Phylogenetic Nomenclature: History, Properties and Advantages

In this article we will discuss about Phylogenetic Nomenclature:- 1. Subject-Matter of Phylogenetic Nomenclature 2. History of Phylogenetic Nomenclature 3. Properties 4. Advantages.

Subject-Matter of Phylogenetic Nomenclature:

The current Linnaean system of nomenclature as embodied in the pre-existing botanical, zoological and bacteriological codes, has been found to be unsuitable to govern the naming of clades and species.

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. It is a group in which every member shares a common ancestor that is not shared with any other group (a unique common ancestor).

They are theoretically the most significant entities above the organism level as they compose the tree of life. The major drawback of the pre-existing code is that it fails to provide names that explicitly and unambiguously refer to a particular clade or species.

The name of a species often changes with time i.e. a species name changes whenever a species is referred to a different genus as a result of phylogenetic or phonetic consideration.

Often under the pre-existing code, supra-specific names are associated with clades and because these names are operationally defined in terms of ranks and types, they often fail to retain their associations with particular clades.

Due to these reasons, an entity whose hypothesized composition has not changed may be given a different name under the pre-existing codes based on considerations of rank in case of a clade or genus in case of a species.

The former is particularly objectionable given the wide recognition that rank assignment is subjective and biologically meaningless. Thus, to avoid this, and in order to promote clear communication and efficient storage and retrieval of biological information, the Phylocode or Phylogenetic Code of Biological Nomenclature has been proposed which is designed for naming species and clades.

The starting date of the Phylocode has not been determined and is cited as 1^st January 2000 in the draft code. The present version of Phylocode only governs clade names. The rules governing species names will be added in future.

While developing the Phylocode, much thought has been given to minimize disruption of the existing nomenclature and it has been designed in such a way, so that it can be used concurrently with the pre-existing codes or (after rules governing species names are added) as the sole code governing the names of taxa, if it is ultimately accepted by the scientific community.

The main intention of this Code is not to replace existing names but to provide an alternate system by which both the existing and newly proposed names can be applied together. Thus, rules and recommendations have been included to ensure that most names will be used in ways that approximate their current usage.

The names of clades will however be redefined in terms of phylogenetic relationships rather than taxonomic rank as previously done under the Linnaean system, so that they will not be subjected to subsequent change with time due to changes in rank.

As according to the Linnaean and phylogenetic system, the membership of a taxon associated with a name may sometimes differ, suggestions have been provided to indicate which code governs a name when there is a possibility of confusion. However, names that were provided with published phylogenetic definitions before 1^st January 2000, will not be considered to be established under the Phylo Code.

History of Phylogenetic Nomenclature:

The theory of Phylogenetic Nomenclature which was built on the suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree, was in development since the early 1980’s until they were finally published in a series of theoretical papers in the 1990’s, the most noteworthy among them are a series of papers by de Queiroz and Gautheir (1990,1992,1994).

Several other papers have also discussed or applied phylogenetic nomenclature. Three symposia were also conducted, which focused on phylogenetic nomenclature. These include the annual meeting of the American Institute of Biological Sciences in San Diego, California, U.S.A. in 1995 entitled ” Translating Phylogenetic Analysis into Classification” organized by Richard G. Olmstead.

The second symposia (Southwestern Botanical Systematics Symposium) was organized by J. Mark Porter in 1996 at the Rancho Santa Ana Botanic Garden in Claremont, California, U.S.A. and was entitled “The Linnean Hierarchy: Past, Present and Future”.

The third symposium was organized at the XVI Internationational Botanical Congress in 1999 at St. Louis, Missouri, U.S.A. by Phlip Cantio and Tarsten Eriksson entitled “Overview and Practical Implications of Phylogenetic Nomenclature”.

The preparation of the Phylocode however began in the autumn of 1997. A workshop was later organized at the Harvard University Herbaria, Cambridge, Massachusetts, U.S.A. from 7^th August to 9^th August, 1998 and was attended by 27 people from five countries.

An initial draft of the Phylocode prepared by Philip Cantino and Kervin de Queiroz was provided to the participants in advance, which was later revised on the basis of decisions made at this workshop.

The draft derived some terminologies and rules from the BioCode and several rules from one or more of the pre-existing codes, particularly the Botanical and Zoological Codes. However, many rules of the Phylocode are totally unique, and have no counterpart in any code based on the Linnaean Taxonomic categories because of fundamental differences in the definitional foundations of this system.

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

Properties of Phylogenetic Nomenclature:

The phylogenetic system of nomenclature has the following properties:

(a) In-spite of the hierarchical relation between the taxa, the system is rankles, as assignment of rank is not part of the naming process, thus, having no bearing on the spelling or application of taxon names.

(b) This system provides rules for naming clades. The rules for naming species will be provided soon. Till then, the naming of the species will be governed by the pre-existing codes.

(c) According to this system, the categories “species” and “clade” are not ranks, but are considered as different kinds of biological entities. A species is a segment of a population lineage, whereas, a clade is a monophyletic group of species. Both of them, which are discovered by systematics, rather than being created, are products of evolution, and even if not named have an objective existence.

(d) In contrast to the pre-existing code, where supra specific names have types, according to the Phylocode, a supra specific 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 specifies as they specify the clade to which the name applies and function, somewhat like types in providing reference points that determine the application of a name.

(e) This code allows taxonomists to restrict the application of names with respect to clade composition. If one wishes to ensure that a name refers to a clade that either excludes or includes a particular sub-taxa, this code has the provision of including a qualifying clause in the definition specifying conditions under which the name cannot be used.

(f) Since there is a basic difference in the rules governing how supra-specific names are defined according to the Phylogenetic and earlier traditional systems, this has led to operational differences in the determination of synonymy and homonymy.

As for example, according to the pre-existing system, synonyms are names of the same rank based on types within the group of concern, regardless of prior associations with particular clades.

On the other hand according to the phylogenetic system, synonyms are names whose phylogenetic definitions specify the same clade, regardless of prior associations with particular ranks. However precedence determines the correct name of a taxon when synonyms or homonyms exist as according to the pre-existing codes.

All established names, need to be registered which will reduce the frequency of accidental homonyms.

Although precedence is based on the date of establishment under the Phylocode, under exceptional circumstances there is a provision for later established names to be conserved over earlier names for the same taxon, at the discretion of the International Committee on Phylogenetic Nomenclature.

Advantages of Phylogenetic Nomenclature:

The Phylogenetic system of Nomenclature has the following advantages over the traditional system:

(a) According to the pre-existing codes, it is often difficult to name a newly discovered clade, which either requires the use of an unconventional intermediate rank (e.g. superfamily) or shifting of less or more inclusive clades to lower or higher ranks. This causes a major source of instability leading to a cascade of name changes resulting in a delay in naming clades, until an entire classification is developed.

As a result of this, taxonomy falls progressively farther behind knowledge of phylogeny, as well supported clades remain unnamed. With the latest burst of new information about phylogeny due to the recent advances in molecular biology and computer technology, this is a serious drawback as most of the phylogenetic information are not being translated into taxonomy, with the use of pre-existing system.

The use of the Phylocode will allow researches to overcome this disadvantage and name newly discovered clades much more easily, as they are discovered.

(b) The Phylocode will also improve nomenclatural stability, when it is extended to the naming of species, where it will remove instability in species names leading to revision of generic limits under the pre-existing codes.

However, when species will be named according to the principles of Phylocode, there will be absence of hierarchical information in species names and one will be unable to infer phylogenetic relationship from the species name in the way one can infer genus assignment from species names governed by the pre-existing codes.

This is because, according to the Phylocode, the primary purpose of the name of a taxon is to provide a means of referring unambiguously to a taxon, and not to indicate its relationship. However, the phylogenetic position can easily be indicated, by associating the species name with the names of one or more clades to which it belongs.

(c) The abandonment of ranks in Phylocode will also eliminate the error caused by many researchers who treat taxa at the same rank as if they are comparable in some biological meaningful way, due to which they commit the error of counting clades or species that possess properties relevant to the question of’ interest, or tracing the evolution of these properties on a phylogenetic tree, leading to faulty reasoning.