PTDs for Fungi

PhyloCode logoSome things just take longer than you thought they ever would. A case in point is the PhyloCode, the guiding text of phylogenetic taxonomy, and its “companion volume”, Phylonyms, which is intended to present phylogenetic taxon definitions for all the major clades of life.

Rank-free phylogenetic taxonomy, which employs explicit tree-based phylogenetic taxon definitions (PTDs), had its origins in theoretical discussions of the 1980s and was refined in the 1990s through a series of workshops and other activities supported by the International Society for Phylogenetic Nomenclature (ISPN). I participated in two of the workshops, at Harvard in 1998, and at Yale in 2002. When plans to produce Phylonyms and link it to publication of the PhyloCode were formed, I recruited several eminent colleagues, Meredith Blackwell, Tim James, Joey Spatafora, John Taylor, and Rytas Vilgalys, to draft PTDs for Fungi, Dikarya, Ascomycota and Basidiomycota. I thought that having worked examples of PTDs for several major group of fungi would help stabilize clade concepts and promote the integration of tree-thinking and fungal taxonomy. Never once did I imagine that it would take more than a decade for the PTDs to see publication. Our first version of the PTDs were submitted in 2008, then revised and resubmitted in 2017. As of this writing, the manuscript for Phylonyms has still not gone to the publisher, although it seems likely that it will soon be submitted.

Despairing about the prospects for Phylonyms and the PhyloCode, my coauthors and I decided to submit the fungal PTDs to IMA Fungus, the journal of the International Mycological Association (this was done with the approval of the editors of the PhyloCode). The PTDs have recently been published (IMA Fungus vol. 5, no. 2, art. 5) in essentially the same form as they will take in Phylonyms.

In the years since we first submitted our PTDs, there have been major developments in fungal taxonomy. For example, a new phylum, Entorrhizomycota, has been proposed, and several different delimitations of Fungi have been advanced (with or without nucleariids, Microsporidia, Cryptomycota, and aphelids). We hope it is not too late for our PTDs to contribute to the ongoing discussion about the meanings of “Fungi”, “Dikarya”, “Ascomycota” and “Basidiomycota”.

Fig 1

Fig. 1. Phylogenetic taxon definitions and specifiers for Fungi, Dikarya, Ascomycota and Basidiomycota. Capital letters following species names indicate the clade(s) for which they serve as specifiers (F for Fungi, and so on). There are two species of Taphrina in the tree: T. wiesneri, which was included in the reference phylogeny for Basidiomycota, and T. neoformans, which was used in the reference phylogeny for Ascomycota. A. Topology based on James et al. (2006: fig. 1) and Bauer et al. (2015: fig. 2). B. Topology based on Spatafora et al. (2016: fig. 1) and the alternative topology of Bauer et al. (2015), which was described but not illustrated.

Many thanks to Meredith, Tim, Joey, John and Rytas, for their patience, the editors of IMA Fungus, for their support of this publication, and the editors of the PhyloCode and Phylonyms, for their flexibility and perseverance.

Viva PhyloCode!