Society of Systematic Biologists Cladistic Taxonomy, Phylogenetic Systematics, and Evolutionary Ranking Author(s): Martin L. Christoffersen Source: Systematic Biology, Vol. 44, No. 3 (Sep., 1995), pp. 440-454 Published by: Oxford University Press for the Society of Systematic Biologists Stable URL: https://www.jstor.org/stable/2413605 Accessed: 30-01-2019 13:57 UTC JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at https://about.jstor.org/terms Society of Systematic Biologists, Oxford University Press are collaborating with JSTOR to digitize, preserve and extend access to Systematic Biology This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 440 Syst. SYSTEMATIC Biol. BIOLOGY VOL. 44 44(3):440-454,1995 Cladistic Taxonomy, Phyl Evolutionary Rankin Martin L. Christoffersen Departamento de Sistematica e Ecologia, Universidade Federal da Paraiba, 58059-900, Joao Pessoa, Paraiba, Brasil The ancient discipline of biologicalrated tax? by the codes, simply conflict with onomy has been very slow to incorporate phylogenetic representations (Griffiths, major shifts in world views throughout the 1974a, 1974b, 1976). For example, manda? millennia. Impervious to the derision tory of categories, the names of genera as scientists from the more glamorousparts fields of binomials, typification and syn? of research, many taxonomists today sim?tied to Linnaean categories, and re? onymy ply take for granted secular traditions dundant of taxon names (Christoffersen, de Queiroz and Gauthier, 1992) all describing and naming the diversity 1987; of tiature. They may persist stoically forconflict a life? with evolutionary approaches. The time in such a self-appointed descriptive codes thus help perpetuate essentialistic role, avoiding theory, philosophy, and ex? taxonomic traditions rather than promote planation. Some of these taxonomists may conceptual evolutionary innovations. venture intuitive classifications for their Conceptual Lineages named groups but will often delegate to others the task of deriving evolutionary Taxonomists, like other segments of th meanings from their proposals. scientific community, are presently divi Evolutionary concepts have still not pen? ed into several factions that support con etrated the core of nomenclature. The in? flicting conceptual systems. Following ternational codes (International Commis? Hull's (1984) and Mishler's (1987) analog sion on Zoological Nomenclature, 1985; with biological phylogenies, these differe International Botanical Congress, 1988; In? research groups, rather than being define by the presence of some necessary and su ficient set of shared ideas, are viewed as eties, 1992) are totally couched in a tradi? tional Linnaean framework developed intellectual lineages, with strong historic coherence, social cohesion, and adversaria more than 100 years before the widespread acceptance of evolutionary ideas. Purport? relations with other lineages. I propose edly not to interfere with taxonomic free? tentative phylogeny for these intellectua dom, the codes provide no rules for the systems of biological taxonomy (Fig. 1). F recognition and definition of taxa and cat? those that would have preferred to se characters (shared ideas) and Characte egories. Yet the available rules significantly constrain taxonomic practice by tying tax(individual spokespersons) on the phyl on names to categorical ranks. This struc? genetic tree, I defer to Carpenter (198 ternational Association of Microbial Soci? ture interferes with the codes7 own avowed who provided a numerical cladistic stud goals of providing explicit, universal, and of phylogeneticists and a review of prev stable names for taxonomy because a taxonous single-character classifications of t name must be changed every time it isthree main contemporary schools of ta placed in a different category (de Queiroz onomy. and Gauthier, 1994). Furthermore, several Different concepts of taxonomy, system taxonomic conventions, variously incorpo-atics, and classification have been advocat? ed by various authors (e.g., Simpson, 196 1 E-mail: cendse09@brufpb .bitnet. Blackwelder, 1967; Mayr, 1969; Nelson This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 1995 POINTS OF VIEW 441 schools of taxonomy (Fig. 1) are as follows. Aristotelian taxonomy proceeds by logical subdivision, in which each member of a pair of taxa is characterized, respectively, by the presence and absence of a chosen feature. All present attempts to derive a taxonomy from an identification key reflect this process. In Linnaean taxonomy, there is an explicit attempt to distinguish the im? portant (stable, essential) properties from the unimportant (variable, nonessential) properties. In traditional taxonomy, groups are reconstructed based on perceived sim? ilarities and differences among taxa. Qui- Figure 1. A possible phylogeny o narian taxonomists (e.g., MacLeay, 1819) eages in biological taxonomy looked for idealistic groupings in circles of A-M cestor-descendant lineages; N: mon five, supposed reveal the harmonious multiple lineages or to single lineag and lawful relations of numbers as evi? populations. A = Aristotelian taxo an (essentialistic, tax dence oftypological) the rational plan of creation. In? tional taxonomy; Dt evolutionary = extinct quin corporating theory, conven? = conventional taxonomy; F = om tional taxonomy involves interpretation of latory, practical, utilitarian) taxo and differences as reflecting taxonomy; H = similarities phenetic (numeric netics); I = orthodox taxonomy; degrees of phylogenetic relationships. Om- (Mayrian, Simpsonian, synthetic, nispective taxonomists explicity reject any s tic, eclectic) taxonomy (phyletics); connections between a practical and utili? onomy; L = phylogenetic taxonomy distics); M = cladistic taxonomy (pattern, tarian taxonomy and the processes thought to be responsible for biological di? methodological, transformed ); N = phylogenetic sys? tematics (phylogenetics). versity (e.g., Blackwelder, 1964). In natural taxonomy, groups are supposed to be dis? 1970; Griffiths, 1974a; Wiley, 1981; covered in nature rather than fabricated in the mind of the taxonomist. Phenetic tax? de Queiroz, 1988). When these denominations onomists attempt to quantify data and es? tablish groups by overall similarity. In or? become interchangeably qualified by such thodox taxonomy, multiple criteria are terms as traditional, numerical, phenetic, used to access taxa (similarity, diversity, evolutionary, cladistic, and phylogenetic size of gaps, ecology, behavior, etc.). In (Fig. 1), their meanings become multifari? evolutionary taxonomy, species are rede? ous, extensively overlapping, and suffi? fined as evolutionary units (Mayr, 1942; ciently confusing so as to lose much of Simpson, 1961), and phenetic, patristic, their heuristic and interpretative value (cf. Charig, 1982; Hill and Crane, 1982; and de cladistic data are combined into a sin? gle taxonomic system (e.g., Mayr, 1981; Queiroz and Donoghue, 1990b; Nixon and Stuessy, 1987, 1990). In Hennigian taxono? Wheeler, 1990). Terms and concepts are my, the principle of common descent is necessarily context bound and should be granted a central role at all levels in the allowed to change through time. I provide taxonomic hierarchy. In the last two de? here successively more inclusive defini? cades, a philosophical split has developed tions for the basic concepts of taxonomy, systematics, and classification. I hope mywithin phylogenetic systematics (e.g., Mishler, 1987; de Queiroz and Donoghue, assignment of several commonly used 1990a) (Fig. 1). Pattern cladists are empir? qualifying terms to distinct conceptual icists that avoid all assumptions and pre? systems (Fig. 1) will reduce ambiguity, even if total agreement is not possible. conceptions about process in constructing Brief characterizations of the several a taxonomy (Brady, 1985; Nelson, 1985; This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 442 SYSTEMATIC BIOLOGY VOL. 44 (Hennig, 1966:6). Characters are instanta? Rieppel, 1988b). Phylogenetic taxo neoustheorists morphologies (de Queiroz, 1985: are evolutionary that de 296) that are compared among "specimens a most useful taxonomic concepts at similar stages in their life history" (Wi? ods from general evolutionary ley, 1981:119). Character generalities are es? (de Queiroz, 1985). Notwithstand tablished the ontogenetic method (Nel? basic difference in by general outloo son, 1978; Nelson promote and Platnick, 1981; phylogeneticists still soc Patterson, 1982, 1983) and the outgroup sion by sharing the same Henn method (Watrous and journal. Wheeler, 1981; Far? sights, meetings, and In ris, 1982; Maddison et al., 1984). Nelson with the evolutionary species c (1985) called ontogenystill a direct method these two factions may be co and outgroup analysis an indirect method interbreeding populations. Below, for the reconstruction of the taxonomic hi? deemphasize the individuality of taxonomy and erarchy. attempt to incorp In cladistic contribution?r taxonomy, only groups based most fundamental on synapomorphies (shared derived char? operational, cladistic analysis?a acters) arephylogenetic recognized as monophyletic procedure within sy taxa and named. Because ancestral lin? ics. Cladistic Taxonomy eages are not recognizable by positive cla? distic data and because ancestor-descen? lineages in principle do not form a I define taxonomy as the practice dant of rec? hierarchical pattern, only nested sets of ognizing, naming, and ordering taxa into monophyletic taxa are admitted in the tax? a system of words consistent with any onomy. kind of relationships among taxa that the Taxa become operationally diag? nosed investigator has discovered in nature. Un?by uniquely held characters, and der this definition, taxonomy becomes species thebecome simply the smallest of these clusters (Nelson, 1989b). By associ? most basic activity in biology, dealing ex? ating species names with the least inclu? clusively with the discovery, ordering, and sive monophyletic groups, it will always communication of patterns of biological be possible to discover smaller groups in the future with the refinement of data (e.g., Cladistic taxonomy uses a cladogram (sensu Nelson and Platnick, 1981) as molecular the data). Thus, species will not be taxa. comparable units and will tend to be much graphical model for constructing a biolog? more numerous than those conventionally ical system. A cladogram is a predomi? recognized. Furthermore, some organisms nantly bifurcating, asymmetric, nontrunor populations will not belong to any cate dendrogram, with no defined vertical group because ontologically and horizontal axes. A cladogram is monophyletic thus they are direct ancestors or belong to lin? a more general statement than a phyloge? netic tree, because it does not attempteages to in which apomorphies have not yet developed. depict actual ancestors (de Queiroz, 1988: The logic of cladistic taxonomy requires 250; Rieppel, 1990:187). A cladogram cor? no distinction between species and mono? responds to a set of possible trees rather taxa nor between variable and than to a single tree (Platnick, 1985; cf.phyletic Wi? ley, 1981). Cladograms are constructedfixed by characters ("character" sensu Nixon and Wheeler's [1990] "attribute"). Individ? maximizing the congruence of several ual organisms logically become the small? types of derived characters, usually mor? est terminal entities for cladistic analysis phological or molecular. Character congru? (Vrana and Wheeler, 1992). Monophyletic ence is accessed by the methodological principle of parsimony (Farris, 1982). taxa Theare not usually ranked to avoid pro? basic elements of taxonomy are semaphoducing what Colless (1977) called a "cor? ronts, or organisms "during a certain, nucopia the? of categories." Fossil taxa are treat? ed in the same way as extant taxa, thus oretically infinitely small, period of life" This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 1995 points avoiding of truncated hierarchies. of view 443 the time practices. Cladistic taxonomy may be iden?axis tified with what has been called the taxic The notion of actual ancestry is incom?approach to systematics (Stanley, 1975; patible with a logically stringent pattern Eldredge, 1979; Rieppel, 1988a). Pattern analysis. In the initial version of cladistics cladistics is a logical and internally consis? (Nelson, 1971), taxa were defined bytent approach in which evolutionary theo? shared characters, and the lines in the ry, rather than a unifying concept, is cladogram indicated relative recency of viewed as an after-the-fact generalization common ancestry between pairs of taxa. Into be deduced from taxonomy Brady this way, the notion of hypothetical com?(1985:113) is one philosopher that support? mon ancestors became associated with ed a strict independence of "that aspect of cladograms. This procedure, however, still systematics concerned with the identifica? of the empirical patterns" from "the? produces a temporalized version oftion a clado? gram resembling a phylogenetic tree, oriesthus of process." But is it necessary for blurring the conceptual gap between cladists clato use methodological essentialism dists and phylogenetic taxonomists. to construct both cladograms and taxono? In the more radical version of trans? formed cladism (Platnick, 1979, 1982, 1985), pattern cladism (Patterson, 1982), or methodological cladism (Hill and Crane, 1982), evolution is not considered a neces? sary prerequisite for the practice of taxon? omy. The same model may be called a syn? apomorphy scheme, where the connecting mies? Phylogenetic Systematics The theory of evolution was developed partly as a generalization from taxonomy (Nelson, 1978, 1985; Patterson, 1983; de Queiroz, 1985). Thus, the use of taxonomic methods in general and the use of cladistic lines in the scheme indicate no more than methods in particular do not seem to re? quire any assumption about evolution. shared sets of character generalities. Such a synapomorphy scheme, or strictly atem? However, "if systematics is an attempt to poral and acausal cladogram, represents a reconstruct evolutionary history, then this hierarchy of static homologies obtained assumption will dictate which cladistic methods are useful" (de Queiroz, 1985: from downward classification by logical subdivision (Platnick, 1977; Patterson, 281). Phylogenetic systematics is the at? 1983; Rieppel, 1988a). One of the implica? tempt to deduce evolutionary history from tions of this approach is that all taxa are the axiom of evolution. treated as classes that are defined by char? I define systematics as the theory, prin? acters (Beatty, 1982). Platnick (1977, 1985) ciples, and practice of identifying (discov? and Patterson (1978) tried to avoid this es- ering) systems, i.e., of ordering the diver? sentialistic connotation of cladistics by im? sity of organisms (parts) into more general plying that taxa are only recognized by systems of taxa (wholes) according to the apomorphic characters. According to this most general causal processes. Under this conception, characters would be diagnostic definition, systematics differs from taxon? rather than defining. This approach, how? omy basically in not attempting to divorce ever, leaves cladistic taxa without defini? the practice of building a general biologi? tions. If cladistic theory corresponds to the cal system from our theoretical knowledge notion that there is order in nature, it is of how general biological processes (in agnostic about what taxa represent for bi? contrast to particular biological mecha? ology. nisms) are supposed to affect the resultant Pattern cladistics represents the most empirical, operational, and objective stage attained by Hennigians. It represents the logical consequence of striving after the most formal cladistic principles and of adopting the least theory-laden taxonomic patterns of diversity. Feedback loops be? tween pattern and process information are considered fundamental for a constant re? shaping of the best system for biology. This view is similar to the concept of Mayr (1969) and approaches what Nelson (1970) This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 444 systematic called biology vol. 44 "comparative biology," netic tree or a temporalized cladogram, in tematics must deal with the transformation which ancestor-descendant lineages may of form through space and time, thus also be given names. Usually, nested sets of integrating information on pattern and multiple lineages are also given names and process from ontogeny, paleontology, and all taxa may be further ranked into a series biogeography. Systematics is thus both of categories. Of course, there seems to be broader in scope than taxonomy and nec?no logical requirement for naming both sets and ancestor-descendant se? essarily more theory laden. It integratesnested a transformational approach (Eldredge, quences in the same system. In a new phy? 1979; Rieppel, 1988a) with the predomi? logenetic system proposed by Papavero et nantly taxic perspective of taxonomy. Riep? al. (1992), for example, only the lines of the pel (1988a:170) treated pattern and process phylogenetic tree are given names. It is analyses as "different ways of seeing," in? also not necessary to rank taxa within the compatible with while complementary system. to Such possibilities for choice as to each other. The world may appear static or which particular phylogeny-based dendro? dynamic, discontinuous or continuous, hi? gram to use as a model for the biological erarchical or linear, as revealed by the taxic system, how to name taxa, and whether or versus transformational approach. These not to rank taxa have led to several ap? approaches are complementary in thatproaches a within phylogenetic systematics. serial or linear hierarchy may be translated Cladistic Analysis into a subordinated hierarchy by the spec? ification of inclusive taxa, whereas the sub?Basic methods of phylogenetic taxono? ordinative hierarchy may be changed to my a are the same as those described for cla? serial arrangement of forms by specifying distic taxonomy, but several additional re? actual ancestors. Phylogenetic systematics quirements and qualifications are necessary. involves integration of these two world In phylogenetic taxonomy, not all kinds of views by recognition of two ontological characters empirically observed in sema- kinds of taxa: species, which are continu?phoronts as instantaneous morphologies ous strings of ancestor-descendant popu? should be used in the cladistic analysis. lations ranked serially (the transformation? Phylogenetic methods are based on the al approach), and monophyletic taxa, premise that there exists a nested hierar? which are discontinuous taxa ranked hi? chical pattern of relationships. It is thus erarchically (the taxic approach) (Rieppel, not appropriate to apply cladistic methods 1988a:105). to entities that are not expected to be re? The preferred modern graphic models lated hierarchically. Characters are associ? for basing biological systems within ated phy?with different patterns of evolutionary logenetic systematics are ramifying, asym? relationships at different hierarchical lev? metric dendrograms (phylogenetic trees or example, mutations at the molecu? els. For cladograms), which may be viewed as lar level may produce ontogenetic changes somewhat stylized and simplified deriva? in organisms, variable characters in popu? tions of traditional phylogenetic trees. lations, fixed characters in species, and There are two ways of applying names to transformation series in monophyletic such dendrograms (Griffiths, 1974a, 1974b): groups. Only fixed characters and trans? (1) the naming of time-extended lineages formation series produce branching pat? of ancestor-descendant populationsterns (e.g., of genealogical relationships. This taxa A-M in Fig. 1) and (2) the naming ofcorresponds closely to Hennig's view nested sets of these lineages (e.g., taxon N (1966:31, fig. 6) contrasts among ontoge? in Fig. 1). In cladistic taxonomy, annetic ahis- (within organisms), tokogenetic torical cladogram serves as a model for populations), and phylogenetic (be? (within representing relationships, and only tween nest? species) descent systems, in which ed sets are given names. In phylogenetic only the phylogenetic system produces hi? erarchies. Nixon and Wheeler (1990) liketaxonomy, the model becomes a phyloge- This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 1995 points of view 445 in phylogenetic systematics. When static wise noted that only ch morphologies are treated as lineage characters, fixed in terminal both ontogenetic and evolutionary polari? ing patterns. ties seem to exist at the same hierarchical The implication for cladistic analysis is level. But when characters are viewed dy? that there are sensible limits to the appli? cation of cladistic methods. If these bound? namically as sequences of individual on? aries are trespassed, cladistic methods willtogenies to be compared among organ? still produce a hierarchical pattern of char?isms, ontogenetic polarities are seen to belong to one hierarchical level (i.e., they acters, however poorly resolved, even when these are known not to form hier? exist within characters) whereas evolution? ary polarities are seen to belong to a dis? archical relationships in nature. Bryant (1992:259) noted that "as an inductivetinct hierarchical level (i.e., they exist be? tween characters). Failure to make these summary of the data set, a cladogram has hierarchical distinctions may lead to errors no separate empirical content; it provides in cladistic analyses. Ontogenetic polari? only a consensus of the hierarchical infor? mation in the data matrix." ties of instantaneous characters, because of alterations in developmental timing (hetThus, allelic polymorphisms, ontogenet? erochrony; see Gould, 1977), do not nec? ic transformations, and populational vari? essarily coincide with phylogenetic polar? able characters must be correctly interpret? of ontogenies. The sequence of ed in a phylogenetic context. Amorim et ities al. particular ontogenetic transformations (1993) showed that it is not possible to within an organism (character adjacency transpose the phylogenetic concept of syn? in Wheeler's [1990] nomenclature) may be apomorphy to the lower hierarchical levels without further resolution. Two evolution? irrelevant to cladistic analysis. The critical elements from ontogeny to be used in cla? ary events are actually involved: (1) the distic analysis are the relative generalities molecular process of apomorphic modifi? cation of a preexisting gene at a given lo?of different life cycles of organisms. Pattern cus and (2) the populational process of ple-cladists, by avoiding evolutionary assump? tions, may produce taxonomies that are siomorphic allele elimination at the same locus. They named the shared presence of not only evolutionarily neutral but are "at odds with evolutionary thinking" (Beatty, apomorphic alleles syntrepty and the shared absence of plesiomorphic or apo?1982:33). An important consequence for phylogenetic systematics is that the onto? morphic alleles synapousy. Because these genetic method of determining character events occur at different times and may be separated by one or more cladogenetic polarity, like the paleontological method, becomes a special case of the outgroup events, allelic polymorphisms will be in? herited by different species. This concep?method (de Queiroz, 1985:293). In other words, the two methods are not indepen? tual resolution should have important con? dent (Fink, 1982; Kluge, 1985), the distinc? sequences for the parsimony concept as tion between direct and indirect polariza? applied to allele matrices. It also provides tion methods is nonexistent (Wheeler, a plausible basis for the intuitive concept 1990), and ontogeny stands to phylogeny of "underlying synapomorphy" (Saether, 1979). Many characters now interpreted asas a part-whole relationship (Brooks and homoplasies between taxa may be foundWiley, 1985). to correspond to independent events of One of the main problems of contem? synapousy of the plesiomorphic allele. porary cladistic analysis refers to explor? Likewise, independent events of synapou?ing methods for combining different kinds of data for the same taxa (e.g., Doyle, 1992). sy of the apomorphic allele may account Agreement among trees estimated by dif? for many cases of multiple reversals in ferent methods lends greater credibility to cladograms. De Queiroz (1985) clarified how onto? genetic transformations must be handled the estimates of phylogeny (Kim,p 1993: 335). However, molecular phylogenies may This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 446 SYSTEMATIC BIOLOGY VOL. 44 gram will other then be hypothesized to form disagree with each and with homologies. Homologies should be viewed generated from morphology (Garl al., 1993:289). With the among number of m as relationships historical individ? uals, a perspective that at combines taxic ular analyses increasing a the greate and the transformational views of homol? than that of morphological analyses derson et al., 1993) and with over ogy (McKitrick, 1994:2). Genetically and 100 able methods developmentally individualized entities of phylogenetic estim (Huelsenbeck and Hillis, 1993:247), th form intraorganismal homologies. Because intraorganismal historical phenomena may clearly a problem in identifying thos form reticulatedparticular patterns, only interorgan-me ditions under which ismal homologies will reveal and models perform well or hierarchical poorly. relationships. mality criteria such as parsimony ar ful, but they must be recognized fo they are: tools that Phylogenetic help Taxonomy direct perc Phylogenetic taxonomy uses a phyloge? towards reality (Knight et al., 1993:3 ny (sensu Hennig, 1966) or a the temporalized Queiroz (1993) noted that at high cladogram (sensu Rieppel, 1988a) as a onomic levels discordances betwee graphical model for constructing a biolog? and species trees due to ancestral ical vanishingly system. A phylogeny is a predomi? morphisms are sma consequently analysis is a nantly bifurcating, asymmetric, and trun? combined approach to cate dendrogram, with time as its vertical usually preferable at su axis (Griffiths, 1974a, 1974b). It is only by neric levels. At the species and popu addition of the disparity time dimension and of levels, however, the much occu the notation of ancestry that the static ho? on tween phylogenetic patterns based mologies of cladistic analysis can be inter? phology and those based on mol preted as evolutionary novelties character? data (e.g., DeSalle and Grimaldi, monophyleticand taxa (Rieppel, 1988a: Sage et al., 1993;izing Patton Smith, 138). All taxa are defined in termsthat of ge? De Queiroz (1993) suggested c nealogical relationships ratherare than ofmo sus methods of data analysis shared attributes (de Queiroz and Gau? Ho propriate at these lower levels. thier, 1990; de Queiroz,ontogenies 1992). "Distin? gene trees, organismal guishing descriptions should be con? taxon phylogenies belong tonotthree d fused with definitions" (Beatty, 1982:27). hierarchical levels, which show part Definitions are ontological statements relationships among each other. Fu about the existence of entities that resultanaly more, disagreements among these different levels seem to be the rule from genealogical relationships among their parts. Descriptions and diagnoses are rather than the exception. Does it make epistemological statements about how we sense to provide consensus trees for these recognize the parts of those entities (de conflicting data sets? I tend to agree with Queiroz and Gauthier, 1990:307). Bull et al. (1993) that when different his? tories are detected by different data anal?In phylogenetic taxonomy, ancestor-de? scendant relationships are recognized in yses, it may be best to keep the data sets addition to the sister-group relationships separate. The next logical step would be to of cladistics because ancestors belong on? identify the causes of heterogeneity and re? tologically to our evolutionary models. The interpret the results accordingly. time-extended lineages of ancestor-de? If cladistic analysis is to avoid tautology, scendant populations are conveniently homology cannot be resolved only by em? named as species. Under this procedure, pirical observation. Homology is distinct however, the notion of monophyly is in? from synapomorphy (de Queiroz, 1985: with the notion of ancestry be? 280). Similarities must first be analyzed compatible by monophyletic species cannot be an? parsimony criteria and summarized oncause a cestors (Rieppel, 1988a:157). Those authors cladogram. Synapomorphies on this dado- This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 1995 points of view 447 that have breeding) chosen that may serve to to distinguish em at the lowest clusters of sexual levels organisms from clonesin of omy (e.g., asexual organisms. Rosen, Cladistic taxonomy19 has 1982; Donoghue, 1985 surface structure (descriptive adequacy) don, 1987) are oblige but lacks deep structure (explanatory ad? some organisms equacy) (Brooks and Wiley, (viz., 1985). A sys? tors and those tematic technique justified that only in termsha of surface structure has not demonstrated its apomorphies) from t relevance to studies ofEpistem characters of the liv? cies concepts. cial distinction must then be made be? ing world that it classifies. Rather than in? tween real cladospecies and provisional sisting on a dichotomy between surface metaspecies (Donoghue, 1985; Archibald, and deep structure, pattern and process, 1994), some of which may represent organisms actual and groups, cladistics and phy? logenetic taxonomy, these part-whole re? It may be tempting to try to avoid lationships the may be more profitably viewed as complementary. Under such an ap? species problem entirely by using only or? ancestors. ganisms as terminal entities for cladistic proach to systematics, pattern provides analysis (Vrana and Wheeler, 1992).process Underwith a direction, and process pro? this approach, taxa are viewed as relation? vides an explanation for pattern (Rieppel, ships among organisms rather than1988a:451). among The only alternative to the problem of groups. Nelson (1989a, 1989b) concluded Siat a basic taxonomic unit does not exist logical incompatibility between monophy? ly and ancestry is to recognize two distinct and that there is no empirical difference entities in phylogenetic sys? between species and other taxa. Theontological prob? tematics: lem with this view is that it ignores the monophyletic taxa and species. Underin? this approach, there is still a tension empirical observation that "character congruence affects lower levels of between the ge? those who propose to use inter? nealogical hierarchy to a greater breeding degree (e.g., Hennig, 1966; Gould, 1986; than higher levels" (Rieppel, 1989:57). Ridley, The1989) and those who reject all pro? cess definitions in favor of strictly morpho? parsimony method provides a cladogram logical pattern definitions (e.g., Wheeler in which there is maximum congruence and Nixon, 1990; Davis and Nixon, 1992). among character generalities. However, this method does not specify the amount My position is that no distinct biological of character incongruence that would entity re?would exist between the organism and the monophyletic taxon if it were not fute the initial hypotheses of hierarchy and for pro? the biological process of interbreeding. monophyly. Cladistic methods cannot vide a rigid test for the expectation Interbreeding of hi? is the most general process known to maintain a reticulated pattern erarchical order in nature. Something more than observations of organisms is required among organisms through time. Conse? for an understanding of character quently, gener? interbreeding is of primary inter? alities at more inclusive levels. A covering est to phylogenetic systematics (de Quei? roz and theory, involving assumptions about bio?Donoghue, 1988) and should continue logical processes such as tokogenesis and to be the basis of species con? cepts. My theoretical (ontological) species con? interbreeding, appears to be necessary. Otherwise, the recurrent charactercept incondefines a species as a single lineage of ancestor-descendant sexual populations, gruences between different empirical data sets cannot be accounted for. Doubts have genetically integrated by historically contingent consequently been raised as to the adequa? events of interbreeding. This concept is clos? est to what has been called the evolution? cy of the cladistic approach to phylogeny reconstruction at low taxonomic levels ary (Ar? species concept (see Wiley, 1981:25). there are empirical limitations to nold, 1981). Many phylogeneticists haveBecause re? jected the very process assumption (interthe possibility of recognizing evolutionary This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 448 systematic species lowing vol. 44 practice, ulated descent systems I and also are not appro? pro priately named within a hierarchical taxo? operational (epistemologi species, Nixon Nixon in biology nomic system. derived from Cracraf and Wheeler (1990), a Evolutionary species are defined here to produce minimal unitary systems thatid (1992): a thespecies is irreducible cluster retrospectively of have sexual functioned as inde? org there is pendent a parental evolutionary units and for patter which and descent and meaningful that cladistic analysis is is diagno possible. At coarser levels of historical resolution, from other such clusters by a which nation of the characters. controversies between cladists and fixed My theoretical phylogenetic species taxonomists over conce how to dea formational, with i.e., the species dynamic, problem are circumvent? are viewed as ed. It stages is reassuring that in no major the method? process andological ranked sequen disagreements remain at the high? nodes of a phylogenetic er levels of the taxonomic hierarchy. tre mological concept Asexual clones is do taxic, not form species. i.e. No species are viewed general and regular as biological the process sma i to produce (tokogeentities thatknown can be a reticulated recogni come of the netic) evolutionary pattern of descent at the supraorgan p ismal level. Birth that relationships,it develop (1993) pointed out w mental canalization, stabilizing impossible to apply theselection spe with precision and other tosuggestions grojips may cause of organ? o isms to remain similar. But these are pro? ing in the present. Althoug cesses of constraint or inertia rather than taxa at the higher phylogene cohesion (de Queiroz and Donoghue, 1988: be considered retrospective 321). The occasional one-way mechanisms levels and as we approach of lateral gene transfer among unrelated i they become prospective, upon expectations microorganisms (including of plasmid what trans? w fer in bacteria) irreducible or between a virus and a the future. Those ing in the present are do incom metazoan host apparently not qualify and only prospective as general biological processes. decisi Clones of cate whether similarpresently organisms traditionally treated iso as tions will remain species are better independe renamed as monophylet? ic taxa when based on apomorphies. ture. This indeterminacy sh Thefor evolutionary concept given r major concern a species general tem that must here also represent has the advantage that it fits the the graphical model of a phylogenetic tree. ological diversity as a whol The birth of a species corresponds to its nition and naming of the origin from a branching event, whereas its permanent phylogenetic lin death results eithera fromrepresent terminal extinc? tainly adequate as history of life. tion or from Systematic its splitting into two or more g like cartographic daughter species maps, (Rieppel, 1988a:99). cann In words, species become restricted to ed to deliver other more precision the internodes than of the phylogenetic tree. Inbe tionary chronicle has judged adequate practice, speciation forwill the coincide with phyl the resentation (see O'Hara, 1993 process of origination of a separate lineage characterized by a new fixed character. study of gene relationships Those species that are not characterized by lations, however, finer graph tations and different methods of data anal? apomorphies (plesiomorphic synapousies) ysis are needed. Demes are the ephemeral may be reduced to the internodes of the phylogenetic tree, thus providing ancestral evolutionary units at any given time plane, including the present, but they form retiespecies for the phylogenetic tree. Descent This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 1995 points of view 449 relationships populations forming among time-extended lin? p eages recognized as evolutionary species, hierarchical when ne founded nested sets of lineages including an ances? by the division tral species and all of its descendants are isting populations and named as monophyletic taxa. De Queiroz disperse among these these conditions, (1992) and de Queiroz andcharac Gauthier (1990, 1992) identified three possible ways ofm de? fixed in a population ted to the fining descendant higher taxon names phylogenetical?p be transmitted ly: (1) a stem-based definition as associates pol the name with a dade of all organisms a more recent common ancestor population will be transmitted to all sharing of its characters that are fixed in an ancestral descendants, either in the original state withorone designated descendant than with another; (2) a node-based definition asso? ciates the name with a dade stemming phylogenetic species therefore constitute in a modified state. The fixed characters of from the immediate common ancestor of evidence that a hierarchical descent system two designated descendants; and (3) an exists and provide the means for analyzing apomorphy-based definition associates the phylogenetic relationships among these species (Davis and Nixon, 1992:421). When name with a dade stemming from the an? no data on interbreeding are available, in? cestor in which a designated character arose. I agree with de Queiroz and Gau? terbreeding evolutionary systems should thier (1992:474) that both stem-based and not be assumed to be larger than the node-based clades should be named in smallest units detected by fixed characters in a cladistic analysis. If a system with ac? phylogenetic taxonomy. Bryant (1994) di cussed nomenclatural problems in esta tive gene exchange is larger than the small? lishing the valid names for crown clade est unit detected on a cladogram, the smal? In practice, stem clades and crown clad ler unit will not remain diagnosable for will be identified by apomorphies esta very long and will retrospectively no lon? lishing the largest and the smallest clade ger be ranked as a species. with recent representatives. As with spe? My evolutionary species concept satisfies cies, all monophyletic taxa in phylogenet the ontological requirements of reflecting real, discrete, irreducible, and comparable systematics are pattern based in practi evolutionary units, withiii which there isbut a genealogically based in theory. parental pattern of ancestry and descent (Cracraft, 1987). Entities cannot be discrete Evolutionary Ranking I have envisioned a procedural progre and still transform over time. Although sion from taxonomy to systematics. Ran species are best recognized from the anal? ysis of pattern, the emphasis of processing in represents the last epistemological ste the theoretical species concept has the ad? within systematics. This view is contrary to conventional practice, which requir vantage of integrating pattern analysis with process theories in systematics. Al? categorical rank to be established before taxon can receive its name. Once taxa have though monophyletic species definitions such as those of Donoghue (1985) require been recognized and named, they may be a previous cladistic analysis, the evolution? classified into age classes or systematized into biogeographical categories, depending ary species concept proposed herein is not on the dependent on such a prior analysis. The available evidence. Classification is the establishment of morphological describer, ecologist, bioge- classes of biological taxa according to ographer, population biologist, geneticist, some useful criterion. Because taxa may be or molecular biologist can all continue the job of recognizing evolutionary units with? referred to many different classes, then out actually producing phylogenetic tax? clearly no one principle of classification can claim to be uniquely valid. onomies. In addition to the ancestor-descendant Linnaean categories were originally This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 450 SYSTEMATIC based on BIOLOGY VOL. 44 Table 1. Phylogenetic taxonomy of Olbiogastridae Aristotelian essentialistic l (Diptera: Bibionomorpha), with biogeographical With the subsequent addition of labels more added to each taxon name. Biogeographical labels are egories to the system, these ranks based on an area cladogram for the history of inter? hav come quite arbitrary, representing continental relationships. Composite labels indicate no the distributions of successively subordinatedhas ances? than an empty formalism that los theoretical idealistic foundation. After the penetrating analysis of Griffiths tral species (either extinct or not sampled), the last term indicating the recent representatives (AfOr = (1974a, Afro-Oriental; AuN = Northern Australia; CAn = cir- 1974b, 1976) on the difficulties of reconcil? cumantarctic; G = Gondwana; GTe = Temperate Gondwana; GTr = Tropical Gondwana; NoAuN = ing the Linnaean categories with the phy? Neotropical-Northern Australian; NoAuS = logenetic system, many phylogeneticists have abandoned further attempts to clas?Neotropical-Southern Australian; NoN = Northern Neotropical; NoS = Southern Neotropical; P = sify taxa into ranks. Pangaea). The square brackets in the taxonomy follow Historical classification corresponds to a convention of Christoffersen (1989) for indicating re? dundant, phylogenetically uninformative taxa (adapt? Hennig's (1966) original proposal of cor? ed from Amorim, 1992:288). relating absolute ages of origin of taxa with age classes delimited by convention Olbiogastridae P-G from the geologic time scale. Subsequent new subfamily GTe-CAn-NoAuS-NoS difficulties in implementing such a scheme in practice led Hennig (1969, 1981) and some followers (e.g., L0vtrup, 1977; Willmann, 1989) to adopt an alternative nu- mericlature. But none of the alternatives to Olbiogastrinae GTr new tribe [new genus 1] Af Or Olbiogastrini NoAuN new genus 2 AuN Olbiogaster NoN the subjective Linnaean categories has won widespread use. These difficulties notwithstanding, the formation (characters). Griffiths (1974a, demand for evolutionary ranking is still 1974b, 1976) showed compellingly that be? warranted because ranking adds retrieva? cause of the noncomparability among dif? ble information content to the biological ferent characters, we are still very far from system. I like the broader connotation of being able to measure overall differences the term evolutionary, as intended by the among taxa. evolutionary taxonomists, for transmitting Amorim (1992) proposed a method of the idea of added information. However, I systematization in which a label corre? am here advocating Hennigian principles sponding to the biogeographical compo? to attain evolutionary ranking. In this re? nent of each taxonomic level is added to spect, theorists of the evolutionary school the name of a taxon (Table 1). One of the such as Mayr (1969, 1974, 1981) and Mayr great advantages of this proposal is that it and Ashlock (1991) have misunderstood does not interfere with the names of taxa the distinction between classification and in the preexisting classification nor must systematization. The systems structure of the Linnaean categories be abandoned im? real phylogenies is cladistic (branching), ir? mediately. The new label may nevertheless respective of what principle for classifying form the basis for biogeographical catego? taxa is adopted (Griffiths, 1974a). Further? ries. The same biogeographical label indi? more, Mayr and Ashlock's (1991) concept cates taxa that have the same age of origin of evolutionary ranking is not evolutionary and that have ancestral species living in at all because it is based on overall simi? the same geographical area. Thus, infor? larity of included taxa rather than on mation any on the history of biogeographical explicit evolutionary criterion. Cladistic areas may be gradually associated with in? and phenetic data cannot be successively formation on the phylogenetic history of combined into a single taxonomic system taxa into a single biological system. One (cf. Mayr, 1981; Stuessy, 1987) because limitation of this proposal refers to taxa these data are obtained from different and originating before the fragmentation of conflicting analyses of the same basic in- Pangaea. Although progress is being made This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 1995 points of view 451 the reconstruction o tionary ranking. Transformed cladistic cesses in when the divested Paleozoic from evolutionary theory detailed biogeographic becomes a strictly methodological activit still not possible It will not produce the best for taxonomyb be these cases, cause groups Amorim known to form reticulate ( visional labels patterns in nature based will be nevertheles age classes forced (for into a hierarchy.exam When evolution made the basis of taxonomy, a split b etc., for successively tween pattern cladists and phylogenet Triassic and similarly er time periods). taxonomists is no longerThes justified. Und es determined evolutionary assumptions, by the most usef p could be gradually methods developed by cladists can su be s and used fortaxon the construction of a origin of lected the an in graphical ical evidence ever becomes available. Even phylogenetic category taxonomy. At the higher if lev? t els of systematic generalization, all phylo? though provisional age classes will always genetic hypotheses become retrospective narratives. In these cases, there is basic remain partially arbitrary and subjective (Craske and Jefferies, 1989), they are still agreement of between pattern cladists and some heuristic value. phylogenetic taxonomists on how to rec? Ranking according to Amorim's (1992) ognize and name monophyletic taxa. Con? proposal is based on biogeography and ceptual and methodological disagreements at the lower taxonomic levels result be? stratigraphy. Such extrinsic data are best kept separate from the intrinsic datacause of gene trees, organismal ontogenies, phylogenetic taxonomy. The evolutionand of taxon phylogenies may produce in? histories for each of these hier? the earth, however, is causally relatedcongruent to the evolution of its biota (Rosen, 1978). archical levels. My evolutionary species concept is ontologically based on inter? Congruence between these largely empir? ical data sets and their representation side breeding and epistemologically recog? nized by diagnostic characters. Codes of by side in a general reference system nomenclature that do not tie taxon names should provide the best hypothesis against which particular evolutionary mechanisms to categorical ranks are required. Such a release from Linnaean conventions would may be tested. In phylogenetic systematics, only mono? immediately promote stability of taxon names. Furthermore, this action would phyletic taxa with extant representatives are ranked into age classes or biogeopermit ranking to proceed gradually and graphical categories. Species, which are independently of taxonomy. Ranks based time-extended lineages logically distinct on the systematization of biogeographical from monophyletic taxa, and taxa com? components add extrinsic evolutionary in? formation on the age of origin and distri? posed exclusively of fossils, which form bution of the ancestral species of a dade truncated phylogenies and have unstable positions in the system (Griffiths, 1976), and may provide the most useful general reference framework for comparative biol? should not be formally ranked. Fossils may ogysimply be sequenced or indented in the system of extant taxa, with such designa? tions as monophylum (Lauterbach, 1989) for Acknowledgments monophyletic taxa and plesion (Patterson A research scholarship from Conselho Nacional and Rosen, 1977) for the remaining taxa. Desenvolvimento Cientifico e Tecnologico during t Conclusions last 15 years has permitted me to accumulate a com prehensive collection of literature even though I w in relative isolation 2,500 km away from the near procedure provisioned libraries. Researchers on the whole h I have argued for a three-step in phylogenetic systematics: cladistic been anal? particularly generous in sending me reprin Editor Michael Miyamoto has been courteous a ysis, phylogenetic taxonomy, and evolu- This content downloaded from 110.54.162.122 on Wed, 30 Jan 2019 13:57:30 UTC All use subject to https://about.jstor.org/terms 452 systematic biology vol. 44 new families for the Crangonoidea and Alpheoidea constructive in his handling of the (Crustacea, Decapoda,Rieppel, Caridea). Cladistics 3:348ham Griffiths, Olivier Kev Dalton Amorim, 362. through their insig have done much Christoffersen, to focus M. L. 1989. Phylogeny my andideas classifi? anonymous script. cation of Pandaloidea (Crustacea, Caridea). Cladis? referees and one asso tics 5:259-274. on suggestions earlier vers Colless, D. H. 1977. A cornucopia of categories. Syst. t Such joint efforts did much helpful quality of 26:349-352. this Zool. manuscript. Yet Cracraft, J. 1983. Speciesthat concepts andIspeciation made me very conscious can analysis. Pages 159-187 in Current ornithology, Vol? for all the errors and hybrid results ume 1 (R. F. Johnston, ed.). Plenum, New York. References Cracraft, J. 1987. Species concepts and the ontology of evolution. Biol. Philos. 2:329-346. Amorim, D. S. 1992. An empirical system ofCraske, ranking A. J., and R. P. S. Jefferies. 1989. A new of biological classifications using biogeographic mitrate from the Upper Ordovician of Norway, and components. Rev. Bras. Entomol. 36:281-292. a new approach to subdividing a plesion. Palaeon? Amorim, D. S. 1994. Elementos basicos de sistematica tology (Lond.) 32:69-99. filogenetica. Sociedade Brasileira de Entomologia, Davis, J. I, and K. C. Nixon. 1992. 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