The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the...

Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main que...

Phylogenetic nomenclature (e.g., de Queiroz & Gauthier, 1990, 1992, 1994; Camino & de Queiroz, 2000) is an alternative to the traditional system of nomenclature described in the bacteriological, botanical, and zoological codes (e.g., Sneath, 1992; Ride & al., 1999; Greater & al., 2000). The most fundamental difference between phylogenetic and traditional nomenclature concerns the manner in whic...

C. psittaci, C. pneumoniae, C. abortus, and C. suis (6–10). To our knowledge, this member of the family Chlamydiaceae has been seen in amphibians, but not in other vertebrate hosts. The 16S rRNA analysis showed this taxon to belong to a clade with Candidatus Clavochlamydia salmonicola, a taxon found in fi sh. The phylogenetic position of the novel taxon in the family Chlamydiaceae thus roughly ...

Evolutionary events such as incomplete lineage sorting and lateral gene transfers constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer species trees from gene trees under such conditions is to combine three-taxon analyses for several gene...