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Systematic Biology Publication details, including instructions for authors and subscription information: http://www.informaworld.com/smpp/title~content=t713658732 The Adequacy of Morphology for Reconstructing the Early History of Placental Mammals Mark S. Springer a; Angela Burk-Herrick a; Robert Meredith a; Eduardo Eizirik b; Emma Teeling c; Stephen J. O'Brien d; William J. Murphy e a Department of Biology, University of California, Riverside, Riverside, CA, USA b Faculdade de Biociencias, PUCRS, Porto Allegre, RS, Brazil c School of Biological and Environmental Sciences, University College Dublin Belfield, Dublin, Ireland d Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD, USA e Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA

First Published on: 01 August 2007 To cite this Article: Springer, Mark S., Burk-Herrick, Angela, Meredith, Robert, Eizirik, Eduardo, Teeling, Emma, O'Brien, Stephen J. and Murphy, William J. (2007) 'The Adequacy of Morphology for Reconstructing the Early History of Placental Mammals', Systematic Biology, 56:4, 673 - 684 To link to this article: DOI: 10.1080/10635150701491149 URL: http://dx.doi.org/10.1080/10635150701491149

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Glir and . tooth A and and Meng, traits: mammalian Gowri-Shankar the phylogenetic Ron and J om Theslef homoplasy Murphy Gowri-Shankar . versions R. Churakov . J. for Chase, of estimated Retr Carrier Recovering and RNA and this the L A Genes R K. National molecular Acad. H., John analysis and es. Accepting Novacek, . N. L. . M. the for unstable M. mammals likelihood Thorne, impr phylogenetic DeBry cusp Evans, molecular/genomic G. Y in oposed extinct Principal the shape with A Honeycutt. Science K.-P B. . J. phylogenetic mammals. Evol. context, C. for eutherian sequences. f, early Hotta, Lark. a J. Gatesy and C , timing , R. Simmons. Sci. Genet. oved molecular and J. phylogeny patterning Milinkovitch. K F of Novacek. . character , , . of of testing W without Science Koepfli, N R Jernvall, M M dental I. R 12:209–246. of K. and its USA the evidence. blocks. placental systematists 2002. marker and elements O ible, EFER mammalian . partnership S. 307:1091–1094. ichael Theslef extinct . E. , and appr , phylogenetic in the taxa Adler G. W component Keifmann, , and Syst. J. P four a manuscript. Penttila, on H. H r one . of PLoS L methods: 2007. Lark. 99:9930–9935. J. O’Brien. morphological elationships. Mol. M. pelvis. G Genetic . characters. E 2005. morphological their ENC Foundation oach millennium. Kishino. assuming data. H. two R. Jow 2005. D Bioinformatics , by W . hypotheses the , the and of 78:267–283. f, wher apolipopr Higgs, T C. G super mammals. oodburne, of as J. K. eutherian and . Biol. ectodin. Geisler Site eutheria. 2005. Phylogenet. placement 2001. , M E fossil to Fossil Jarvik, Mammal. anonymous McKenna, way M ar Syst. N. S K. early Genome the by W mitochondrial Stem E U. 2001. basis estimating analysis chives Application . J. e specific N ayne, Kavanagh, 4:e91. methods. 2003. Rattray Itoh. submission? Genetics is and This SOAP Jor or T Jernvall. a molecular Natur . r gr evidence Biol. tr to S elatives Mol. otein (M.S.S. constant Science 2003. E. to dinal Lagomorpha for dan, Molecular Syst. diversification BMC ee eatest J. Michael M. inferring for T 2005. and work A. Res. Evol. , Her tease concerning ime 17:573–574. systems rates or of 50:913–925. , G. Evol. e Phylogenet. cleaning of characters. B, r and J. the Relationships Rattray Biol. of Ostrander 432:21 phylogeny of eviewers tr ders. the Mol. Evol. 2004. M. W and ed. 309:2067–2070. 15:1825–1830. clades based Br pr to N. scale and Regulation ee canid rate 10:131–194. living was challenges genome . evolutionary of fossil osius, 28:241–252. ovides P Morpholog- mammalian canid W S. apart Rougier Ohbayashi, 53:333–342. 92:212–219. . dating W data Biol. mitochon- 1–214. of that Biol. esterman, G. Noninde- the of . Springer of Robust multiple partially .J.M.). phylo- on P and 2005. skeletal skeletal molec- O Higgs. euthe- for , origin is and skele- taxa Evol. Evol. com- T pla- fr mor I 7:8. base ho- ap- the N ar and , . om the an r of D D T of of e A e J. - - . . . S O F Springer Springer Smith, T T Swof Springer Nishihara, Murphy Murphy Murphy Murphy Meng, Simmons, Scotland, Scally Ronquist, Ronquist, Reyes, Posada, Novacek, Novacek, McKenna, Madsen, Luo, eeling, abuce, V Springer clade. tiary Mahboudi, land, (*and 19:430–438. Molecules Hopkins placental ular Natl. mammal 173. r 235:1–182. and extant expected mal 2007. logenomics radiation and Douady mammals. O’Brien. Bull. malia, New plinary Icar r placental and manual. genetic genes 2004. DNA Biol. 356:121–125. insertions. Mammalia. Natur allel Amrine, tribosphenic econstr econstr I E for Z.-X., , onycteris W foraging M. phylogeny M. J., evidence adaptive M N. A., 1 mammals Am. Y Acad. d, Massachusetts. Using Congr R., , , , , substitution. e 1:R573–R575. , , , using other D., Pr bat ork W Y O., W Glir ., W M E. M W M S. M. infer S. 409:610–614. M. appr D., R. F , F uction: uction: . D. N. , oc. M. C. 2001a. H., . O. . . L. . M. R. . Hu, University . diversification E . mammalian . , mammals , . mammals. J., Springer using and Springer J., Mus. J., and S., M. lineages, S., J 2001. consolidate and W C., . es): and S., J., Pr J. Natur and L. . Marivaux, B., F Gissi, L. , J. E. Pages Sci. comes Madsen, Roy uent genomic ence T M. P T Bayesian oach methods, P . . C. W 1992. mammals. Ar strategies oc. and , W . eeling, Scally . Stanhope, . Mebr E. M. 2003. radiations Eizirik, for Cifelli, Huelsenbeck, M. and H. R A. K. . . Implications M. London. J. fr . Molecular The Hasegawa, chaeonycteris A. Nat. . J. Perspectives Bayesian USA Genome Mammalian 1975. . J. Natl. Eizirik, Soc. om e mammalian under P J. Murphy C. Pringle, (W G Pevzner major Crandall. J. F . 21–46 Murphy . . Mammalian H. 409:614–618. of ouk, Bioinformatics J. . , 2001b. Stanhope, . Scally 2001. Huelsenbeck. with P r (K. Li. Stanhope. C Pr . Catzeflis, Hist. North J. ole Olmstead, AUP*: O. H. 100:1056–1061. data C. age. B P T and W . methods. clade Acad. T M. the . Mammal. ess, V urner J in 2003. 274:1 owar D. Luckett mixed . . P W and Natur ersion placental Geisler of A. J. in comments in E. Douady S. Res. , . Molecular phylogenetics. Micr Adaci, , , T 275:1–247. T Resolution . placental phylogenetics S. T Rose to , E Douady Baltimor and morphology Phylogeny Johnson, W Africa . and r D two a E R J. r . Phylogenetic , ends . for 1998. A. the 159–1 f Kielan-Jawor Sci. d and phylogeny: evealed The Eizirik, . unravel . yder Hassianycteris fr . for 2005. 17:413–421. tr O. O’Brien, Eizirik, e ochir de models. E. om 2000. a Crider J . 4.0b10. S. phylogeny: ees N. and and major 409:53–57. phylogeny Mol. Cr . and eau, 1998. M. USA , Evol. P osteology Madsen, Jong, phylogenetic Genet. Nevo, , J. 2003. r D 166. . clades. Kao, ModelT etaceous-T 14:817–818. , Okada. einfor paleontology Morphology’s M van fr optera. O’Brien. e. on . mammal Bensalah, W evidence J. F Y and J. J and om Molecular by Biol. . . the of . . , and D. 103:9929–9934. . clades S. Phylogenetic of P M Kao, 8:239–277. the J and R. Bioinformatics Sinauer . W O. der . . MrBayes the tracking Syst. Zhang, Genes M. Szalay G. Science 20:631–639. S. ce and . Ar mitochondrial the Stanhope, r J.-J. . Pages analysis Bennett. S oska. oot est: S. Evol. evolution and 2006. Madsen, J. d , Bull. . M. the of Shaking Mark. chibald, and early Pesole, W and Springer e O’Brien. J. 2004. primates: L. of ertiary the Jaeger tr for Rhombomylus Biol. of . J.-L. Jong, S. T O’Brien. , molecular ee. DeBry W and esting classification placental 2001. Associates, eds.). O. Am. 21:397–403. . evolution 37–49 evidence Pegasoferae, the Romagnoli, Springer 294:2348–2351. Palaeochir origins the ancient . placental 3: Syst. 2005. r T Mammalian W Hartenber using A. ole 52:539–548. 2003. supertr r . and Bayesian eds.). W the ends r M. boundary placental 2007. M. . of major , Mus. elationships , 2003. 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Smirnov J. Hillis, e. Nomencl. T , , -Smith, -Smith, D. oz, A. oz, T S., oz, P W W P J. P urland, P P 150:363–368. W workshop Life. Phylogen. O. ganisms. emphasizing biological otozool. O. brief . . species 2004. . Syst. . . . Lodge, J. D., classification ., . S., D., M D. . D. nomenclatur D., classification. 2007. A. 1999. K., H., of K. 2002. Syst. . up, 1995. K., nomenclatur 2006. Euk. T J. ., Syst. J. and . H. 1998. M. http://www , 2004. R. their r 1997. G. Y and and McNeill, P Biol. with Barta, eview F Linnaean T T and , D. S. . . . D. . . S. G. F Pr and 23: James, Biodiversity richness Micr DePriest, Naming The M. D. W 1998. 1993. 41:199–219. Biogeography 52:1 B. nomenclatur . Biol. E. Oecologia Y H. J. Bryant, otist nomenclatur Spiegel, Binomials, K. Evol. significant on atermann, e. Olmstead, Classifying 48:790–807. J. The H. . of emphasis 449–480. J. Simpson, Gauthier Mozley-Standridge, Lee. 1–17. ambir of S. D. T obiol. Gauthier Donoghue. Nicholson, de pr integrating eukaryotes L A Kingdom axon 46:313–331. in e diversity: S. ynn, the F Linnaean S. e. otists. T 42:317–330. L. r (St . nomenclatur 1999. Queir evised patterns fungi. axon taxa Karpov .discoverlife.or K. T R. Bowser V eginal and pr r 52:399–451. Hawksorth. Louis 47:425–429. . ends 126:1 D. de . and Barrie, Funk, oblem on R. r hyphenated e and 1994. . M. Species Acta oz. oles fr G. 53:153–158. e, species 1992. Queir with and F Mycologia six-kingdom Pr om Kar . the 1998. Estimates version , biocomplexity 14–124. pr P Ecol. Code). traditional hierar , Mann, with A. J. between S. P 2006. otozoa . G in . T Pr otists R. C. R. dispersal ez, and pr Kugr cladograms: J. owar H. . the Farmer Phylogenetic oz, e maintenance otozool. names B Integrating W W oblem emphasis T Evol. versus Silva, i r chy U.G. n aylor M. PhyloCode: 2004. uger R. M. K agstaf curr . of g/ 3 T and and ens, d the Kiger onigstein, . uninomials, [http://www ¨ M. of 90:347–356. pr unicellular A. J. a and Bur , (accessed 9:27–31. ent nomenclatur in Berninger olle, . system phylogenetic the Donoghue, of R oposed J. the of its 21st McCourt, J. naming 2005. 45:1 International f. Nerad, . phylogenetic det, , E. of nomenclatur the Kr micr 1997. A system: 18 near on W codes A phylogenetic R. the . 1 century: Skog, ug, taxonomy . of 1–136. phyla. Andersen, evolutionization the V The J Koeltz cautionary of A o-or A. . solutions. . imponderable. pr our A November C. K C. . clades. and and Demoulin, life. phylogenetic of taxonomy 2001. otists L. r .ohiou.edu/ Fensome, comparison new A T ess, ganisms: P A. Lane, e nomencla- biospher Micr . . Mendoza, system Eriksson, botanical and Biol. Scientific phyloge- multicel- A T P Shear code nomen- . e. r and O and Dif higher ehane, Annu. r T obiol. O. eport Aliso anal- L. axon I phy- Bull. Rev tale. N fer 28, an er A. G. R. T of of of T A S. e. - , . . S O F May Kr Keeling, James, International Hillis, Editor: Associate First The Whittaker Slapeta, Simpson, Redhead, Pleijel, Patterson, Patterson, Micr Mendoza, May V 15:105–1 T Pearlman, Natur constr Lutzoni, Aptr Langer M. A. J. R. Letcher Longcor Curtis, H. Rauhut, G. T tional Phylogenet. cessed T Pr diversity: Curr J. Pneumocystis phylogenetic P 2–9 154(Suppl.):S96–S124. cessed boundary zoa: 448. 241:1441–1449. on, final . axon r r I Euk. , , D. ends ust E C. oc. W oscope. Davies, submitted Celio, Shoemaker R. Sung, Ser W R. in K. orld D. a . T Jack oot, Bradbury F Rogers, acceptance M., Royal for Biol. . e . An ucting J., heter Code dani, , 21:213-251. A. P Y Editor: , M. Micr July December M. , A. Ecol. 443:818–822. , and . J. S. . e, 12. L., W V D. M D. , R D. Sullivan P and Zoological J., C. Health D. 1997. . F illustrated D. . insights G. . . C. A., . . 2007. . A. Ann. R. 14:R693–R696. Reeb, 1988. http://star K. Diederich, H Commission ogeneous Mor J. J. Kauf 15, obiol. J. G. Soc. A Gueidan, P G. 22 Evol. of B., J Evol. Johnson, the . and S. D. . A. W 2002. . McLaughlin, nomenclatur J. J. Slot, . T , 1972. M. , O’Donnell, W Bur 2006). i J Zoological W January Unter Nee. Exploring eds.). Roger and 1 . Powell eira, m . Rev H. Constraints Humber f, early B . 1999. T A. Report. Kohlmeyer How M . T T 4, 53:2–1 Cr aylor Collins 42:331–338. C. fr rypanosoma 20:670–676. Rouse. Biol. ger . Z. Changing ay Pfister E. Evolution A., om . 2006). Cushion, 1995. Nomenclatur guide ous, and L. einer Micr , Society gr , E. I. Arnold, evolution 2007 central.mbl.edu/micr and B. W Roger D , 2007; , Schoch, many oup molecular Sci. The Schmitt, 1. and J on Fraker ang, . , P . O’Rourke, K. http://www The obiol. , alternative 2003. , J . G W e. S. Nomenclatur to . M. J. D Lopez-Gar Zoological R 272:2073–2081. . B of W , . J. in L. . W r . . the of Durnfor diversity B . T Mozley-Standridge, 2004. eviews species J. cruzi views and A. W Hewitt, . species A. Zool. L Morton, aylor micr . . , naming P Ajello. Hughes, Ceci Pr Spatafora, V ucking, J 56:315–344. K. . of ¨ . M. pr . Amtoft, Gray olkmann-Kohlmeyer B. W e, M otozoologists, ecology measur fungi : otozoa Fr The oor . Nomenclatur , Matheny Schultz, London. iadlikowska, Syst. r M. of n’est M enkel, eturned systems W d, alias cia. . .who.int/whr/2004/en/ K. 2002. ganisms Nomenclatur ar . 2005. r pr J. ilson, parts Cr e, of eal B. M B. using K. e Sugiyama, Hansen, J. otistan Evol. ement 2005. (J. pas . 4th pr ockett, of and F ther B E. kingdoms W Matsuura, eukaryotes. and . oscope/portal.php R. The J. , oblem. udel, 31 The fr ¨ Lang, of V Stajich, hite, o A. une Lee, edition. eshwater a Y . R. e f Res. at The Mar Hofstetter the six ahr classification. of Lawr J. class e systematics. tr o H. Sch V the M. and n S. R. D. D. pipe: G. ee G. species ilgalys. , gene c tr R. Natur extent e. 41:162–174. D T A. h earth? Hambleton, uszligler K. ee ¨ Stringer animal-fungal of F W ence, . of M. 1999. , . Binder Mesomyceto- 2007; Porter E. W . typifications. International Lumbsch, S R Y Leedale . Hosaka, eukaryotes. eukaryotes. eukaryotes. of Clades . phylogeny . Grif . . Langer Am. Hibbett, Geiser e , A Rossman, Lee, diversity of 2006. life. C 378:447– Kansas. Interna- . Science . , , fith, Spotts, pr . J , Pages J . P Aliso 2006. . R. Mol. Cox, J . otist N 689 and and , . (ac- (ac- , Re- G.- M M at. A A D. G R E E. F ......