The dorsoventrally flattened skull typifies extant Crocodylia perhaps more than any other anatomical feature and is generally considered an adaptation for semi-aquatic feeding. Although the evolutionary origins have been extensively studied, the developmental origins of craniofacial flattening have yet to be explored. To understand how the skull table and platyrostral snout develop, we quantified embryonic development and post-hatching growth (ontogeny) of the crocodylian skull in lateral view using geometric morphometrics. Our dataset (n=103) includes all but one extant genus and all of the major ecomorphs, including the extremely slender-snouted Gavialis and Tomistoma. Our analysis reveals that the embryonic development of the flattened skull is remarkably similar across ecomorphs, including the presence of a conserved initial embryonic skull shape, similar to prior analysis of dorsal snout shape. Although differences during post-hatching ontogeny of the snout are recovered among ecomorphs the embryonic patterns are not distinct, revealing an important shift in developmental rate near hatching. In particular, the flattened skull table is achieved by the end of embryonic development with no changes after hatching. Further, the rotation of skull roof and facial bones during development is critical for the stereotypical flatness of the crocodylian skull. Our results suggest selection on hatchling performance and constraints on embryonic skull shape may have been important in this pattern of developmental conservation. The appearance of aspects of cranial flatness among Jurassic stem crocodylians suggests key aspects of these cranial developmental patterns may have been conserved for over 200 million years.

The distinctive anatomy of the crocodylian skull is intimately linked with dietary ecology, resulting in repeated convergence on blunt- and slender-snouted ecomorphs. These evolutionary shifts depend upon modifications of the developmental processes which direct growth and morphogenesis. Here we examine the evolution of cranial ontogenetic trajectories to shed light on the mechanisms underlying convergent snout evolution. We use geometric morphometrics to quantify skeletogenesis in an evolutionary context and reconstruct ancestral patterns of ontogenetic allometry to understand the developmental drivers of craniofacial diversity within Crocodylia. Our analyses uncovered a conserved embryonic region of morphospace (CER) shared by all non-gavialid crocodylians regardless of their eventual adult ecomorph. This observation suggests the presence of conserved developmental processes during early development (before Ferguson stage 20) across most of Crocodylia. Ancestral state reconstruction of ontogenetic trajectories revealed heterochrony, developmental constraint, and developmental systems drift have all played essential roles in the evolution of ecomorphs. Based on these observations, we conclude that two separate, but interconnected, developmental programs controlling craniofacial morphogenesis and growth enabled the evolutionary plasticity of skull shape in crocodylians.

The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the “true crocodiles” of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers as well as karyotype analysis of chromosome number and structure to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species’ taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.