Stack, Jack R.2025-05-132025-05-132025-05-12vt_gsexam:43082https://hdl.handle.net/10919/132197Nearly three hundred years have passed since Carl von Linné published the system that gave naturalists the tools to name and organize the colossal diversity of living things on Earth. We estimate that there are between 3 and 100 million species on Earth, approximately 1.2 million of which have been named. However, living species comprise perhaps 1 percent or less of all the species that have existed in the over 3.5-billion-year history of life on Earth. Therefore, a core challenge of systematics is creating a system that can incorporate the living and the dead in a unified network of biological knowledge. Most of our knowledge from extinct species is based on fossils, which are (typically) lamented by systematists for being devoid of soft-tissue, behavioral, and genetic data. However, fossils provide a deep-time perspective on the history of life, including the tempo of evolutionary change, the acquisition of traits, and give us a glimpse at groups that have no living representatives. The goal of my dissertation is to explore problems that arise from attempting to integrate data from living and extinct species to study evolutionary history. I use the ray-finned fishes (Actinopterygii) as a study system due to their excellent, ~380-million-year fossil record and their extraordinary living diversity, which includes one out of every two vertebrate species. My first chapter explores an empirical case study of the instability that can arise when fossil and living taxa are included in the same phylogenetic search. I describe a new species and show how novel methods based in information theory for measuring the variation in phylogenetic trees can be applied to detect and stabilize phylogenetic studies with extinct taxa. My second chapter describes a new species of the Triassic ray-finned fish Saurichthys from newly collected material in the Upper Triassic Dockum Group of northwest Texas. This description is a launching point to discuss using disarticulated microvertebrate actinopterygian remains to inform our conception of the deep history of form and function in fishes. Chapter three is a description of a new species of ray-finned fish based on lower jaw specimens collected from the Late Triassic Thunderstorm Ridge locality in Petrified Forest National Park, Arizona, USA. Placing this new animal into the context of an exceptionally preserved assemblage of fishes provides critical perspective on the early evolutionary history of freshwater fish communities, which host ~44% of living fish species. In my fourth and final chapter, I construct a novel phylogenetic framework to reconstruct the evolutionary relationships of ray-finned fishes in deep time. I explore how novel methods for computing anatomy with vocabularies (ontologies) can help systematists integrate living and fossil species. Overall, I find that fossils provide essential perspective on the deep history of ray-finned fish diversity, form, and function. Therefore, the use of information theory, ontologies, and microfossils to bridge living and fossil species can help us build a more comprehensive knowledge of the history of life on Earth.ETDenCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 InternationalVertebrate paleontologyphylogeneticssystematicsActinopterygiiPaleozoicPermianTriassicmorphologyDissertation