We describe adaptations for a semiaquatic lifestyle in the dinosaur Spinosaurus aegyptiacus. These adaptations include retraction of the fleshy nostrils to a position near the mid-region of the skull and an elongate neck and trunk that shift the center of body mass anterior to the knee joint. Unlike terrestrial theropods, the pelvic girdle is downsized, the hindlimbs are short, and all of the limb bones are solid without an open medullary cavity, for buoyancy control in water. The short, robust femur with hypertrophied flexor attachment and the low, flat-bottomed pedal claws are consistent with aquatic foot-propelled locomotion. Surface striations and bone microstructure suggest that the dorsal "sail" may have been enveloped in skin that functioned primarily for display on land and in water.

Imagine if we could compute across phenotype data as easily as genomic data; this article calls for efforts to realize this vision and discusses the potential benefits.

BackgroundElucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent ‘natural’ phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.ResultsPreviously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.ConclusionsThe newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies.The ontology release files associated with the ontology merge described in this manuscript are available at: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/Current ontology release files are available always available at: http://purl.obolibrary.org/obo/uberon/releases/

The geological and paleoenvironmental setting and the vertebrate taxonomy of the fossiliferous, Cenomanian-age deltaic sediments in eastern Morocco, generally referred to as the “Kem Kem beds”, are reviewed. These strata are recognized here as the Kem Kem Group, which is composed of the lower Gara Sbaa and upper Douira formations. Both formations have yielded a similar fossil vertebrate assemblage of predominantly isolated elements pertaining to cartilaginous and bony fishes, turtles, crocodyliforms, pterosaurs, and dinosaurs, as well as invertebrate, plant, and trace fossils. These fossils, now in collections around the world, are reviewed and tabulated. The Kem Kem vertebrate fauna is biased toward large-bodied carnivores including at least four large-bodied non-avian theropods (an abelisaurid, Spinosaurus, Carcharodontosaurus, and Deltadromeus), several large-bodied pterosaurs, and several large crocodyliforms. No comparable modern terrestrial ecosystem exists with similar bias toward large-bodied carnivores. The Kem Kem vertebrate assemblage, currently the best documented association just prior to the onset of the Cenomanian-Turonian marine transgression, captures the taxonomic diversity of a widespread northern African fauna better than any other contemporary assemblage from elsewhere in Africa.

Intensive research on non-avian dinosaurs in recent decades strongly suggests that these animals were restricted to terrestrial environments 1. Historical views proposing that some groups, such as sauropods and hadrosaurs, lived in aquatic environments 2,3 were abandoned decades ago 4,5,6. Recently, however, it has been argued that at least some spinosaurids, an unusual group of large-bodied Cretaceous theropods, were semi-aquatic 7,8 , but this idea has been challenged on anatomical, biomechanical, and taphonomic grounds and remains controversial 9,10,11. Here we present the first unambiguous evidence for an aquatic propulsive structure in a dinosaur, the giant theropod Spinosaurus aegyptiacus 7, 12. This dinosaur has a tail with an unexpected and unique shape consisting of extremely tall neural spines and elongate chevrons forming a large, flexible, fin-like organ capable of extensive lateral excursion. Using a robotic flapping apparatus to measure undulatory forces in physical tail models, we show that the tail shape of Spinosaurus produces greater thrust and efficiency in water than the tail shapes of terrestrial dinosaurs, comparable to that of extant aquatic vertebrates that use vertically expanded tails to generate forward propulsion while swimming. This conclusion is consistent with a suite of adaptations for an aquatic lifestyle and a piscivorous diet in Spinosaurus 7,13,14. Although developed to a lesser degree, aquatic adaptations are also found in other spinosaurids 15,16 , a clade with a near global distribution and a stratigraphic range of more than 50 million years 14 , documenting a significant invasion of aquatic environments by dinosaurs.

The Kem Kem beds in South Eastern Morocco contain a rich early Upper (or possibly late Lower) Cretaceous vertebrate assemblage. Fragmentary remains, predominantly teeth and jaw tips, represent several kinds of pterosaur although only one species, the ornithocheirid Coloborhynchus moroccensis, has been named. Here, we describe a new azhdarchid pterosaur, Alanqa saharica nov. gen. nov. sp., based on an almost complete well preserved mandibular symphysis from Aferdou N'Chaft. We assign additional fragmentary jaw remains, some of which have been tentatively identified as azhdarchid and pteranodontid, to this new taxon which is distinguished from other azhdarchids by a remarkably straight, elongate, lance-shaped mandibular symphysis that bears a pronounced dorsal eminence near the posterior end of its dorsal (occlusal) surface. Most remains, including the holotype, represent individuals of approximately three to four meters in wingspan, but a fragment of a large cervical vertebra, that probably also belongs to A. saharica, suggests that wingspans of six meters were achieved in this species. The Kem Kem beds have yielded the most diverse pterosaur assemblage yet reported from Africa and provide the first clear evidence for the presence of azhdarchids in Gondwana at the start of the Late Cretaceous. This, the relatively large size achieved by Alanqa, and the additional evidence of variable jaw morphology in azhdarchids provided by this taxon, indicates a longer and more complex history for this clade than previously suspected.

Secondary aquatic adaptations independently evolved more than thirty times from terrestrial vertebrate ancestors 1,2 . For decades, non-avian dinosaurs were believed to be an exception to this pattern. Only a few species have been hypothesized as partly or predominantly aquatic 3,4,5,6,7,8,9,10,11 . However, these hypotheses remain controversial 12,13 largely due to the difficulty of identifying unambiguous anatomical adaptations for aquatic habits in extinct animals. In this study, we demonstrate that the relationship between bone density and aquatic ecologies across extant amniotes provides a reliable inference of aquatic habits in extinct species.We use this approach to evaluate the distribution of aquatic adaptations among non-avian dinosaurs. We find strong support for aquatic habits in spinosaurids, associated with a remarkable increase in bone density, which precedes the evolution of more conspicuous anatomical modifications, a pattern also observed in other aquatic reptiles and mammals 14,15,16 .Spinosaurids are revealed to be aquatic specialists with surprising ecological disparity, including subaqueous foraging behavior in Spinosaurus and Baryonyx, and non-diving habits in Suchomimus.

BackgroundA hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships.DescriptionAs a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies.ConclusionsThe VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.