An evidence-based reassessment of the phylogenetic relationships of conodonts shows that they are not “stem” gnathostomes, nor vertebrates, and not even craniates. A significant group of conodont workers have proposed or accepted a craniate designation for the conodont animal, an interpretation that is increasingly becoming established as accepted “fact”. Against this prevailing trend, our conclusion is based on a revised analysis of traditional morphological features of both discrete conodont elements and apparatuses, histological investigation and a revised cladistic analysis modifying that used in the keystone publication promoted as proof of the hypothesis that conodonts are vertebrates. Our study suggests that conodonts possibly were not even chordates but demonstration of this is beyond the scope of this paper. To summarize, in conodonts there is low cephalization; presence of simple V-shaped trunk musculature and unique large-crystal albid material in the elements; lack of a dermal skeleton including characteristic vertebrate hard tissues of bone, dentine and enamel; lack of odontodes with bone of attachment and a unique pulp system; lack of segmentally-arranged paraxial elements and dermal elements in median fins, all of which supports neither a vertebrate nor a craniate relationship for conodonts.

Recent gnathostomes are composed of two major clades, the chondrichthyans, or cartilaginous fishes, and the osteichthyans, or bony fishes and tetrapods. Recent chondrichthyans include about 1200 elasmobranch (sharks and rays) species, but only about 40 holocephalan (ratfish) species. Nevertheless, an important radiation of chondrichthyans took place in the Carboniferous (360–300 Myr), and gave rise to an important diversity of odd and poorly understood taxa, such as the iniopterygians, that are considered as related to extant holocephalans. However, the relationships between these taxa and the two extant chondrichthyan clades remain controversial. The material studied here by means of computed microtomography scanning using synchrotron radiation X-ray, consists of neurocrania from the Upper Carboniferous of Kansas and Oklahoma (USA), which are remarkably well preserved in three dimensions, and which belong to one of the two families of iniopterygians, the Sibyrhynchidae Zangerl & Case, 1973. A detailed description of these specimens provides more information about the cranial and brain anatomy of this taxon. No three-dimensionally preserved skull of any stem-holocephalan was known in detail to date, contrary to fossil elasmobranchs. The data presented here show the three-dimensionally preserved braincase of a possible stem-holocephalan as these new specimens share with extant chimaeroids some key neurocranial characters. This may provide means for a comparative study of skull anatomy in Paleozoic representatives of the main two chondrichthyan clades.

I present here a revision of the late Pleistocene Haplomastodon chimborazi (Proaño, 1922) material from Bolivar, Ecuador and a comparison with other New World trilophodont gomphotheres, and provide new morphological data in order to develop a novel phylogenetic hypothesis of South American (SA) proboscideans. Haplomastodon Hoffstetter, 1950 includes a single SA species whose valid name is H. chimborazi. Haplomastodon waringi (Holland, 1920) is considered to be an invalid taxon as it is based on undiagnosed material. Phylogenetic analysis supports the monophyly of SA gomphotheres (Cuvieroniinae) H. chimborazi, Cuvieronius hyodon (Fischer de Waldheim, 1814), and “Stegomastodon” platensis (Ameghino, 1888), based on five unambiguous characters. Conflicting evidence regarding the interrelationships of SA gomphotheres leads to three possible alternative hypotheses: two paired associations ((H. chimborazi, “S.” platensis) C. hyodon) and ((C. hyodon, “S.” platensis) H. chimborazi), and a trichotomy. These imply that the ancestral separation of the three SA taxa might be either the result of two successive dichotomous branchings or of a single trichotomous branching event. The latter hypothesis would be consistent with the disjunct fossil distribution of the three SA gomphothere species. “Stegomastodon” platensis is shown to be not closely related to North American (NA) Stegomastodon Pohlig, 1912, supporting its removal from the latter genus. The NA species Rhynchotherium cf. falconeri Osborn, 1923 is placed as the sister taxon of SA gomphotheres, on the basis of four unequivocal characters. NA Stegomastodon and the Asian Sinomastodon Tobien, Chen & Li, 1986 form successive outgroups to the previous clade together with whom they form a monophyletic group which includes all the brevirostrine species considered, along with the “depressed-beaked” gomphothere Rhynchotherium Falconer, 1868. The results of the present phylogenetic analysis indicate a rather high level of homoplasy in the evolution of New World gomphotheres.