The Triassic Period (~252–201.5 Ma) saw a transformative radiation and reorganization of continental tetrapod diversity following the end-Permian Extinction, including an assemblage of diverse forms that do not survive the end-Triassic (herein termed the 'endemic Triassic fauna', =ETF), as well as the earliest fossil representatives of all major modern tetrapod groups (herein termed the 'Living [Triassic to Recent] Fauna', =LTF; i.e. Salientia, Caudata, Gymnophiona, Mammaliaformes, Squamata, Rhynchocephalia, Testudinata, Crocodylomorpha, and Dinosauria). With few exceptions, only the LTF assemblage survives the end-Triassic Extinction (~201.5 Ma), highlighting the Late Triassic (~227–201.5 Ma) record as essential for understanding this pivotal transition and the evolutionary and ecological origins of post-Triassic non-marine tetrapod faunas, including those of present day. Micro-microvertebrate bonebeds are arguably the best proxy for tracking continental vertebrate biodiversity, however gaps in their Late Triassic record obscure patterns and drivers of evolutionary, ecological, and environmental change during the rise of LTF communities. In my dissertation, I use new data collected from Upper Triassic microvertebrate bonebeds from North America, and particularly the Thunderstorm Ridge site (PFV 456) in Petrified Forest National Park, Arizona, U.S.A, to fill gaps in the evolutionary record of specific groups (e.g., lissamphibians and lepidosaurs), as well as the vertebrate paleocommunity record of Triassic equatorial Pangaea. My first chapter describes and analyzes an assemblage of gymnophionomorph (stem caecilian) bones from PFV 456 which represent the oldest-known caecilian fossils globally. As the oldest caecilian fossils, they provide new support for the dissorophoid temnospondyl affinities of caecilians and other living amphibians, evidence of a step-wise acquisition of caecilian anatomies associated with fossoriality, and evidence of an ancient pattern of equatorial biogeographic restriction in caecilians from the Triassic to the present day. My second chapter describes and analyzes an assemblage of lepidosauromorphs from the Late Triassic of Equatorial Pangaea, providing new insights into the step-wise evolution tooth and jaw morphologies near the divergence of living lepidosaur clades (Squamata and Rhynchocephalia), and showing evidence for the Triassic acquisition in stem squamates and non-squamate lepidosaurs of dental features conserved in living squamates. The third chapter uses apomorphy-based identifications to describe the vertebrate diversity of the Thunderstorm Ridge site (PFV 456), providing evidence for the most species rich continental vertebrate community yet-known from the Triassic, with 55 vertebrate taxa. Nearly all LTF clades are present, predating similar assemblages from the early Jurassic by over 20 million years, and indicating that the assembly of the first LTF communities by at least 220 million years ago, long before the Triassic-Jurassic Extinction event (~201.5). The presence of this exceptional diversity may be linked to the climatic and environmental settings of equatorial Pangaea during the Triassic. / Doctor of Philosophy / The Triassic Period, lasting about 50 million years from approximately 252 to 201.5 million years ago, was a period of transformation for life living on land. During the Triassic, we see the first fossil evidence for the evolution of the tetrapod (animals with a backbone and limbs) groups familiar to us from the present-day Earth, including frogs, salamanders, caecilians, mammals, lizards, the tuatara, turtles, crocodilians, and dinosaurs. Understanding the early evolution of these groups is limited by gaps in the Triassic fossil record, particularly for groups with small-bodies and delicate skeletons like frogs, salamanders, caecilians, and lizards. The poor Triassic records of these groups also limits understandings of when and where tetrapod communities resembling those of the present-day first assembled, and whether events like the Triassic-Jurassic Extinction event (~201.5 million years ago) shaped the organization of these communities. To fill these gaps, I have focused on collecting data from microvertebrate bonebeds, layers of rock that preserve the small, delicate bones of small-bodied vertebrates that are typically rare elsewhere. New microvertebrate data collected from Late Triassic rocks in North America, and particularly the 220 million year old Thunderstorm Ridge site (PFV 456) in Petrified Forest National Park, Arizona, U.S.A., provide evidence for exceptionally diverse tetrapod communities, opening a window onto the early evolution of living tetrapods and their ecological interactions. In my first chapter I describe and analyze the bones of a stem caecilian amphibian from the Thunderstorm Ridge site. These are the oldest caecilian fossils on Earth, and they provide new evidence for the evolutionary relationships, ecologies, and biogeography of these enigmatic living amphibians. In my second chapter I describe and analyze the jaws and teeth of early lizards and their close relatives from North American Late Triassic microvertebrate sites, showing that the tooth and jaw morphologies of living lizards like geckos and skinks first evolved in their Triassic relatives. In my third chapter, I describe and identify the 55 vertebrate taxa recovered from the Thunderstorm Ridge site, showing that it is the most diverse tetrapod community known from the Triassic. The diversity of early members of living tetrapod groups at Thunderstorm Ridge suggests that tetrapod communities resembling those of the present-day first assembled in the Triassic, at least 20 million years prior to the Triassic-Jurassic Extinction.

L’anatomie interne des crânes des stégocéphales Stanocephalosaurus (Temnospondyli), Laosuchus (Chroniosuchia) et Diplocaulus (Lepospondyli) a pu être révélée par l’utilisation de la tomographie à rayons X et a permis de mieux comprendre leur paléobiologie : 1) l’oreille moyenne de Stanocephalosaurus serait adaptée à la perception de sons dans le milieu subaquatique ; 2) des canaux sensoriels intra-osseux ont été identifiés chez Laosuchus. La morphologie endocrânienne a ensuite été utilisée dans une analyse phylogénétique portant sur les relations de parentés controversées entre stégocéphales et lissamphibiens. Cette analyse montre que la monophylie des lissamphibiens serait due à un phénomène d’attraction des longues branches, résultant de l’optimisation de la simplification crânienne, identifiée comme une convergence. Les morphologies de la boite crânienne, du stapes et du palais favorisent une origine diphylétique des lissamphibiens parmi les temnospondyles. / The intracranial anatomy of the stegocephals Stanocephalosaurus (Temnospondyli), Laosuchus (Chroniosuchia) and Diplocaulus (Lepospondyli) has been revealed by X-rays tomography and allowed to better understand their paleobiology: 1) the middle ear of Stanocephalosaurus would be an underwater adapted hearing system; 2) intraosseous sensorial canals have been identified in Laosuchus. The endocranial morphology have been included in a phylogenetic analysis on the debated relationships between stegocephals and lissamphibians. This analysis shows that the monophyly of Lissamphibia may result from a long-branch attraction, due to the optimisation of the cranial simplification, here as identified convergent. The morphologies of braincase, stapes and palate favour a biphyletic origin of lissamphibians among temnospondyls.

Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in cryptobranchid salamanders, suggesting a conserved system of female heterogamety in this group. At much deeper scales, phylogenetic analyses of hundreds of protein-coding genes across all major amphibian lineages are employed to reveal the backbone topology and evolutionary timescales of the amphibian tree of life, suggesting a new set of hypotheses for relationships among extant amphibians. Yet, genomic data on their own are no panacea for the thorniest questions in evolutionary biology, and this work also demonstrates the power of a model testing framework to dissect support for different phylogenetic and population genetic hypotheses across different regions of the genome.