 1988).

Phylogenetic efinitions n no way di-minish he significance f such interme-diateforms, ut they ocus ttention wayfrom urely definitional ssues to phylo-genetic nes. For example, n the caseofArchaeopteryx,he nteresting ssue is notwhether hese fossils ruly an be calledbirds; ather, t s their hylogenetic ela-tionships. Given that these relationshipshave been determined, hen the questionofwhether rchaeopteryxs a bird dependsentirely n how "bird" is defined e.g.,Thulborn, 984; Gauthier, 986). Thus, fArchaeopteryxsthe ister roup f ll otherknown feathered ertebrates nd "birds"is defined s the most ecent ommon n-

cestor f paleognaths nd neognaths ndits descendants, hen Archaeopteryxs nota bird. But, f "bird" s defined s the firstfeathered ertebrate nd tsdescendants r


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as all archosaurs haring more recentcommon ncestor with extant irds thanwith crocodylians, henArchaeopteryxs abird. And although t maybe more radi-tional, onvenient, r useful oadopt oneof hevarious ossible efinitions f bird"and hence settle he ssue of whether Ar-chaeopteryxs or is not part of this taxon,the choice s a definitional ather han abiological ssue.

Becausephylogenetic efinitions re-cisely pecify he imits f taxa, hey lsoclarify uestions bout imes f origin ndconsequently bout temporal durations,both ofwhich re susceptible o confusionunder raditional efinitions Rowe,1988).Under character-based efinitions, is-crepancies n the agesassigned o a taxoncan result, ven n the bsence f conflict-ing data, from nconspicuous ifferencesin the definition f the name. What ap-pears o be the ame taxon s udgedby tsnameand many, erhaps most, f ts "de-fining" haracters, ay n fact e two dif-ferent axa n terms f the common nces-tors mplied by slightly ifferent ets ofcharacters. or xample,Mammalia f omeauthors s based solely on the characterdentary-squamosal rticulation etweencranium nd mandible,whereas ther u-thors ase a taxon f he ame name n thisand additional characters Rowe, 1988).Giventhat ome of the additional harac-ters rose before r after hedentary-squa-mosal rticulation, s indeed t apears heydid (Rowe,1988), hen the name "Mam-malia" does not alwaysrefer o the same

clade Fig.3).Becausehese ifferent ladesform nested eries, heir gesmust iffer.Therefore, stimates f the age of Mam-maliamay differ iven the same hypoth-esized relationships nd known fossilssimply ecausecertain ossilswill be con-sideredmammals ccording o some defi-nitions f "Mammalia" ut not others.

The general problem described bovewasrecognized y Hennig 1965, 981; eealsoJefferies, 979;Lauterbach, 989). n-

deed, hree ifferent eanings f taxon'stime f origin ecognized y Hennig rep-resent pecialcasesof the three lasses ofphylogenetic efinitions dentified n this

ECD

C\J Cu)= 0U) c CDM ) U)

o 0 ? : H

Mammalia

FIG. 3. Ambiguities n the boundaries of taxa un-der character-based efinitions f taxon names. If dif-ferent uthors define the name "Mammalia" with re-spect to different ets of the characters indicated bybars in diagram), then "Mammalia" will refer o dif-ferent lades, some more nclusive than others. There-fore, he three fossils will be mammals according tosome definitions ut not according to others.

paper. Theseare 1) the time t which er-tain ineages epresented y extant rgan-isms ast hared common ncestor Hen-nig's * group, Jefferies's rown group,Lauterbach'smonophylum ensu tricto;specialcase of the node-based efinition),(2)the time t which the stem ineageofthat lade separated rom ts sister roup(Jefferies's otalgroup, Lauterbach's an-monophylum; specialcaseof the stem-baseddefinition), nd 3)the ime t whichthe "typical" haracters f the extant ep-resentatives f the clade arose n its stemlineage a specialcase of the apomorphy-baseddefinition). given name could bedefined n any of these three ways, buteach would refer o a different ncestor

and, therefore, o a more r less inclusiveclade. This fact has important conse-quencesfor arious ime-related henom-ena, such as estimates f the originationtimes nd durations f taxa and the cali-bration f molecular locks.

Phylogenetic efinitions void such m-biguities oncerning he imits f taxa, e-cause the ncestors n question re clearlyspecified. his s not to say that differentauthors annot se the amename o refer

to different lades.However, hylogeneticdefinitions f the same name as used bydifferent uthors hould reveal whetherthat namerefers othe ameor to different


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316 SYSTEMATIC ZOOLOGY VOL. 39

cu0

0 ~~~00. E0 CL~~~ 0.0 (0~~~Eg E ~~~~~~~~~~~~~~o

FIG.4. Synonymy nder hylogenetic efinitions."Lacertilia"defined s the lade temming rom hemost recent ommon ncestor f Iguania,Gekkota,Scincomorpha,nd Anguimorpha) nd "Squamata"(defined s the lade temming rom he most ecentcommon ncestor f Lacertilia, erpentes, nd Am-phisbaenia) efer o the ame ancestor circle) f therelationships mong these taxa are as illustrated.Therefore, Lacertilia" nd "Squamata" re synony-mous.

ancestors, nd f they o not, his uggestspossible disagreements oncerning hy-logenetic elationshipsseeSynonymy, e-low).

SynonymyThe issue of taxonomic synonymy,

whether ifferent amesrefer o the ameentity, s clarified y phylogenetic efini-tions.Under haracter-basednd enumer-ativedefinitions, ynonymy ften sa mat-ter- f degree. When the definitions fdifferent amesare identical n terms fcharacters nd included taxa, then syn-onymy eems obvious, but how closelymust hey orrespond f hey re not den-tical?And what criteria re to be used indeciding his ssue?Under raditional ef-initions f taxon names, the answers tothese uestions re not traightforward.ncontrast, hylogenetic efinitions rovidea nonarbitrary nd unambiguous riterion

for ynonymy: ames are synonymous fand only f they efer oclades stemmingfrom hesameancestor.

For example, uppose that 1) "Squa-

mata" s defined s the most recent om-mon ancestor f Lacertilia, erpentes, ndAmphisbaenia, nd its descendants; 2)"Lacertilia" s defined s the most recentcommon ancestor of Iguania, Gekkota,Scincomorpha,nd Anguimorpha, nd itsdescendants; and (3) the relationshipsamongthese taxa are as shown n Figure4 (Estes t al., 1988).Without onsideringphylogenetic elationships,hedefinitionsof the two names seem to indicate that"Squamata" efers o more nclusive ladethan does "Lacertilia." his s contradictedby he phylogenetic elationships. he def-initions f both "Squamata" and "Lacer-tilia" refer o the same ancestor-the oneat the base of the diagram Fig. 4).There-fore, iven the definitions tated nd therelationships llustrated, hese names aresynonymous. hat the two names previ-ouslymayhave been viewed as referringto different lades is accountedfor by amistake bout the content f Lacertilia,namely, hat erpentes nd Amphisbaeniawere thought ot to be parts f t.

Of course, hylogenetic efinitions anclarify ssues f ynonymy nly n the on-text f relevant knowledge bout phylo-genetic relationships. The situation sgreatly implified y, but t is not depen-dent n, there eing single ccepted hy-logeny. Thus, n Figure5a, the name de-fined s the cladestemming rom hemostrecent ommon ncestor f Aand D issyn-onymous with the name defined s theclade temming rom he most ecent om-mon ncestor f Band E,even though herelationships f C are controversial. yn-onymy lsowouldobtain f he definitionsof one, the other, r both names ncludedreference o C as one of the descendantsof the specified ncestor.

Certain differences mong competingphylogenetic ypotheses ender uestionsof ynonymy nresolvable. uppose, singthe previous xample, hat two differentnames are defined under the alternativephylogenetic ypotheses Fig. 5b, c): onefor he

cladestemmingrom he most

e-cent ommon ncestor f A, B, C, D, and Eand the other or he ladestemming romthe most ecent ommon ncestor f A, B,


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A B D E

c c

a

A B D E A B D E

C C

b c

FIG. 5. Synonymy n cases of uncertain phylogenetic relationships. a) The name of the node-based taxon.stemming rom he most recent common ancestor of A and D is synonymous with the name of the node-based taxon stemming from the most recent common ancestor of B and E, despite uncertainty bout therelationships f C. (b, c) Names of node-based taxa defined with respect o the most recent ommon ancestorsof A, B, C, D, and Eand of A, B,and C are synonymous nder one of the possible resolutions. f the relationshipsof C (b), but not the other c). Circles indicate ancestors pecified by the definitions.

and C. According o one of the two hy-potheses he names re synonymous Fig.5b),but according o the alternative heyare not Fig. 5c). Accepting ne of thesehypotheses nd rejecting he other re-solves the issue of synonymy, ut if therelationships re considered unresolvedand both hypotheses re retained, he ssueof synonymy annot be resolved. Thissituation hould be viewed as a strengthrather han weakness f phylogenetic ef-initions. t emphasizes hat ynonymy anbe resolved nly n the context f the rel-evant phylogenetic nformation.

Although the implicit phylogeneticmeaning f taxonnames sgenerally learwhen only extant rganisms re consid-ered, mbiguities ften rise when consid-ering fossils e.g., Patterson nd Rosen,1977; Jefferies, 979; Hennig, 1981;Lau-terbach, 989). or xample, here s no dis-agreement bout the content f Amniotawhen only extant rganisms re consid-ered. n this ontext, hephylogenetic ef-inition f Amniota" might e stated s themost recent common ncestor f Mam-malia, Chelonia, Archosauria, nd Lepi-

dosauria, nd ts descendantsa node-baseddefinition f the crown roup). Neverthe-less, the mplicit meaning f "Amniota,"as this name s most ommonly sed, s theclade temming rom he first ertebrate opossess an egg with an amnion an apo-morphy-based efinition). n the xtant i-ota, the content f Amniota nder thesealternative efinitions s identical; how-ever, f extinct rganisms re also consid-ered, hen hese wo definitions ayrefertodifferent lades, ne more nclusive hanthe other. n otherwords, he mniote ggmay have arisen prior o the most recentcommon ncestor f extant mniotes. Astem-based efinition f the "total" group(Jefferies, 979) s also possible;for xam-ple, Gardiner 1982, 1983) implicitly e-fined Amniota" s Recent mniotes ndall organisms hat re more losely elatedto them than to extant mphibians. Re-gardless f whichdefinition f "Amniota"is favored, he different ossibilities llus-trate general oint: lthough t s usuallypossible o dentify series f ancestors sbeing mplicitly ssociatedwith he nameof a traditional axon e.g.,Fig.4),the pre-


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cise ancestor n this series often will beambiguous. urthermore, lthough hereexists n awareness f these distinctions,traditional ractice as been o usethe amename for both crown and "total" clades(e.g.,Jefferies, 979;Hennig, 1981;Lauter-bach,1989).Given he mbiguity esultingfrom ssociating he amenamewith ladesstemming rom ifferent ncestors n a lin-eage, t eems preferable o give differentnameto the crown ladeon the one handand the "total" lade on the other.

As can be seen from he preceding is-cussion, there necessarily will be ambi-guities bout synonymy uring he tran-sition o a system ased on phylogeneticdefinitions. ssociations f names withparticular ncestors ave heretofore eenimplicit ather han xplicit, nd the formsof definition urrently n use often endersuch associations mbiguous. This situa-tion hould encourage he redefinition ftaxon ames n explicit hylogenetic erms;however, ue consideration houldbe giv-en to diverse criteria, ncluding mplicitassociationswith ancestors, urrent ndhistorical sage, lternative ames,prior-ity see below), nd utility o the greatestnumber f biologists.

PriorityThe consequences f phylogenetic ef-

initions or ynonymy ear on another s-sue, priority, hich s often esolved n aphylogenetically nsatisfactory ayundertraditional axonomic onventions. n thetraditional ystem e.g., CZN, 1985), pri-ority s tied to categorical anks.This sit-uation can lead to drastic hanges n themeanings fnames i.e., he ncestors ithwhich henames re mplicitly ssociated)as the result of simple changes n rank.Thus, ombining everal axa of the samerank nto a single one requires hat theoldestname s the valid one for hat axon.This practice an result n changing heancestor ithwhich hename s mplicitlyassociated o that f more nclusive lade.Similarly, artitioning single taxon of aparticular ank nto everal axa t that amerank often esults n restricting heorigi-nal taxon'sname to a less inclusive lade.

Theproblem f hanging he lades withwhich names re associated s aggravatedby trying o achieve a phylogenetic ax-onomywithin he raditional innean ys-tem. This results rom ttempts o elimi-nate paraphyletic axa, which are oftenaccompanied y changes n ranks ssoci-atedwith particular ames n order o sat-isfy he convention f mandatory atego-ries.Forexample, he taxaAgamidae* ndChamaeleonidaehave traditionally eenassigned herank f family, nd t hasbeensuggested hat Agamidae*may be para-phyletic with respect o Chamaeleonidae(Estes et al., 1988; Frost and Etheridge,1989). f the relationships re asillustratedin Figure , then Agamidae" s paraphy-letic ccording o ts raditional efinition.Nevertheless, ne might nterpret hisname s having n mplicit ssociation ithancestorA, the most recent ommon n-cestor f ts ncluded ubtaxa u-w). "Cha-maeleonidae," n the other hand, s im-plicitly ssociatedwith ncestor .

Such being the case, uniting Agami-dae" and Chamaeleonidae nto a singlefamily ould eliminate paraphyletic ax-on. If this s done, then according o tra-ditional, rank-based notions of priority(e.g., CZN, 1985), he name of the cladestemming rom ncestorA will be "Cha-maeleonidae,"because this is the oldername n the family roup Frost nd Eth-eridge, 989).Given he desirability f ta-ble phylogenetic eanings f names, hisactionhas the undesirable onsequence fchanging he association f a name fromoneclade o more nclusive ne. Thename"Chamaeleonidae,"which was formerlyassociatedwith the cladestemming romancestor C, is now associatedwith thatstemming rom ncestor A, the ancestorwith which Agamidae"was formerly s-sociated.

It might e argued that he associationof "Agamidae"with ancestorA is unjus-tified-that t is preferable o consider"Agamidae," he name of a paraphyletictaxon, o have had no implicit hyloge-netic definition. his does not, however,solve the problem f the change n thecladewith which, Chamaeleonidae"s as-


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sociated.Furthermore, he name "Acro-donta" Cope, 1864) lready as been usedfor the clade stemming rom ncestor A(Estes t al., 1988).Acrodonta, owever, sconsidered o be assigned rank bove thefamily evel in traditional axonomies.Therefore, Acrodonta" ouldbereplacedby "Chamaeleonidae," imply ecause heformer s not a name of the family roup.

From he preceding xample, t can beseen that he traditional ractice f deter-mining priority ccording o ranks s ob-fuscatory rom he perspective f phylo-genetic axonomy.he ssociationsfnameswith particular ladeschange s the resultof arbitrary ecisions about categoricalranks, nd names ppliedto monophyleticentities re rejected imply becausetheyare not of the ppropriate ank.Given hata rank-based oncept f priority onfusesthe associations f names with particularclades, phylogenetic oncept f priorityshould not be basedon ranks.

In phylogenetic axonomy, he conceptofpriority houldnot be basedon first seof name t given ank r group f ranks,but on first se of a name in associationwith particular lade ancestor). hus, ocontinuewith hesameexample, Agam-idae" and "Chamaeleonidae"would re-main associatedwith the same ancestors(Aand C,respectively).f he relationshipsare as illustrated Fig. 6), then Chamae-leonidaewould be considered subgroupof Agamidaerather han separate axonof the samerank. The names re not syn-onymous, nd the former paraphyly" fAgamidae s seen as a mistake bout itscontent. Alternatively, ecause the name"Acrodonta" as already eenusedfor hemore nclusive lade, Agamidae," nameformerly ssociatedwith a paraphyleticgroup, might be. abandoned n favor of"Acrodonta"Estes t l., 1988). f hename"Acrodonta" id not xist, tmight epref-erable to coin a new name for his claderather han using Agamidae."Any ne ofthese lternatives s reasonable rom phy-logenetic perspective, ecause none ofthem changes the associations f nameswith particular lades ancestors).

The principle of coordination ICZN,

Acrodonta

"Agamidae" ChamaeleonidaeU_ v w x y z

FIG.6. Changes in the clade with which a nameis associated under the traditional, ank-based crite-rion of priority. f "Agamidae" and Chamaeleonidaeare combined into a single taxon assigned the rankof family, he name of this family s "Chamaeleoni-dae" because this is the older name in the familygroup. The result is a change in association of thename "Chamaeleonidae" from the clade stemmingfrom ncestor C to that stemming from ncestor A.

1985),which deals with priority f au-thorship ather hanof the name tself, sanother omenclatural ulethat ettles s-sues of priority n a phylogenetically n-satisfactory ay. According othe princi-ple of coordination, ll names n a givenrank-based roup e.g., genus group, am-ily group) re credited o the first uthorto useanyname n the groupbasedon thesamenomenclatural ype.Thus, lthoughCope (1886)coinedthe name "Iguaninae"for particular axon f quamate eptiles,his nsight scredited o Bell 1825)merelybecauseBellcoined Iguanidae" nd bothnames belong to the family group (deQueiroz, 1987). This rule would be un-problematical f it applied only to situa-tions n which he differencesnthe namesinvolved only differences n categoricalranks and their associated suffixes, orexample, f the family guanidaehad beenlowered n its entirety osubfamily ank.The rule applies, however, even if thenames refer o different ntities, or ex-ample,when "Iguanidae"refers o a moreinclusive taxon than does "Iguaninae."From he viewpoint f conveying n au-thor's ssociation f a name with partic-ular taxon, this rule confuses matters,whether n phylogenetic r in Linneantaxonomy. t reflects n overemphasis n


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320 SYSTEMATICZOOLOGY VOL.39

categorical anks. s n the ase of priority,authorship n phylogenetic taxonomyshould not be based on the first se of aname n a particular ank-based roup, ut

on mplicit r xplicit ssociation f namewith particular lade ancestor).CONCLUSION

Since Hennig's e.g., 1965, 1966) nflu-ential writings nd their popularization,phylogenetic ystematics as enjoyed on-siderable uccess nd made great rogress.In contrast, hylogenetic axonomy, hatbranch f ystematics oncernedwith ep-resenting he relationships ncovered y

phylogenetic nalysis, as lagged behind.The development f phylogenetic axon-omyhas been hindered n part y the m-plicit r explicit ssumption hat t s to beachieved within the traditional inneanframework. his assumption s one ex-ampleof a general henomenon n whichexisting axonomic ractices re taken forgranted nd the evolutionary orld viewis overlaidupon them s a superficial n-terpretation. ut f the Darwinian Revo-

lution s ever to occur n biologicaltax-onomy Patterson, 978;de Queiroz, 988;O'Hara, 1988), hen the role of the prin-ciple of descent must change. It mustchange from n after-the-fact nterpreta-tion oa central enet rom hich heprin-ciples and methods f taxonomy re de-duced. The principle of phylogeneticdefinitions xemplifies his change. Pre-viously, axawere onsidered o be definedby characters nd only nterpreted fter-

the-fact s products f evolution. Underthe principle f phylogenetic efinitions,evolutionary onsiderations nter irectlyinto hedefinitions f their ames. Just sthe concept f synapomorphy ranted heprinciple f common escent central olein systematic nalysis, o the concept ofphylogenetic efinitions rants his con-cept central ole n taxonomy.

ACKNOWLEDGMENTS

We thank D. Cannatella, M. Donoghue, R. Estes, R.Etheridge, . Fink, D. Frost, M. Ghiselin, A. Graybeal,D. Hillis, D. Hull, P. Mabee, R. O'Hara, C. Patterson,E. Sober, E. Wiley, A. Wyss, and an anonymous re-

viewerfor heir omments n earlier rafts f thispaper.Thisresearch as supported y a Tilton ost-doctoral ellowship rom he California cademy fSciences oK.deQ. nd National cienceFoundationgrant SR 87-09455 o J.G.

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Received 3 February 990; accepted 5 June 990

De Queiroz and Gauthier, 1990 Phylogenetic Definitions of Taxon Names

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