A mitogenomic perspective on the phylogeny and biogeography of living caecilians (Amphibia: Gymnophiona)

The caecilians, members of the amphibian Order Gymnophiona, are the least known Order of tetrapods, and their intra-relationships, especially within its largest group, the Family Caeciliidae (57% of all caecilian species), remain controversial. We sequenced thirteen complete caecilian mitochondrial genomes, including twelve species of caeciliids, using a universal primer set strategy. These new sequences, together with eight published caecilian mitochondrial genomes, were analyzed by maximum parsimony, partitioned maximum-likelihood and partitioned Bayesian approaches at both nucleotide and amino acid levels, to study the intra-relationships of caecilians. An additional multiple gene dataset including most of the caecilian nucleotide sequences currently available in GenBank produced phylogenetic results that are fully compatible with those based on the mitogenomic data. Our phylogenetic results are summarized as follow. The caecilian family Rhinatrematidae is the sister taxon to all other caecilians. Beyond Rhinatrematidae, a clade comprising the Ichthyophlidae and Uraeotyphlidae is separated from a clade containing all remaining caecilians (Scolecomorphidae, Typhlonectidae and Caeciliidae). Within this large clade, Scolecomorphidae is the sister taxon of Typhlonectidae and Caeciliidae but this placement did not receive strong support in all analyses. Caeciliidae is paraphyletic with regard to Typhlonectidae, and can be divided into three well-supported groups: Caeciliidae group 1 contains the African caeciliids Boulengerula and Herpele; Caeciliidae group 2 contains Caecilia and Oscaecilia and it is the sister taxon of Typhlonectidae; Caeciliidae group 3 comprises the remaining species of caeciliids. The mitochondrial genome data were also used to calculate divergence times for caecilian evolution using the penalized likelihood method implemented in the program R8S. The newly obtained dating results are compatible with (but a little older than) previous time estimates mainly based on nuclear gene data. The mitogenomic time tree of caecilians suggests that the initial diversification of extant caecilians most probably took place in Late Triassic about 228 (195–260) Ma. Caeciliids currently distributed in India and the Seychelles diverged from their African and American relatives most probably in Late Jurassic about 138 (112–165) Ma, fairly close to the time (130 Ma) when Madagascar–India–Seychelles separated from Africa and South America. The split between the Indian caeciliid Gegeneophis and Seychellean caeciliids occurred about 103 (78–125) Ma, predated the rifting of India and the Seychelles (65 Ma).     

The First Virtual Cranial Endocast of a Lungfish (Sarcopterygii: Dipnoi)

Lungfish, or dipnoans, have a history spanning over 400 million years and are the closest living sister taxon to the tetrapods. Most Devonian lungfish had heavily ossified endoskeletons, whereas most Mesozoic and Cenozoic lungfish had largely cartilaginous endoskeletons and are usually known only from isolated tooth plates or disarticulated bone fragments. There is thus a substantial temporal and evolutionary gap in our understanding of lungfish endoskeletal morphology, between the diverse and highly variable Devonian forms on the one hand and the three extant genera on the other. Here we present a virtual cranial endocast of Rhinodipterus kimberleyensis, from the Late Devonian Gogo Formation of Australia, one of the most derived fossil dipnoans with a well-ossified braincase. This endocast, generated from a Computed Microtomography (µCT) scan of the skull, is the first virtual endocast of any lungfish published, and only the third fossil dipnoan endocast to be illustrated in its entirety. Key features include long olfactory canals, a telencephalic cavity with a moderate degree of ventral expansion, large suparaotic cavities, and moderately enlarged utricular recesses. It has numerous similarities to the endocasts of Chirodipterus wildungensis and Griphognathus whitei, and to a lesser degree to ''Chirodipterus'' australis and Dipnorhynchus sussmilchi. Among extant lungfish, it consistently resembles Neoceratodus more closely than Lepidosiren and Protopterus. Several trends in the evolution of the brains and labyrinth regions in dipnoans, such as the expansions of the utricular recess and telencephalic regions over time, are identified and discussed.     

Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)

Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.     

High-resolution X-ray computed tomography of an Early Cretaceous gekkonomorph (Squamata) from Öösh (Övörkhangai; Mongolia)

We describe the braincase of AMNH FR 21444, a gecko-like squamate from the Early Cretaceous of Mongolia, based on high-resolution X-ray computed tomography scans (CT scans) and incorporate it in a phylogenetic analysis of 36 squamate taxa scored for 226 morphological characters. Our analysis corroborates the Eublepharidae-Gekkonoidea split as the basal gekkotan dichotomy, but retrieves Teratoscincus as the sister-taxon to pygopodines + diplodactylines. The combination of plesiomorphic and apomorphic character states within AMNH FR 21444 demonstrates a decoupled evolutionary history between the braincase and the rest of the skull and mandible within gekkonomorph squamates. Enclosure of the lateral head vein and mandibular branch of the trigeminal nerve are both plesiomorphic for gekkonomorphs. The mechanisms responsible for the transition from the plesiomorphic skull roof of basal gekkonomorphs to the modern gekkotan condition cannot be anticipated given the current data.     

Braincase,palatoquadrate and ear region of the plagiosaurid Gerrothorax pulcherrimus from the Middle Triassic of Germany

Abstract: The complete neurocranium plus palatoquadrate of the plagiosaurid temnospondyl Gerrothorax pulcherrimus from the Middle Triassic of Germany is described for the first time, based on outer morphological observations and micro‐CT scanning. The exoccipitals are strong elements with paroccipital processes and well‐separated occipital condyles. Anterolaterally, the exoccipitals contact the otics, which are mediolaterally elongated and have massive lateral walls. The otics contact the basisphenoid, which shows well‐developed sellar processes. Anteriorly, the basisphenoid is continuous with the sphenethmoid region. In its posterior portion, the sphenethmoid gives rise to robust, laterally directed laterosphenoid walls, a unique morphology among basal tetrapods. The palatoquadrate is extensively ossified. The quadrate portion overlaps the descending lamina of squamosal and ascending lamina of pterygoid anteriorly, almost contacting the epipterygoid laterally. The epipterygoid is a complex element and may be co‐ossified with otics and laterosphenoid walls. It has a broad, sheet‐like footplate and a horizontally aligned ascending process that contacts the laterosphenoid walls. The degree of ossification of the epipterygoid, however, is subject to individual variation obviously independent from ontogenetic changes. The stapes of Gerrothorax is a large, blade‐like element that differs conspicuously from the plesiomorphic temnospondyl condition. It has a prominent anterolateral projection which has not been observed in other basal tetrapods. Morphology of neurocranium and palatoquadratum of Gerrothorax most closely resembles that of the Russian plagiosaurid Plagiosternum danilovi, although the elements are less ossified in the latter. The extensive endocranial ossification of Gerrothorax is consistent with the general high degree of ossification in the exo‐ and endoskeleton of this temnospondyl and supports the view that a strong endocranial ossification cannot be evaluated as a plesiomorphic character in basal tetrapods.     

An Expanded Combined Evidence Approach to the Gavialis Problem Using Geometric Morphometric Data from Crocodylian Braincases and Eustachian Systems

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 comparative study of locomotion in the caecilians Dermophis mexicanus and Typhlonectes natans (Amphibia: Gymnophiona)

We compared locomotion of two species of caecilian using x-ray videography of the animals traversing smooth-sided channels and a pegboard. Two channel widths were used, a body width channel and a body width + 20% channel. The terrestrial caecilian, Dermophis mexicanus , used internal concertina locomotion in both channels and lateral undulation on the pegboard. The aquatic caecilian, Typhlonectes natans , was not able to move at all in the body width channel. In the wider channel Typhlonectes proceeded at the same speed as Dermophis while using normal, rather than internal, concertina locomotion. On the pegboard, Typhlonectes used lateral undulation and achieved 2.5 times the speed managed by Dermophis. A phylogenetic analysis of this, and other, evidence shows that (1) internal concertina evolved in the ancestor to extant caecilians and (2) internal concertina locomotion was secondarily lost in the aquatic caecilians.     

First giraffid skulls (Bohlinia attica) from the late Miocene Maragheh fauna,Northwest Iran

An almost complete skull and a second partial skull of Bohlinia attica (Artiodactyla: Giraffidae) from the late Miocene of Maragheh in northwestern Iran is described along with a complete upper dentition from Samos in Greece. These specimens enrich what is known of this species. The skull has massive bent ossicones. The braincase is horizontal to the face in lateral view. The upper premolars have strongly curved styles. The metapodials of this species are elongate with a deep plantar trough. The braincase is short and the occipital does not extend caudally. The type material of Bohlinia is from Pikermi but this taxon is also known from localities in F.Y.R.O. Macedonia, Greece, Turkey, Bulgaria, Iraq, and Iran. The new specimens are similar to others except that the ossicone terminates in a knob and the palatine choanae are positioned caudally. This taxon along with Honanotherium, which is most similar but with shorter metapodials and simpler premolars, can be placed in the subfamily Bohlininae.     

New specimens of the early Eocene stem group galliform Paraortygoides (Gallinuloididae), with comments on the evolution of a crop in the stem lineage of Galliformes

Two new specimens of the fossil stem group galliform Paraortygoides messelensis Mayr 2000 (Gallinuloididae) are described from the Middle Eocene of Messel in Germany, including a complete skeleton in which the hitherto unknown skull of this species is preserved. The shorter and more protruding crista deltopectoralis of the humerus, also for the first time visible in one of the new specimens, shows gallinuloidids to be the sister taxon of all other, extinct and extant, galliform birds. Gallinuloidids distinctly differ from modern Galliformes in several other plesiomorphic osteological features, mainly of the pectoral girdle, of which the absence of a spina interna on the sternum is here reported for the first time. It is assumed that major evolutionary transformations in the stem lineage of Galliformes are related to the evolution of a large crop, which appears to have been absent in gallinuloidids. The vegetarian food component of gallinuloidids thus probably mainly consisted of soft plant matter rather than coarse material such as seeds.     

Sexual size dimorphism in caecilian amphibians: analysis, review and directions for future research

Sexual dimorphism, widespread in the animal kingdom, describes differences between the sexes in size, shape and many other traits. Sexual size dimorphism (SSD) plays a significant role in understanding life history evolution and mating systems. The snakelike morphology of limbless caecilian amphibians lacking obvious secondary sexual characters (in contrast to frogs and salamanders) impedes accurate intrasexual comparisons. In this study, sexual size dimorphism in the oviparous caecilian Ichthyophis cf. kohtaoensis, a phylogenetically basal caecilian, was analysed. Females were larger in all body and head characters tested. However, when adjusted to body size (total length), females differed only in their cloacal shape. Clutch volume was positively correlated to female body size, thus female fecundity increased with body size supporting the hypothesis of a fecundity-selected SSD in the oviparous Ichthyophis cf. kohtaoensis. A review of the present SSD data for caecilians shows that many species are monomorphic for body size but show dimorphism in head size, while other species demonstrate female-biased SSD. Male-biased SSD has not been reported for caecilians. To understand life history evolution in caecilians, further studies on the reproductive biology of other taxa are urgently needed, in particular for rhinatrematids and uraeotyphlids. New data will allow phylogenetically controlled comparative analyses to fully explore the pattern of SSD among caecilian lineages.     

The Neurocranium of the Stereospondyl Mastodonsaurus Giganteus

New and rich material of the stereospondyl amphibian Mastodonsaurus giganteus from Kupferzell in southern Germany allows for the first time a detailed study of the neurocranium of this species. Both sections and uncrushed specimens preserved in three dimensions were examined. The sphenethmoid ranges from the sella turcica region far to the anterior almost towards the nasal capsules, which remained unossified. The basisphenoid persisted as cartilage, whose morphology can be traced from imprints in surrounding bones. The otic is a single but complex element which underwent major ontogenetic changes. During development, the posterior braincase became increasingly ossified and finally formed a single, compound unit. In addition, otic and sphenethmoid are broadly co-ossified in large specimens. The basioccipital is present but rudimentary, wedged in between the exoccipital and parasphenoid and without contribution to the occipital condyles. The course of the optic, trigeminal, and facial nerves is studied in detail. The homology of the passages is assessed by means of phylogenetic arguments and comparative anatomical data, based on observations on nearest living crown groups.     

A new eusuchian crocodyliform with novel cranial integument and its significance for the origin and evolution of Crocodylia

Crocodyliforms were one of the most successful groups of Mesozoic tetrapods, radiating into terrestrial, semiaquatic and marine environments, while occupying numerous trophic niches, including carnivorous, insectivorous, herbivorous, and piscivorous species. Among these taxa were the enigmatic, poorly represented flat-headed crocodyliforms from the late Cretaceous of northern Africa. Here we report a new, giant crocodyliform from the early Late Cretaceous (Cenomanian) Kem Kem Formation of Morocco. Represented by a partial braincase, the taxon has an extremely long, flat skull with large jaw and craniocervical muscles. The skull roof is ridged and ornamented with a broad, rough boss surrounded by significant vascular impressions, likely forming an integumentary structure unique among crocodyliforms. Size estimates using endocranial volume indicate the specimen was very large. The taxon possesses robust laterosphenoids with laterally oriented capitate processes and isolated epipterygoids, features allying it with derived eusuchians. Phylogenetic analysis finds the taxon to be a derived eusuchian and sister taxon to Aegyptosuchus, a poorly understood, early Late Cretaceous taxon from the Bahariya formation. This clade forms the sister clade of crown-group Crocodylia, making these taxa the earliest eusuchian crocodyliforms known from Africa. These results shift phylogenetic and biogeographical hypotheses on the origin of modern crocodylians towards the circum-Tethyean region and provide important new data on eusuchian morphology and evolution.     

Unexpected bird-like features and high intraspecific variation in the braincase of the Triassic relative of dinosaurs

Abstract

Silesaurus opolensis Dzik, 2003 from the Late Triassic (late Carnian) of Poland is a key taxon for understanding the evolution of early dinosaurs. High intraspecific variation observed in the S. opolensis braincase brings caution in taxonomic and diversity studies of early dinosauromorphs. The external and internal osteology of three almost complete braincases of S. opolensis show that this taxon shares several similarities with other early dinosauriforms, which supports a close relationship among these forms. However, the paroccipital processes of S. opolensis are directed ventrally like in birds, reaching the level of the ventral margin of the basioccipital condyle. In dinosauromorphs, these processes usually have an almost horizontal orientation (presumed to be the plesiomorphic condition). Modifications observed in birds and S. opolensis have resulted in the dorsoventral expansion of M. complexus and M. depressor mandibulae, which occupy the dorsolateral part of the posterior side of the skull. In adult birds, these muscles act strongly on the initial upstroke of the head during drinking. Therefore, the inferred condition of these muscles in S. opolensis may imply that Silesauridae evolved toward bird-like feeding behaviour.     

Discovery of a new family of amphibians from northeast India with ancient links to Africa

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India-an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.