There are still unknowns in the phylogenetic relationships and morphological evolution of the early evolution of vertebrates. Palaeospondylus gunni from the Middle Devonian represents one such enigma, whose phylogenetic position has remained unknown for the past 120 years. Homologies of skeletal elements in Palaeospondylus cranium was not well understood, since the interpretation of the skeletal homologies depends on the higher taxon being compared. Until recently, data about the morphotypes of the extant vertebrates had been incomplete, and the precise morphology of Palaeospondylus cranium itself was not observable. In the past decade, progress has been made in developmental biology of extant vertebrates, in particular the hagfish and coelacanth embryos. Interestingly, there is a morphological similarity between Palaeospondylus and the hagfish embryo at a certain developmental stage, and we once proposed that Palaeospondylus was a stem-hagfish. However, the proof was not conclusive, and we decided to conduct a detailed observation of Palaeospondylus fossils. To observe the complete cranial skeleton of Palaeospondylus, we searched for specimens in which the entire cranium was still embedded within the matrix and only the tail was exposed on the rock. We found two hopeful specimens and observed them using synchrotron radiation X-ray micro-computed tomography, eventually showing complete cranial skeletons in both specimens with their microstructures. Based on the skeletal histology, including the distribution of cell lacunae, and the pattern of displacement of skeletal elements observed so far, we were able to identify the skeletal boundaries in Palaeospondylus cranium. The cranial morphology of Palaeospondylus corresponds to the morphotype of tetrapodomorph crania, in particular the combination of the intracranial joint, basicranial fenestra, distinct basipterygoid process and lateral commissure carrying a hyomandibular articulation. The skeletal element articulated with the caudal end of the Palaeospondylus cranium, which had been particularly enigmatic, was found to be the hyomandibula. While the hyomandibula is large relative to the Meckel's cartilage, the proportional length of the hyomandibula relative to the other cranial skeletal elements in Palaeospondylus is not necessarily unusual for tetrapodomorphs. The strangeness of the cranial morphology of Palaeospondylus is attributable largely to the unusually small size of the Meckel's cartilage. The homology correspondences enabled us to perform cladistic analyses for the first time, showing the inference that Palaeospondylus is closely related to stem-tetrapods such as Acanthostega and 'elpistostegalians'. The absence of teeth, dermal bones, and skeletal elements of paired appendages in Palaeospondylus indicates that there was a heterochronic evolution in which these did not develop concurrently with other organs of the body. Palaeospondylus fossils tend to be preserved in specific layers, where Palaeospondylus and Mesacanthus of approximately the same body size were accumulated. It is possible that the same body size may have sorted during transportation before burial. Therefore, it is difficult to conclude whether the bodies hitherto found as Palaeospondylus reflect the entire ontogenetic stages of this animal. Palaeospondylus may have been a larval form, with teeth, dermal bones, and paired appendages appearing as it grew, or the form preserved as Palaeospondylus fossils may have been an adult.
Unveiling the enigmatic Middle Devonian vertebrate, Palaeospondylus