PhyloCode: a phylogenetic Code of Biological Nomenclature




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PhyloCode: A Phylogenetic Code of Biological Nomenclature

Philip D. Cantino and Kevin de Queiroz

(equal contributors; names listed alphabetically)

Advisory Group: William S. Alverson, David A. Baum, Harold N. Bryant, David C. Cannatella, Peter R. Crane, Michael J. Donoghue, Torsten Eriksson*, Jacques Gauthier, Kenneth Halanych, David S. Hibbett, David M. Hillis, Kathleen A. Kron, Michael S. Y. Lee, Alessandro Minelli, Richard G. Olmstead, Fredrik Pleijel*, J. Mark Porter, Heidi E. Robeck, Greg W. Rouse, Timothy Rowe*, Christoffer Schander, Per Sundberg, Mikael Thollesson, and Andre R. Wyss.


*Chaired a committee that authored a portion of the current draft.

Most recent revision: April 8, 2000

Table of Contents
Preface

Preamble


Division I. Principles

Division II. Rules

Chapter I. Taxa

Article 1. The Nature of Taxa

Article 2. Clades

Article 3. Hierarchy and Rank

Chapter II. Publication

Article 4. Publication Requirements

Article 5. Publication Date

Chapter III. Names

Section 1. Status

Article 6

Section 2. Establishment

Article 7. General Requirements

Article 8. Registration

Chapter IV. Clade Names

Article 9. General Requirements for Establishment of Clade Names

Article 10. Selection of Clade Names for Establishment

Article 11. Specifiers and Qualifying Clauses

Chapter V. Selection of Accepted Names

Article 12. Precedence

Article 13. Homonymy

Article 14. Synonymy

Article 15. Conservation

Chapter VI. Provisions for Hybrids

Article 16.

Chapter VII. Orthography

Article 17. Orthographic Requirements for Establishment

Article 18. Subsequent Use and Correction of Established Names

Chapter VIII. Authorship of Names

Article 19.

Chapter IX. Citation of Authors and Registration Numbers

Article 20.

Chapter X. Governance

Article 21.

Glossary


Table 1. Equivalence of Nomenclatural Terms

Appendix A. Registration Procedures and Data Requirements


Preface
The development of the PhyloCode grew out of a recognition that the current Linnaean system of nomenclature, as embodied in the preexisting botanical, zoological, and bacteriological codes, is not well suited to govern the naming of clades and species. These are the entities that compose the tree of life, and for this reason they are among the most theoretically significant entities above the organism level. In order to promote clear communication and efficient storage and retrieval of biological information, clades and species require names that explicitly and unambiguously refer to those entities and do not change with time. The preexisting codes fail to provide such names for either kind of entity. Supraspecific names are often associated with clades under the preexisting codes, but because those names are operationally defined in terms of ranks and types, they often fail to retain their associations with particular clades. And species names change whenever species are referred to a different genus, whether as the result of phylogenetic or phenetic considerations. In both cases, an entity whose hypothesized composition has not changed may be given a different name under the preexisting codes based on considerations of rank (if a clade) or genus assignment (if a species). The former is particularly objectionable given the wide recognition that rank assignment is subjective and biologically meaningless.
In contrast to the preexisting codes based on the Linnaean system of nomenclature, the PhyloCode will provide rules for the express purpose of naming the parts of the tree of life--both species and clades--by explicit reference to phylogeny. In doing so, the PhyloCode extends "tree-thinking" to nomenclature. This parallels the extension of tree-thinking into taxonomy, as manifested in the concept of species as lineage segments and the concept of supraspecific taxa as clades. The nomenclatural and taxonomic developments are complementary but independent. Lineages and clades can be named using the traditional Linnaean system of nomenclature (albeit with the problems noted above), and a nomenclatural system based on phylogenetic principles does not require equating taxa with species and clades. Nevertheless, the PhyloCode is designed for naming species and clades. (Only clade names are governed in this version of the PhyloCode, but rules governing species names will be added in the future.)
The PhyloCode is designed so that it can be used concurrently with the preexisting codes or (after rules governing species names are added) as the sole code governing the names of taxa, if the scientific community ultimately decides that it should. The intent is not to replace existing names but to provide an alternative system for governing the application of both existing and newly proposed names. In developing the PhyloCode, much thought has been given to minimizing the disruption of the existing nomenclature. Thus, rules and recommendations have been included to ensure that most names will be used in ways that approximate their current usage. However, names that apply to clades will be redefined in terms of phylogenetic relationships rather than taxonomic rank and will therefore not be subject to the subsequent changes that occur under the Linnaean system due to changes in rank. Because the taxon membership associated with a name will sometimes differ somewhat under the Linnaean and phylogenetic systems, suggestions are provided for indicating which code governs a name when there is a possibility of confusion.
The starting date of the PhyloCode has not yet been determined and is cited as 1 January 200n in the draft code. Names that were provided with published phylogenetic definitions before that date are not considered to be established under the PhyloCode. The starting date will be scheduled to coincide with the publication of a companion volume that will provide phylogenetic definitions for many widely used clade names. This volume will also provide an opportunity for the authors of names that were given phylogenetic definitions before the starting date to republish them in accordance with the PhyloCode and thereby establish their nomenclatural precedence. The delayed starting date will provide the time needed to prepare the companion volume and establish a registration system. It will also permit sufficient time for experimentation with the PhyloCode with no permanent nomenclatural consequences. Some changes in the code will no doubt result. It is hoped that many people will avail themselves of this opportunity to explore the ramifications of phylogenetic nomenclature in the taxa with which they are familiar.
Properties of Phylogenetic Nomenclature. The phylogenetic system of nomenclature embodied in the PhyloCode has the following properties: 1) The system is rankless. Although taxa are hierarchically related, assignment of rank is not part of the naming process and has no bearing on the spelling or application of taxon names. 2) Rules are provided for naming clades and will eventually be provided for naming species. In this system, the categories "species" and "clade" are not ranks but different kinds of biological entities. A species is a segment of a population lineage, while a clade is a monophyletic group of species. Both are products of evolution that are discovered, rather than created, by systematists, and both have an objective existence regardless of whether they are named. 3) In contrast to the preexisting codes, supraspecific names do not have types in the sense that this term is used in the preexisting codes (although some clade names may have a preexisting genus name as a root). Instead, a supraspecific name is given a phylogenetic definition and applies to whatever clade fits that definition, regardless of its hypothesized composition. Species, specimens, and synapomorphies cited within these definitions are called specifiers because they are used to specify the clade to which the name applies. Thus, specifiers function somewhat like types in providing reference points that determine the application of a name. Until the PhyloCode includes rules governing species names, the names of species used as specifiers must be those governed by the preexisting codes. 4) Another novel aspect of the PhyloCode is that it permits the taxonomist to restrict the application of names with respect to clade composition. If a taxonomist wishes to ensure that a name refers to a clade that either includes or excludes particular subtaxa, the definition may contain a qualifying clause specifying conditions under which the name cannot be used. 5) Fundamental differences between the phylogenetic and traditional systems in how supraspecific names are defined lead to operational differences in the determination of synonymy and homonymy. For example, under the PhyloCode, synonyms are names whose phylogenetic definitions specify the same clade, regardless of prior associations with particular ranks; in contrast, under the preexisting codes, synonyms are names of the same rank based on types within the group of concern, regardless of prior associations with particular clades. 6) As with the preexisting codes, precedence determines the correct name of a taxon when synonyms or homonyms exist. In general, precedence is based on the date of establishment under the PhyloCode, but a later-established name may be conserved over earlier names for the same taxon under exceptional circumstances at the discretion of the International Committee on Phylogenetic Nomenclature. The requirement that all established names be registered will reduce the frequency of accidental homonyms.

Advantages of Phylogenetic Nomenclature. Phylogenetic nomenclature has several advantages over the traditional system. In the case of clade names, it eliminates a major source of instability under the preexisting codes--name changes due solely to shifts in rank. It also facilitates the naming of new clades as they are discovered. Under the preexisting codes, it is often difficult to name clades one at a time, the way that new species are named, because a taxon name is affected by its rank, which in turn depends on the ranks of more and less inclusive taxa. In a group in which the standard ranks are already in use, naming a newly discovered clade requires either the use of an unconventional intermediate rank (e.g., supersubfamily) or the shifting of less or more inclusive clades to lower or higher ranks, thus causing a cascade of name changes. This problem encourages systematists to delay naming clades until an entire classification is developed. In the meanwhile, well supported clades are left unnamed, and taxonomy falls progressively farther behind knowledge of phylogeny. This is a particularly serious drawback at the present time, when recent advances in molecular biology and computer technology have led to a burst of new information about phylogeny, much of which is not being translated into taxonomy. The availability of the PhyloCode will permit researchers to name newly discovered clades much more easily than they can under the preexisting codes. For many researchers, naming clades is just as important as naming species. In this respect, the PhyloCode reflects a philosophical shift from naming and classifying species to naming both species and clades. This does not mean, however, that all clades must be named. Criteria that influence the decision whether to name a clade include level of support, phenotypic distinctiveness, economic importance, etc.
When the PhyloCode is extended to species, it will improve nomenclatural stability here as well, by removing the linkage to a genus name. A major source of instability in species names under the preexisting codes (except the viral code, which does not use binomial nomenclature), revision of generic limits, will thereby be eliminated. There will, of course, be a consequent absence of hierarchical information in species names governed by the PhyloCode; specifically, one will not be able to infer phylogenetic relationship from these names in the way that one can infer genus assignment from species names governed by the preexisting codes. However, an underlying principle of the PhyloCode is that the primary purpose of a taxon name is to provide a means of referring unambiguously to a taxon, not to indicate its relationships. From this perspective, the loss of nomenclatural stability of species names under the preexisting codes is too high a price to pay for incorporating taxonomic information (genus assignment) into the names. Moreover, although such information will not be built into species names under the PhyloCode, phylogenetic position can easily be indicated by associating the species name with the names of one or more clades to which it belongs.
Another benefit of phylogenetic nomenclature is that abandonment of ranks eliminates the most subjective aspect of taxonomy. The arbitrary nature of ranking is not widely appreciated by non-taxonomists. This misunderstanding leads to faulty reasoning on the part of some researchers, who treat taxa at the same rank as if they are comparable in some biologically meaningful way. That is, they commit the error of counting genera or families rather than counting clades or species that possess properties relevant to the question of interest or tracing the evolution of these properties on a phylogenetic tree. This kind of error is not possible in a rankless system.
History. The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and Gauthier (1990, 1992, 1994), which built on earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree (Ghiselin 1984; Rowe 1987; de Queiroz 1988). The theory was in development for several years before the first of these theoretical papers was published, and explicit phylogenetic definitions were used in some earlier papers (Gauthier, 1984, 1986; de Queiroz,1985, 1987; Gauthier et al., 1988; Estes et al., 1988; Rowe,1988). Several other papers contributed to the development of phylogenetic nomenclature (Rowe and Gauthier, 1992; Bryant 1994, 1996, 1997; de Queiroz 1994, 1997a,b; Sundberg and Pleijel 1994; Schander and Thollesson 1995; Lee 1996a, b, 1998, 1999a, b; Wyss and Meng 1996; Cantino et al. 1997; Kron 1997; Baum et al., 1998; Cantino 1998, 2000; Eriksson et al., 1998; Hibbett and Donoghue 1998; Moore 1998; Schander 1998a, b; Cantino et al., 1999; Pleijel, 1999; Sereno 1999). Other papers have discussed or applied phylogenetic nomenclature, including several by members of the PhyloCode advisory group. Three symposia have focused on phylogenetic nomenclature. The first one (1995), organized by Richard G. Olmstead and entitled "Translating Phylogenetic Analyses into Classification," took place at the annual meeting of the American Institute of Biological Sciences in San Diego, California, U.S.A. The 1996 Southwestern Botanical Systematics Symposium at the Rancho Santa Ana Botanic Garden in Claremont, California, U.S.A., organized by J. Mark Porter and entitled "The Linnean Hierarchy: Past Present and Future," focused in part on phylogenetic nomenclature. Philip Cantino and Torsten Eriksson organized a symposium at the XVI International Botanical Congress in St. Louis, Missouri, U.S.A. (1999), entitled "Overview and Practical Implications of Phylogenetic Nomenclature."
The preparation of the PhyloCode began in the autumn of 1997, following a decision by Michael Donoghue, Philip Cantino, and Kevin de Queiroz to organize a workshop for this purpose. The workshop took place August 7-9, 1998, at the Harvard University Herbaria, Cambridge, Massachusetts, U.S.A., and was attended by 27 people from five countries: William S. Alverson, Harold N. Bryant, David C. Cannatella, Philip D. Cantino, Julia Clarke, Peter R. Crane, Noel Cross, Michael J. Donoghue, Torsten Eriksson, Jacques Gauthier, Kancheepuram Gandhi, Kenneth Halanych, David S. Hibbett, David M. Hillis, Kathleen A. Kron, Michael S. Y. Lee, Alessandro Minelli, Richard G. Olmstead, Fredrik Pleijel, J. Mark Porter, Kevin de Queiroz, Heidi E. Robeck, Timothy Rowe, Christoffer Schander, Per Sundberg, Mikael Thollesson, and André R. Wyss. An initial draft of the code prepared by Cantino and de Queiroz was provided to the workshop participants in advance and was considerably revised by Cantino and de Queiroz as a result of decisions made at the meeting. The initial draft of Article 21 was written by F. Pleijel, A. Minelli, and K. Kron and subsequently modified by M. Donoghue and P. Cantino. The initial drafts of Recommendations 10D and 11.8B were contributed by T. Rowe. Article 8 and Appendix A were written largely by T. Eriksson. William M. Owens provided the Latin terms in Article 9.3. Whenever possible, the writers of the PhyloCode used the draft BioCode (Greuter et al. 1998) as a model for the unification of the preexisting codes. Thus, the organization of the PhyloCode, some of its terminology, and the wording of certain rules is derived from the BioCode. Other rules are derived from one or more of the preexisting codes, particularly the Botanical and Zoological Codes (Greuter et al. 1994; International Commission on Zoological Nomenclature 1985, 1999). However, many rules in the PhyloCode have no counterpart in the any code based on the Linnaean taxonomic categories because of fundamental differences in the definitional foundations of the systems.

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