Apomorphy-based Definitions Research Articles

Relating Ediacaran Fronds

AbstractEdiacaran fronds are key components of terminal-Proterozoic ecosystems. They represent one of the most widespread and common body forms ranging across all major Ediacaran fossil localities and time slices postdating the Gaskiers glaciation, but uncertainty over their phylogenetic affinities has led to uncertainty over issues of homology and functional morphology between and within organisms displaying this ecomorphology. Here we present the first large-scale, multigroup cladistic analysis of Ediacaran organisms, sampling 20 ingroup taxa with previously asserted affinities to the Arboreomorpha, Erniettomorpha, and Rangeomorpha. Using a newly derived morphological character matrix that incorporates multiple axes of potential phylogenetically informative data, including architectural, developmental, and structural qualities, we seek to illuminate the evolutionary history of these organisms. We find strong support for existing classification schema and devise apomorphy-based definitions for each of the three frondose clades examined here. Through a rigorous cladistic framework it is possible to discern the pattern of evolution within and between these clades, including the identification of homoplasies and functional constraints. This work both validates earlier studies of Ediacaran groups and accentuates instances in which previous assumptions of their natural history are uninformative.

What is an ‘elasmobranch’? The impact of palaeontology in understanding elasmobranch phylogeny and evolution

The Subclass Elasmobranchii is widely considered nowadays to be the sister group of the Subclass Holocephali, although chimaeroid fishes were originally classified as elasmobranchs along with modern sharks and rays. While this modern systematic treatment provides an accurate reflection of the phylogenetic relationships among extant taxa, the classification of many extinct non-holocephalan shark-like chondrichthyans as elasmobranchs is challenged. A revised, apomorphy-based definition of elasmobranchs is presented in which they are considered the equivalent of neoselachians, i.e. a monophyletic group of modern sharks and rays which not only excludes all stem and crown holocephalans, but also many Palaeozoic shark-like chondrichthyans and even close extinct relatives of neoselachians such as hybodonts. The fossil record of elasmobranchs (i.e. neoselachians) is reviewed, focusing not only on their earliest records but also on their subsequent distribution patterns through time. The value and limitations of the fossil record in answering questions about elasmobranch phylogeny are discussed. Extinction is seen as a major factor in shaping early elasmobranch history, especially during the Triassic. Extinctions may also have helped shape modern lamniform diversity, despite uncertainties surrounding the phylogenetic affinities of supposedly extinct clades such as cretoxyrhinids, anacoracids and odontids. Apart from these examples, and the supposed Cretaceous extinction of 'sclerorhynchids', elasmobranch evolution since the Jurassic has mostly involved increased diversification (especially during the Cretaceous). The biogeographical distribution of early elasmobranchs may be obscured by sampling bias, but the earliest records of numerous groups are located within the Tethyan realm. The break-up of Gondwana, and particularly the opening of the South Atlantic Ocean (together with the development of epicontinental seaways across Brazil and Africa during the Cretaceous), provided repeated opportunities for dispersal from both eastern (European) and western (Caribbean) Tethys into newly formed ocean basins.

Optimality of phylogenetic nomenclatural procedures

Nomenclatures resulting from the application of various procedures are viewed as communication tools whose optimality can be compared. The traditional, node-based, branch-based, apomorphy-based, and cladotypic procedures are compared based on theoretical cases. The traditional procedure collects several major drawbacks: endings related to ranks are of low information content on taxa hierarchy; with respect to procedures using uninominal species names, in case of a partly unbalanced and/or partly unresolved phylogeny, the application of the procedure results into supernumerary names; a traditional taxon name is prone to be polysemic, depending upon someone’s opinion on the rank and composition of the taxon, and upon conflicting hypotheses on the phylogenetic position of name-bearing types. Alternative systems vary in merit. Names of apomorphy-defined taxa are prone to be polysemic due to possible ambiguity in the formulation of the defining character state. The cladotypic nomenclatural procedure is similar in that respect, but a set of rules allow ambiguity to be limited. The main issue of node- and branch-based procedures is that cases of synonymy cannot be settled if the inner phylogeny of taxa cannot be resolved. Cases of irresolvable synonymy can occur under apomorphy-based and cladotypic procedures, but the problem can be circumvented by the use of taxa whose defining character state is not subject to ambiguous mapping. Node-, branch- and apomorphy-based definitions as governed by the PhyloCode can produce nonsensical statements, but this problem can be fixed by the adjunction of falsifiable assumptions in use under the cladotypic procedure. Cladotypic definitions must involve a fourth assumption formulated as ‘cladotypes belong to different species’ (cladogenesis assumption). The present contribution suggests that the cladotypic procedure outperforms all other proposed procedures, producing an optimal formal lexicon useful for naming and communicating about species and taxa.

On the manual morphology of Compsognathus longipes and its bearing on the diagnosis of Compsognathidae

Compsognathus longipes sits at an important point in theropod evolution at the base of Coelurosauria. Despite its relative completeness and oft-cited morphology, however, the manual morphology has been unclear. This work provides the first detailed study of the morphology of the manus of Compsognathus longipes. It shows that Compsognathus longipes had two fully formed functional digits as well as a reduced, perhaps even non-functional, third digit. That conclusion runs counter to the usual interpretation that Compsognathus longipes had only two phalanges, rather than the expected complement of three, in digit II. This work also identifies a unique suite of metacarpal I morphologies that are used to diagnose a subclade among species often referred to as ‘Compsognathidae’. These features are used to construct an apomorphy-based definition of a new clade name: Compsognathidae. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 569–581.

Phylogeny of Phagotrophic Euglenids (Euglenozoa) as Inferred from Hsp90 Gene Sequences

Molecular phylogenies of euglenids are usually based on ribosomal RNA genes that do not resolve the branching order among the deeper lineages. We addressed deep euglenid phylogeny using the cytosolic form of the heat-shock protein 90 gene (hsp90), which has already been employed with some success in other groups of euglenozoans and eukaryotes in general. Hsp90 sequences were generated from three taxa of euglenids representing different degrees of ultrastructural complexity, namely Petalomonas cantuscygni and wild isolates of Entosiphon sulcatum, and Peranema trichophorum. The hsp90 gene sequence of P. trichophorum contained three short introns (ranging from 27 to 31 bp), two of which had non-canonical borders GG-GG and GG-TG and two 10-bp inverted repeats, suggesting a structure similar to that of the non-canonical introns described in Euglena gracilis. Phylogenetic analyses confirmed a closer relationship between kinetoplastids and diplonemids than to euglenids, and supported previous views regarding the branching order among primarily bacteriovorous, primarily eukaryovorous, and photosynthetic euglenids. The position of P. cantuscygni within Euglenozoa, as well as the relative support for the nodes including it were strongly dependent on outgroup selection. The results were most consistent when the jakobid Reclinomonas americana was used as the outgroup. The most robust phylogenies place P. cantuscygni as the most basal branch within the euglenid clade. However, the presence of a kinetoplast-like mitochondrial inclusion in P. cantuscygni deviates from the currently accepted apomorphy-based definition of the kinetoplastid clade and highlights the necessity of detailed studies addressing the molecular nature of the euglenid and diplonemid mitochondrial genome.

The Phylogenetic Definition of Reptilia

Naming taxa is an important endeavor in the documentation of life by systematists, whether it is conducted in the context of traditional rank-based classification or within a phylogenetic framework. Proponents of the phylogenetic approach distinguish between the diagnosis of a group and its definition (Ghiselin, 1984; Rowe, 1987, 1988), and this distinction forms the basis for a phylogenetically based method of naming taxa formerly referred to as Phylogenetic Taxonomy (de Queiroz and Gauthier, 1990, 1992, 1994) and now called Phylogenetic Nomenclature (PN; Cantino et al., 1999; Gauthier and de Queiroz, 2001; Bryant and Cantino, 2002). Emphasis in naming has been placed on ancestry using phylogenetic definitions, and the widespread adoption of nodeand stem-based definitions (apomorphy-based definitions have yet to receive as widespread acceptance, but see Gauthier and de Queiroz, 2001; Anderson, 2002; Laurin and Anderson, 2004) has led to a proliferation of new names and definitions. This shift in nomenclatural practice has, unfortunately, fostered a growth in redundant names and definitions for well-known taxa (Benton, 2000). The PhyloCode (Cantino and de Queiroz, 2003) has modified the rule of priority as used in other codes (i.e., International Code of Zoological Nomenclature) to determine which of two or more possible names with equivalent definitions is valid (Brochu and Sumrall, 2001), or which of several definitions for a given name is valid (Cantino and de Queiroz, 2003). Unfortunately, it is now apparent that some of the definitions for wellknown taxon names established early in the emergence of PN were not devised following conventions now widely accepted, by either defining groups in an overly restrictive manner, or via selection of reference taxa without due consideration of the ramifications of differing tree topologies (Anderson, 2002; Laurin and Anderson, 2004). It has become evident in broad-scale amniote taxonomy that the first published definition for Reptilia (Gauthier et al., 1988a), which would have priority under a binding PhyloCode, is problematic because of the dramatic controversies over the affinities of the specifier taxon Testudines (see Zardoya and Meyer, 2001 for review of hypotheses for turtle relationships). Recent morphological and molecular studies have challenged conventional hypotheses concerning the affinities of turtles, and this has led to unexpected and undocumented changes in the composition of the well-known taxon Reptilia, with additional ramifications for the nomenclature of some of its included taxa. We examine the consequences of the application of priority to the nomen Reptilia as our understanding of early amniote interrelationships has progressed over the past two decades, and offer a new definition that brings the phylogenetic concept of this taxon name into line with both currently accepted conventions of PN and historical usage. This new definition corrects an error created by the combination of the selection of a higher taxon (rather than a species) as a specifier, and an unexpected topology. We believe that now is an appropriate time to examine the definitions established when PN was in its earliest stages, and hope to correct what we consider to be a poorly formulated definition upon publication of a binding PhyloCode.

The use of apomorphies in taxonomic defining

Nixon & Carpenter (2000: 306) describe the procedure of a good taxonomist for defining as being ... equivalent to a formal based on diagnosis, i.e., the largest inclusive group bearing the designated homologies. Nixon and Carpenter's homologies are presumably synapomorphies, following Patterson (1982) who defined homology in terms of synapomorphies. The phylogenetic definition of Nixon and Carpenter is not following Phylogenetic Nomenclature (PN); they advocate Linnaean taxonomy. Lee (2001), commented that Nixon & Carpenter (2000), contrary to their intention, do not discredit PN's apomorphy-based and unintentionally argue in favour of the superiority of those definitions to others, including Linnaean. Lee furthermore correctly remarks that Nixon and Carpenter's procedure is not the practice of defining names, but instead identical to the apomorphy-based definition. Then, what are definitions? Lee (2001: 176) mentions that they ...delimit taxa very vaguely, by specifying a rank and type.... This statement fits the way in which names are defined. Before discussing whether Lee or Nixon and Carpenter are right or wrong, I will consider what constitutes defining. A feature of PN is that names are defined according to tree topology (see de Queiroz & Gauthier, 1992, 1994). Stuessy (2000, 2001) argues that clades can be defined, but names not. Thus, while are the family that includes genus sounds like a of the name Pinaceae, it is not. The name is then merely a label to communicate about the family that contains Pinus as its type. Stuessy's arguments receive replies by de Queiroz (2000) and de Queiroz & Cantino (2001). De Queiroz (2000) argues that even according to the Codes of Nomenclature names are defined, since family Asteraceae is defined by the type genus Aster. Stuessy (2001) argues back that de Queiroz mistakes christening for defining. De Queiroz and Cantino (2001) agree that names serve to facilitate communication and that they are given to taxa in a process of christening, but still insist that names can be defined. They point out that under the system names are d fined ostensively by pointing, for example to type genus Aster. In general, biologists seem of the opinion that names can and should be defined (Harlin & Sundberg, 1998). I question this, and am sure that I am not the only one. Harlin & Sundberg (1998) and Harlin (1998) point out that in traditional taxonomy as well as in PN, names are viewed as having the same meaning as the defining d scr ptions. In other words, names have intension. However, Harlin & Sundberg (1998) and Harlin (1998) suppor the view that taxa are historical entities. Thus, a name and its meaning are not the same, since the meaning is s bject to historical change. A name would thus not have intension (meaning) and cannot be defined. Since a taxon changes through history, the only way to fix the reference to its name is by pointing, i.e., ostensively (Harlin & S ndberg, 1998; Harlin, 1998). To thus fix a reference, one could point to, for example, specifiers in PN. However, in doing this, the name is not defined. References to names are fixed to facilitate communication. This means that Pinaceae is a label without inten-

Apomorphy-Based Definition Also Pinpoints a Node, and PhyloCode Names Prevent Effective Communication

Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are “node based,” “stem based,” and “apomorphy based.” All of them define a clade name by pinpointing a node; whereas node-based and stem-based definitions require two or more taxon “specifiers” to define names, an apomorphy-based definition requires two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based definition is completely different from the “type” in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning. Communication through such PhyloCode names is very ineffective or impossible.

Species and phylogenetic nomenclature

TAXONVolume 51, Issue 3 p. 507-510 Points of ViewsFree Access Species and phylogenetic nomenclature Michael S. Y. Lee, Michael S. Y. Lee lee.mike@saugov.sa.gov.au Department of Palaeontology, The South Australian Museum and Department of Environmental Biology, University of Adelaide, North Terrace, Adelaide, SA5000 AustraliaSearch for more papers by this author Michael S. Y. Lee, Michael S. Y. Lee lee.mike@saugov.sa.gov.au Department of Palaeontology, The South Australian Museum and Department of Environmental Biology, University of Adelaide, North Terrace, Adelaide, SA5000 AustraliaSearch for more papers by this author First published: 01 August 2002 https://doi.org/10.2307/1554863Citations: 8AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume51, Issue3August 2002Pages 507-510 ReferencesRelatedInformation

Revision ofAmphidurosHartman, 1959 (Polychaeta, Hesionidae, Gyptini)

Abstract A revision is presented of the taxonomy of Amphiduros Hartman, 1959 based on re-examined types, newly collected topotypes, and other specimens. Amphiduros axialensis Blake & Hilbig, 1990 is referred to Amphiduropsis, new genus. Amphiduros fuscescens (Marenzeller, 1875), A. izukai Hessle, 1925, A. pacificus Hartman, 1961 and A. setosus Hessle, 1925 cannot be conclusively diagnosed, wherefore the three latter are synonymised with A. fuscescens. Amphiduros fuscescens is newly recorded from Papua New Guinea and the Great Barrier Reef; the taxon appears to have a circumtropical and warm-water temperate distribution. Following a parsimony analysis based on morphological characters, Amphiduros and Amphiduropsis constitute a monophyletic group, either with Gyptis Marion & Bobretzky in Marion, 1874, or part of Gyptis, as sister taxon. In parallel to the traditional Linnean nomenclature, I present an alternative phylogenetic nomenclature of the group, with apomorphy-based definitions of taxon names and wit...

Phylogenetic Taxonomy, a Farewell to Species, and a Revision of Heteropodarke (Hesionidae, Polychaeta, Annelida)

Cladistic relationships between 7 parts of the hesionid polychaete group Heteropodarke are assessed in a parsimony analysis based on 34 morphological characters. Taxon names are de- fined by apomorphy-based phylogenetic definitions, without reference to Linnean ranks or types. Species entities are omitted and denied any role in taxonomy; taxon names refer to monophyletic groups only. Linnean binomial species names are not employed, and all taxa are assigned uninomi- als. Previously known parts of Heteropodarke (Africana Hartmann-Schroder, 1974; Formalis, Perkins, 1984; Heteromorpha Hartmann-Schroder, 1962; Lyonsi Perkins, 1984; Xiamenensis Ding, Wu, and Wes- theide, 1997) are reexamined, and Bidentata, new taxon, and Zmyrina (informal name) are de- scribed from Papua New Guinea and Belize, respectively. The new taxon Crassichaetae is named for a subgroup of Heteropodarke, which is diagnosed by enlarged, anteriorly situated falcigers, and in- cludes Africana, Heteromorpha, Lyonsi, and Xiamenensis . Within this group Africana and Heteromorpha are treated as taxa inquirendae. {Apomorphy-based definitions; Linnean nomenclature; phylogenetic taxonomy; polychaetes; ranks; species concepts; species names; types.}

Phylogenetic taxonomy of the Coelurosauria (Dinosauria: Theropoda)

Phylogenetic taxonomy, that component of phylogenetic systematics concerned with the verbal representation (rather than the reconstruction or estimation) of phylogenetic relationships, was developed by de Queiroz and Gauthier (1990, 1992, 1994). Under phylogenetic taxonomy, all taxon names are names of clades (i.e., an ancestor and all of that ancestor's descendants). De Queiroz and Gauthier (1990, 1992, 1994) described three possible ways of denning clade names within the phylogenetic taxonomic system: 1) node-based definitions (Figure 1.1), of the form “the most recent common ancestor of Taxon A and Taxon B, and all of that ancestor's descendants”; 2) stem-based definitions (Figure 1.2), of the form “Taxon A and all taxa sharing a more recent common ancestor with Taxon A than with Taxon B”; and 3) apomorphy-based definitions (Figure 1.3), of the form “the first taxon with derived character X and all of that ancestor's descendants.” Bryant (1994) noted that, while the first two definition types will always be stable, apomorphy-based definitions are potentially confusing if that derived character is found to occur in more than one lineage (i.e., is homoplastic). Under the phylogenetic system of taxonomy, definitions of taxon names are independent with respect to previous diagnosis (as particular character states may be found to occur in other lineages or in more inclusive clades) and composition (as particular member taxa may subsequently be found to lie outside the defined clade boundary). This paper is the initial work in an ongoing study by Holtz and Padian (1995, in preparation) to clarify the phylogenetic taxonomy of major clades of theropods and related taxa.