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© Taylor and Francis 2007 Downloaded By: [University of California Irvine] At: 19:33 26 March 2007 O:10.1080/10635150601145365 DOI: online 1076-836X / print 1063-5157 ISSN: Copyright Biol. Syst. 130 xatognssfrwihawl-ae hlgn is phylogeny well-dated a available. which of for group objec- any organisms classifying an extant for standard provide universal thereafter and tive would among to arbitrary. consensus they inherently windows a by systematists, are temporal ratified rank formally the once each However, of forms with boundaries associated extant be The any life. across of ranks taxonomic equilibrate a by standardized time. and evolutionary added calibrated yardstick: the universal being with now but of un- schemes) benefit (as Linnaean hierarchical traditional re- be der each also arranged, would classification hierarchically sulting are clades phylogeny Because 2006.) any al., in et e.g., Moreau data; 2003; the al., sequence to et Springer especially molecular thanks extensive clades of progress many availability rapid for made estimate, being to is difficult dates notoriously nodal (Although be the resides. can which clade that in de- for (band) rank node window taxonomic basal temporal a the assigned by be termined would compris- clade species any biogeographic extant ing evidence), clocks, other or molecular fossils, data, (from nodes dated internal with reliably tree phylogenetic any to biological For and diversity. of retrieval interpretation evolutionary and an storage encapsulate information univer- for a provide system to sal 1982): of (Mayr, both functions to ideal closer two taxonomy its moving by situation rem- could this classification edy for 1999) Johns, and Avise 1966; scant received have it 2005). implement (Dubois, to attention how and criterion be universal that might what by 2000), equivalent Minelli, prin- less 1973; Valen, in or should more rank be taxonomic ciple same the afforded that taxa proclaimed sometimes is it Although are monophyletic. Aves) paraphyletic (e.g., are others whereas Reptilia) delimited, (e.g., traditionally as taxa some that is nonstandard- ization of aspect Another en- variation. or groups evolutionary genetic, disparate phenotypic, of such amounts comparable whether compass almost on provides particular information primates for and no flies designation fruit other) of any assemblages (or problem, genus-level “apples-versus-oranges” a an of as because such more, others than older some as example, such For genera classifications. biological current in eprlbnigcudpoieasml a to way simple a provide could banding Temporal (Hennig, strategy “temporal-banding” a principle, In nonstandardized grossly are assignments Taxonomic 61:3–3,2007 56(1):130–133,  c oit fSseai Biologists Systematic of Society 1 eateto clg n vltoayBooy nvriyo aiona rie aiona967 S;Emi:[email protected] E-mail: USA; 92697, California Irvine, California, of University Biology, Evolutionary and Ecology of Department Drosophila Pan r nodro magnitude of order an are or Gorilla 2 3 ooaSre,Sd elns aiona933 USA 92373, California Redlands, B Side Street, Sonora 231 some iet tnadz Taxonomies Standardize to Time J OHN n,further- and, ; rtro (Van criterion .A C. 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M ITCHELL 2 T Drosophila IMECLIP [D:mi] bold P Fe ono,2000] Johndoe, [F:eo ROPOSAL oioda or Hominoidea; rcee as bracketed , [....] Drosophila with ) and , 56 Downloaded By: [University of California Irvine] At: 19:33 26 March 2007 ovn aiu aao rmts as ri is ns n horsetail and ants, flies, text. fruit the bats, in primates, mentioned plants of taxa various volving Timeclip 2007 fteapoiaeeouinr etso h aain taxa the of sense depths informative evolutionary question. an approximate consumers the give of would treatises), they scientific primary but for reserved best (such are origin details of dates precise seminars. specify or not publications would Timeclips in as used such as settings well suitable as other lists 2500–3600 taxonomic traditional to attached 550–2500 500–550 410–440 Archaean 440–500 Proterozoic [R:ar] Cambrian 350–410 [Q:pr] 250–290 205–250 Ordovician [P:ca] Silurian [O:od] 145–205 290–350 Myrmicinae [N:si] Devonian Carboniferous [M:dv] Chiroptera, 65–145 Permian [L:cb] Triassic [K:pe] 56–65 Jurassic [J:tr] Cretaceous [I:ju] Yangochiroptera, [H:cr] Paleocene 33–56 Pteropodidae [G:pa] Hominoidea, 24–33 5–24 2–5 0–0.01 Eocene Oligocene 0.01–2 [F:eo] Miocene [E:ol] Pliocene [D:mi] Pleistocene [C:pc] Recent [B:pl] [A:re] nicinquiry. sci- sug- further entific for often hypotheses might interesting as boundary) themselves K-T gest the at as- holocaust the teroid as (such as events physical (such with events radiations) adaptive biological pos- of episodes, associations geological historical the well-known sible to linking evolutionary taxa timeclips of approximate with origins Furthermore, their 1). of (Table terms ages compare in and arrange taxa to these observer any enabling thereby timeclips, appropriate receive likewise could groups two these within clades well-dated Other respectively. ocene, timeclips with [G:pa] appended simply but taxonomic tained the proposal, to new demoted designations subordinal the and Under to renamed status. be elevated generic could and Chiroptera or renamed level, be example, for scheme, Chi- under temporal-banding original assemblages (order the these clade equilibrate bat To the 1). of (Fig. roptera) members extant did (genus as clade zoic, plant horsetail the Equisetum of members extant ies, ae nmlclrgntcdt n osldiscover- fossil and data genetic molecular on Based T ABLE eoigoiiaindtsi h oeeadPale- and Eocene the in dates origination denoting .Sgetdtmcisadafwtxnmceape in- examples taxonomic few a and timeclips Suggested 1. Geological ea hi iesfiaineryi h Ceno- the in early diversification their began ) episode Equisetum T IMECLIP idw(Mya) window Temporal n hrpeawudb re- be would Chiroptera and E XAMPLES Pan Yinpterochiroptera Equisetum Vespertilionoidea, Noctilionoidea, Emballonuroidea, Rhinolophoidea, , Gorilla o aamnindin mentioned taxa (of i.1o ntetext) the in or 1 Fig. Euvlnylist” “Equivalency Equisetum , Drosophila [F:eo] ONSO VIEW OF POINTS could, and taotta aetm.Sc yohssmgtte be investigation. then scientific might further hypotheses of Such worthy time. same that place about taking at also were with that associated radiations ecologically plant be Angiosperm might it think that prolifera- as to evolutionary such tion, this stimulated for be hypotheses causal might about for- Myrmicinae timeclip than to a attached earlier seeing readers (much Thus, supposed). Cretaceous merly oc- the ants myrmicine during of curred radiation they early evidence, an From fossil that interest. and concluded of data be sequence can DNA dates extensive evolutionary how of tion eas tpnonsgp nkoldeta ih war- might investigation). that further knowledge rant in important gaps is pinpoints itself it information because (this taxa age evolutionary These to attached. be as clades, interpreted need be many simply timeclips would for no these unknown origi- for currently course, but focus are Of sole dates the analyses. nation been phylogenetic have to traditional addition often of in that dates, desirable topologies nodal encourage branch estimate would to protocol efforts timeclip scientific a of adop- mere tion the Finally, appended. are names timeclips taxon which is traditional to of system use timeclip continued Further- the the by desirable. retained under scientifically stability taxonomic is more, flexibility such information, new but with considered change be to should subject and taxon provisional given Any a various to studies. attached empirical for timeclip from phylogenies emerge groups secure taxonomic as piecemeal, porated clades. across these paces different grossly at proceeded evolution have to morphological seems why and intriguing how raises groups about Hominoidea, questions taxonomic than these ancient more of far all are that or age, evolutionary that knowing simply setum and example, within For phenotypes clades. timeclips across other so or behaviors, equation, in anatomies, tempos rate evolutionary of any comparisons stimulate in would denominator time the Furthermore, is phylogenetics. all comparative nearly of in areas communication and research facilitate thus would and taxonomies current do than information more ahrta honaa;ti osntma htthis that exis- timeclip Our saved mean ” in . not be . unchanged. does should been remain . this . should . information has and away; thrown years, merits, than 250 of rather than more number for a tence has . nomen- . . and clature taxonomy zoological A of system current classification. (2005): “the Dubois by stated biological was stance conventional compromise for popular abandon frameworks or overhaul, Linnaean retain, to whether oeue l 20)rcnl rvddaohrillustra- another provided recently (2006) al. et Moreau nte datg sta ielp ol eincor- be could timeclips that is advantage Another far convey and standardize would system timeclip A ytmtssfryashv nae ndbtsabout debates in engaged have years for Systematists , Drosophila n hrpeaaeo ogl similar roughly of are Chiroptera and , T IMECLIP S YNOPSIS B ENEFITS netesedis incertae ihrespect with [H:cr] Equi- 131 Downloaded By: [University of California Irvine] At: 19:33 26 March 2007 ae foii,tmciswudadmtral othe to materially add would approximate timeclips their origin, to of according dates taxa tra- Linnaean sort and ditional signify to biologists enabling By evolutionary disciplines. relevant other molecu- or paleontology, from biology, lar discoveries phylogenetic new of familiar poration the retain to system way Linnaean practical a provides proposal 132 aiu a iegsi h re hrpea(eln ta. 05.Frsmlct,tesvntmoa ad soitdwt ucsieeoh of epochs vary. successive durations with actual associated their bands but temporal width, seven in the simplicity, equal For as 2005). here al., drawn are et (Teeling Era Chiroptera Cenozoic order the the in lineages bat various F IGURE .Pyorm rw ntesm eprlai o osti ln pce ntegenus the in species plant horsetail for axis temporal same the on drawn Phylograms 1. and iutnosypooeteincor- the promote simultaneously YTMTCBOOYVOL. BIOLOGY SYSTEMATIC l ye fsinicrsac ncmaaiephyloge- comparative in 2006). (Avise, research netics nearly scientific facilitate of general types in all and genotypes, and thought notypes of phe- organismal avenues of rates novel evolutionary comparative promote about life, of forms parate dis- across to ranks taxonomic help nonstandardized classifications, equilibrate biological of content information Equisetum DsMri ta. 03 and 2003) al., et Marais (Des 56 Downloaded By: [University of California Irvine] At: 19:33 26 March 2007 uos .20.Pooe ue o h noprto fnmn of nomina of incorporation the for rules Proposed 2005. A. Dubois, 2003. Pryer. M. K. and Britton, M. D. Smith, R. A. L., D. Annu. Marais, taxonomy. Des Phylogenetic 1992. Gauthier. J. and K., Queiroz, de tempo- standardized a for Proposal 1999. Johns, phylogenetic C. G. A and nature: C., J. in Avise, pathways Evolutionary 2006. C. J. Avise, 2007 O:10.1080/10635150601156305 DOI: online 1076-836X / print 1063-5157 ISSN: Copyright Biol. Syst. uainbe ein.Ti samsae eas there because mistake, a is auto- deleting This other regions. manually some data “unalignable” perhaps or their program, 1994) alignment al., with mated et parameters (Thompson default Clustal data. in use molecular of simply alignment investigators Some consider many carefully homology, not of do issues ignore to gists homology. of assignment the Simpli- is 1996). alignment Wheeler, fied, (see path- optimization homology direct in presumed ways reconstructed nucleotides, arguably, homologous or putatively but of molecular sequences, in columns individual rather, data not The are step. studies critical phylogenetic a in of- as is overlooked However, alignment ten of modification. process the with phylogenetics, molecular descent of paradigm and traditions Linnaean nomenclatures. established while taxonomies maintaining existing enrich still greatly on could tac- discussion that timeclip-like open tics on and invite strategy now temporal-banding we the Thus, ad- proposal here. timeclip the vanced than utilitarian radi- more less far and/or seem cal which of some other proposals various taxonomic to devoted been Phyloge- have Nomenclature) for netic Society (International organization formal ihrrne olgcltx nthe in taxa zoological higher-ranked 164:737–751. Sci. Plant J. Int. horsetails, extant of setum evolution and relationships Phylogenetic 23:449–480. Syst. Ecol. Rev. Natl. Proc. species. 96:7358–7363. extant USA for Sci. classification Acad. biological of scheme ral York. New Press, University Cambridge approach. lhuhi ol eutikbefrmorpholo- for unthinkable be would it Although Darwin’s to pivotal is homology of concept The a even and symposia, special literature, extensive An 61:3–4,2007 56(1):133–146, ae nclrpatDAsqec aa(eLadTrnL-F). and (recL data sequence DNA chloroplast on based ,  c oit fSseai Biologists Systematic of Society 4 urn drse:Vrii iifraisIsiue iifraisFclt,Wsigo tet ignaIsiueo Technology, of Institute Virginia Street, Washington Facility, Bioinformatics Institute, Bioinformatics Virginia Addresses: Current pnoso utpeSqec lgmn,ada miia Comparison Empirical an and Alignment, Sequence Multiple on Opinions 2 fRpaaiiyadAcrc ewe O n tutrlAlignment Structural and POY between Accuracy and Repeatability of eateto noooy ea & nvriy olg tto,Txs783 S;Emi:[email protected] E-mail: USA; 77843, Texas Station, College University, A&M Texas Entomology, of Department 1 R eateto clg,EouinadNtrlRsucs ugr nvriy e Brunswick, New University, Rutgers Resources, Natural and Evolution Ecology, of Department EFERENCES 3 eateto ilg,Cleeo h oyCos ocse,Msahsts060 USA; 01610, Massachusetts Worcester, Cross, Holy the of College Biology, of Department K ARL nentoa oeo Zoological of Code International .K M. e esy091 S;Emi:[email protected] E-mail: USA; 08901, Jersey New JER , 1 J OSEPH lcsug igna201 USA 24061, Virginia Blacksburg, -al [email protected] E-mail: ONSO VIEW OF POINTS .G J. Equi- ILLESPIE soit dtr aeaSoltis Pamela Editor: Associate 2006; July 11 returned reviews 2006; February 21 submitted First Taxon equivalent? phyla different in categories and Are 1973. O’Brien, L. Valen, J. Van S. Bates, P. Madsen, O. Springer, S. M. C., E. Teeling, Placental 2003. O’Brien. J. S. and Eizink, E. Murphy, J. W. S., M. Springer, 2006. Pierce. E. N. and Archibald, B. S. Vila, R. Bell, D. C. S., C. Moreau, or taxa, higher and species of names the and ranks The 2000. Cam- A. Press, Minelli, Belknap thought. biological of growth The 1982. E. Mayr, Press, Illinois of University systematics. Phylogenetic 1966. W. Royal Hennig, Trans. Philos. Introduction. 2004. Knapp. S. and C., H. Godfray, n oqe Soe 98,adTCfe [Notredame T-Coffee and 1998], Divide [Stoye, of 1994], al., variety Conquer et a and [Thompson in Clustal performed (e.g., be programs can methods 1). (Table Automated aligned manually were rRNA utilized that pers in papers Cladistics phylogenetic of survey Biology a Systematic In 1. pro- Figure is in another one vided to relationship types their the and of alignment of diagram A alignment. alignment computer-based manual and categories; broad two into divided be 2004). Kjer, Xia 2003; 2001; Whiting, al., and et Ogden Wheeler 2003; al., 2000; et 1997; al., et Ellis, Hickson and 1995, Morrison Kjer, 1995; (e.g., Wheeler, trees different 1991; produce Mindell, will them, into assump- go the that and tions alignments, where examples many are 22:333–373. 307:580–584. Science bio- record. illuminates fossil bats the for and phylogeny geography molecular A 2005. Murphy J. W. 100:1056–1061. USA Sci. Acad. Natl. Proc. boundary. Cretaceous-Tertiary the and diversification mammal Angiosperms. of Age the in 312:101–104. Diversification Science ants: the of Phylogeny San Sciences, of Academy California sciences. Francisco. of philosophy and 339–351 Pages history. natural of in language the of inertia dangerous a Massachusetts. bridge, Illinois. Urbana, 359:559–569. B Lond. Soc. 27:365–426. Zoosystema nomenclature. ological Nomenclature prahst lgmn o hlgntcsuiscan studies phylogenetic for alignment to Approaches nlacpac 0Ags 2006 August 10 acceptance final utrsadisiuin fntrlhsoy sasi h history the in Essays history: natural of institutions and Cultures , 2 , 4 AND rmtels er,w n ht7%o h pa- the of 76% that find we years, 3 last the from .Sm eea usin,cnet,adtrso bi- of terms and concepts, questions, general Some 1. . K AREN , oeua ilg n Evolution, and Biology Molecular .O A. BER 3 and 133