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Syst. Biol. 48(2):329–351, 1999 Denitions in PhylogeneticTaxonomy:Critique and Rationale PAUL C. SERENO Department of Organismal Biologyand Anatomy, Universityof Chicago, 1027E. 57thStreet, Chicago, Illinois 60637, USA; E-mail: [email protected] Abstract.—Ageneralrationale forthe formulation andplacement of taxonomic denitions in phy- logenetic taxonomyis proposed, andcommonly used terms such as“crown taxon”or “ node-based denition” are more precisely dened. In the formulation of phylogenetic denitions, nested refer- ence taxastabilize taxonomic content. Adenitional conguration termed a node-stem triplet also stabilizes the relationship between the trio of taxaat abranchpoint,in the face of local changein phylogenetic relationships oraddition/ deletion of taxa.Crown-total taxonomiesuse survivorship asa criterion forplacement of node-stem triplets within ataxonomic hierarchy.Diversity,morphol- ogy,andtradition alsoconstitute heuristic criteria forplacement of node-stem triplets. [Content; crown; denition; node;phylogeny; stability; stem; taxonomy.] Doesone type ofphylogenetic denition Mostphylogenetic denitions have been (apomorphy,node,stem) stabilize the taxo- constructedin the systematicliterature since nomiccontent of ataxonmore than another then withoutexplanation or justi cation for in the face oflocal change of relationships? the particulartype ofde nition used. The Isone type of phylogenetic denition more justication given forpreferential use of suitablefor clades with unresolved basalre- node- andstem-based de nitions for crown lationshipsor uncertain outgroups? Which andtotal taxa, respectively ,isincomplete or type ofphylogenetic denition is preferable inaccurate,as reviewed below. forclades whose members areentirely living Totaltaxa and crown taxarequire stem- or extinct? basedand node-based de nitions, respectively. — Questionslike these havenot been rigor- Given thata totaltaxon includes allcur- ouslyaddressed in phylogenetic taxonomy. rently knownand potential extinct out- Rather,attention has been focused on(1) the groupsthat are most closely related to a adaptationof traditionalrules governing particularcrown taxon (T able 1),the total synonymyand redundancy foruse within taxonmust have a stem-basedde nition the phylogenetic system,and (2) the recom- (de Queirozand Gauthier, 1992). The stem- mendationthat “ widely recognized”names basedstructure of the denition ensures the arebetter restrictedto crown taxa than to inclusionof all taxa up to,but excluding, the more-inclusive taxawith extinct basal mem- commonancestor shared with its sister to- bers (de Queirozand Gauthier, 1990, 1992; taltaxon. This justi cation is suf cient, be- Roweand Gauthier ,1992;Bryant, 1994, 1996; causeneither anapomorphy- nor a node- Lee, 1996).Despite increasinguse of phy- basedde nition would include allpotential logenetic denitions in systematics,a gen- extinctoutgroups. eralrationale has yet tobe proposedfor Acrowntaxon, in contrast,does not the formulationand placement of phyloge- require anode-based denition, although netic denitions, and manycommonly used one iscommonly assumed. De Queiroz termssuch as “ crowntaxon” and “ node- andGauthier (1992:469) simply remarked, basedde nition” have yet tobe specically “Namescan be associatedunambiguously dened. withcrown clades using node-based def- initions.”Likewise, Roweand Gauthier (1992)and McKenna andBell (1997)pro- LACK OF A GENERAL RATIONALE posednode-based denitions for Mammalia DeQueirozand Gauthier(1990, 1992) rst withoutexplaining why denitional type articulatedthe general structureof phylo- ispreferable. Lee (1996:1103)remarked, “ A genetic denitions, outlining apomorphy-, crown-cladede nition results when both node-, andstem-based de nitions (Fig. 1). taxaimplicated in anode-based denition 329 330 SYSTEMATICBIOLOGY VOL. 48 denition will moreeffectively stabilizetax- onomiccontent. Thus, there isno current justication for exclusive use of node-based denitions to delimit crowntaxa. Node- basedcrown taxa, in conjunctionwith stem- basedtotal taxa, however, yield alocaldef- initionalcon guration that can provide jus- tication for preferential use of node-based crowntaxa (see Node-Stem Triplet below). Node-basedcrown taxaare more stable,infor- mative,and accurate thantaxa de ned by ex- tinct speciesand have been (or shouldbe) as- FIGURE 1.Node-based and stem-based phyloge- sociatedwith “ widelyused” names. —Gauthier netic denitions, which usually havebeen shown (1986:12)stated that restricting “ Aves”to graphicallyby encircling portions of acladogram(de Queiroz andGauthier, 1992), are indicated here byadot “living taxa”maximizes “ stabilityand phy- (node-based)or arrow (stem-based). logenetic informativeness,”and de Queiroz andGauthier (1992:468) suggested that“ bi- ologistscommonly use the widely known arerepresented by extantforms.” And Wyss nameA veswhen makinggeneralizations andMeng (1996:559)stated that the deni- thatapply toextant birds alone.” With re- tionsof crown taxa “ arethus node-based in gardto the taxonMammalia, Rowe and their formulation,”without presenting any Gauthier(1992:372) observed that “ noone reasoningfor such a conclusion. in severalcenturies hasmistakenly assigned Any group of extantspecies mayjust aRecentmammal to some other taxon.” aswell be united by astem-basedde ni- McKenna andBell (1997:32)remarked that tion.The crowntaxon Amniota, for example, “acrowngroup islikely toremain relatively couldhave a stem-basedde nition, such as: stable.” “anyRecent tetrapod more closely related to Despite these andsimilar statements in Mammaliathan to Anura and all extinct de- the literature,node- orstem-based crown scendantsof their mostrecent commonan- taxaare not demonstrably more stable in cestor.”A stem-basedde nition for a crown terms of meaning or content.Any node- or taxon,in fact,may be preferable if the basal stem-basedde nition that speci cally iden- relationshipsamong extant taxa within a ties amostrecent commonancestor clearly crownclade are poorly established, as seems species the boundariesof aclade,regard- tobe the casewith Amniota (see alsoRo- lessof the living orextinct status of the ref- dentia:Wyss and Meng, 1996)(Fig. 2b). All erence taxaor the particularphylogeny to members of the crowntaxon will be in- which the denition is applied (Lee, 1996). cluded, even if basalingroup relationships In termsof taxonomic content, rede n- arepoorly resolved, because astem-based ing Mammaliaas a crowntaxon does not denition is based on reference toan out- immediatelyclarify which extinct taxa will group taxon(or taxa). be included orexcluded. Mammaliaas Asingle suboscinebird, for example, acrowntaxon appears more stable only wouldsuf ce asan outgroup reference if extincttaxa are ignored andattention taxonfor a stem-basedde nition of the isfocused onthe greatphylogenetic dis- crowntaxon Oscines. A node-based de- tanceto their nearest living sistergroup. nitionof the samecrown taxon would re- Even so,inclusion of someliving mam- quire listingmany oscine subgroups toen- malsmay be uncertain.Rowe and Gau- sure inclusionof all living species currently thier’s(1992:375)preferred node-based def- regardedas oscines. On the otherhand, if initionof Mammalia(“ the lastcommon the basaldichotomy within a crowntaxon ancestorof Monotremata and Theria” ; see iswell establishedand outgroup relation- alsoMcKenna andBell, 1997:32,35.)may shipsare uncertain (Fig. 2a),a node-based be synonymouswith Theria, if monotremes 1999 SERENO—RATIONALE FOR PHYLOGENETIC DEFINITIONS 331 TABLE 1.De nitions forterms used in this paper. Term Denition Taxonomicde nition relational statement specifying the taxonomic content of ataxon Taxonomicdiagnosis descriptive statement specifying the apomorphies (derived characterstates) thatserve to identify membersof ataxon Taxonomiccontent existing andpotential taxaor individuals thatby denition areincluded within ataxon Reference taxon taxonserving asareference in aphylogenetic denition Crown taxon aliving species, ora clade thatcan be dened by living species, whose immediate outgroup is extinct Total taxon clade composed of acrown taxonplus all extinct outgroups more closely related to it thanto anothercrown clade Stem taxon anextinct species orclade for which immediate outgroup includes atleast one living member Node-basedde nition statement specifying aclade composed of the most recent commonancestor of two ormore reference taxaand all descendants Stem-basedde nition statement specifying aclade composed of all descendantsmore closely related to one reference taxon(or taxa)than another (or others) Complementaryde nitions phylogenetic denitions with the samereference taxa(as in anode-stem triplet) Reciprocal denitions phylogenetic denitions with the samereference taxabut in reverse order (asin opposing stem-basedtaxa of anode-stem triplet) Node-stemtriplet trio of taxawith complementary denitions consisting of anode-based taxonand two subordinatestem-based taxa Taxonomicequivalence statement of equivalence (or equation)in which the taxonomic content of one taxonequals that of subordinatetaxa plus their commonancestor (e.g.,A =B+C,asin anode-stem triplet) proveto be moreclosely related to marsu- thanto suppose thatthe ancientbird hadthis pials,as indicated by somerecent molecu- sequence (Lee, 1996).Accelerated character- larevidence (Penny andHasegawa, 1997). statetransformation, in otherwords, is not Stability of taxonomiccontent is not re- morecorrect, accurate, or informative than latedto the living orextinct status of ref- delayed transformation.
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  • Principles of Plant Taxonomy Bot

    Principles of Plant Taxonomy Bot

    PRINCIPLES OF PLANT TAXONOMY BOT 222 Dr. M. Ajmal Ali, PhD 1 What is Taxonomy / Systematics ? Animal group No. of species Amphibians 6,199 Birds 9,956 Fish 30,000 Mammals 5,416 Tundra Reptiles 8,240 Subtotal 59,811 Grassland Forest Insects 950,000 Molluscs 81,000 Q: Why we keep the stuffs of our home Crustaceans 40,000 at the fixed place or arrange into some Corals 2,175 kinds of system? Desert Others 130,200 Rain forest Total 1,203,375 • Every Human being is a Taxonomist Plants No. of species Mosses 15,000 Ferns and allies 13,025 Gymnosperms 980 Dicotyledons 199,350 Monocotyledons 59,300 Green Algae 3,715 Red Algae 5,956 Lichens 10,000 Mushrooms 16,000 Brown Algae 2,849 Subtotal 28,849 Total 1,589,361 • We have millions of different kind of plants, animals and microorganism. We need to scientifically identify, name and classify all the living organism. • Taxonomy / Systematics is the branch of science deals with classification of organism. 2 • Q. What is Plant Taxonomy / Plant systematics We study plants because: Plants convert Carbon dioxide gas into Every things we eat comes Plants produce oxygen. We breathe sugars through the process of directly or indirectly from oxygen. We cannot live without photosynthesis. plants. oxygen. Many chemicals produced by the Study of plants science helps to Study of plants science helps plants used as learn more about the natural Plants provide fibres for paper or fabric. to conserve endangered medicine. world plants. We have millions of different kind of plants, animals and microorganism.