DEVELOPING A PROTOCOL FOR THE CONVERSION OF RANK-BASED TAXON NAMES TO PHYLOGENETICALLY DEFINED CLADE NAMES, AS EXEMPLIFIED BY TURTLES

Journal of Paleontology, Sep 2004 by Joyce, Walter G, Parham, James F, Gauthier, Jacques Armand

ABSTRACT-

We present a rank-free phylogenetic nomenclature for 25 well-established ancient clades of living turtles. This is the first attempt to document fully the nomenclatural history of a clade with the intent of proposing a coherent nomenclatural system to replace the traditional rank-based nomenclature. Because of the imperative to retain connectivity to the literature for information retrieval, due consideration is given to balancing the desire to develop a consistent system against the desire to conserve traditional associations between names, taxa (i.e., clades), and characters. Novel issues and problems that emerged during this review include: the unclear name/clade association of traditional names; the creation of synonymy lists from which to choose a name; difficulties associated with selecting a single criterion for choosing among multiple 'subjectively synonymous' names; identifying authorship for a converted traditional name; and the potential loss of nomenclatural information due to 'functional homonyms.' This work may provide a useful road map to those intent on converting their traditional rank-based nomenclatures to explicitly phylogenetic nomenclatures under the precepts of the PhyloCode.

INTRODUCTION

THE GENERAL principles of phylogenctic nomenclature embodied in the draft PhyloCode (PhyloCode, 2003) were outlined more than a decade ago (de Queiroz, 1988; de Queiroz and Donoghue, 1988; de Queiroz and Gauthier, 1990), and their implications have inspired a lively debate among practitioners of this type of nomenclature (e.g., de Queiroz and Gauthier, 1992, 1994; Rowe and Gauthier, 1992; Bryant, 1994; de Queiroz, 1994; Schander and Thollesson, 1995; Chiappe, 1996; Holt/, 1996; Lee, 1996; Lee and Spencer, 1997; Sereno, 1998, 1999; Padian et al., 1999; Gaulhier and de Queiroz, 2001; Bryant and Cantino, 2002). We apply those principles in proposing a comprehensive phylogenetic nomenclature for the 50 primary clades of turtles that we feel sure many zoologists will want to talk about. Our stated purpose is not to provide an overview or critique of the differences between both nomenclalural systems, but rather to propose a coherent, rank-free nomenclature to replace the current rank-based nomenclature governed (implicitly or explicitly) by the International Code of Zoological Nomenclature (ICZN, 1999).

Our proposed nomenclature is incomplete, thanks in no small part to the fact that knowledge of turtle phylogeny is still growing. However, there are at least three additional reasons for this shortcoming. First, and perhaps most importantly, there are unresolved questions about the conversion of Linnaean binomials-in which species names are unique but not constant due to changing generic assignments-into a nomenclatural system in which all genealogical entities of interest, be they species or clades (sensu PhyloCode, 2003, Glossary), have their own unchanging names (Cantino et al., 1999). A second problem is that there is no widely accepted protocol for associating a particular node-, stem-, or apomorphy-based clade with one among a realm of possible candidate names from the traditional taxonomic literature (e.g., Sereno, 1998, 1999). This is largely because the limits of the circumscription of many traditional rank-based taxa are often fuzzy, making it difficult to construct a coherent argument that any given taxon name governed (explicitly or implicitly) by the ICZN must objectively refer to a particular clade as well (Gauthier and de Queiroz, 2001; see below). Finally, any nomenclatural history necessitates a laborious review of an old and rare scientific literature that is often difficult to find. We consequently focus our efforts toward converting the names associated with the most widely studied, uncontroversial, long-recognized phylogcnetic units, which include extant species, and intentionally leave the conversion of currently ill-supported eladcs, or clades that contain fossils only, to subsequent reviewers.

Among extant vertebrates, turtles are an ideal clade to lead the transition from a rank-based nomenclatural system (ICZN, 1999) to a rank-free nomenclatural system that is based on phylogenetically defined clade names (PhyloCode, 2003). With fewer than 300 living species, turtles are manageable, yet diverse enough, with a long and complex history of ideas about phylogeny and nomenclature, to raise novel questions regarding the procedures of nomenclatural transition as proposed in the PhyloCode (2003).

Given the lack of transitional protocols, a primary goal of this paper is to identify difficulties that may be associated with the systematic conversion of names, explore promising solutions, and develop a protocol that allows the efficient mass conversion of names from one system to the other while maintaining optimal connection to their current meaning (i.e., their currently accepted circumscriptions). On this basis, we propose an internally consistent phylogenetic nomenclature for all well-accepted crown clades of extant turtles, and their stem counterparts, with the ultimate goal of nomenclatural precision, stability, and universality.