History
Ultimately, phylogenetic nomenclature is a result of the general acceptance of branching in the course of evolution, represented in the diagrams of Jean-Baptiste Lamarck and later writers like Charles Darwin and Ernst Haeckel. In 1866, Haeckel for the first time constructed a single tree of all life (see figure) and immediately proceeded to translate it into a classification. This classification was rank-based, as was usual at the time, but did not contain taxa that Haeckel considered polyphyletic In it, Haeckel introduced the rank of phylum which carries a connotation of monophyly in its name (literally meaning "stem").
Ever since, it has been debated in which ways and to what extent the phylogeny of life should be used as a basis for its classification, with views ranging from "numerical taxonomy" (phenetics) over "evolutionary taxonomy" (gradistics) to "phylogenetic systematics". From the 1960s onwards, rankless classifications were occasionally proposed, but in general the principles of rank-based nomenclature were used by all three schools of thought.
Most of the basic tenets of phylogenetic nomenclature (lack of obligatory ranks, and something close to phylogenetic definitions) can, however, be traced to 1916, when Edwin Goodrich interpreted the name Sauropsida, erected 40 years earlier by T. H. Huxley, to include the birds (Aves) as well as part of Reptilia, and coined the new name Theropsida to include the mammals as well as another part of Reptilia. Goodrich did not give them ranks, and treated them exactly as if they had phylogenetic definitions, using neither contents nor diagnostic characters to decide whether a given animal should belong to Theropsida, Sauropsida, or something else once its phylogenetic position was agreed upon. Goodrich also opined that the name Reptilia should be abandoned once the phylogeny of the reptiles would be better known.
The principle that only clades should be formally named became popular in some circles in the second half of the 20th century. It spread together with the methods for discovering clades (cladistics) and is an integral part of phylogenetic systematics (see above). At the same time, it became apparent that the obligatory ranks that are part of the traditional systems of nomenclature produced problems. Some authors suggested abandoning them altogether, starting with Willi Hennig's abandonment of his earlier proposal to define ranks as geological age classes.
The first use of phylogenetic nomenclature in a publication can be dated to 1986. Theoretical papers outlining the principles of phylogenetic nomenclature, as well as further publications containing applications of phylogenetic nomenclature (mostly to vertebrates), soon followed (see Literature section).
In an attempt to avoid a schism in the biologist community, "Gauthier suggested to two members of the ICZN to apply formal taxonomic names ruled by the zoological code only to clades (at least for supraspecific taxa) and to abandon Linnean ranks, but these two members promptly rejected these ideas" (Laurin, 2008: 224). This led Kevin de Queiroz and the botanist Philip Cantino to start drafting their own code of nomenclature, the PhyloCode, for regulating phylogenetic nomenclature.
Read more about this topic: Phylogenetic Nomenclature
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