To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
The phylogenetic position of the Indian gharial (Gavialis gangeticus) is disputed - morphological characters place Gavialis as the sister to all other extant crocodylians, whereas molecular and combined analyses find Gavialis and the false gharial (Tomistoma schlegelii) to be sister taxa. Geometric morphometric techniques have only begun to be applied to this issue, but most of these studies have focused on the exterior of the skull. The braincase has provided useful phylogenetic information for basal crurotarsans, but has not been explored for the crown group. The Eustachian system is thought to vary phylogenetically in Crocodylia, but has not been analytically tested. To determine if gross morphology of the crocodylian braincase proves informative to the relationships of Gavialis and Tomistoma, we used two- and three-dimensional geometric morphometric approaches. Internal braincase images were obtained using high-resolution computerized tomography scans. A principal components analysis identified that the first component axis was primarily associated with size and did not show groupings that divide the specimens by phylogenetic affinity. Sliding semi-landmarks and a relative warp analysis indicate that a unique Eustachian morphology separates Gavialis from other extant members of Crocodylia. Ontogenetic expansion of the braincase results in a more dorsoventrally elongate median Eustachian canal. Changes in the shape of the Eustachian system do provide phylogenetic distinctions between major crocodylian clades. Each morphometric dataset, consisting of continuous morphological characters, was added independently to a combined cladistic analysis of discrete morphological and molecular characters. The braincase data alone produced a clade that included crocodylids and Gavialis, whereas the Eustachian data resulted in Gavialis being considered a basally divergent lineage. When each morphometric dataset was used in a combined analysis with discrete morphological and molecular characters, it generated a tree that matched the topology of the molecular phylogeny of Crocodylia.
A number of hypotheses have been suggested for the origin of birds and feathers. Although distributions of functional complexes have frequently been used to test phylogenetic hypotheses, analysis of the origin of feathers remains hampered by the incomplete fossil record of these unmineralized structures. It is also complicated by approaches that confuse the origins of birds, feathers, and flight without first demonstrating that these relate to the same historical event. Functional speculation regarding the origin of feathers usually focuses on three possible alternatives: (1) flight; (2) thermal insulation; or (3) display. Recent fossil finds of Late Cretaceous feathered dinosaurs in China have demonstrated that feathers appear to have originated in taxa that retained a significant number of primitive nonavian features. Current evidence strongly suggests that birds are theropod dinosaurs, and that the most primitive known feathers are found on non-flying animals. This further suggests that feathers did not evolve as flight structures. Thermoregulatory, display, and biomechanical support functions remain possible explanations for the origin of feathers. As the earliest function of feathers was probably not for aerial locomotion, it may be speculated that the transitional animals represented by the Chinese fossils possessed skin with the tensile properties of reptiles and combined it with the apomorphic characteristics of feathers.
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ABSTRACT A partial skull from the early Eocene London Clay of the Isle of Sheppey, England, is referable to the gavialoid clade Eosuchus, otherwise known from the late Paleocene of continental Europe and North America. It differs slightly from Paleocene forms, but there is insufficient material on which to base a new species. This extends the range of Eosuchus beyond the Paleocene and represents the first unambiguous occurrence of a gavialoid in the early Eocene.
ABSTRACT We describe a new crocodile, Crocodylus thorbjarnarsoni, sp. nov., on the basis of skulls and jaws from Pliocene and Pleistocene deposits in the Lake Turkana Basin of Kenya. The new species has a comparatively broad, deep snout and resembles an extinct horned crocodile from the Quaternary of Olduvai Gorge (C. anthropophagus), but the squamosal 'horns' are not as well developed. The skull table has a strongly trapezoidal outline different from those of the living Nile crocodile (C. niloticus) and crocodiles from late Miocene deposits in the Turkana Basin. The largest specimens are from animals up to 7.5 m in total length. It would have been the largest predator in its environment, and the early humans found in the same deposits were presumably part of its prey base. A phylogenetic analysis, including the new species and an improved sample of extinct crocodyline diversity, suggests a more complex phylogenetic and biogeographic history for the clade in Africa and the eastern Indian Ocean region than previously supposed. The analysis limits the known geographic and stratigraphic range of Rimasuchus lloydi, previously thought to occur throughout Africa from the early Miocene through the Pleistocene of northern Africa. Crocodylus niloticus is not known with certainty from units older than the Quaternary, and most late Miocene fossils from the Turkana Basin previously referred to C. niloticus can instead be referred to C. checchiai. The current first appearance datum for Crocodylus in Africa is approximately 7 Ma.
Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.
A well-preserved crocodyliform specimen from the Maastrichtian or Paleocene of Mali preserves the braincase and posterior dermatocranium. It is referred to Dyrosauridae on the basis of several derived features (a prominent anterior process of the postorbital, discrete occipital processes on the exoccipitals, significant quadratojugal contribution to jaw joint) and tentatively referred to Rhabdognathus on the basis of supratemporal fenestra shape. The lacrymal and prefrontal are relatively short compared with those published for other dyrosaurids. The palatines border the internal choanae anteriorly, and the choanae are divided by a midline septum derived from the pterygoids. The prefrontal pillars are mediolaterally broad and contact the palate ventrally. One stapes is preserved in place. The basicranial pneumatic system is very unusual, in that the anterior and posterior branches of the median eustachian canal are both separate at the palatal surface, and the pterygoids form part of the border for the anterior branch. The lateral eustachian openings lie within fossae on the lateral surface of the braincase and face laterally, with a descending process of the exoccipital nearly intersecting the opening. The braincase and surrounding dermal bones are elongate anteroposteriorly, and the postorbital's posterior ramus extends along the posterodorsal margin of the infratemporal fenestra. The quadrate ramus projects ventrally. These observations clarify character optimizations in previous phylogenetic analyses of Crocodyliformes.
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