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Linnaeaii, rank-based, and phylogenetic : Restoring primacy to the link between names and taxa Kevin de Queiroz

de QueiroK, K. 2005. Linnaean, rank-based, and phylogenetic nomenclature: Restoring pri- macy to the link between names and taxa. - Acta Univ. Lips. Symb. Bor. Upa. 33:3, 127-140. Uppsala, ISBN 91-554-6192-1. Linnaeus and other 18"" Century naturaii.sts practiced nomenclature in a way that associated laxon names more strongly with taxa (group.s) than with the categorical ranks of the taxonomic ("Linnaean") . For IS'"* century naturalists, ranks functioned merely as devices for indicating hierarchical position that did not alTccl I he application of names. Conse- quently, taxa did not change their names simply because of changes in rank. For example, the name RepiiUa did not change when the rank of the taxon designated by that name was changed from to division or . During the 19''' Century, a different approach to nomenclature emerged that made rank assignment centra! to the application of taxon names. Under this rank- based approach, which forms the ba.sis of the current botanical and zoological ctxlcs, names are implicitly defined in tenns of ranks and types and are therefore more strongly associated with ranks than with the taxa to which they refer. Consequently, taxa change their names simply because of changes in rank. Forexample, if the rank of die taxon/Icícacrae is changed from to .subfamily, its name must change to Aceroklnae. Phylogenetic nomenclature is a new approach that ties taxon names to explicitly evolutionary concepts of taxa through definitions that describe taxa in terms of ancesu-y and descent. This approach once again associates ia.\on names more strongly with taxa than with ranks and thus represents a return, updated with evolutionary principles, to an approach similar to that practiced by Linnaeus and other 18'''Century naturalists, Kevin de Queiroz. Departivem of Vcrtebrati' , National Museum of Natural Hislory. Smitksoimin ¡n.^titulioii, Waxliinf^ton. DC. 20560-0162. USA. E-mail: dei/ue iik^ai. edu

In addressing the future of biological nomencla- fundamental difference, phylogenetic nomencla- ture, it seems appropriate to consider phyltigenetic ture often differs significantly from traditional notn end ature (e.g. de Queiroz and Gauthier 1990, rank-based nomenclature concerning which 1992, 1994, de Queiroz and Cantino 2Û()lb) - a names are to be considered synonyms and - new approach to biological nomenclature in which nyms, and thus also the accepted names of partic- the application of laxon names is based on explic- ular taxa. Although phylogenetic nomenclature itly evolutionary methods. This approach contrasts can be considered radical in this respect, in other with the traditional rank-based approach - adopted respects it is not radical at all but instead represents hy the current Bacteriological (lUMS !992), Zoo- a return to an approach similar to that practiced by logical (ICZN 1999), and Botanical (IBC 2000) Linnaeus and other early naturalists. codes - in which evolutionary considerations are In this paper, I will discuss the relationships be- entirely taxonomic (i.e. they determine only what tween 18'" Century, rank-based, and phylogenetic kinds of groups are to be recognized as taxa), and nomenclature, emphasizing the relationships be- nomcnclatui c (i.e. the use of taxon names) is ba.scd tween taxon names, on the one hand, and taxa on categorical or taxonotiiic ranks. Because of this (groups) versus categorical ranks, on Ihe other, I

Symb. Bot. Up.'í. 33:3 128 Kevin de Queiroz will first describe how nomenclature was practiced categories, they use those categories in a way that hy ¡8"' Century naturalists. In particular, I will differs significandy from the way in which the cat- provide evidence thai the primary associations of egories were used by Linnaeus and other early tax- taxon names were with taxa (groups) rather than onomists. with ranks (laxonomic categories). I will then de- I have called attention to Linnaean nomencla- scribe the rank-based approach to nomenclature ture both because of the importance of Linnaeus' thai emerged during the 19"^ Century and forms contributions to and nomenclature and the foundation of the currcni international codes because this paper is part of a tribute to one of his (e.g. lUMS 1992, ICZN 1999, IBC 2000). In par- great works, the PiiinUintm. Nevertheless, ticular, [ will describe how the rank-based ap- the approach thai I really wish to describe is not proach changed the primary associations of taxon the approach of Linnaeus in particular hut that of names from taxa to taxonomic ranks. Next, I will 18''' Century European naturalists in general - or describe the recently proposed phylogenetic ap- more specifically, that of European naturalists proach that forms the basis of the draft fAy/wCoi/e from the time when they adopted the use of cate- (Camino and de Quciroz 2000, 2003), giving a gorical ranks, following Linnaeus, until sometime brief overview of its similarities to, as well as its in the middle of the 19"' Century, when the alterna- differences from, traditional rank-based nomen- tive rank-based approach to nomenclature clature. Finally, 1 will describe how the phyloge- emerged. netic approach restores the primary association be- In describing how nomenclature was practiced tween names and taxa. Although phylogenetic no- by Linnaeus and other eariy naturalists, the point I menclature de-emphasize s taxonomic ranks, want to make is that for these eariy taxonomists which are commonly considered one of the hall- taxon names were more clo.sely associated with marks of , 1 hope to show that taxa than with categorical ranks. This point can be this new approach is, with respect to the function demonstrated by showing that when particular of categorical ranks, more similar to nomenclature taxa (groups) were assigned to different ranks, the as it was practiced by Linnaeus and other early names of those taxa did not change and thus re- naturalists than is the later rank-based approach tained their associations with the taxa to which that underiies the current codes of botanical and they originally referred, rather than with the ranks zoological nomenclature. with which they had previously been associated. To dcmonslrate this, I need to adopt a conceptual- ization of taxa that approximates that of 18* Cen- Linnaean and Late IS"" Century tury naturalists.Therefore, I will adopt aconceptu- Nomenclature ahzation of taxa as sets of , particulariy I will use the term Linnaean nomenclature for the those sharing distinctive characters (see de Quei- nomenclatural principles and practices adopted by roz, 1997). Carolus Linnaeus (1707-1778). Linnaean nomen- Because this symposium commemorates the clature in this sense should not be confused with publication of Linnaeus" Species Plaiiiaiuin, I the taxon names used by Linnaeus, which is Lin- wouid have liked to use names from that work to naean nomenclature in a ditïerent sense. More im- illustrate my point. However, 1 am a zoologist, portantly, it should not be confused with the no- which is to say that I am sufficiently unfamiliar menclatural approach that forms the basis of the with the historical use of taxon names that current international codes of nomenclature. Al- using those names as examples would have greatly though these codes are based on the taxonomic delayed the completion of my paper. For this rea- rank-categories adopted by Linnaeus (i.e. regnum, son, I will emphasize zoological taxon names, par- classis, ordo, , species) with the addition of ticularly those of vertebrates, the group with which both primary (e.g. division, , family) and I am most familiar. secondary (e.g. subclass, inlraorder, superfamily) In addition, it is not particularly informative to

Synih. Bot. Upx. JJ:J Linnaeun, rank-based, and pkylogeneiic nomenclature 129

compare Linnaeus' use of taxon names with use of Class Amphibia Tribe Amphibia the same names hy earher authors, at least not as Order Reptilia Division Replilia they relate to differences in rank assignments. The reason is that taxonomic ranks were used infre- Figure I. Application of taxon names by late 18''' and quently by earlier authors; their consistent and sys- early 19'" Century naturalists. For ihesc early naturalists, tematic use derives largely from the work of Lin- categórica! ranks served to indicate the nested or mutu- ally exclusive relation.ships of taxa but had no effect on naeus, Therefore. I will illustrate my point with the application of taxon names. Therefore, a taxon could zoological names used by Linnaeus and later 18'*' be designated by the same name regardless of the rank to and early 19"' Century authors. Of particular inter- which it was assigned. In this example, the same names. est are cases in which a taxon recognized by Lin- Amphibia and Replilia, were used by Linnaeus (e.g., ] 758, 1766) for nested taxa thai he ranked as a class and naeus (or some other author) was also recognized an order (left), and by Scopoli ( 1777), who ranked the by a subsequent author but assigned to a different same taxa a^ a tribe and a division (right). taxonomie rank. [n these cases, the change in rank did not re- quire a change in the name of the taxon. I do not These taxa were once again excluded from Am- mean to say that the names of taxa never changed. phibia in the 13"" Edition of Ihe Authors who recognized taxa of similar or identi- (Linnaeus and Gmelin 1788). (1 have not at- cal composition but based their taxonomic systems tempted a thorough survey of the various editions on different characters often gave different names of Linnaeus" Systema Naturae but instead have to those taxa, since it was common to use taxon chosen the hrst ( 1735), sixth (1748), tenth ( 1758), names that described the characters upon which and twelfth (1766) editions as the sources of my the systems were ba.sed. For example, several au- examples.) thors recognized a taxon composed of what would With the preceding clarifications tn mind, the later be considered and (ex- point I want to make is that the categorical ranks to cluding and ); however, some of which particular taxa were assigned sometimes those authors emphasized the u.se of both aquatic changed without any significant changes concern- and terrestrial habitats by at least some of those ing the composition or diagnostic characters of organisms and used the name Atnphibict (< Greek those taxa, but such changes did not necessitate amphihios = double ) for that taxon (e.g. Lin- changes in taxon names (Fig. 1), For example, Lin- naeus 1735, 1748, Linnaeus and Gmelin 1788, naeus ( 1735, 1748, see also Linnaeus and Gmelin Shaw 1802), while others emphasized the mode of 1788) assigned the taxon Amphibia {nox including locomotion and used the name Repulía or Reptiles any "") to the rank of class. Later, Merrem (< Latin reptare = to creep or crawl) (e.g. Laurenti (1820) assigned the same taxon to a higher cate- 1768, Brongniari 1800, I805,0ppel 1811). gorical rank. (Merrem did not explicitly .state the In addition, sometimes the composition of a rank of this taxon; that rank is inferred to have taxon would change significantly (i.e. not merely been above the rank of class because the laxon's through the inclusion of newly discovered spe- two primary subgroups were ranked as classes.) cies), yet the same name would be used. For exam- Despite this difference in ranks, Merrem (1820) ple, in the first edition of Systeina Naturae, Lin- used the same name. Amphibia, for this taxon. In naeus ( 1735) included only taxa that would later later editions of the Systema Naturae, Linnaeus be considered amphibians and reptiles in his class (e.g., 1758, 1766) recognized a taxon of a some- Ampliihia (.see also Linnaeus 1748). Later, how- what different composition (i.e., including certain ever, Linnaeus (e.g. 1758, 1766) included in a "fishes") as the cla.ss Amphibia. Scopoli (1777) taxon of the same name and rank various organ- recognized the same taxon but ranked it as a tribe; isms that he had previously included in his class nevertheless, he used the same name. Amphibia. Pices, such as lain prey s (Petmmyzon), sharks [Sq- Another example concerns the name Reptllla, ualus), skates {Raja), and sturgeons {Acipenser). which Linnaeus (1748, 1758, 1766, see also Lin-

Symb. Boi. Ups. 33:3 130 Kevin de Queiroz naeus and Gmelin 1788) used for a subgroup of Table 1. Mandatory standardized ranking signify- Amphibia that he assigned to the rank of order (he ing endings used by the rank-based codes of bot- also used the name Repiikx for this taxon). Sco- any and zoology poli ( 1777) used the same name for a laxon of sim- ilar composition despite assigning it to the rank of Categorical Rank '-^ Zoology" division. Most other laie 18"' and early 19"" Cen- _ tury authors who used the name Repiiiia or Wí-/;- Ordo (order) -ales Siibordo (suborder) -meae - (iVe.î (e.g. Laurenti 1768, Daudin 1802-3, Lamarck Supi;rramilia (superfamily) - -iiidea 1809) applied that name to a more inclusive taxon Familia (family) -aceae -idae corresponding in composition to the one that Lin- Subfamilia (subfamily) -oideae -inae naeus (e.g. 1735, 1748, .see also Linnaeus and Tribus (iribe) -eue -illi Gmelin 1788) called Amphibia (i.e. including not Subu-ibus (subtribe) -inae -ina only Linnaeus' order Reptilia but also his order ' IBC (2000): Ans. 17.1, 18.1, 19.1, 19.3, Serpentes). They used the same name that Lin- -ICZN (1999): Art. 29,2. naeus had used for an order despite ranking the ' In botany, ibc standardized, rank-signifying endings laxon as a class. for orders and suborders arc only mandatory for names Thus, for 18"" Century taxonomists, changes in based on the names of included fain i 11 es based on ge- neric names (automatically typified names), thai Ls, as the assignments of taxa to categorical ranks did not opposed 10 names taken from dLstinctive characters of necessitate changes in the names of those taxa. the taxon (descriptive name.s) (IBC 2000: Art. 16.1). This situation indicates that the categorical ranks Standardized, rank-signifying endings are also recom- did not have a significant nomenclatural function. mended (but not mandatory) for names of laxa assigned Instead, the ranks served a more or less exclusively to the higher ranks division, .subdivision, class, and sub- class (IBC 2000: Rec, !6A), laxouomie function of indicating the relative hier- archical positions (inclusiveness) of taxa. The in- dependence of 18"" Century nomenclature from categorical ranks contrasts sharply with situations family). Table 1 summarizes the standardized rank- in what has now become traditional nomenclatural signifying endings used in botany and zoology. practice, in which the application of taxon names Although rank-based nomenclature is com- is based on categorical ranks. monly referred to as Linnaean, this characteriza- tion is misleading. Despite being based on the hi- erarchy of taxonomic categories derived from Rank-based Nomenclature those used by Linnaeus (commonly termed the Twill use the term rank-based nomenclature for an Linnaean hierarchy) and in using binominal spe- approach to nomenclature in which taxon names cies names, the rank-based approach differs signif- are tied to particular categorical ranks and rank icantly from that adopted by Linnaeus and other assignment is necessary for the application of eariy naturalists in granting greater importance to taxon names. A particular name is applied to the associations of taxon names with categorical whichever taxon contains the designated type and ranks than with taxa. On the other hand, this prop- is assigned to the categorical rank associated with erty is manifested in some of Linnaeus' (e,g, 1737, that name. For example, the name Aceraceae is !751) practices regarding genera (see also Larson applied to whichever taxon contains the type of the 1971: 131, de Queiroz 1997: i 33). In any ease, I genus Acer and is assigned to the rank of family. have reserved the adjective Linnaean for the ap- As in this example, at least some of the names in proach used by Linnaeus himself. Because the no- rank-based nomenclature have intrinsic compo- menclatural system that underlies the modern nents - mandatory, standardized, rank-specific codes contains many components developed in the endings {-aceae in the example) - that tic those 250 years since the lime of Linnaeus, and because names to particular categorical ranks (in this case, its use depends on categorical ranks {including

Symb. Bot. üps. 33:3 Linnaeah, rank-based, and phyiogenetic nomenclature 131

Infraorcfer Acrodonta Family Chamaeleonidae Family Chamaeleonidae Subfamily Chamaeleoninae Figure 2. Application of laxon names under rank-hascd nomenclature. In this approach, the name of a laxon depends on the rank to which thai taxon is assigned. Therefore, if the same taxon is a.ssigncd to a different categorical rank, it must be designated by a different name. In ihis example, two nested taxa are designated by the names Acmiionkt and Chamaeleonidae when the taxa are ranked as an infraorder and a family (left), but the same two taxa are designated by the names Chamaeleonidae and Chamaeleoninae when the taxa arc ranked as a family and a .subfamily (right). Notice also that the name Cliamaeieonsdae refers to different (less and moi'c inclusive) taxa under the two ranking schemes. Compare with Figure 1. several that were not u.sed by Linnaeus), that sys- drastic change in the relationships between taxon tem is more accurately termed rank-based rather names, on the one hand, and taxa versus ranks, on than Linnaean {see also Stuessy 2000). the other. Compared with eariier nomenclatural Rank-based nomenclature became widely at;- practices (see previous section), the rank-based cepted sometime during 19"' Century, though J approach reversed the relative strengths of the as- have not attempted a th oro tig h investigation of its sociations of taxon names by placing greater em- origin and history. One of its most obvious mani- phasis on their associations with particular ranks festations is the use of standardized, rank-specific than on their associations with particular taxa. Cat- endings (Table I). In zoology, the earliest explicit egorical ranks no longer served simply as devises endorsement of such endings as a general nomen- for indicating position in the taxonomic hierarchy; clatura! convention that [ have so far been able to now they became fundamental to the application findis that of Swainson{ 1835), who stated that the of taxon names. This situation is evident in cases names of al! families arc terminated in -idae and where the rank of a taxon changes without any those of subfamilies in -inae, though the former other changes regarding the conceptualization of convention had been adopted in practice by earlier the taxon (e.g. in terms of hypothesized composi- authors (e.g. Gray 1825). In an early attempt to tion, diagnostic characters, or phyiogenetic rela- develop a code of zoological nomenclature, Strick- tionships). In such cases, the name shifts its asso- land (1837:175) proposed the general rule (16), ciation from one taxon to another to maintain its attributed to Swainson, that "the names of tribes, association with a particular rank. families and subfamilies should have a distinctive For example, if three nested taxa were earlier termination," though he did not specify what those assigned to the ranks of suborder, family, and sub- terminations should be. Later, the so-called Strick- family, but later assigned to the ranks of family, landian Code (Strickland et al. 1843:272-3), an subfamily, and tribe, the names of those taxa important precursor of the zoological code, would have to be changed (i,e. through changes in adopted the recommendation that "families should their rank-spccilic endings) to reflect the changes be uniformly named by adding the termination in ranks (Fig. 2). Thus, if the taxon originally -idae to the name of the earliest known, or most ranked as a family were named Aceraceae, its typically characterized genus in them; and ... their name would have to be changed to AcemUleae: if subdivisions, termed sulifamilies, should be simi- it were originally named Chamaeleonidae, its larly constructed, with the termination -inae." name would have to be changed to Chamaeleoni- Most importantly, similar rules were adopted in the nae. Concomitantly, the original names would original international codes of both zoological and have to shift their asstjciations to more inclusive (ICZN 1905: Art. 4. IBC taxa. Thus, the name Aceraceae (and Chamaeleo- 1906: Art. 23) and perpetuated in ail subsequent nidae) would have to be applied to the more inclu- versions of those codes up to the present ones sive taxon that was formerly ranked as a suborder. (ICZN 1999: Art. 29.2, IBC 20(H): Arts. 17-19). These examples illu.strate that under rank-based The adoption of these and related rules lead to a nomenclature, taxon names are more closely asso-

Symb. Bot. Ups. 33:3 ) 32 Kevin de Queiroz

ciated with particular ranks than they are with par- actly the same). For example, if the genera Crota- ticular taxa. Consequently, when the ranks of taxa phytiis and Gambelia were to be united into a sin- are changed, the relevant taxon names retain Iheir gle genus Cmiaphytus; the two formerly recog- associations with the original ranks of the taxa to nized taxa could still be referred to using the which they previously referred rather than their as- names Croiaphytux and Gambelia by treating sociations with the taxa themselves. In effect, those names as the names of subgenera. Conse- taxon names have become disassociated from taxa quently, the names wouid {ignoring their status as (whether conceptualized in terms of composition, the names of genera versus subgenera) remain a.s- diagnostic characters, or phylogenetic relation- sociated with the same taxa. On the other hand, ships) in that they are tied to those taxa only in the usirjg the same name for a genus and one of its context of a pajticular ranked taxonomy. The only subgenera violates a fundamental principle of at permanent associations of taxon names are with least the zoological code, which states that one of particular ranks and types. its primary objectives is "to ensure that the name The primary association of names with ranks in of each taxon is unique and distinct" (ICZN 1999: rank-based nomenclature is not restricted to names Preamble). with .standardized rank-specific endings. Genera, The behavior of rank-ba.sed nomenclature in the lor example, do not have rank-signifying endings face of changes in taxonomic ranks derives from under either the botanical or the zoological code. the fact that names have fixed associations with Nonetheless, the names of genera behave similarly particular ranks. Some names (e.g. family and sub- to those of taxa with rank-signifying endings. family names) have standard endings that tie them Thus, if two closely related genera are united to particular ranks (e.g. [CZN 1999: Art. 29.2; IBC (lumped) in the absence of any change in the hy- 2000: Art, 18.1, 19.D.These names are automati- pothesised relationships among their included spe- cally typified in that the names are based on the cies, both of the original genus names shift their names of their types (ICZN 1999: Art. 29.1; IBC associations to the more inclusive group that for- 2000: Art. 10.6). Other names (e.g. those of genera merly contained both genera (though only one, of and subgenera) do not have standard endings that course, would be used as the accepted name of the tie them to particular ranks, and therefore they taxon). For example, if the lizard genera Crotaphy- must be explicitly tied to those ranks, for example, tus and Gambelia, which are the only members of by a declaration that a name is the name of a new a more inclusive taxon commonly ranked as either genus (e.g. [BC 2000: Art. 35.1 ). These names are a subfamily (Cmlaphytinae) or a family (Crota- not automatically typified; therefore, their types pkyliilae), are united into a single genus, then both must be independently designated (ICZN ¡999: names, Crotapiiytus aña Gambelia, will be applied Arts. 67-69; [BC 2000: Arts. 10.2, 37.1). to that genus and thus considered synonyms (Cro- In rank-based nomenclature, both the associa- laphytiis, which has priority over Gambelia, will tion with a particular rank and lypiiication are nec- be the accepted name). In other words, both names essary for the application of taxon names. Typifi- will shift their references from less inclusive taxa cation is necessary to determine which of several to a more inclusive one rather than retaining their taxa assigned to a particular rank is to be desig- associations with the original taxa. This situation nated by a particular name (e.g. the name Acer- demonstrates that the names are more closely as- aceae is not to be applied to any family whatsoever sociated with the rank of genus than with particu- but only to the one that contains the type of the lar taxa {groups of species). genus/IcÉír). Converseiy, association with a partic- In the case of names associated with the rank of ular rank is necessary to determine which of sev- genus, this situation can be partially ameliorated eral nested taxa containing the relevant type is to through the use of subgenera, because the names be designated by a particular name (e.g. the name of genera and subgenera, unlike those associated Aceraceae is not to be applied to any taxon what- with higher ranks, can be identical (i.e. spelled ex- soever that contains the type but only to the one

Syiiib. Bot. Ups. 33:3 Linnaean, rank-based, and phylogenetic nomenclature 133

Order Squamata Superorder Squamata Suborder "Lacertilia" Order "Lacertilia"

Suborder Serpentes Order Serpentes Figure 3. Application of taxon names under cunent practices when names are untypified. In these cases, the applica- tion of taxon names is not determined by ranks despite the fact that other aspects of the names are regulated by the rank-based codes. Therefore, the same taxtin can be designated by the same name regardless of the rank to which it is assigned. In this example, the same names, Sqmimaui, "Laceniliü'' and Scrpi'iUcs, are applied lo the same three taxa regardless of whether those taxa are ranked as an order and twt> suborders (e.g. Romer 1956, 196t>, Kuhn 1966, Carroll 1988; left) or as a superorder and two orders (e.g. Gans 1978, Estes 1983, Underwood 1967, 1971; right). Compare with Figures 1 and 2. that is ranked as a family). In this sense, the com- An, 16.1 ). On (he other hand, these names are rel- bination of rank association and typification con- atively unregulated; in particular, there are no rules stitutes an itnplicil definition based on rank and for establishing their relative precedence (e.g. IBC type (de Queiroz and Gauthier 1994, de Queiroz 1999: An. 11.9). 1997, de Queiroz and Cantino 2001b). Il provides an unambiguous criterion for applying a taxon name to a taxon. It is also the reason that taxon Phylogenetic Nomenclature names are more .strongly lied to ranks than to taxa. In the approach called phylogenetic nameachitiire, In spite of the situation just described, some taxon names are tied to explicitly phylogenetic contemporary names continue to be applied in concepts of taxa through definitions of taxon much the same way that they were by Linnaeus natnes that describe taxa in terms of ancestry and and other early naturalists - that is, even though descent (e.g. dc Queiroz and Gauthier 1990, 1992, they are at least partly regulated by the rank-based 1994, de Queiroz and Cantino 2001b). The three codes (e.g. ICZN 1999; Art. 1.2.2; IBC 2000: Arts. most general types of phylogenetic definitions - 16, 17). These names are not typified, meaning termed node-haxed, stem-based, and apomorpiiy- that their references are not tied to a subordinate hased - are illustrated in Figure 4, the legend of taxon or specitnen, the type. More importantly, which also includes definitions of some relevant they are not tied to any pat ticular categorical rank. terms. The .statements in question are called defini- Such names include zoological names above the tions becau.se they specify the meanings of words, rank of supcrfamily and descriptive botanical in this case, taxon names (de Queiroz 2000, de names above the rank of family. Because these Queiroz and Cantino 2001a). They should not be names are not tied to any particular rank, they con- confused with what are commonly called defini- tinue to be applied in a manner that is unaffected tions in taxonomy - that is, lists of characters that by rank assignment (Fig. 3). For example, the cur- distinguish the organisms of a panicular taxon rently recognized taxon Squama ta ("lizards'" and from those of other taxa and thus serve to diagnose ) and its subordinate taxa "Lacertilia" ("liz- the taxon in question. Although such lists serve to ards") and Serpentes (snakes) are assigned to the define laxa as conceptualized prior to the adoption respective ranks of order and suborder by some of an evoiutionary worldview (i.e. as groups of or- authors (e.g. Römer 1956, 1966, Kuhn 1966, Car- ganisms sharing particular characters), they do not roll 1988) and .superorder and order by others (e.g. specify how taxon names are to be applied (i.e. in Gans 1978, Estes 1983, sec also Underwood 1967, different taxonomic contexts) and therefore do not 1971). However, because the application of these Cjualify as definitions in the nomenclatural (as op- names is not based on categorical ranks, the taxa in po.sed to the taxonomic) sense. question retain the same names regardless of their Phylogenetic definitions function like the im- assignments lo different ranks {see also IBC 2000: plicit definitions of rank-based nomenclature in

Syini). Bot. Ups. 33:3 134 Kevin de Queiroz

Node-Based Stem-Based Apomorptiy-Based (B and C) Clade (B not A) Clade (X in C)

Figure 4. Three gênerai classes of pliylogenetic dcfinilions. The de signal i on s of tiiree Liasses of deñnilions - noäe- based, siem-híixed. and apomorpliy-hased - are given above, stiortliand example definitions are given beiow the designations, and diagrams illustrating application of the example definitions arc given below, [n the node-based definition, Chide iB and C} í,\¿r\ái'i

thai ihey provide unambiguous criteria for apply- set of rules and recommendations that represents ing names 1« taxa. A given name is applied, in the an alternative to the codes of rank-based noinen- context of a specified phylogenetic hypothesis, to claiure. This approach can be considered an out- whichever clade fits the .stated definition {i.e. re- growth of the phylogenetic or cladistic approach to gardless of the clade's precise compo.sition, excepl (e.g. Hennig 1966, Eldredge and Crac- for the necessary inclusion of internal specifiers raft 1980, Wiley 1981) in that I) the principle of and the necessary exclusion of external specifier.s). common ancestry or cladistic relationship (Cain For example, if the name Mamnialia is defined and Harrison 1960} is fundamental to the applica- phylogenetically as referring to the clade stem- tion of names, 2) categorical ranks are de-empha- ming from the most recent common ancestor of sized, following Hennig (e.g, ¡969, 1981, 1983) {Omithnrhynchus aiuitinus) and hu- and some other proponents of phylogenetic sys- mans (Homo sapiens), then certain taxa may tematics (e.g. L0vtrup 1977, Ax 1987), and 3} or may not be included within Mammalia depend- or monophyletic groups are emphasized as ing on their hypothesized phylogenetic relation- the eniiiies to be named, following Hennig (e.g. ships - that is, depending on whether or not they 1966) and other proponents of phylogenetic sys- are inferred to be descended from the last common tematics (e.g. Eldredge and Cracrafl 1980, Wiley ancestor of platypuses and . 1981, Ax 1987). Phylogenetic nomenclature was proposed in the Nevertheless, phylogenetic nomenclature is last part of the 20"* Century (e.g. dc Queiroz and logically independent from Hennig's principle that Gauthier 1990, 1992, 1994, Sundberg and Plcijcl all formally recognized taxa must be mono- 1994, Schander and ThoUesson 1995) and forms phyletic. On the one hand, Hennig's principie can the theoretical foundation of the draft PhyloCode be adopted in the context of either rank-based or (Cantino and de Queiroz 2000, 2003), a proposed phylogenetic nomenclature, though in the fonner

Symb. Bot. Ups. 3.1-3 lÁnnaean, rank-based, and phylogenetic nomenclature 135 case laxon names do not necessarily retain iheir rank-based definition ofthe name/tceraceoe is the associations with particular monophyletic taxa. laxon ranked as a family that contains the type of On the other hand, phylogenetic nomenclature the genus Acer. These statements can be consid- can, in theory, accommodate other evolutionary ered definitions in thai they specify the references approaches (see de Queiroz and Gauthier of words (in this case, taxon names). They func- 1990:311 ), such as the traditional evolutionary ap- tion analogously to phylogenetic definitions in that proach to taxonomy that allows paraphylctic taxa they provide unambiguous criteria for applying (e.g. Simpson 1961, Davis and Heywood 1963, names in the context of different taxonomic hy- Mayr 1969), though proponents of phyiogenetic potheses (phylogenetic trees in the case of phylo- nomenclature do not advocate this practice. genetic definitions, sets of ranked groups in the Phylogenetic nomenclature shares severa! basic case of rank-based definitions). And like phyloge- goals and methods with rank-based nomenclature. netic definitions, they are applied, in the context of Both systems have the same fundamental goals of a specified taxonomy (in this case, a set of categor- providing unambiguous methods for applying ically ranked groups), to whichever ranked group names to (axa, for selecting a single accepted name fits the Slated definition (i.e. regardless of the for a taxon from among competing synonyms or group's precise composition, except for the neces- homonyms, and for promodng nomenclatural sta- sary inclusion of the type). bility and continuity to the extent that doing so The difference between rank-based and phyio- does not contradict new systematic conclusions. genetic nomenclature regarding methods for ap- Neither system infringes upon the judgment of plying names lo taxais the cause of a fundamental taxonomisis with respect to inferring the composi- difference concerning the relative strengths with tion of uixa or to assigning taxonomic ranks (con- which the two approaches as.sociate names with trary to a widely held misconception, phylogenetic laxa versus ranks. Under rank-based nomencla- nomenclature does not prohibit the use of ranks). ture, the method for applying names to taxa is Both systems use piecedence, a clear order of pref- based on ranks and types; consequently, taxon erence, to determine the accepted name of a taxon names are more strongly associated with ranks when .synonyms or homonyms exist. Both systems than with taxa. Under phyiogenetic nomenclature, use priority with regard to the date of publication ihe method for applying names is based on .speci- as the primary criterion for establishing prece- fied phylogenetic relationships; consequently, dence. And both phylogenetic and rank-based sys- taxon names are more strongly associated with tems allow a later-es tab I i shed name to be con- taxa, as conceptualized and described by the spec- served over an earlier name for the same taxon (i.e. ified phyiogenetic relationships, than with ranks. for priority to be set aside) if using the earlier name For the case of rank-based nomenclature, 1 de- contradicts the fundamental goal of promoting no- scribed in the previous section how taxon names menclatural stability and continuity. change their references from less inclusive to more Phylogenetic nomenclature also differs from inclusive taxa, or vice versa, when the ranks of rank-based nomenclature in a number of ways (see those taxa are changed. Cantino and de Queiroz 2000, 2003, de Queiroz For the case of phyiogenetic nomenclature, and Cantino 2001 b); however, the most fundamen- changes in rank alone have no effect on the appli- tal difïerencc concerns the methods that the alter- cation of taxon names (Fig, 5). For example, sup- native systems use for applying names to taxa (de pose that the names Squamata and Serpentes were Queiroz 1997). As noted above, phylogenetic no- defined as referring to the clades stemming from menclature uses explicit definitions that describe the most recent common ancestors of the species laxa in terms of ancestry and descent. In contrast, curremly included in those taxa. (The name Lacer- rank-based nomenclature uses implicit definitions iiiia, traditionary applied to a paraphylctic group, that describe taxa in terms of ranks and types. To would, if defined similarly, be a synonym of Sijua- repeat one of my earlier examples, the implicit inata.) Under these definitions, the names Squa-

Synih. Bot. Ups. 3.13 136 Kevin de Queiroz

Order Squamata Superorder Squamata Suborder Serpentes Order Serpentes

Squamata Sqitíinwta

Sßfpentes Serpentes

SubonJsr

Suparuitter

Figure 5. Application oftaxon names under phylogenetic nomenclature. In this approach, names arc applied accord- ing to their phylogenetic definitions, which are independent of categorical ranks. Therefore, the same laKon is designated by the same name regardless of the rank to which it is assigned. In this example, the same two nested taxa are designated by the same names, Sqummim and Serpolles, regardless of whether they are ranked as an order and a suborder (left) or as a superorder and an order (right). For this example, the names have been defined hypothetic ally using the following node-based definitions: Squamata = the least inclusive clade containing A and C; Serpentes = the least inclusive clade containing C and D. The name üjcertilin, defined as referring to the least inclusive clade containing A and B, is synonymous with XguaíHíi/a in thecontcxt of the phylogenetic hypothesis used in the example. Compare with Figures 1, 2, and 3, mala and Serpentes would remain associated with will not always remain associated with the same the same clades (and sets of species) regardless of sets of species (de Queiroz and Gauthier 1990, de whether those taxa were ranked as an order and a Queiroz 1997). Changes in the hypothesized com- suborder, a superorder and an order, or anything position of taxa can occtir under phylogenetic no- else. Phylogenetic nomenclature Ihus applies menclature just as they can occur under rank- names siinüariy to the nomenclatural practices of based nomenclature. However, under pbyltjgenetic Linnaeus and other early naturalists, as well as lo nomenclature, such changes can occur only when the current codes for names that are untypified and hypotheses about relevant phylogenetic relation- thus lack ¡mplicil rank-based definitions. ships change. In contrast, under rank-based no- The clo.ser association of taxon names with taxa menclature, changes in composition can also occur than with ranks under phylogenetic nomenclature solely as the result of changes in the assignments also holds for laxon names with terminations con- of taxa to categorical ranks. noting particular ranks under rank-based nomen- The important point is that, relative to the situa- clature {Fig. 6). Consequently, under phylogenetic tion under rank-based nomenclature, phylogenetic nomenclature, those endings would no longer have nomenclature effectively reverses the relative any significance with regard to categorical ranks. strengths of the associations between taxon name.s, For example, taxa with names such as Chamaele- one the one hand, and ranks versus taxa, on the onidae and Aceraceae might be ranked as families, other. In so doing, phylogenetic nomenclature not or ihey might be ranked as subfaitiilies, or they only differs from rank-based nomenclature but might not be ranked at all. Moreover, those names also resembles nomenclature as practiced by Lin- would be applied to the same laxa, all else being naeus and other late IS"* and early 19"" Century equal (i.e. with respect to hypothesized phyloge- naturalists. Of course, phylogenetic nomenclature netic relationships), regardless of their associa- also differs in important ways from the nomenclat- tions with particular categorical ranks {Fig, 6). ural practices of 18"' and early 19"* Century natu- Under phyk)genetic nomenclature, taxon names ralists. The most obvious and important difference

Symh. not. Ups. 33:3 Linnaean, rank-based, and phyhgenetic nomenclature 137

Infraorder Acrodonta Family Acrodonta

Family Chamaeleonidae Subfamily Chamaeleonidae

Acn xkmta Acnxkmta

Chamaeleoniífáe Chamaeleonidae

A B C D A BCD

Family Sjtvfamily

Infraorder Family Figure 6. Application of taxon names under phylogenetic nomenclature for cases involving endings that signify rank under riink-based nomenclature. Because taxon naines are applied independently of categorical ranks in phyloge- netic nomenclature, the standardized, rank-signifying endings of rank-based nomenclature no longer have any signif- icance in terms of ranks. In this example, ihe names Acrodoma and ChamaeieonUIae remain unchanged regardless of whether the taxa designated by tliosc names are ranked as an infraorder and family (left) or as a family and a subfamily fright). For this example, the names have been defined hypothetically using the following node-based definitions: Acrodoma = the least inclusive clade containing A and C; Chumuekonidaf = the least inclusive clade containing C and D. Compare with Figures 1,2, 3, and 5. is thai in 18"" and early 19"'Century nomenclature, isz 1995, Novacek 1992) to the species known at conceptualizations of (axa were non-evolutionary; the lime of Linnaeus (1758), the species of Mam- in phylogenetie nomenclature, they are explicitly malia would be precisely the same as those in- evolutionary. cluded in Mammalia by Linnaeus. Despite this fundamenial difference regarding the conceptualization of taxa, at least some of the taxa recognised by IS'''and early 19'" Centuty nat- Conclasion uralists correspond closely in terms of their com- Phylogenetie nomenclature represents an alterna- position with clades. In such cases, names under tive to traditional rank-based nomenclature. Al- phylogenetie noinenclature are applied to more or though rank-based nomenclature is commonly less the same entities, at least in terms of composi- characterized as Linnaean (a misleading tenoinol- tion. For example, consider the following phyloge- ogy that I confess to having been partly responsi- netie definitions of the name Aífimmíi/i£i: I) (node- ble for perpetuating), phylogenetie nomenclature based) the least inclusive clade containing platy- more closely approximates the nomenclaiural puses (Ornithorhynchus analinus), opossums (Di- practices of Linnaeus and other IS"* Century natu- delphis marsiipiatis), and humans (Homo sapi- ralists in granting greater importance to the associ- ens); 2) (stem-based) the most inclusive clade con- ations of taxon names with taxa than with categor- taining humans (Homo sapiens) but not birds (e.g. ical ranks. In other words, phylogenetie nomencla- Aqitila chrysaetos) or turtles (e.g. Emys orbicula- ture is not so much at odds with true Linnaean ris) or squamates (e.g. Lacerta vivípara); 3) (apo- nomenclature as it is with the rank-based approach morphy-based) the clade stemming from the first to nomenclature that developed in the 19'*" Century ancestor of humans (Hmna sapiens) to evolve and came to the foundation of the original mammary glands. If any of these three definitions international codes of nomenclature (e.g. ICZN were to be applied in the context of recent esti- 1905, IBC 1906) and their contemporary descend- mates of vertebrate phylogeny (e.g. Lau tin and Re- (e.g. ICZN 1999, IBC 2000). The critical dif-

Sywh. BoL Ups. 33:3 13S Kevin de Queiroz fcrence concerns how the three approaches use Linnaeus and other 18"^ Century naturalists. 18"' categorical ranks. Century nomenclature developed in a non-evolu- Giventhat the primary purpose of a taxon name tionary theoretical context, and therefore, its taxon is to refer to a taxon, then the use of categorical concepts were non-evolutionary. In contrast, taxon ranks by Linnaeus and other early naturalists was concepts in phylogenetic nomenclature arc explic- appropriate. For these early naturalists, categorical itly evolutionary. ranks functioned simply as devices for indicating Phylogenetic nomenclature thus combines both relative position in the taxonomic hierarchy, serv- Linnaean and modem components. On the one ing much the same purpose as a branching dia- hand, it embodies the general approach of Lin- gram, a Venn diagram, or an indented list • (hat is, naeus and his immediate successors, who treated to indicate which taxa were considered nested and categorical ranks merely as devices for represent- which mutually exclusive. Taxon names were ing hierarchical relationships that had no bearing more .strongly lied to taxon concepts than to cate- on the application of taxon names. On the other gorical ranks, and therefore, the assignments of hand, it embraces the most important theoretical taxa to categorical ranks did not alïeet the spelling development in biology since the time of Linnaeus or application of taxon names. Consequently, the - ihe principle of , or descent with modi- categorical rank ofa taxon could be changed with- fication - which it uses to specify the references of out requiring a change in the name of the taxon. taxon names under modern evolutionary concepts In contrast, the use of categorical ranks in rank- of taxa. In short, phylogenetic nomenclature repre- based nomenclature is inappropriate; ranks have sents Linnaean wisdom updated with evolutionary become too important. Instead of functioning sim- principles, and it therefore provides a fitting tribute ply as devices for indicating relative position in the to Linnaeus on the 250"^ anniversary of his Species taxonomic hierarchy, ranks have become critical to Flaniarum. the application and spelling of taxon names. Con- sequently, changes in the rank of a taxon require Acknowledgements changes in the name of thai taxon, even when other aspects of the taxon concept remain the same. I wish to thank and Phil Cantino Thus, regardless of whether taxa are conceptual- for collaborations related to the development of ized in terms of included organisms, diagnostic phylogenetic nomenclature, 1 am grateful to Mi- characters, or phylogenetic relationships, laxon kael Thollesson and Magnus Popp for the invita- names are more strongly tied to ranks than to taxa. tion to speak in the symposium coiomemorating Given that categorical ranks are less biologically (he 250'^ anniversary nf the publication of Lin- significant than arc these other properties, this em- naeus' Species Plamarum and to contribute a pa- phasis on ranks is misplaced. It also compromises per to its proceedings. 1 would also like to thank taxonomic freedom, thus contradicting an explic- Leslie Overstreet for assistance with 1T^ and 18"' itly slated goal of the zoológica! code {ICZN 1999: Century literature, and Jacques Gauthier, Phil Preamble). Because one must rank a taxon to name Cantino, Mikael Thollesson, an anonymous re- it, the use of ranks has effectively become manda- viewer, and especially Fredrik Pleijel for com- tory. ments on an earlier version of this paper Phylogenetic nomenclature represents a return to the general nomenclatura! approach adopted by References Linnaeus and other late IS"" and early 19'" Century naturalists in which taxon names have their pri- Ax, R 1987. The phylogenetic system. The systématisa- mary associations with laxa, rather than with cate- tion of organisms on ihc basis of their phylogenesis. Englisti edition. -John Wiley & Sons, Chichester. gorical ranks. On the other hand, phylogenetic no- Brongnian, A. 1800. Essai ti'une classification naturelle menclature also ditïcrs in at lea.st one important des reptiles, - Bulletin des Sciences, par la Société respect irom nomenclature as it was practiced by ['hilomatique 2:89-91 + 1 plate.

Symi). Bot. Upx. 33:3 Linnaean, rank-baaed, and phyiogenetic nomenclature 139

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