Lee, M. S. Y. 2005. Choosing stable reference taxa in phylogenetic nomenclature. Zoologica Scripta 34: 313-318. (original) (raw)

Stability and Universality in the Application of Taxon Names in Phylogenetic Nomenclature

Systematic Biology, 2006

A major task for biological nomenclature and taxonomy is to provide names and tools for communication about biodiversity. This is even more important in times of bioinformatics where scientists often search GenBank and other databases for phylogenetic information. Comparative studies on a large number of unrelated taxa by scientists that are not taxonomic specialists are likely to become even more common in the future. Hence, a nomenclatural system that helps scientists to unequivocally find information about a particular taxon has high priority.

Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names

Zoologica Scripta, 2008

Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names. -Zoologica Scripta, 37 , 337-347. When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.

Phylogenetic nomenclature, hierarchical information, and testability.

2013

In a continuing debate about the usefulness of phylogenetic nomenclature, Platnick (2012) has apparently conceded the two main points of our previous paper (de Queiroz and Donoghue 2011) by providing no counter-arguments. First, contrary to Platnick's previous assertions, when appropriate comparisons are made (i.e., between taxonomies consisting of the same-named groups), there are no differences in information content, as measured by implied three-taxon statements, between hierarchical taxonomies whose names are governed by rank-based versus phylogenetic nomenclature. The reason is that three-taxon informativeness is a property of the clades that are recognized (the taxonomy) rather than of the rules governing their names (the nomenclatural system). Second, phylogenetic nomenclature outperforms its rank-based counterpart when the approaches are compared using a nomenclaturally relevant criterion. Specifically, phylogenetically defined names result in fewer unnecessary name changes in the context of new phylogenetic hypotheses.

On the other "phylogenetic systematics"

Cladistics, 2000

De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor “widely held belief” systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new “Phylogenetic Systematics” - instead we have been presented with a vague and sketchy manifesto based upon the assertion that “clades are individuals” and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for “node pointing,” yet even their own examples show that the opposite is true, and their “node pointing” system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the “node pointing” system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.

Conceptual issues in phylogeny, taxonomy, and nomenclature

Bijdragen tot de Dierkunde

Phylogenetic hypotheses are designed and tested (usually in implicit form) on the basis of a set of presumptions, that is, of statements describing a certain order of things in nature. These statements are to be accepted as such, no matter whatever evidence for them exists, but only in the absence of reasonably sound evidence pleading against them. A set of the most current phylogenetic presumptions is discussed, and a factual example of a practical realization of the approach is presented.