New concepts and methods for phylogenetic taxonomy and nomenclature in zoology, exemplified by a new ranked cladonomy of recent amphibians (Lissamphibia)

Although currently most taxonomists claim to adhere to the concept of ‘phylogenetic taxonomy’, in fact most of the zoological classifications currently published are only in part ‘phylogenetic’ but include also phenetic or gradist approaches, in their arbitrary choices of the nodes formally recognised as taxa and in their attribution of ranks to these taxa. We here propose a new approach to ‘phylogenetic taxonomy and nomenclature’, exemplified by a phylogenetic classification or cladonomy of the extant amphibians (subclass Lissamphibia of the class Amphibia) derived from a supermatrix-based phylogenetic analysis using 4060 amphibian species, i.e. about half of the 8235 species recognised on 31 October 2020. These taxa were represented by a mean of 3029 bp (range: 197–13849 bp) of DNA sequence data from a mean of 4 genes (range: 1‒15). The cladistic tree thus generated was transferred into a classification according to a new taxonomic and nomenclatural methodology presented here, which allows a bijective or isomorphic relationship between the phylogenetic hypothesis and the classification through a rigorous use of suprageneric ranks, in which their hierarchy mirrors the structure of the tree. Our methodology differs from all previous ones in several particulars: [1] whereas the current International Code of Zoological Nomenclature uses only three ‘groups of names’ (species, genus and family), we recognise four nominal-series (species, genus, family and class); [2] we strictly follow the Code for the establishment of the valid nomen (scientific name) of taxa in the three lower nominal-series (however, in a few situations, we suggest improvements to the current Rules of the Code); [3] we provide precise and unambiguous Criteria for the assignment of suprageneric nomina to either the family- or the class-series, excluding nomina proposed expressly under unranked or pseudoranked nomenclatural systems; [4] in the class-series, for which the Code provides only incomplete Rules concerning availability, we provide precise, complete and unambiguous Criteria for the nomenclatural availability, taxonomic allocation and nomenclatural validity and correctness of nomina; [5] we stress the fact that nomenclatural ranks do not have biological definitions or meanings and that they should never be used in an ‘absolute’ way (e.g., to express degrees of genetic or phenetic divergence between taxa or hypothesised ages of cladogeneses) but in a ‘relative’ way: two taxa which are considered phylogenetically as sister-taxa should always be attributed to the same nomenclatural rank, but taxa bearing the same rank in different ‘clades’ are by no means ‘equivalent’, as the number of ranks depends largely on the number of terminal taxa (species) and on the degree of phylogenetic resolution of the tree; [6] because of this lack of ‘equivalence’, some arbitrary criteria are necessary to fix a starting point for assigning a given suprageneric rank to some taxa, from which the ranks of all other taxa will automatically derive through a simple implementation of the hierarchy of ranks: for this purpose we chose the rank family and we propose a ‘Ten Criteria Procedure’ allowing to fix the position of this rank in any zoological classification. As a result of the implementation of this set of Criteria, we obtained a new ranked classification of extant lissamphibians using 25 suprageneric ranks below the rank class (11 class-series and 14 family-series ranks), and including 34 class-series and 573 family-series taxa, and where the 575 genera we recognise are referred to 69 families and 87 subfamilies. We provide new nomina and diagnoses for 10 class-series taxa, 171 family-series taxa, 14 genus-series taxa and 1 species. As many new species of amphibians are permanently described, this classification and its nomenclature will certainly have to change many times in the future but, using the clear, explicit, complete, automatic and unambiguous methodology presented here, these changes will be easy to implement, and will not depend on subjective and arbitrary choices as it has too often been the case in the last decades. We suggest that applying this methodology in other zoological groups would improve considerably the homogeneity, clarity and usefulness of zoological taxonomy and nomenclature.