PhyloCode

Abstract: Based on a molecular phylogeny, a new phylogenetic taxonomy that is compatible with both the International Code of Zoological Nomenclature (ICZN) and the PhyloCode is proposed for Glassfrogs and ...

Abstract: Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.

Abstract: Cantino, P. D., and K. de Queiroz. 2004. PhyloCode: A phylogenetic code of biological nomenclature. [http://www.ohiou. edu/phylocode/] de Queiroz, K. 1992. Phylogenetic definitions and taxonomic philosophy. Biol. Philos. 7:295-313. de Queiroz, K. 1997. The Linnaean hierarchy and the evolutionization of taxonomy, with emphasis on the problem of nomenclature. Aliso 15:125-144. de Queiroz, K. 2005. Linnaean, rank-based, and phylogenetic nomenclature: Restoring primacy to the link between names and taxa. Symb. Bot. Ups. 33(3):127-140. de Queiroz, K., and P. D. Cantino. 2001. Phylogenetic nomenclature and the PhyloCode. Bull. Zool. Nomencl. 58:254-271. de Queiroz, K., and J. Gauthier. 1990. Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39:307-322. de Queiroz, K., and J. Gauthier. 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst. 23:449-480. de Queiroz, K., and J. Gauthier. 1994. Toward a phylogenetic system of biological nomenclature. Trends Ecol. Evol. 9:27-31. International Botanical Congress. 2000. International Code of Botanical Nomenclature. Edition adopted by the Sixteenth International Botanical Congress, St. Louis, Missouri, July-August 1999. Koeltz Scientific Books, Konigstein. International Commission on Zoological Nomenclature. 1999. International Code of Zoological Nomenclature, 4th edition. International Trust for Zoological Nomenclature, London. International Union of Microbiological Societies. 1992. International Code of Nomenclature of Bacteria and Statutes of the International Committee on Systematic Bacteriology and Statutes of the Bacteriology and Applied Microbiology Section of The International Union of Microbiological Societies. American Society for Microbiology, Washington. Laurin, M., K. de Queiroz, P. Cantino, N. Cellinese, and R. Olmstead. 2005. The PhyloCode, types, ranks, and monophyly: A response to Pickett. Cladistics 21:605-607. Pickett, K. M. 2005. The new and improved PhyloCode, now with types, ranks, and even polyphyly: A conference report from the First International Phylogenetic Nomenclature Meeting. Cladistics 21:7982.

Abstract: 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 practice, phylogenetic nomenclature will be disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the dierence between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.