The actinopterygian crown group (comprising all living ray-finned fishes) originated by the end of the Carboniferous. However, most late Paleozoic taxa are stem actinopterygians, and broadly resemble stratigraphically older taxa. The early Permian †Brachydegma caelatum is notable for its three-dimensional preservation and past phylogenetic interpretations as a nested member of the neopterygian crown. Here, we use computed microtomography to redescribe †Brachydegma, uncovering an unanticipated combination of primitive (e.g., aortic canal; immobile maxilla) and derived (e.g., differentiated occipital ossifications; posterior stem of parasphenoid; two accessory hyoidean ossifications; double jaw joint) endoskeletal features relative to most other Paleozoic actinopterygians. Some of these features were previously thought restricted to the neopterygian crown. The precise phylogenetic position of †Brachydegma is unclear, with placements either on the polypterid stem, or as an early-diverging stem neopterygian. However, our analyses decisively reject previous placements of †Brachydegma in the neopterygian crown. Critically, we demonstrate that key-endoskeletal components of the hyoid portion of the suspensorium of crown neopterygians appeared deeper in the tree than previously thought.

This dataset includes an evolving phylogenetic matrix of morphological characters. The matrix can be found in .nex and .tnt formats. Analyses of this matrix using various algorithms that are part of the TNT software, resulted in phylogenetic trees that are also part of this dataset. Finally, the tree resulting from a bayesian analysis using MrBayes is also included in this dataset.

Most trees can be opened either on Mesquite or directly with TNT, after loading the relevant phylogenetic matrix file.