Background

The International Code of Phylogenetic Nomenclature (PhyloCode) is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny. The PhyloCode will be formally published in 2012, although the exact date has not yet been determined.

The PhyloCode grew out of a workshop at Harvard University in August 1998, where basic decisions were made about its scope and content. Many of the workshop participants, together with a few other people who subsequently joined the project, have served as an advisory body (see the PhyloCode preface for the history of development and a list of people involved). In 2004 The International Society for Phylogenetic Nomenclature was founded in Paris at the first society meeting.

The current draft of the PhyloCode represents several years of work and some rules may still be refined before the code is implemented. For example, the current draft governs only the naming of clades (see Dayrat et al., 2008) and rules governing species names may be added in future (see Cellinese et al., 2012). Since the code does not currently cover species names, the examples in the present draft use Linnaean binomials when species names are cited in the phylogenetic definitions of clade names.

We hope that many members of the scientific community will examine the draft PhyloCode and send suggestions for improvement. Although the code has initially been developed by a small group of people, it is intended for the benefit of all biologists who name clades or use clade names.

RegNum database

According to the PhyloCode, clade names should be registered in a database and published in peer-reviewed publications. To develop such a registry, an informatics project managed by Mikael Thollesson (Uppsala University) was launched and RegNum was originally developed with Java tools as part of a master thesis by Jonas Ekstedt. Currently, Nico Cellinese and Greg Traub at University of Florida are developing the next version of RegNum with Ruby-on-Rails and MySQL. A prototype is now available but still under construction. This new tool includes two components: 1) PhyloRegNum, a name repository storing and managing phylogenetic definitions; and 2) PhenoRegNum, a phenotype repository linking ontologies to the apomorphies used in phylogenetic definitions. PhenoRegNum is linked to BioPortal and allows users to explicitly define apomorphies by using existing phenotype ontologies and creating formal EQ statements. Additionally, we have implemented links with NCBI, and uBio while the integration with TreeBASE and TOLKIN is underway.

The source code will soon be available for download from this site. For more information please contact Nico Cellinese: ncellinese(at)flmnh.ufl.edu.