Two misconceptions of phylogeny and classification

A recent contribution embodies the assumptions that organisms may be excluded from relationship with others on the basis of autopomorphy, and that its position in a classification is an inherent characteristic of an organism. Both of these assumptions are fallacious.     

A molecular phylogeny and classification of Verbenaceae

? Premise of the study: Verbenaceae consist of trees, shrubs, lianas, and herbs distributed primarily in Latin America, where they occur in a wide array of ecosystems. A second center of diversity exists in Africa. Competing morphology-based classifications that rely on different traits conflict in significant ways. A broad phylogenetic study was undertaken to assess those classifications and to examine the historical geography of the family. ? Methods: Analysis of seven chloroplast DNA regions for 109 species, representing all genera except one monotypic genus, provide inference into evolutionary relationships in Verbenaceae. ? Key results: The phylogeny shows that none of the traditional classifications reflect phylogenetic relationships very well. Eight clades are recognized as tribes (Casselieae, Citharexyleae, Duranteae, Lantaneae, Neospartoneae trib. nov., Petreeae, Priveae, and Verbeneae). Two genera, Dipyrena and Rhaphithamnus, remain unplaced in these larger clades. Petreeae, which consist of Neotropical lianas, are sister to the rest of the family. Lantaneae and Verbeneae together form a derived clade that comprises approximately two-thirds of the species in Verbenaceae. ? Conclusions: We present a new tribal classification, including one new tribe, Neospartoneae trib. nov., to accommodate three small genera of Argentine species (Diostea, Neosparton, and Lampaya). Phylogenetic inference suggests a South American origin for Verbenaceae, with approximately six colonization events having given rise to the Old World species.     

A molecular phylogeny and classification of Bignoniaceae

Bignoniaceae are woody, trees, shrubs, and lianas found in all tropical floras of the world with lesser representation in temperate regions. Phylogenetic analyses of chloroplast sequences (rbcL, ndhF, trnL-F) were undertaken to infer evolutionary relationships in Bignoniaceae and to revise its classification. Eight clades are recognized as tribes (Bignonieae, Catalpeae, Coleeae, Crescentieae, Jacarandeae, Oroxyleae, Tecomeae, Tourrettieae); additional inclusive clades are named informally. Jacarandeae and Catalpeae are resurrected; the former is sister to the rest of the family, and the latter occupies an unresolved position within the "core" Bignoniaceae. Tribe Eccremocarpeae is included in Tourrettieae. Past classifications recognized a large Tecomeae, but this tribe is paraphyletic with respect to all other tribes. Here Tecomeae are reduced to a clade of approximately 12 genera with a worldwide distribution in both temperate and tropical ecosystems. Two large clades, Bignonieae and Crescentiina, account for over 80% of the species in the family. Coleeae and Crescentieae are each included in larger clades, the Paleotropical alliance and Tabebuia alliance, respectively; each alliance includes a grade of taxa assigned to the traditional Tecomeae. Parsimony inference suggests that the family originated in the neotropics, with at least five dispersal events leading to the Old World representatives.     

Angiosperm classification and phylogeny: a criticism

This is a criticism of Dahlgren's recent classification of angiosperms (1980) and his basic diagram of angiosperm phylogeny. The first is shown to include unnatural orders and super-orders; the second is accordingly as questionable. Basic factors for phylogenetic taxonomy in the angiosperms are considered. Leptocauly leads to parallel evolution and specific multiplication. Nomenclatural artifices for taxonomic equivalence are exposed; the name 'pseudon' is suggested for a conjectural taxon.     

Genome analysis,phylogeny, and classification

The implications of genome analysis for evolutionary theory and systematics are treated. The precise relationship between the theoretical and operational definitions of chromosome homology is shown to be uncertain. It is pointed out that genera defined by genome analysis may be either monophyletic or non-monophyletic, and that the genus is not a basic unit of evolution. Characters obtained by genome analysis may be useful in a phylogenetic context, provided they are treated as all other characters.     

Commentary on two misconceptions of phylogeny and classification

A recent brief communication criticizes a morphometric study of the structure of Daubentonia (Oxnard, 1981). The criticisms are invalid because they apply to the concept of the detailed character state in a localized anatomical region, a type of morphological information different than the broad measurement that embodies many characters. The criticisms themselves display, moreover, exactly those problems of prior assumption that the underlying philosophy of multivariate morphometric studies as used by Oxnard (1981) tries to eliminate.     

Angiosperm classification and phylogeny: a rectifying comment

A commentary is given on the criticism of Dahlgren's recent classification of angiosperms by Corner ( Botanical Journal of the Linnean Society, 82: 81–87 (1981)). In his dissatisfaction with the current, (almost) generally accepted nomenclatural concepts he has chosen to use my classification as a target. It is agreed that nomenclature is not 'fair' to plant groups playing the most important role in building up the biosphere, and that nomenclatural constructions do not reflect the consideration given to various parts of the plant. Corner does not seem to be familiar with the fact that his so-called 'pseudons' are common to all current systems of classification, nor that the termination '-florae' has been used by Thorne (1968) and in a number of publications since. This suffix does not imply that the botanists using it neglect vegetative characters, nor characters from fruits and seeds. Other misunderstandings are also pointed out. In no case has it been satisfactorily demonstrated by Corner that my orders or superorders are unnatural entities (even though a number of them most likely are).     

Molecular phylogeny and the higher classification of eutherian mammals

Reconstructing the evolutionary relationships among the orders of eutherian mammals constitutes a formidable phylogenetic task. It entails the identification of a single true phylogenetic tree out of 10(12)-10(28) possible ones. For almost half a century, the field of mammalian Phylogeny has been dominated by a pessimistic view, according to which the great burst of mammalian radiations more than 65 million years ago has rendered the ordinal phylogeny of mammals insolvable. In the last few years, this pessimism has started to dissipate as several superordinal relationships were identified through the use of molecular data. DNA and protein sequences have the potential to supply millions of phyloge netically useful characters, and therefore, the Phylogeny of the orders of mammals may be resolved into a consistently bifurcating tree in the not-sodistant future.     

A review of the phylogeny and classification of the Asteraceae

The Asteraceae are commonly divided into two large subfamilies, the Cichorioideae (syn. Lactucoideae; Mutisieae, Cardueae, Lactuceae, Vernonieae, Liabeae, Arctoteae) and the Asteroideae (Inuleae, Astereae, Anthemideae, Senecioneae, Calenduleae, Heliantheae, Eupatorieae). Recent phylogenetic analyses based on morphological and chloroplast DNA data conclusively show that the Mutisieae-Barnadesiinae are the sister group to the rest of the family and that the Asteroideae tribes form a monophyletic group. The Vernonieae and Liabeae are sister tribes and the Eupatorieae are nested within a paraphyletic Heliantheae; otherwise tribal interrelationships are still largely uncertain. The Mutisieae-Barnadesiinae are excluded from the Mutisieae and elevated to the new subfamily Barnadesioideae. The two subfamilies Barnadesioideae and Asteroideae are monophyletic, whereas the status of the Cichorioideae remains uncertain. Analyses of chloroplast DNA data support the monophyly of the Cichorioideae; however, morphological data indicate that the subfamily is paraphyletic. Further studies are needed to test the monophyly of the Cichorioideae, as well as to further resolve tribal interrelationships in the two larger subfamilies.     

A phylogeny of Lophocoleaceae-Plagiochilaceae-Brevianthaceae and a revised classification of Plagiochilaceae

The Lophocoleaceae-Plagiochilaceae-Brevianthaceae clade is a largely terrestrial, subcosmopolitan lineage of jungermannialean leafy liverworts that may include significantly more than 1000 species. Here we present the most comprehensively sampled phylogeny available to date based on the nuclear ribosomal internal transcribed spacer region and the chloroplast markers rbcL and rps4 of 372 accessions. Brevianthaceae (consisting of Brevianthus and Tetracymbaliella) form a sister relationship with Lophocoleaceae; this lineage is in turn sister to Plagiochilaceae. Plagiochila is resolved monophyletic subsequent to exclusion of Plagiochila radiculosa; this species is placed in a new genus Cryptoplagiochila. Chiastocaulon and a polyphyletic Acrochila nest in Plagiochilion; these three genera are united under Chiastocaulon to include the Plagiochilaceae species with dominating or exclusively ventral branching. The generic classification of the Lophocoleaceae is still unresolved. We discuss alternative approaches to obtain strictly monophyletic genera by visualizing their consistence with the obtained consensus topology. The presented phylogeny will serve as a basis for follow-up studies including several thousand accessions. These studies will enable revision of current hypotheses on species diversity and distribution of Lophocoleaceae-Plagiochilaceae-Brevianthaceae and allow for a reconstruction of their evolution in time and space.     

Molecular phylogeny and proposed classification of the simian picornaviruses.

The simian picornaviruses were isolated from various primate tissues during the development of general tissue culture methods in the 1950s to 1970s or from specimens derived from primates used in biomedical research. Twenty simian picornavirus serotypes are recognized, and all are presently classified within the Enterovirus genus. To determine the phylogenetic relationships among all of the simian picornaviruses and to evaluate their classification, we have determined complete VP1 sequences for 19 of the 20 serotypes. Phylogenetic analysis showed that A13, SV19, SV26, SV35, SV43, and SV46 are members of human enterovirus species A, a group that contains enterovirus 71 and 11 of the coxsackie A viruses. SA5 is a member of human enterovirus species B, which contains the echoviruses, coxsackie B viruses, coxsackievirus A9, and enterovirus 69. SV6, N125, and N203 are related to one another and, more distantly, to species A human enteroviruses, but could not be definitely assigned to a species. SV4 and SV28 are closely related to one another and to A-2 plaque virus, but distinct from other enteroviruses, suggesting that these simian viruses are members of a new enterovirus species. SV2, SV16, SV18, SV42, SV44, SV45, and SV49 are related to one another but distinct from viruses in all other picornavirus genera, suggesting that they may comprise a previously unknown genus in Picornaviridae. Several simian virus VP1 sequences (N125 and N203; SV4 and SV28; SV19, SV26, and SV35; SV18 and SV44; SV16, SV42, and SV45) are greater than 75% identical to one another (and/or greater than 85% amino acid identity), suggesting that the true number of distinct serotypes among the viruses surveyed is less than 20.     

Issues in the classification of multimodal communication signals

Communication involves complex behavior in multiple sensory channels, or "modalities." We provide an overview of multimodal communication and its costs and benefits, place examples of signals and displays from an array of taxa, sensory systems, and functions into our signal classification system, and consider issues surrounding the categorization of multimodal signals. The broadest level of classification is between signals with redundant and nonredundant components, with finer distinctions in each category. We recommend that researchers gather information on responses to each component of a multimodal signal as well as the response to the signal as a whole. We discuss the choice of categories, whether to categorize signals on the basis of the signal or the response, and how to classify signals if data are missing. The choice of behavioral assay may influence the outcome, as may the context of the communicative event. We also consider similarities and differences between multimodal and unimodal composite signals and signals that are sequentially, rather than simultaneously, multimodal.     

Contribution of genosystematics to current concepts of phylogeny and classification of bryophytes

This paper is a survey of the current state of molecular studies on bryophyte phylogeny. Molecular data have greatly contributed to developing a phylogeny and classification of bryophytes. The previous traditional systems of classification based on morphological data are being significantly revised. New data of the authors are presented on phylogeny of Hypnales pleurocarpous mosses inferred from nucleotide sequence data of the nuclear DNA internal transcribed spacers ITS1-2 and the trnL-F region of the chloroplast genome.