PhyloCode: Concept, History and Advantages | Taxonomy

In this article we will discuss about PhyloCode (Phylogenetic Code) which presently governs only clade names:- 1. Concept of PhyloCode 2. History of PhyloCode 3. Implications 4. Advantages.

Concept of Phylocode:

The Linnaean system of binomial nomenclature is now becoming unsuitable to govern the naming of clade and species. Clade is a group in which every member shares a common ancestor (a unique common ancestor). A clade is a group for which all the descendants of the last common ancestor of the members of the group are included in the group.

In the pre-existing code the name of a species changes whenever a species is referred to a different genus as a result of phylogenetic or phenetic consideration. In this the supraspecific names are associated with clade as they are operationally defined in terms of ranks and types.

The phyloCode (Phylogenetic code) Botanical nomenclature is proposed to promote clear communication and efficient storage and retrieval of biological information. The code was cited on 1^st January 2000. Presently phyloCode governs only clade names.

History of PhyloCode:

Theoretical foundation of the phyloCode was developed by de Queiroz and Gauthier in a series of papers published in 1990, 92, 94. Earlier to it many paper on phylogeneted definition were published by Gauthier 1984, Gauthier and Padian 1985, Gauthier 1988, Rode, 1988 etc. The first version of phyloCode was published in 2000.

The early symposia increased awareness of phylogentic nomenclature. The first one is organized by Richard G. Olmstead “Translating Phylogenetic Analyses into Classifications” took place in 1995 in annual meeting of American Institute of Biological Sciences in San Diago, California, USA.

South Western Botanical Systematic Symposium in 1996 held at the Rancho Santa Ana Botanic Garden in Claremont, California, USA. It was organised by J. Mark Porter entitled “The Linnean Hierarchy: Past, Present and Future”. It was focused in part on phylogenetic nomenclature.

Philip Cantiro and Torsten Eriksson organised a symposium at the XVI International Botanical Congress in St. Louis, Missouri, USA in 1999, entitled “Overview and Practical Implications of Phylogenetic Nomenclature”.

Preparation of PhyloCode began in the autumn of 1997, following a decision by Michael Donoghue, Philip Cantino and Kevin de Queiroz to organise a work shop. This work shop took place from 7-9 August 1998 at the Harvard University, Herbaria, Cambridge Massachusetts, USA. An initial draft of the code was prepared by Cantino and de Queiroz.

The first public draft of the phyloCode was published in April 2000. Nixon and Carpenter 2000, Black Well 2002, Jorgenson 2004, Carpenter 2003, Barkley 2004, Riepel 2006, Stevens, 2006 etc. criticised it many times.

Langer 2001, and Stevans 2002, pointed out both advantages and disadvantages. Gauthier and de Queiroz 2001 discussed properties of different kinds of phylogentic definitions.

Joycee 2004, Donoghue 2005, Sereno 2005, suggested the application of widely used names to a particular category of clades.

The conversion of rank-based names to phylogenetically defined names was given by Joycee 2004.

The choice of specifies was given by Wilkinson 2006, Lee 2005, Sereno 2005.

The development of an integrated approach to naming crown and total clads was given by de Queiroz, 2007.

Second workshop on phylogentic nomenclature was held at Yale University between 28-30 July 2002, organized by Michael Donoghue, Jacques Gauthier, Philip Cantino and Kevin de Quieroz. Sixteen proposed changes in the rules and recommendations were discussed, 11 of which were approved.

The first public draft of the PhyloCode covered only Clade names.

Then in 2002 is was decided that:

(i) The rules for clade names and rules for species names would be published in separate documents.

(ii) The timing of implementation of the two documents would be independent.

The rules for clade names are implemented before the names of species. The decision was reconsidered in 2006.

In 2007 a different approach to species names was adopted by CPN.

The first International Phylogenetic Nomenclature meeting took place between 6-9^th July 2004 at Museum National d’Historie Naturelle in Paris. It was chaired by Michael Lanin.

International Society for Phylogenetic Nomenclature (ISPN) bears full responsibilities including ratifying the first edition of Phylocode and approving any subsequent modification (Art. 22). ISPN suggests the basis for the set of rules and recommendations which were eventually adopted by CPN.

The result of May 2006, meeting was reconciliation between traditional binomial species names and phylogenetic nomenclature including mandatory genus category and the fact that many genus are not monophyletic. This approach was adopted by CPN 2007 (May) and incorporated into current version of code as a new Article 21.

Article 21 has following features:

(1) Regulation of species names is left entirely to the rank—based codes.

(2) Genus portion of binomen, called the ‘prenomen’ under the phylocode is treated as simply the first part of species name and need not be established under this code.

(3) Some mechanism be used to indicate whether the prenomen is also an established clade name under this code, and examples of possible symbols are provided.

(4) Guidelines and examples are provided for selecting a prenomen when publishing a new species name in various situations.

(5) Protologue include evidence indicating that the name species represents a separately evolving lineage or citation of such evidence published elsewhere.

(6) When a species name is published under appropriate rank-based code, the second part of the binomen may be treated as though it were the name of the species.

The species uninomen may be combined with the names of clades other than prenomen. If the uninomen is not accompanied by prenomen, the author and publication year of the uninomen be cited.

The development of the International code of Phylogentic Nomenclature or PhyloCode grew out of the recognition that the current rank—based system of nomenclature, as embodied in current botanical, zoological, and bacteriological codes, are not well suited to govern the naming of clades.

Clades along-with species are the entities that make up the tree of life. Supraspecific names are not always associated with clades under the rank based codes, they often fail to retain their associations with particular clades because the names are operationally defined in term of ranks and types.

In contrast to rank based codes the phylocode will provide rules for the purpose of naming clades through explicit reference to phylogeny. The phyloCode extends “tree-thinking” to biological nomenclature.

The purpose of the phyloCode is not to replace existing names but to provide an alternative system for governing the application of both existing and newly purposed norms. Rules and recommendations have been included to ensure that most names will be applied in ways that approximate their current and/or historical use.

Names that apply to clades will be redefined in term of phylogenetic relationships rather than taxonomic rank and therefore will not be subject to the subsequent changes that occur under the rank based system due to changes in rank.

If a clade name is based on a genus name, the type of the genus under the appropriate rank based code must be used as an internal specifier under the phyloCode (Art. 11.7).

In the recent report on the first International Phylogenetic Nomenclature Meeting, Pickett (2005), the conclusion came as the “Architects of the phylocode have reversed their positions one some points of contention.

The starting date of the phyloCode will be scheduled to coincide with the publication of a volume providing phylogenetic definition for many widely used clade name and the name of many large clades.

The phylogenetic system of nomenclature embodied in phyloCode exhibits both similarities to and differences from the rank based system of the traditional codes.

Similarities:

1. Both systems have the same fundamental goals of providing unambiguous methods for applying names to taxa, selecting a single accepted name for a taxon from among completing synonyms or homonyms; and promoting nomenclatural stability and continuity to the extent that doing so does not contradict new results and conclusions.

2. Neither system infringes upon the judgment of taxonomists with respect to inferring the composition of taxa to assigning taxonomic ranks.

3. Both systems use precedence and clear order of preference, to determine the correct name of a taxon when synonyms or homonyms exists.

4. Both systems use the date of publication i.e., chronological priority as the primary criterion for establishing precedence.

5. Both phylogenetic and rank based systems have conservation mechanisms that allow a later-established name to be given precedence even an earlier name for the same taxon if using the earlier name would be contrary to fundamental goal of promoting nomenclatural stability and continuity.

Differences:

1. Phylogenetic system is independent of taxonomic rank. Although taxa are hierarchically related, the assignment of taxonomic rank is not part of the naming process and has no bearing on the spelling and application of taxon names. Consequently the phylogenetic system does not require ranked taxonomies.

2. In phylogenetic system the categories “Species” and “Clades” are not ranks but different kinds of biological entities where species is a segment of population lineage, and Clade is monophyletic group of species or organism.

Both are the product of evolution. As a consequence, once a taxon is named, the composition and diagnostic characters of the taxon became questions to be decided by empirical evidence rather than by personal decisions.

3. In addition to applying name to nested and mutually exclusive taxa, as in traditional nomenclature, the phylogentic system allows names to be applied to partially overlapping taxa (clades). This provision is necessary to accommodate situations involving taxa (both species and clades) of hybrid origin.

4. In contrast to rank based codes, which use definitions based on ranks and types to determine the application of names, phylogentic nomenclature uses explicit phylogenetic definitions. Species, specimens, and apomorphies cited within these definitions are called specifiers because they are used to specify the clade to which the name applies.

Specifiers function analogously, the types of rank based nomenclature in providing reference points that determine the application of a name. They differ from types in that may either be included in or excluded from taxon being named, and multiple specifiers may be used.

5. Fundamental difference between Phylogentic and rank based system in how names are defined leads to operational differences in the determination of synonymy and homonymy e.g., under the Phylocode, synonyms are names whose phylogenetic definitions specify the same clade, regardless of prior associations with particular ranks; in contrast under the rank based codes; synonyms are name of same name rank whose type are included within a single taxon at that rank regardless of prior association with particular clades.

6. PhyloCode is that which permits taxonomists 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 taxa, this result may be achieved through the use of additional internal or external specifiers i.e., beyond the minimal number needed to specify a clade, or the definition may contain a qualifying clause specifying condition under which the name cannot be used.

7. PhyloCode includes recommended naming convention that promote an integrate system of names for crown the total clades. The resulting pairs of names enhance the cognitive efficiency of the system and provide hierarchical information within the name.

8. Establishment of a name under the PhyloCode requires both publication and registration. The purpose of registration is to create a comprehensive database of established names which will reduce the frequency of accidental homonyms and facilitate the retrieval of nomenclatural information.

Implications of PhyloCode:

The initial draft of Article 21 was written by F.Pleijel, A.Minelli and K.Kron which was modified by M.Donoghue and P.Cartino. The initial drafts of Recommendations 10 D and 11.8 B were written largely by I.Eriksson and the Latin terms in Article 9.3 were provided by W.M.Owens. Properties of Phylocode

The following are the properties of Phylogenetic system:

(1) The system is rankles as assignment of rank is not a part of naming process.

(2) Rules are framed for naming of clades.

(3) The categories ‘species’ and ‘clade’ are not ranks. A species is a segment of a population lineage, and clade is a monophyletic group of species.

(4) In PhyloCode a supraspecific name is given a phylogenetic definition and is applied to the clade which fits that definition, irrespective of its hypothesized composition. Species specimens and synapomorphies cited within these definitions are called specifiers as they clade to which the name applies and function somewhat like types.

(5) Applications of names is restricted with respect to clade composition.

(6) Basic difference is there in the rules governing the super specific names. According to phylocode and earlier traditional systems there is the operational difference in the determination of synonymy and homonymy.

Pre-existing system suggests that synonyms are names of the same rank based on types within the group of concern, regardless of prior association with particular clades. According to phylogenetic system, synonyms are names whose phylogenetic definitions specify the same clade; regardless of prior association with particular ranks.

Advantages of PhyloCode:

1. PhyloCode allows naming the intermediate ranks such as superfamily etc.

2. It improves nomenclatural stability. The phylogenetic position can easily be indicated by associating the species name with the names of one or more clades to which it belongs.

3. The abandonment of ranks in Phylocode also eliminates the error caused by many taxonomists who treat taxa at the same rank.

4. It eliminates a major source of instability under the rank based codes- changes in clade names due solely to shifts in rank.

5. It facilitates the naming of new clades as they are discovered. Under the rank based codes, it is often difficult to name clades one at a time, similar to the way that new species are named because the name of taxons is affected by taxon’s rank, which in turn depends on the ranks of more and less inclusive taxa.

6. Phylogenetic nomenclature permits the abandonment of categorical ranks, which would eliminate the most subjective aspect of traditional taxonomy. A rankless system of taxonomy, which is permitted but not required by the phyloCode, encourages the development of mere appropriate uses of taxonomies in such studies.

7. Advantage of the phylocode over the rank based codes is that it applies at all levels of the taxonomic hierarchy. In contrast, the ICZN does not extend its rank based method of definition level of superfamily and the ICBN extends that method of definition only to some names above that rank of family and the principle of priority is not mandatory for those names.

Suprageneric Nomenclature:

Names of taxa above the rank of family have not been rigorously studied. Provisions in the current International Code of Botanical Nomenclature dealing with names above the rank of family have improved considerably over previous edition of the code.

The Suprageneric names is the names above the rank of family published after 1 Jan, 1935 must be accomponished with a description and diagnosis in Latin or a reference to a validly published description or diagnosis in Latin.

This has resolved many inconsistencies practiced over the years regarding when suprageneric nomenclature as least for spermatophytes and Pterophytes began and the parenthetical use of authorships for suprageneric names.

The following articles are mentioned here because of their importance to suprageneric names:

Art. 3:

The principal suprageneric ranks are kingdom, division or phylum, class, order and family.

Art. 4:

The rank of tribe may be inserted between family and genus. Additional ranks are formed typically by adding the prefix “-Sub” to form subkingdom, subdivision or subphylum, subclass, suborder, subfamily and subtribe. Some workers adopted prefix “Super” as Superkingdom.

Art. 5:

The relative order of the ranks may not be altered. The ranks in use and Superkingdom, Kingdom, Subkingdom, Superdivision, Subdivision, Division Superclass, Class Subclass, Superorder, Order, Suborder, Superfamily, Family, Subfamily, Supertribe, Tribe and Subtribe.

Art. 13:

4 Aug. 1789 is the date when this article is established. It is the starting date for supergeneric names of spermatophytes and pteridophytes.

Art. 16:

The article is redrafted in the St. Louis Code making the provisions and nature of names above the rank of family, e.g.,

Division: Magnoliophyta Takht. and Zimmeem ex-Roveal

Subdivision: Magnoliophytina frohne & U Jensen ex. Roveal

Class: Magnoliopsida Brongn

Subclass: Magnoliidae Novak ex Takht

Super Order: Magnolianae Takht

Order: Magnoliales Brom head

Suborder: Magnoliineae Engl.

Art. 17:

It has two provisions:

(i) Establishes the ending for names at the ranks of order (“-ales”) and suborder (“-ineae”).

(ii) Permits to use of certain classical terms such as “cohorts”, “nixus”, “alliance”, and ‘Reihe’ when proposed in a position equivalent to order to be considered as having published at the rank of order.

Art. 18:

Deals with the establishment of family names. All family names end in “- aceae”.

Art. 19:

Deals with names at the ranks of subfamily, tribe and subtribe. It ends in “-oideae”. Tribe and subtribe should terminate in ‘ -eae’ and ‘-inae’.

Art. 32:

Contrary to often accepted practices, all names regardless of rank must be accompanied by validating description or diagnosis. Numerous modern authors simply use suprageneric names without concern for their validity. In case many supragenric names are find the reference in the form of a name, typically a descriptive name associated with one base on a generic stem.

In dealing with suprageneric names one must have a full understanding of the literature to evaluate the validity of these names. Autonyms are not operative for names at ranks above that the genus. Art. 32.8 is not applicable to suprageneric names which are mononomials.

Art. 33:

Suprageneric names are not combinations and therefore articles dealing with combination are not applicable. Suprageneric names frequently are “transferred” from one rank to another.

Art. 35:

It deals with indication of rank.

Art. 36:

All names regardless of rank proposed after 1 Jan. 1935 must be accompanied by a validating description or diagnosis in Latin or have a reference to an effectively published description in Latin.

Art. 41:

Provisions provide some guidelines for the establishment of suprafamilial names was referred to and special committee.