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

Giant stem tetrapod was apex predator in Gondwanan late Palaeozoic ice age

Current hypotheses of early tetrapod evolution posit close ecological and biogeographic ties to the extensive coal-producing wetlands of the Carboniferous palaeoequator with rapid replacement of archaic tetrapod groups by relatives of modern amniotes and lissamphibians in the late Carboniferous (about 307 million years ago). These hypotheses draw on a tetrapod fossil record that is almost entirely restricted to palaeoequatorial Pangea (Laurussia)1,2. Here we describe a new giant stem tetrapod, Gaiasia jennyae, from high-palaeolatitude (about 55° S) early Permian-aged (about 280 million years ago) deposits in Namibia that challenges this scenario. Gaiasia is represented by several large, semi-articulated skeletons characterized by a weakly ossified skull with a loosely articulated palate dominated by a broad diamond-shaped parasphenoid, a posteriorly projecting occiput, and enlarged, interlocking dentary and coronoid fangs. Phylogenetic analysis resolves Gaiasia within the tetrapod stem group as the sister taxon of the Carboniferous Colosteidae from Euramerica. Gaiasia is larger than all previously described digited stem tetrapods and provides evidence that continental tetrapods were well established in the cold-temperate latitudes of Gondwana during the final phases of the Carboniferous-Permian deglaciation. This points to a more global distribution of continental tetrapods during the Carboniferous-Permian transition and indicates that previous hypotheses of global tetrapod faunal turnover and dispersal at this time2,3 must be reconsidered.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Triassic stem caecilian supports dissorophoid origin of living amphibians

Living amphibians (Lissamphibia) include frogs and salamanders (Batrachia) and the limbless worm-like caecilians (Gymnophiona). The estimated Palaeozoic era gymnophionan-batrachian molecular divergence¹ suggests a major gap in the record of crown lissamphibians prior to their earliest fossil occurrences in the Triassic period^2-6. Recent studies find a monophyletic Batrachia within dissorophoid temnospondyls^7-10, but the absence of pre-Jurassic period caecilian fossils^11,12 has made their relationships to batrachians and affinities to Palaeozoic tetrapods controversial^1,8,13,14. Here we report the geologically oldest stem caecilian-a crown lissamphibian from the Late Triassic epoch of Arizona, USA-extending the caecilian record by around 35 million years. These fossils illuminate the tempo and mode of early caecilian morphological and functional evolution, demonstrating a delayed acquisition of musculoskeletal features associated with fossoriality in living caecilians, including the dual jaw closure mechanism^15,16, reduced orbits¹⁷ and the tentacular organ¹⁸. The provenance of these fossils suggests a Pangaean equatorial origin for caecilians, implying that living caecilian biogeography reflects conserved aspects of caecilian function and physiology¹⁹, in combination with vicariance patterns driven by plate tectonics²⁰. These fossils reveal a combination of features that is unique to caecilians alongside features that are shared with batrachian and dissorophoid temnospondyls, providing new and compelling evidence supporting a single origin of living amphibians within dissorophoid temnospondyls.

The menisci are not shock absorbers: A biomechanical and comparative perspective

The lateral and medial menisci are fibrocartilaginous structures in the knee that play a crucial role in normal knee biomechanics. However, one commonly cited role of the menisci is that they function as "shock absorbers." Here we provide a critique of this notion, drawing upon a review of comparative anatomical and biomechanical data from humans and other tetrapods. We first review those commonly, and often exclusively, cited studies in support of a shock absorption function and show that evidence for a shock absorptive function is dubious. We then review the evolutionary and comparative evidence to show that (1) the human menisci are unremarkable in morphology compared with most other tetrapods, and (2) "shock" during locomotion is uncommon, with humans standing out as one of the only tetrapods that regularly experiences high levels of shock during locomotion. A shock-absorption function does not explain the origin of menisci, nor are human menisci specialized in any way that would explain a unique shock-absorbing function during human gait. Finally, we show that (3) the material properties of menisci are distinctly poorly suited for energy dissipation and that (4) estimations of meniscal energy absorption based on published data are negligible, both in their absolute amount and in comparison to other well-accepted structures which mitigate shock during locomotion. The menisci are evolutionarily ancient structures crucial for joint congruity, load distribution, and stress reduction, among a number of other functions. However, the menisci are not meaningful shock absorbers, neither in tetrapods broadly, nor in humans.

Tracking the Origin and Early Evolution of Reptiles

The origin of Reptilia and the biostratigraphic and palaeobiogeographic distribution of its early representatives are still poorly understood. An independent source of information may come from the extensive Carboniferous footprint record of reptiles, which is arguably richer and more complete than the skeletal record. Nevertheless, previous studies often failed to provide useful information because they were based on poorly preserved material and/or characters non-exclusive of reptile tracks. In fact, a large part of the supposed early reptile tracks can be assigned to the anamniote ichnotaxon Hylopus hardingi. Here, we revise the ichnotaxon Hylopus hardingi based on anatomy-consistent material, attribute it to anamniote reptiliomorphs, and distinguish it from Notalacerta missouriensis, the earliest ichnotaxon that can be attributed to reptiles, and the somewhat younger Varanopus microdactylus (attributed to parareptiles, such as bolosaurians) and Dromopus lacertoides (attributed to araeoscelid reptiles and non-varanodontine varanopids). These attributions are based on correlating morphofunctional features of tracks and skeletons. Multivariate analysis of trackway parameters indicates that the late Bashkirian Notalacerta missouriensis and Hylopus hardingi differ markedly in their trackway patterns from Late Mississippian Hylopus hardingi and Late Pennsylvanian reptile tracks, which appear to share a derived amniote-like type of gait. While the first occurrence/appearance of reptile tracks in the tetrapod footprint record during the late Bashkirian corresponds to the first occurrence/appearance of reptiles in the skeletal record, footprints significantly enlarge the paleobiogeographic distribution of the group, suggesting an earlier radiation of reptiles during the Bashkirian throughout North America and possibly North Africa. Dromopus appeared in the Kasimovian together with the diapsid group Araeoscelidia, but footprints from Western-European occurrences enlarge the paleobiogeographic distribution of diapsids and varanopids. Varanopus and bolosaurian parareptiles appear in the Gzhelian of North America. Older parareptiles are, however, known from the late Moscovian. In all, the footprint record of early reptiles supplements the skeletal record, suggesting possible future lines of research.

The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.

Evolutionary Change in Locomotion Close to the Origin of Amniotes Inferred From Trackway Data in an Ancestral State Reconstruction Approach

Among amniote and non-amniote tetrapod trackways from late Carboniferous to early Permian deposits, certain trackway measures vary notably. Some of this variability can be attributed to evolutionary changes in trackmaker anatomy and locomotion style close to the origin of amniotes. Here we demonstrate that steps in early amniote locomotion evolution can be addressed by applying methods of ancestral state reconstruction on trackway data – a novel approach in tetrapod ichnology. Based on (a) measurements of 186 trackways referred to the Carboniferous and early Permian ichnogenera Batrachichnus, Limnopus, Hylopus, Amphisauropus, Matthewichnus, Ichniotherium, Dimetropus, Tambachichnium, Erpetopus, Varanopus, Hyloidichnus, Notalacerta and Dromopus, (b) correlation of these ichnotaxa with specific groups of amphibian, reptiliomorph, synapsid, and reptilian trackmakers based on imprint morphology and (c) known skeletal-morphology-based phylogenies of the supposed trackmakers, we infer ancestral states for functionally controlled trackway measures in a maximum likelihood approach. The most notable finding of our analysis is a concordant change in trackway parameters within a series of ancestral amniote trackmakers, which reflects an evolutionary change in locomotion: In the ancestors of amniotes and diadectomorphs, an increase in body size was accompanied by a decrease in (normalized) gauge width and glenoacetabular length and by a change in imprint orientation toward a more trackway-parallel and forward-pointing condition. In the subsequent evolution of diadectomorph, synapsid and reptilian trackmakers after the diversification of the clades Cotylosauria (Amniota + Diadectomorpha) and Amniota, stride length increased whereas gauges decreased further or remained relatively narrow within most lineages. In accordance with this conspicuous pattern of evolutionary change in trackway measures, we interpret the body size increase as an underlying factor that triggered the reorganization of the locomotion apparatus. The secondary increase in stride length, which occurred convergently within distinct groups, is interpreted as an increase in locomotion capability when the benefits of reorganization came into effect. The track-trackmaker pair of Ichniotherium sphaerodactylum and Orobates pabsti from the early Permian Bromacker locality of the Thuringian Forest, proposed in earlier studies as a suitable ancestral amniote track-trackmaker model, fits relatively well with our modeled last common ancestor of amniotes – with the caveat that the Bromacker material is younger and some of the similarities appear to be due to convergence.

The postcranial anatomy of Whatcheeria deltae and its implications for the family Whatcheeriidae

Here we describe the postcranial skeleton and present the first full-body reconstruction of the early tetrapod Whatcheeria deltae from the Viséan of Iowa. The skeletal proportions, including an elongate neck and large limbs, are unlike those of other Devonian and Mississippian tetrapods. The robust limbs of Whatcheeria appear adapted for a walking gait, but the lateral lines of the cranium are fundamentally unsuited for sustained subaerial exposure. Thus, although Whatcheeria bears a general resemblance to certain terrestrially adapted Permian and Triassic members of crown tetrapod lineages, its unusual form signals a broader range of early amphibious morphologies and habits than previously considered. From the exceptionally rich collection it is evident that most Whatcheeria specimens represent immature individuals. Rare specimens suggest an adult body size of at least 2 m, over twice that of the holotype. Further comparison suggests that the Pederpes holotype might also be a juvenile and reveals a combination of hindlimb characters unique to Whatcheeria and Pederpes. These new data contribute to a revised diagnosis of the family Whatcheeriidae and a re-evaluation of fragmentary Devonian–Carboniferous fossils reported as ‘whatcheeriid’ but sharing no synapomorphies with the more precisely defined clade.