Jacques A. Gauthier

Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names

Defining the names of taxa in terms of common ancestry, that is, using phylogenetic definitions of taxon names, departs from a tradition of character-based definitions by granting the concept of evolution a central role in taxonomy. Phylogenetic definitions bear on other taxonomic principles and practices, including the following: (1) Names cannot be applied to nonmonophyletic taxa as the result of mistaken ideas about relationships or characters. Such mistakes do not affect conclusions about the monophyly of taxa but about their content and/or diagnoses. Because nonmonophyletic taxa can only be named deliberately, they are easily avoid- ed. (2) Definitions are clearly distinguished from descriptions and diagnoses. Definitions are ontological statements about the existence of entities that result from the relationships of common ancestry among their parts; descriptions and diagnoses are epistemological statements about how we recognize the parts of those entities. (3) By precisely specifying the clade (ancestor) with which a name is associated, phylogenetic definitions clarify the limits of taxa, and this in turn clarifies related phenomena such as time of origin and duration. (4) Unlike the case for character-based intensional definitions and enumerative extensional definitions, phylogenetic definitions provide an unambiguous criterion for synonymy of taxon names: names are syn- onymous if they refer to clades stemming from the same ancestor. (5) Because of their relevance to synonymy, phylogenetic definitions also are relevant to priority, of both names and authorship. In phylogenetic taxonomy, priority is based not on first use of a name at a particular rank or rank-group but on first use of a name in association with a particular ancestor. (Definition; diagnosis; nomenclature; phylogeny; priority; synonymy; taxonomy.)

Toward a phylogenetic system of biological nomenclature

Despite the widely held belief that modem biological taxonomy is evolutionary, some of the most fundamental concepts and principles in the current system of biological nomenclature are based on a nonevolutionary convention that pre-dates widespread acceptance of an evolutionary world view by more than a century. The development of a phylogenetic system of nomenclature requires reformulating these concepts and principles so that they are no longer based on the Linnean categories but on the tenet of common descent.

DEVELOPING A PROTOCOL FOR THE CONVERSION OF RANK-BASED TAXON NAMES TO PHYLOGENETICALLY DEFINED CLADE NAMES, AS EXEMPLIFIED BY TURTLES

Abstract 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.

Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record

Abstract We assembled a dataset of 192 carefully selected species—51 extinct and 141 extant—and 976 apomorphies distributed among 610 phenotypic characters to investigate the phylogeny of Squamata (“lizards,” including snakes and amphisbaenians). These data enabled us to infer a tree much like those derived from previous morphological analyses, but with better support for some key clades. There are also several novel elements, some of which pose striking departures from traditional ideas about lizard evolution (e.g., that mosasaurs and polyglyphanodontians are on the scleroglossan stem, rather than parts of the crown, and related to varanoids and teiids, respectively). Long-bodied, limb-reduced, “snake-like” fossorial lizards—most notably dibamids, amphisbaenians and snakes—have been and continue to be the chief source of character conflict in squamate morphological phylogenetics. Carnivorous lizards (especially snakes, mosasaurs and varanoids) have proven a close second. Genetic data, presumably less burdened by the potential for adaptive convergence related to fossoriality, were expected to resolve these conflicts. Although recent gene phylogenies seem to do so, they also differ radically from any phylogeny based on the phenotype, especially for the most ancient crown squamate divergences that occured during the latter half of the Mesozoic. Our study relied on traditionally prepared specimens as well as high-resolution computed tomography scans that afforded unprecendented access to the cranial anatomy of Squamata. This, along with the inclusion of stem fossils, provided an unparalleled sample of the phenotype enabling us to more fully explore the extreme incongruences between molecular and morphological topologies for the squamate tree of life. Despite this extensive new database, we were unable to find morphological support for the major rearrangement of the deep divergences in Squamata proposed by recent molecular studies. Instead, our data strongly support the same fundamental topology suggested by most previous morphological studies—an Iguania-Scleroglossa basal split, a sister-group relationship between Gekkota and Autarchoglossa, and the divergence between Anguimorpha and Scincomorpha—and documents the extreme degree of morphological homoplasy required by those molecular topologies.

Palaeoecology of triassic stem turtles sheds new light on turtle origins.

Competing hypotheses of early turtle evolution contrast sharply in implying very different ecological settings—aquatic versus terrestrial—for the origin of turtles. We investigate the palaeoecology of extinct turtles by first demonstrating that the forelimbs of extant turtles faithfully reflect habitat preferences, with short‐handed turtles being terrestrial and long‐handed turtles being aquatic. We apply this metric to the two successive outgroups to all living turtles with forelimbs preserved, Proganochelys quenstedti and Palaeochersis talampayensis, to discover that these earliest turtle outgroups were decidedly terrestrial. We then plot the observed distribution of aquatic versus terrestrial habits among living turtles onto their hypothesized phylogenies. Both lines of evidence indicate that although the common ancestor of all living turtles was aquatic, the earliest turtles clearly lived in a terrestrial environment. Additional anatomical and sedimentological evidence favours these conclusions. The freshwater aquatic habitat preference so characteristic of living turtles cannot, consequently, be taken as positive evidence for an aquatic origin of turtles, but must rather be considered a convergence relative to other aquatic amniotes, including the marine sauropterygians to which turtles have sometimes been allied.

Transitional fossils and the origin of turtles

The origin of turtles is one of the most contentious issues in systematics with three currently viable hypotheses: turtles as the extant sister to (i) the crocodile–bird clade, (ii) the lizard–tuatara clade, or (iii) Diapsida (a clade composed of (i) and (ii)). We reanalysed a recent dataset that allied turtles with the lizard–tuatara clade and found that the inclusion of the stem turtle Proganochelys quenstedti and the ‘parareptile’ Eunotosaurus africanus results in a single overriding morphological signal, with turtles outside Diapsida. This result reflects the importance of transitional fossils when long branches separate crown clades, and highlights unexplored issues such as the role of topological congruence when using fossils to calibrate molecular clocks.

Mass extinction of lizards and snakes at the Cretaceous–Paleogene boundary

The Cretaceous–Paleogene (K-Pg) boundary is marked by a major mass extinction, yet this event is thought to have had little effect on the diversity of lizards and snakes (Squamata). A revision of fossil squamates from the Maastrichtian and Paleocene of North America shows that lizards and snakes suffered a devastating mass extinction coinciding with the Chicxulub asteroid impact. Species-level extinction was 83%, and the K-Pg event resulted in the elimination of many lizard groups and a dramatic decrease in morphological disparity. Survival was associated with small body size and perhaps large geographic range. The recovery was prolonged; diversity did not approach Cretaceous levels until 10 My after the extinction, and resulted in a dramatic change in faunal composition. The squamate fossil record shows that the end-Cretaceous mass extinction was far more severe than previously believed, and underscores the role played by mass extinctions in driving diversification.

The laterosphenoid bone of early archosauriforms

ABSTRACT The laterosphenoid is an ossification of the pila antotica neurocranial cartilage in the anterior sidewall of the braincase of crocodylians and birds. Contrary to published reports, the bone is present in the basal archosauriforms Proterosuchus fergusi, Euparkeria capensis, and Erythrosuchidae, taxa that diverged prior to the origin of the archosaurian crown group. Its presence is thus a synapomorphy of Archosauriformes rather than of Archosauria. The bone appears to have been induced by shifting jaw muscle origins from the skull roof to the anterolateral wall of the braincase. Additional innovations in the archosauriform feeding apparatus, such as a mandibular fenestra, appear to reflect changes in jaw muscles that may, in turn, facilitate predaceous habits. We review the historical development of the names of bones in the anterior sidewall of the amniote braincase and argue for the use of the term laterosphenoid, rather than either pleurosphenoid or orbitosphenoid, for this bone in all Archosau...

A transitional snake from the Late Cretaceous period of North America

Snakes are the most diverse group of lizards, but their origins and early evolution remain poorly understood owing to a lack of transitional forms. Several major issues remain outstanding, such as whether snakes originated in a marine or terrestrial environment and how their unique feeding mechanism evolved. The Cretaceous Coniophis precedens was among the first Mesozoic snakes discovered, but until now only an isolated vertebra has been described and it has therefore been overlooked in discussions of snake evolution. Here we report on previously undescribed material from this ancient snake, including the maxilla, dentary and additional vertebrae. Coniophis is not an anilioid as previously thought; a revised phylogenetic analysis of Ophidia shows that it instead represents the most primitive known snake. Accordingly, its morphology and ecology are critical to understanding snake evolution. Coniophis occurs in a continental floodplain environment, consistent with a terrestrial rather than a marine origin; furthermore, its small size and reduced neural spines indicate fossorial habits, suggesting that snakes evolved from burrowing lizards. The skull is intermediate between that of lizards and snakes. Hooked teeth and an intramandibular joint indicate that Coniophis fed on relatively large, soft-bodied prey. However, the maxilla is firmly united with the skull, indicating an akinetic rostrum. Coniophis therefore represents a transitional snake, combining a snake-like body and a lizard-like head. Subsequent to the evolution of a serpentine body and carnivory, snakes evolved a highly specialized, kinetic skull, which was followed by a major adaptive radiation in the Early Cretaceous period. This pattern suggests that the kinetic skull was a key innovation that permitted the diversification of snakes.

Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister‐relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super‐alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.