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We contend that the move away from providing character evidence with phylogenies has diminished fish systematics and systematics in general, and amounts to a crisis. Present practices focus on solutions to matrices rather than on character homology, and rely on algorithms and statistics rather than biology to determine relationships. Optimization procedures in tree-building programs are phenetic and no longer employ homology, the original foundation of cladistics. Evidence for phylogenies is presented in a manner that obscures character conflict and makes meaningful debate difficult. The role of morphological characters has largely been reduced to their optimization and reinterpretation on the revealed "truth" of molecule-based topologies. All of this has resulted in a schism between molecular and morphological phylogeneticists. We examine several examples, focusing on Percomorpha and Gobioidei, to illustrate the shortcomings of recent approaches. We feel that phylogenetics can only move forward by recognizing that molecules are small-scale morphology; molecular data are not substantively different from larger-scale morphological data and should be treated in much the same manner. Careful investigation of homology and transparent presentation of evidence will keep our work and our science relevant. We suggest four measures that need reintroduction to phylogenetic practice in order to bring systematics back to its fundamental principles: (1) examine data quality, character distribution, and evidence; plot characters to identify and examine character conflict, and weigh evidence for homology, (2) explore the nature of character information-data become characters only after they are understood, (3) question assumptions of methods, common practice is not necessarily indicative of the ideal analysis, (4) in particular, question and investigate optimization as a method and what its impact is on character homology and the meaning of synapomorphies; use biology, not algorithms to make homology decisions.Since, in principle, a data matrix containing characters for different minerals can be analyzed with PAUP to obtain a dendrogram, the application of cladistic techniques alone does not make an analysis phylogenetic.

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We address the problem of reconciling human phylogeny and linguistic history and conclude that its resolution requires (i) development of a valid objective method of quantifying linguistic relationships, (2) delimitation and subsequent characterisation of human populations and languages by large-scale demographic census, (3) integration of genetic and linguistic data with other types of information, (4) parallel analyses of the relationships between genetic and linguistic entities using specifically phylogenetic algorithms, and (5) clarification of the biological and philosophical relationship between human lineages and potentially dependent cultural phenomena such as speech. Also, increased discourse between linguists and biologists is needed to distinguish homologous from analogous processes in the two disciplines and thereby standardise terms and concepts. Even if these criteria are eventually satisfied, different processes and rates of evolution and radiation in human populations and languages will continue to complicate attempts to recover "racial" phylogenies. Although profound, these difficulties may not be insuperable, particularly if initial studies sample a regional rather than a global catchment.

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. 1997. Dismantling the Trachinoidei: evidence of a scorpaenoid relationship for the Champsodontidae. Ichthyol. Res., 44 (2): 143-176. AbstractAn examination of the osteology and myology of the Champsodontidae reveals a number of apomorphic features (e.g., double-headed palatine, large pelvic radial, epaxial muscle inserting on the medial pelvic-fin ray, posterior levator internus inserting on the third epibranchial). The evidence for a Champsodontidae/Chiasmodontidae relationship is examined through a re-evaluation of the basal characters used to define the suborder Trachinoidei. The Champsodoutidae are removed from the Trachinoidei and a chiasmodontid sister relationship is rejected. After investigation of severaI possible alternative relationships (Paracanthopterygii, Gobioidei, Callionymoidei, Kurtoidei, Apogonidae, Blennioidei, Trichodontidae), champsodontids are hypothesized to be members of the perciform suborder Scorpaenoidei. This hypothesis is based largely on the synapomorphy of a parietal spine with an opening for passage of the supratemporal sensory canal, a unique condition of champsodontids and some scorpaenoids. A shared Type 1 epaxial muscle morphology, with separate fibre insertions on the distal tips of the spine-bearing dorsal-fin pterygiophores, is unusual and probably derived among perciforms. Champsodontids also share with some scorpaenoids Type 5 spinoid scales and the origin of Baudelot's ligament from the first vertebra rather than the basi-occipital, although neither of these features is unique to these taxa. The occurrence of an enclosed sensory. canal on the parietals of Trichodontidae suggest that their relationships might also lie with the Scorpaenoidei. Arguments pertaining to the removal of champsodontids from the trachinoids apply equally to the hypothesized membership of the Cheimarrichthyidae, Pinguipedidae, Percophididae, Trichonotidae, Creediidae, Chiasmodontidae, and notothenioids in the Trachinoidei. Inclusion of these taxa within the Trachinoidei is not well-supported, and their relationships require further investigation.

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