Clade Names Research Articles

Systematics and character evolution in Durio s. lat. (Malvaceae/Helicteroideae/Durioneae or Bombacaceae-Durioneae)

Abstract A molecular phylogenetic study of Durio s.lat. was conducted based on sequences of the internal transcribed spacer (ITS) of nuclear ribosomal DNA for 30 ingroup exemplars, representing 16 species, and two taxa of Cullenia as outgroups. The phylogeny suggests the existence of two well-circumscribed clades composed, respectively, of species with poricidal pollen locules ( Boschia) and species with pollen locules that open with longitudinal slits ( Durio s.str.). The latter clade is subdivided into two strongly supported clades: /Tubulidurio, with highly fused filaments and free calyx lobes, and /Palatadurio, with largely free filaments and connate calyx lobes. We provide phylogenetic definitions for the names of these well-supported clades. Reconstruction of floral evolution is consistent with the hypothesis that vertebrate pollination is ancestral for Durio s.lat. and Cullenia. However, there have been further shifts in pollination system within Durio s.lat., which may account for some of the current diversity of floral characters. The correlation of fruit and aril characteristics suggests that there are two major dispersal syndromes, involving either birds (fruits opening on trees; aril red/yellow and odorless) or terrestrial mammals (fruits opening only after falling to the ground; aril pale colored and pungent). The distribution of extant taxa implies a Malesian origin and radiation of the study group, with a single dispersal of Cullenia to India and Sri Lanka. However, the fossil pollen record raises the possibility that Durio and relatives may have migrated to Southeast Asia from the Indian subcontinent after it collided with Asia. A molecular clock analysis suggests that the earliest divergence within the study group occurred about 20 to 32 mya and, hence, does not favor either biogeographic scenario.

Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?

Recent radical proposals to overhaul the methods of biological classification are reviewed. The proposals of phylogenetic nomenclature are to translate cladistic phylogenies directly into classifications, and to define taxon names in terms of clades. The method has a number of radical consequences for biologists: taxon names must depend rigidly on the particular cladogram favoured at the moment, familiar names may be reassigned to unfamiliar groupings, Linnaean category terms (e.g. phylum, order, family) are abandoned, and the Linnaean binomen (e.g. Homo sapiens) is abandoned. The tenets of phylogenetic nomenclature have gained strong support among some vocal theoreticians, and rigid principles for legislative control of clade names and definitions have been outlined in the PhyloCode. The consequences of this semantic maelstrom have not been worked out. In pratice, phylogenetic nomenclature will bc disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the difference between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phlylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.

Species names in phylogenetic nomenclature.

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.

Application of Phylogenetic Taxonomy to Poorly Resolved Crown Clades: A Stem-Modified Node-Based Definition of Rodentia

Phylogenetic taxonomy (de Queiroz and Gauthier, 1990, 1992) entails the naming of clades, a procedure distinct from and sec? ondary to the process of clade recognition. Current procedures for defining taxon names in terms of common ancestry were developed in the context of well-resolved (usually dichotomously branching) phy? logenies. Because of the recent discovery of a fossil bearing importantly on the origin of rodents (Meng et al., 1994), we intro? duce here a new way of stating phyloge? netic definitions for the names of clades

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.

Exploring Alternative Systems of Classification

Classification involves the development of a system of naming clades that can represent evolutionary relationships accurately and concisely. Using the acid-loving heath plants (Ericales) as an example, one can explore the application of different classification methods. The Linnean system of naming retains the traditional hierarchical framework (named ranks) and allows for the application of many cuqently used names. The "phylogenetic systematic" approach recommends the removal of an absolute hierarchy but allows retention of traditionally used endings such as -aceae. Historical usage of these names can lead to confusion when the names are used within a discussion or text, especially when a cladogram is not presented at the same time. Another method is suggested that removes the Linnean endings and adds the same ending (ina) to all clade names. This effectively eliminates absolute rank and clearly indicates that the group name represents a clade. The names used in this method and the "phylogenetic systematic" method do not indicate relative rank. Numbering systems and indentation are two ways in which relative rank has been conveyed. Indented lists have been the preferred method, often in combination with suffixes that indicate absolute rank. If absolute rank is eliminated, relative rank can still be reflected by indentation as in the "phylogenetic systematic" method. Relative rank can be conveyed by always presenting a cladogram in conjunction with a classification. In practice, relative rank is also effectively communicated within the context of discussion, thus a precise system of indicating relative rank within a formal classification may not be necessary.

The definitions of species and clade names: A reply to Ghiselin

The definitions of species and clade names: A reply to Ghiselin

Ostensive definitions of the names of species and clades

Ostensive definitions of the names of species and clades

Comments on the Phylogenetic Definition of Taxon Names and Conventions Regarding the Naming of Crown Clades

Comments on the Phylogenetic Definition of Taxon Names and Conventions Regarding the Naming of Crown Clades

Comments on the Phylogenetic Definition of Taxon Names and Conventions Regarding the Naming of Crown Clades

Comments on the Phylogenetic Definition of Taxon Names and Conventions Regarding the Naming of Crown Clades

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.