An ontological morphological phylogenetic framework for living and extinct ray-finned fishes (Actinopterygii)

The ray-finned fishes include one out of every two species of living vertebrates on Earth and have an abundant fossil record stretching 380 million years into the past. The division of systematic knowledge of ray-finned fishes between paleontologists working on extinct animals and neontologists studying extant species has obscured the relationships of fossil and living species and the origin of the actinopterygian crown group. In addition, the relationships of enigmatic groups of Paleozoic-Mesozoic ray-finned fishes that have been inferred as early members of the neopterygian total group, such as the †Bobasatraniidae and †Guildayichthyidae, are obscured by the divisions within and between paleontological and ichthyological knowledge. I built a systematic framework of living and extinct ray-finned fishes to trace the roots of the phylogenetic diversity of Actinopterygii in deep time and to infer the position of the †Bobasatraniidae and †Guildayichthyidae. I built this framework by integrating systematic data from paleontology and ichthyology with anatomical ontologies for ray-finned fish skeletal morphology from the Phenoscape Knowledgebase (https://phenoscape.org). Using ontologies allowed me to analyze dependencies within the character set, informing model construction in Bayesian phylogenetic analysis. The phylogenetic analyses indicate that †Bobasatraniidae and †Guildayichthyidae form a clade within Actinopterygii separate from Neopterygii, Acipenseriformes, and Polypteridae. Additional insights from the novel framework are support for the placement of the early Permian †Brachydegma as a member of pan-Neopterygii and the Mesozoic †Coccolepidae as a late-surviving clade of stem-group actinopterygians. Further, I demonstrate an approach to morphological phylogenetics that unites systematic knowledge of living and fossil species in a fully accessible, computable, and repeatable format. Unification of systematic knowledge from living and extinct ray-finned fishes allowed me to: (1) infer the divergence times and interrelationships of pan-Actinopterygii and (2) place the traits of Actinopterygii into the context of the 380 million year history of ray-finned fish morphological evolution.