We present a rank-free phylogenetic nomenclature for 25 well-established ancient clades of living turtles. This is the first attempt to document fully the nomenclatural history of a clade with the intent of proposing a coherent nomenclatural system to replace the traditional rank-based nomenclature. Because of the imperative to retain connectivity to the literature for information retrieval, due consideration is given to balancing the desire to develop a consistent system against the desire to conserve traditional associations between names, taxa (i.e., clades), and characters. Novel issues and problems that emerged during this review include: the unclear name/clade association of traditional names; the creation of synonymy lists from which to choose a name; difficulties associated with selecting a single criterion for choosing among multiple 'subjectively synonymous' names; identifying authorship for a converted traditional name; and the potential loss of nomenclatural information due to 'functional homonyms.' This work may provide a useful road map to those intent on converting their traditional rank-based nomenclatures to explicitly phylogenetic nomenclatures under the precepts of the PhyloCode.

Developing a protocol for the conversion of rank-based taxon names to phylogenetically defined clade names, as exemplified by turtles

In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relationships,
we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We
have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod
clades. A stem-based ( total-group) definition of Tetrapoda is preferred over apomorphy- and node-based
(crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP*
search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differences
between these trees concern: (1) the internal relationships of ai¨stopods, the three selected species of which
form a trichotomy; (2) the internal relationships of embolomeres, with Archeria crassidisca and Pholiderpeton scutigerum
collapsed in a trichotomy with a clade formed by Anthracosaurus russelli and Pholiderpeton attheyi ; (3) the internal
relationships of derived dissorophoids, with four amphibamid species forming an unresolved node with a clade
consisting of micromelerpetontids and branchiosaurids and a clade consisting of albanerpetontids plus basal
crown-group lissamphibians ; (4) the position of albenerpetontids and Eocaecilia micropoda, which form an unresolved
node with a trichotomy subtending Karaurus sharovi, Valdotriton gracilis and Triadobatrachus massinoti ; (5) the
branching pattern of derived diplocaulid nectrideans, with Batrachiderpeton reticulatum and Diceratosaurus brevirostris
collapsed in a trichotomy with a clade formed by Diplocaulus magnicornis and Diploceraspis burkei. The results of the
original parsimony run – as well as those retrieved from several other treatments of the data set ( e.g. exclusion
of postcranial and lower jaw data ; character reweighting ; reverse weighting ) – indicate a deep split of early
tetrapods between lissamphibian- and amniote-related taxa. Colosteids, Crassigyrinus, Whatcheeria and baphetids
are progressively more crownward stem-tetrapods. Caerorhachis, embolomeres, gephyrostegids, Solenodonsaurus
and seymouriamorphs are progressively more crownward stem-amniotes. Eucritta is basal to temnospondyls,
with crown-lissamphibians nested within dissorophoids. Westlothiana is basal to Lepospondyli, but evidence for
the monophyletic status of the latter is weak. Westlothiana and Lepospondyli form the sister group to diadectomorphs
and crown-group amniotes. Tuditanomorph and microbrachomorph microsaurs are successively
more closely related to a clade including proximodistally : (1) lysorophids; (2) Acherontiscus as sister taxon to
adelospondyls; (3) scincosaurids plus diplocaulids ; (4) urocordylids plus ai¨stopods. A data set employing cranial
characters only places microsaurs on the amniote stem, but forces remaining lepospondyls to appear as sister
group to colosteids on the tetrapod stem in several trees. This arrangement is not significantly worse than the tree
topology obtained from the analysis of the complete data set. The pattern of sister group relationships in the
crownward part of the temnospondyl-lissamphibian tree re-emphasizes the important role of dissorophoids in
the lissamphibian origin debate. However, no specific dissorophoid can be identified as the immediate sister taxon
to crown-group lissamphibians. The branching sequence of various stem-group amniotes reveals a coherent set
of internested character-state changes related to the acquisition of progressively more terrestrial habits in several
Permo-Carboniferous forms.

Early tetrapod relationships revisited.

This is an abbreviated version of a paper that appears in full in the Electronic supplement to Taxon. Phylogenetic definitions are provided for the names of 20 clades of vascular plants (plus 33 others in the electronic supplement). Emphasis has been placed on well-supported clades that are widely known to non-specialists and/or have a deep origin within Tracheophyta or Angiospermae. These treatments follow the draft PhyloCode and illustrate the application ofphylogenetic nomenclature in a variety of nomenclatural and phylogenetic contexts. Phylogenetic nomenclature promotes precision in distinguishing crown, apomorphy-based, and total clades, thereby improving communication about character evolution and divergence times. To make these distinctions more transparent without increasing the number of entirely different names that must be learned, the following naming conventions (which have been adopted in the most recent draft of the PhyloCode) are employed here: widely known names are applied to crown clades, and the corresponding total clade (i.e., crown plus stem) is named "Pan-X", where "X" is the name of the crown (e.g., Pan-Spermatophyta for the total clade of plants that share more recent ancestry with extant seed plants than with any other crown clade). If a name "X" that is based etymologically on an apomorphy is applied to the crown, the name "Apo-X" is applied to the clade for which this trait is synapomorphic (e.g., Apo-Spermatophyta for the clade originating from the first plant with seeds). Crown clade names can be defined by three kinds of definitions, two of which are used here: standard node-based and branch-modified node-based. The latter is particularly useful when outgroup relationships of a crown clade are better known than basal relationships within the clade. Criteria and approaches used here to choose among competing preexisting names for a clade, to select a definition type, to choose appropriate specifiers, and (in some cases) to restrict the use of a name to certain phylogenetic contexts may be widely applicable when naming other clades. The phylogenetic definitions proposed here should help focus future discussions of the PhyloCode on real definitions rather than simplified hypothetical ones.

/pdf/towards-a-phylogenetic-nomenclature-of-tracheophyta-1gj7bstl5l.pdf

Towards a phylogenetic nomenclature of Tracheophyta

https://www.cell.com/trends/parasitology/pdf/S1471-4922(12)00194-8.pdf

Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed.

Bertrand, Y., and M. Harlin. 2006. Stability and universality in the application of taxon names in phylogenetic nomenclature. Syst. Biol. 55:848–858. Bininda-Emonds, O. R. P. 2004. The evolution of supertrees. Trends Ecol. Evol. 19:315–322. Bryant, H. N., and P. D. Cantino. 2002. A review of criticisms of phylogenetic nomenclature: Is taxonomic freedom the fundamental issue? Biol. Rev. 77:39–55. Cantino, P. D., and K. de Queiroz. 2007. International Code of Phylogenetic Nomenclature, Version 4b. Available at http://www.ohiou. edu/phylocode. Cantino, P. D., and R. G. Olmstead. 2004. Phylogenetic nomenclature of Lamiaceae. Abstracts of the First International Phylogenetic Nomenclature Meeting (Paris): 13. Available at http://www.ohiou. edu/phylocode/events.html. Cantino, P. D., R. G. Olmstead, and S. J. Wagstaff. 1997. A comparison of phylogenetic nomenclature with the current system: A botanical case study. Syst. Biol. 46:313–331.

/pdf/taxon-sampling-affects-inferences-of-macroevolutionary-3rvde1j5vb.pdf

Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees.

The proposal to implement a phylogenetic nomenclatural system (governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy, in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.

Harold N. Bryant

Papers

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?