Hearing without a tympanic ear

The ability to sense and localize sound is so advantageous for survival that it is difficult to understand the almost 100 million year gap separating the appearance of early tetrapods and the emergence of an impedance-matching tympanic middle ear - which we normally regard as a prerequisite for sensitive hearing on land - in their descendants. Recent studies of hearing in extant atympanate vertebrates have provided significant insights into the ancestral state(s) and the early evolution of the terrestrial tetrapod auditory system. These reveal a mechanism for sound pressure detection and directional hearing in 'earless' atympanate vertebrates that may be generalizable to all tetrapods, including the earliest terrestrial species. Here, we review the structure and function of vertebrate tympanic middle ears and highlight the multiple acquisition and loss events that characterize the complex evolutionary history of this important sensory structure. We describe extratympanic pathways for sound transmission to the inner ear and synthesize findings from recent studies to propose a general mechanism for hearing in 'earless' atympanate vertebrates. Finally, we integrate these studies with research on tympanate species that may also rely on extratympanic mechanisms for acoustic reception of infrasound (<20 Hz) and with studies on human bone conduction mechanisms of hearing.

Palatal morphology predicts the paleobiology of early salamanders

Ecological preferences and life history strategies have enormous impacts on the evolution and phenotypic diversity of salamanders, but the yet established reliable ecological indicators from bony skeletons hinder investigations into the paleobiology of early salamanders. Here, we statistically demonstrate by using time-calibrated cladograms and geometric morphometric analysis on 71 specimens in 36 species, that both the shape of the palate and many non-shape covariates particularly associated with vomerine teeth are ecologically informative in early stem- and basal crown-group salamanders. Disparity patterns within the morphospace of the palate in ecological preferences, life history strategies, and taxonomic affiliations were analyzed in detail, and evolutionary rates and ancestral states of the palate were reconstructed. Our results show that the palate is heavily impacted by convergence constrained by feeding mechanisms and also exhibits clear stepwise evolutionary patterns with alternative phenotypic configurations to cope with similar functional demand. Salamanders are diversified ecologically before the Middle Jurassic and achieved all their present ecological preferences in the Early Cretaceous. Our results reveal that the last common ancestor of all salamanders share with other modern amphibians a unified biphasic ecological preference, and metamorphosis is significant in the expansion of ecomorphospace of the palate in early salamanders.

Brain Reconstruction Across the Fish-Tetrapod Transition; Insights From Modern Amphibians

The fish-tetrapod transition (which incorporates the related fin-limb and water-land transitions) is celebrated as one of the most important junctions in vertebrate evolution. Sarcopterygian fishes (the “lobe-fins”) are today represented by lungfishes and coelacanths, but during the Paleozoic they were much more diverse. It was some of these sarcopterygians, a lineage of the tetrapodomorph fishes, that gave rise to tetrapods (terrestrial vertebrates with limbs bearing digits). This spectacular leap took place during the Devonian Period. Due to the nature of preservation, it is the hard parts of an animal’s body that are most likely to fossilize, while soft tissues such as muscular and brain tissues, typically fail to do so. Thus, our understanding of the adaptations of the hard skeletal structures of vertebrates is considerably greater than that of the soft tissue systems. Fortunately, the braincases of early vertebrates are often ossified and thereby have the potential to provide detailed morphological information. However, the correspondence between brain and endocast (an internal mold of the cavity) has historically been considered poor in most “lower” vertebrates and consequently neglected in such studies of brain evolution. Despite this, recent work documenting the spatial relationship in extant basal sarcopterygians (coelacanth, lungfish, axolotl, and salamander) has highlighted that this is not uniformly the case. Herein, we quantify and illustrate the brain-endocast relationship in four additional extant basal tetrapod exemplars: neobatrachian anurans (frogs) Breviceps poweri and Ceratophrys ornata; and gymnophionans (caecilians) Gegeneophis ramaswamii and Rhinatrema bivittatum. We show that anurans and caecilians appear to have brains that fill their endocasts to a similar degree to that of lungfishes and salamanders, but not coelacanth. Ceratophrys has considerably lower correspondence between the brain and endocast in the olfactory tract and mesencephalic regions, while Breviceps has low correspondence along its ventral endocranial margin. The brains of caecilians reflect their endocasts most closely (vol. ∼70%). The telencephalon is tightly fitted within the endocast in all four taxa. Our findings highlight the need to adequately assess the brain-endocast relationship in a broad range of vertebrates, in order to inform neural reconstructions of fossil taxa using the Extant Phylogenetic Bracket approach and future studies of brain evolution.

Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences

Recent efforts have led to the development of extremely sophisticated methods for incorporating tree-wide data and accommodating uncertainty when estimating the temporal patterns of phylogenetic trees, but assignment of prior constraints on node age remains the most important factor. This depends largely on understanding substantive disagreements between specialists (paleontologists, geologists, and comparative anatomists), which are often opaque to phylogeneticists and molecular biologists who rely on these data as downstream users. This often leads to misunderstandings of how the uncertainty associated with node age minima arises, leading to inappropriate treatments of that uncertainty by phylogeneticists. In order to promote dialogue on this subject, we here review factors (phylogeny, preservational megabiases, spatial and temporal patterns in the tetrapod fossil record) that complicate assignment of prior node age constraints for deep divergences in the tetrapod tree, focusing on the origin of crown-group Amniota, crown-group Amphibia, and crown-group Tetrapoda. We find that node priors for amphibians and tetrapods show high phylogenetic lability and different phylogenetic treatments identifying disparate taxa as the earliest representatives of these crown groups. This corresponds partially to the well-known problem of lissamphibian origins but increasingly reflects deeper instabilities in early tetrapod phylogeny. Conversely, differences in phylogenetic treatment do not affect our ability to recognize the earliest crown-group amniotes but do affect how diverse we understand the earliest amniote faunas to be. Preservational megabiases and spatiotemporal heterogeneity of the early tetrapod fossil record present unrecognized challenges in reliably estimating the ages of tetrapod nodes; the tetrapod record throughout the relevant interval is spatially restricted and disrupted by several major intervals of minimal sampling coincident with the emergence of all three crown groups. Going forward, researchers attempting to calibrate the ages for these nodes, and other similar deep nodes in the metazoan fossil record, should consciously consider major phylogenetic uncertainty, preservational megabias, and spatiotemporal heterogeneity, preferably examining the impact of working hypotheses from multiple research groups. We emphasize a need for major tetrapod collection effort outside of classic European and North American sections, particularly from the southern hemisphere, and suggest that such sampling may dramatically change our timelines of tetrapod evolution.

Phylogeny of Paleozoic limbed vertebrates reassessed through revision and expansion of the largest published relevant data matrix

The largest published phylogenetic analysis of early limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69-122) recovered, for example, Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the "temnospondyl hypothesis" on the origin of Lissamphibia (TH) to be more parsimonious than the "lepospondyl hypothesis" (LH)-though only, as we show, by one step. We report 4,200 misscored cells, over half of them due to typographic and similar accidental errors. Further, some characters were duplicated; some had only one described state; for one, most taxa were scored after presumed relatives. Even potentially continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded. After these issues are improved-we document and justify all changes to the matrix-but no characters are added, we find (Analysis R1) much longer trees with, for example, monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega either crownward or rootward of Acanthostega; and Anthracosauria either crownward or rootward of Temnospondyli. The LH is nine steps shorter than the TH (R2; constrained) and 12 steps shorter than the "polyphyly hypothesis" (PH-R3; constrained). Brachydectes (Lysorophia) is not found next to Lissamphibia; instead, a large clade that includes the adelogyrinids, urocordylid "nectrideans" and aïstopods occupies that position. As expected from the taxon/character ratio, most bootstrap values are low. Adding 56 terminal taxa to the original 102 increases the resolution (and decreases most bootstrap values). The added taxa range in completeness from complete articulated skeletons to an incomplete lower jaw. Even though the lissamphibian-like temnospondyls Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4; unconstrained) and TH (R5) rises to 10 steps, that between LH and PH (R6) to 15; the TH also requires several more regains of lost bones than the LH. Casineria, in which we tentatively identify a postbranchial lamina, emerges rather far from amniote origins in a gephyrostegid-chroniosuchian grade. Bayesian inference (Analysis EB, settings as in R4) mostly agrees with R4. High posterior probabilities are found for Lissamphibia (1.00) and the LH (0.92); however, many branches remain weakly supported, and most are short, as expected from the small character sample. We discuss phylogeny, approaches to coding, methods of phylogenetics (Bayesian inference vs. equally weighted vs. reweighted parsimony), some character complexes (e.g. preaxial/postaxial polarity in limb development), and prospects for further improvement of this matrix. Even in its revised state, the matrix cannot provide a robust assessment of the phylogeny of early limbed vertebrates. Sufficient improvement will be laborious-but not difficult.

Histological characterization of denticulate palatal plates in an Early Permian dissorophoid

Denticles are small, tooth-like protrusions that are commonly found on the palate of early tetrapods. Despite their widespread taxonomic occurrence and similar external morphology to marginal teeth, it has not been rigorously tested whether denticles are structurally homologous to true teeth with features such as a pulp cavity, dentine, and enamel, or if they are bony, tooth-like protrusions. Additionally, the denticles are known to occur not only on the palatal bones but also on a mosaic of small palatal plates that is thought to have covered the interpterygoid vacuities of temnospondyls through implantation in a soft tissue covering; however, these plates have never been examined beyond a simple description of their position and external morphology. Accordingly, we performed a histological analysis of these denticulate palatal plates in a dissorophoid temnospondyl in order to characterize their microanatomy and histology. The dentition on these palatal plates has been found to be homologous with true teeth on the basis of both external morphology and histological data through the identification of features such as enamel and a pulp cavity surrounded by dentine. In addition, patterns of tooth replacement and ankylosis support the hypothesis of structural homology between these tiny teeth on the palatal plates and the much larger marginal dentition. We also provide the first histological characterization of the palatal plates, including documentation of abundant Sharpey’s fibres that provide a direct line of evidence to support the hypothesis of soft tissue implantation. Finally, we conducted a survey of the literature to determine the taxonomic distribution of these plates within Temnospondyli, providing a broader context for the presence of palatal plates and illustrating the importance of maintaining consistency in nomenclature.

Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia

The origin of the limbless caecilians remains a lasting question in vertebrate evolution. Molecular phylogenies and morphology support that caecilians are the sister taxon of batrachians (frogs and salamanders), from which they diverged no later than the early Permian. Although recent efforts have discovered new, early members of the batrachian lineage, the record of pre-Cretaceous caecilians is limited to a single species, Eocaecilia micropodia The position of Eocaecilia within tetrapod phylogeny is controversial, as it already acquired the specialized morphology that characterizes modern caecilians by the Jurassic. Here, we report on a small amphibian from the Upper Triassic of Colorado, United States, with a mélange of caecilian synapomorphies and general lissamphibian plesiomorphies. We evaluated its relationships by designing an inclusive phylogenetic analysis that broadly incorporates definitive members of the modern lissamphibian orders and a diversity of extinct temnospondyl amphibians, including stereospondyls. Our results place the taxon confidently within lissamphibians but demonstrate that the diversity of Permian and Triassic stereospondyls also falls within this group. This hypothesis of caecilian origins closes a substantial morphologic and temporal gap and explains the appeal of morphology-based polyphyly hypotheses for the origins of Lissamphibia while reconciling molecular support for the group's monophyly. Stem caecilian morphology reveals a previously unrecognized stepwise acquisition of typical caecilian cranial apomorphies during the Triassic. A major implication is that many Paleozoic total group lissamphibians (i.e., higher temnospondyls, including the stereospondyl subclade) fall within crown Lissamphibia, which must have originated before 315 million years ago.

The complex evolutionary history of the tympanic middle ear in frogs and toads (Anura)

Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species. Following that initial loss, independent regains of some or all TME structures were inferred within two minor clades and in a radiation of >400 species. The reappearance of the TME in the latter clade was followed by at least 10 losses of the entire TME. The many losses and gains of the TME in anurans is unparalleled among tetrapods. Our results show that anurans, and especially bufonid toads, are an excellent model to study the behavioural correlates of earlessness, extratympanic sound pathways, and the genetic and developmental mechanisms that underlie the morphogenesis of TME structures.

Cranial Morphology of the Carboniferous-Permian Tetrapod Brachydectes newberryi (Lepospondyli, Lysorophia): New Data from µCT

Lysorophians are a group of early tetrapods with extremely elongate trunks, reduced limbs, and highly reduced skulls. Since the first discovery of this group, general similarities in outward appearance between lysorophians and some modern lissamphibian orders (specifically Urodela and Gymnophiona) have been recognized, and sometimes been the basis for hypotheses of lissamphibian origins. We studied the morphology of the skull, with particular emphasis on the neurocranium, of a partial growth series of the lysorophian Brachydectes newberryi using x-ray micro-computed tomography (μCT). Our study reveals similarities between the braincase of Brachydectes and brachystelechid recumbirostrans, corroborating prior work suggesting a close relationship between these taxa. We also describe the morphology of the epipterygoid, stapes, and quadrate in this taxon for the first time. Contra the proposals of some workers, we find no evidence of expected lissamphibian synapomorphies in the skull morphology in Brachydectes newberryi, and instead recognize a number of derived amniote characteristics within the braincase and suspensorium. Morphology previously considered indicative of taxonomic diversity within Lysorophia may reflect ontogenetic rather than taxonomic variation. The highly divergent morphology of lysorophians represents a refinement of morphological and functional trends within recumbirostrans, and is analogous to morphology observed in many modern fossorial reptiles.

Cranial Morphology of the Brachystelechid 'Microsaur' Quasicaecilia texana Carroll Provides New Insights into the Diversity and Evolution of Braincase Morphology in Recumbirostran 'Microsaurs'

Recumbirostran ‘microsaurs,’ a group of early tetrapods from the Late Carboniferous and Early Permian, are the earliest known example of adaptation to head-first burrowing in the tetrapod fossil record. However, understanding of the diversity of fossorial adaptation within the Recumbirostra has been hindered by poor anatomical knowledge of the more divergent forms within the group. Here we report the results of μCT study of Quasicaecilia texana, a poorly-known recumbirostran with a unique, broad, shovel-like snout. The organization of the skull roof and braincase of Quasicaecilia is found to be more in line with that of other recumbirostrans than previously described, despite differences in overall shape. The braincase is found to be broadly comparable to Carrolla craddocki, with a large presphenoid that encompasses much of the interorbital septum and the columella ethmoidalis, and a single compound ossification encompassing the sphenoid, otic, and occipital regions. The recumbirostran braincase conserves general structure and topology of braincase regions and cranial nerve foramina, but it is highly variable in the number of ossifications and their extent, likely associated with the reliance on braincase ossifications to resist compression during sediment compaction and mechanical manipulation by epaxial and hypaxial musculature. Expansion of the deep ventral neck musculature in Quasicaecilia, autapomorphic among recumbirostrans, may reflect unique biomechanical function, and underscores the importance of future attention to the role of the cervical musculature in contextualizing the origin and evolution of fossoriality in recumbirostrans.

Micro-CT Study of Rhynchonkos stovalli (Lepospondyli, Recumbirostra), with Description of Two New Genera

The Early Permian recumbirostran lepospondyl Rhynchonkos stovalli has been identified as a possible close relative of caecilians due to general similarities in skull shape as well as similar robustness of the braincase, a hypothesis that implies the polyphyly of extant lissamphibians. In order to better assess this phylogenetic hypothesis, we studied the morphology of the holotype and three specimens previously attributed to R. stovalli. With the use of micro-computed x-ray tomography (μCT) we are able to completely describe the external and internal cranial morphology of these specimens, dramatically revising our knowledge of R. stovalli and recognizing two new taxa, Aletrimyti gaskillae gen et sp. n. and Dvellacanus carrolli gen et sp. n. The braincases of R. stovalli, A. gaskillae, and D. carrolli are described in detail, demonstrating detailed braincase morphology and new information on the recumbirostran supraoccipital bone. All three taxa show fossorial adaptations in the braincase, sutural articulations of skull roof bones, and in the lower jaw, but variation in cranial morphology between these three taxa may reflect different modes of head-first burrowing behaviors and capabilities. We revisit the homology of the supraoccipital, median anterior bone, and temporal bone of recumbirostrans, and discuss implications of alternate interpretations of the homology of these elements. Finally, we evaluate the characteristics previously used to unite Rhynchonkos stovalli with caecilians in light of these new data. These proposed similarities are more ambiguous than previous descriptions suggest, and result from the composite nature of previous descriptions, ambiguities in external morphology, and functional convergence between recumbirostrans and caecilians for head-first burrowing.

The braincase of Eocaecilia micropodia (Lissamphibia, Gymnophiona) and the origin of Caecilians

The scant fossil record of caecilians has obscured the origin and evolution of this lissamphibian group. Eocaecilia micropodia from the Lower Jurassic of North America remains the only stem-group caecilian with an almost complete skull preserved. However, this taxon has been controversial, engendering re-evaluation of traits considered to be plesiomorphic for extant caecilians. Both the validity of the placement of E. micropodia as a stem caecilian and estimates of the plesiomorphic condition of extant caecilians have been questioned. In order to address these issues, the braincase of E. micropodia was examined via micro-computed tomography. The braincase is considered to be a more reliable phylogenetic indicator than peripheral regions of the skull. These data reveal significant new information, including the possession of an ossified nasal septum, ossified anterior wall of the sphenethmoid, long anterolateral processes on the sphenethmoid, and paired olfactory nerve foramina, which are known only to occur in extant caecilians; the latter are possibly related to the evolution of the tentacle, a caecilian autapomorphy. A phylogenetic analysis that included 64 non-amniote taxa and 308 characters represents the first extensive test of the phylogenetic affinities of E. micropodia. The results place E. micropodia securely on the stem of extant caecilians, representing a clade within Temnospondyli that is the sister taxon to batrachians plus Gerobatrachus. Ancestral character state reconstruction confirms the braincase of E. micropodia to be largely representative of the plesiomorphic condition of extant caecilians. Additionally, the results refine the context within which the evolution of the caecilian form can be evaluated. The robust construction and pattern of the dermal skull of E. micropodia is interpreted as symplesiomorphic with advanced dissorophoid temnospondyls, rather than being autapomorphic in its robust construction. Together these data increase confidence in incorporating E. micropodia into discussions of caecilian evolution.