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2008 POINTS OF VIEW 173 Wiens, J. J. 2001. Character analysis in morphological phylogenetics: Wilkins, A. S. 2002. The evolution of developmental pathways. Sinauer Problems and solutions. Syst. Biol. 50:689–699. Associates, Sunderland, Massachusetts. Wiens, J. J., and R. E. Etheridge. 2003. Phylogenetic relationships of Wright, S. 1934a. An analysis of variability in the number of digits in hoplocercid lizards: Coding and combining meristic, morphometric, an inbred strain of guinea pigs. Genetics 19:506–536. and polymorphic data using step matrices. Herpetologica 59:375– Wright, S. 1934b. The results of crosses between inbred strains 398. of guinea pigs differing in number of digits. Genetics 19:537– Wiens, J. J., and M. R. Servedio. 1997. Accuracy of phylogenetic analysis 551. including and excluding polymorphic characters. Syst. Biol. 46:332– 345. Wiens, J. J., and M. R. Servedio. 1998. Phylogenetic analysis and in- First submitted 28 June 2007; reviews returned 10 September 2007; traspecific variation: Performance of parsimony, likelihood, and dis- final acceptance 18 October 2007 tance methods. Syst. Biol. 47:228–253. Associate Editor: Norman MacLeod Syst. Biol. 57(1):173–181, 2008 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150801910469 Crown Clades in Vertebrate Nomenclature: Correcting the Definition of Crocodylia JEREMY E. MARTIN1 AND MICHAEL J. BENTON2 1UniversiteL´ yon 1, UMR 5125 PEPS CNRS, 2, rue Dubois 69622 Villeurbanne, France; E-mail: [email protected] 2Department of Earth Sciences, University of Bristol, Bristol, BS9 1RJ, UK; E-mail: [email protected] Downloaded By: [Martin, Jeremy E.] At: 19:32 25 February 2008 Acrown group is defined as the most recent common Dyke, 2002; Forey, 2002; Monsch, 2005; Rieppel, 2006) ancestor of at least two extant groups and all its descen- but rather expresses dissatisfaction with the increasingly dants (Gauthier, 1986). Despite criticism, crown-group common use of crown-group definitions, with a particu- definitions are widely used, especially for certain clades lar focus on the use of the term Crocodylia. Names should of vertebrates. As an example, crown-group Crocodylia be given to stable clades for the sake of nomenclatural was established by Clark (in Benton and Clark, 1988), and stability, independent of which nomenclatural system is there has been increasing use of crown Crocodylia rather preferred. than traditional or total Crocodylia since that date. Orig- Lee (1996) demonstrated that crown clades were as inally, the Crocodylia embraced forms dating from the good as any other kinds of clades in terms of clarity of Late Triassic to the present. These were divided into three definition and biological usage. Our question is there- classes, Protosuchia, Mesosuchia, and Eusuchia, the first fore the following: why is it necessary to redefine some- two of which were accepted as probably or certainly pa- thing already established and accepted for almost 250 raphyletic. The new convention was cemented by Brochu years with a new definition that is no more stable and (2003), who gave a new definition of crown Crocodylia even more confusing than the previous one? Moreover, according to the conventions of phylogenetic nomencla- consistency with traditional taxonomy is recommended ture (PN), as the last common ancestor of Gavialis gangeti- by the PhyloCode (e.g., Articles 10 and 11; Cantino and cus, Alligator mississipiensis, and Crocodylus niloticus, and de Queiroz, 2003). The basis for the definition of crown all of its descendents. This led to an interesting reversal clades was set up by Gauthier (1986) and Gauthier et al. in the hierarchy, so that crown-clade Crocodylia is a sub- (1988), who argued that crown clades possess three main set of Eusuchia, rather than the other way round, as had advantages: (a) they allow us to reconstruct soft tissues been the case. and other unfossilizable characters of extinct members; Reasons for redefining the boundaries of major verte- (b) they promote stability in discussion; and (c) they con- brate groups are linked to the advent of cladistics. Such form most closely to the original concept of the name. We nomenclatural revisions have been accelerated by the will develop our ideas around these three points, the aim need for clarity in the application of the principles of PN being to survey the literature in order to determine the (de Queiroz and Gauthier, 1992, 1994). Many proponents traditional meaning of Crocodylia. of crown-clade definitions assume that crown clades are a key element of PN and the Phylocode, but this is not the case (Cantino and de Queiroz, 2004). The assumption of ISASEPARATE CLASS FOR CROWN CLADES NECESSARY? a linkage arose because earlier papers by architects of the Motivations for the usage of crown-clade definitions Phylocode (e.g., de Queiroz and Gauthier, 1992) included came with the advent of cladistics in the mid-1980s. Pro- crown clades as a part of the manifesto for change, and ponents of PN may define taxa in three ways: node- Phylocode supporters generally support crown clades. based, stem-based, and apomorphy-based definitions. This article does not aim to criticize the principles of Acrown clade is founded on a node-based definition PN (see Benton, 2000, 2007; Nixon and Carpenter, 2000; and it is specifically bracketed by extant taxa. Crown 174 SYSTEMATIC BIOLOGY VOL. 57 clades were first defined by Hennig (1966), but the characters, whether hard or soft, probably arose below earliest proposal for their usage appears in Gauthier the crown-clade Aves node. A further example concerns (1986). A key advantage of crown clades has been the soft characters of Rowe’s (1988) crown Mammalia, stated (Gauthier, 1986; Gauthier et al., 1988; Gauthier which almost certainly pertain to, or originated within, and de Queiroz, 2001) to be that inferences about the larger clades—we know from fossils, for example, that biology of contained taxa are maximized. Some au- mammalian hair was present into a wider group of mam- thors have extended this statement to say that the num- mals, perhaps even to traditional Mammalia (Meng et al., ber of soft-part apomorphies is maximized also, but 2006). Gauthier and de Queiroz (2001) are quite clear that this is A weaker argument might be that soft-tissue char- wrong. acters of extinct members of crown clades may be re- Rowe (1988) was the first to apply a crown-group def- constructed with greater confidence than those for ex- inition to mammals. Mammalia was restricted to all taxa tinct members of total clades because there is evidence stemming from the most recent common ancestor of at from both sides of the basal split. So, for example, soft- least two extant lineages as proposed by Patterson and tissue characters of crown Archosauria must share at- Rosen (1977) and Gauthier et al. (1988). Lucas (1992) ex- tributes of both modern birds and modern crocodilians. pressed dissatisfaction with this practice because crown It is hard though to determine why this is objectively bet- clades restrict traditional namings to more exclusive ter than bracketing total-group Archosauria by birds and clades, and this in turn triggers further renaming through crocodilians on the one hand, and lizards and snakes on the phylogeny of the concerned group and redefinition the other. In both cases, there is still the uncertainty about of accepted names, and so brings confusion. As stated leakage of soft characters below the node subtended by by Lucas (1992), and then by Bryant (1994), the use of extant representatives (the example of mammalian hair names within the frame of codes of nomenclature allows above). stability and long-established names should be retained It may not be possible to infer soft-part characters whenever possible, so avoiding conflict of usage among in crown or other clades. For example, among crown- Downloaded By: [Martin, Jeremy E.] At: 19:32 25 February 2008 workers in order to avoid confusion. group Crocodylia, lingual salt glands are absent in ex- Gauthier et al. (1988) argued that crown clades are su- tant alligatorids and present in extant crocodylids. This perior to other clades that include at least one extinct means that all the extinct taxa bracketed by alligatorids taxon as a specifier because soft-part characters may and crocodylids have to be coded with a question mark, be safely assumed, even for fossil members. However, demonstrating that all soft-tissue characters cannot be the extant phylogenetic bracket (EPB) concept (Witmer, coded for the crown group. As a consequence, Brochu 1995) allows assumptions about soft-tissue characters (1999) pointed out that we simply do not know whether in more inclusive clades as well. Thanks to the EPB, it nonalligatorid alligatoroids followed the same osmoreg- is philosophically just as easy to determine unfossiliz- ulatory rules as their closest living relatives. The soft- able characters in dinosaurs as in Cretaceous eusuchians. tissue argument, as originally defended by Gauthier et Extant crocodylians as well as birds possess a four- al. (1988), is therefore not a valid reason to make a sepa- chambered heart (see Seymour et al., 2004, for a review). rate class for crown clades, which in this respect are the The discovery of a four-chambered heart in an ornithis- same as all other clades. chian dinosaur (Fisher et al., 2000), if correct, could be said to validate the use of the EPB. ARE CROWN CLADES MORE STABLE? Crown clades do not differ from other kinds of clades Lee (1996) demonstrated that crown clades are no more in the confidence with which soft-part characters may be stable than total clades, contrary to Gauthier (1986) and inferred. For example, the EPB approach does not allow Gauthier et al. (1988). Crown clades are hypothesis de- us to determine the extent to which feathers were present pendent because they contain fossils, as do all other in a clade wider than Aves (in the traditional sense, con- clades (Benton, 2000).
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  • A Synapomorphy-Based Multiple Sequence Alignment Method. Cladistics, 19:261

    A Synapomorphy-Based Multiple Sequence Alignment Method. Cladistics, 19:261

    Cladistics Cladistics 19 (2003) 261–268 www.elsevier.com/locate/yclad Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search Ward C. Wheeler* Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79thSt., New York, NY 10024-5192, USA Accepted 7 April 2003 Abstract A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple- alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These ‘‘lines of correspondence’’ link ancestor–descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion–deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the im- provement of heuristic cladogram cost calculations are discussed.