A general rationale for the formulation and placement of taxonomic definitions in phylogenetic taxonomy is proposed, and commonly used terms such as "crown taxon" or "node-based definition" are more precisely defined. In the formulation of phylogenetic definitions, nested reference taxa stabilize taxonomic content. A definitional configuration termed a node-stem triplet also stabilizes the rela...

Proteins containing an Rho GTPase-activating protein (RhoGAP) domain work as molecular switches involved in the regulation of diverse cellular functions. The ability of these GTPases to regulate a wide number of cellular processes conies from their interactions with multiple effectors and inhibitors, including the RhoGAP family, which stimulates their intrinsic GTPase activity. Here, a phylogen...

Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the G...

The problem in phylogenetic tree construction, is to find the tree which best describes the relationship between a set of objects. We are mostly interested in the case when the objects are species or taxa. carrot whale chimpanzee human Figure 5.1: Phylogenetic tree of 4 species Phylogenetic Tree Construction is based on Cladistics, the systematic classification of groups of organisms on the bas...

Conservation of proximity of a pair of genes across multiple genomes generally indicates that their functions could be linked. Here, we present a systematic evaluation using 42 complete microbial genomes from 25 phylogenetic groups to test the reliability of this observation in predicting function for genes. We find a relationship between the number of phylogenetic groups in which a gene pair i...