The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps

The skull of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae)

We provide a detailed and first description of the skull, hyoid apparatus, and trachea of the Turks and Caicos rock iguana, Cyclura carinata (Squamata: Iguanidae). Cyclura is a radiation of iguanas restricted to islands of the Caribbean Sea. Species of Cyclura have high rates of endemism, and all species are severely threatened with extinction. Our anatomical description of this threatened iguana is based on high-resolution computed tomography scans of one adult, one putative adult or near adult, and one juvenile specimen, and includes three-dimensional segmented renderings and visualizations. We discuss some observations of intraspecific and ontogenetic variation, and provide a brief comparison with specimens of another species of Cyclura and published descriptions of other iguanas. Our study provides a cranial osteological framework for Cyclura and augments the body of knowledge on iguana anatomy generally. Finally, we posit that our description and future studies may facilitate identification of fossil Cyclura, which could help understand the paleobiogeography of the genus.

Saurodesmus robertsoni Seeley 1891-The oldest Scottish cynodont

Predating Darwin's theory of evolution, the holotype of Saurodesmus robertsoni is a long-standing enigma. Found at the beginning of 1840s, the specimen is a damaged stylopodial bone over decades variably assigned to turtles, archosaurs, parareptiles, or synapsids, and currently nearly forgotten. We redescribe and re-assess that curious specimen as a femur and consider Saurodesmus robertsoni as a valid taxon of a derived cynodont (?Tritylodontidae). It shares with probainognathians more derived than Prozostrodon a mainly medially oriented lesser trochanter and with the clade reuniting tritylodontids, brasilodontids, and mammaliaforms (but excluding tritheledontids) the presence of a projected femoral head, offset from the long axis of the femoral shaft; a thin, plate-like greater trochanter; a distinct dorsal eminence proximal to the medial (tibial) condyle located close to the level of the long axis of the femoral shaft and almost in the middle of the width of the distal expansion; and a pocket-like fossa proximally to the medial (tibial) condyle. Saurodesmus robertsoni is most similar to tritylodontids, sharing at least with some forms: the relative mediolateral expansion of the proximal and distal regions of the femur, the general shape and development of the greater trochanter, the presence of a faint intertrochanteric crest separating the shallow intertrochanteric and adductor fossae, and the general outline of the distal region as observed dorsally and distally. This makes Saurodesmus robertsoni the first Triassic cynodont from Scotland and, possibly, one of the earliest representatives of tritylodontids and one of the latest non-mammaliaform cynodonts worldwide. Moreover, it highlights the need for revisiting historical problematic specimens, the identification of which could have been previously hampered by the lack of adequate comparative materials in the past.

Extreme neck elongation evolved despite strong developmental constraints in bizarre Triassic reptiles-implications for neck modularity in archosaurs

The Triassic radiation of vertebrates saw the emergence of the modern vertebrate groups, as well as numerous extinct animals exhibiting conspicuous, unique anatomical characteristics. Among these, members of Tanystropheidae (Reptilia: Archosauromorpha) displayed cervical vertebral elongation to an extent unparalleled in any other vertebrate. Tanystropheids were exceptionally ecologically diverse and had a wide spatial and temporal distribution. This may have been related to their neck anatomy, yet its evolution and functional properties remain poorly understood. We used geometric morphometrics to capture the intraspecific variation between the vertebrae comprising the cervical column among early archosauromorphs, to trace the evolutionary history of neck elongation in these animals. Our results show that the cervical series of these reptiles can be divided into modules corresponding to those of extant animals. Tanystropheids achieved neck elongation through somite elongation and a shift between cervical and thoracic regions, without presacral vertebrae count increase-contrary to crown archosaurs. This suggests a peculiar developmental constraint that strongly affected the evolution of tanystropheids. The data obtained just at the base of the archosauromorph phylogenetic tree are crucial for further studies on the modularity of vertebral columns of not only Triassic reptile groups but extant and other extinct animals as well.

Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic

Background

Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups.

Methods

We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found.

Results

Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.

The oldest known rhynchocephalian reptile from the Middle Triassic (Ladinian) of Germany and its phylogenetic position among Lepidosauromorpha

Skeletal remains of a small lepidosaurian reptile from the Middle Triassic (Ladinian: Longobardian) Erfurt Formation, exposed in a commercial limestone quarry near Vellberg (Germany), represent the oldest rhynchocephalian known to date. The new taxon, Wirtembergia hauboldae, is diagnosed by the following combination of features: Premaxilla with four teeth, first being largest and decreasing in size from first to fourth. Jugal with tiny, spur-like posterior process. Lateral surface of dentary strongly convex dorsoventrally for much of length of bone, bearing distinct longitudinal ridge and sculpturing in large specimens. Coronoid eminence of dentary low, subrectangular, and with dorsoventrally concave lateral surface in larger specimens. Dentition with pleurodont anterior and acrodont posterior teeth. Posterior (=additional) teeth with (in side view) triangular, at mid-crown level labiolingually somewhat flattened crowns, and with oval bases. Phylogenetic analysis recovered the new rhynchocephalian as the earliest-diverging member of its clade known to date.

The dawn of an Era: New contributions on comparative and functional anatomy of Triassic tetrapods

The Triassic period stands as a crucial moment for understanding tetrapod evolution, marking the emergence and early diversification of numerous lineages that persist in today's ecosystems. Birds, crocodiles, testudines, lizards, and mammals can all trace their origins to the Triassic, which is distinguished by several adaptive radiation events that fostered unparalleled diversity in body plans and lifestyles. Beyond this macroevolutionary significance, the Triassic period serves as fertile ground for scientific inquiry, especially in tetrapod studies. The aim of this Special Issue is to assemble a diverse array of new contributions focused on continental Triassic tetrapods globally, encouraging collaboration among researchers across generations, pooling their efforts to comprehend this pivotal moment in tetrapod evolutionary history. This issue encompasses almost 40 varied contributions, spanning topics from comparative and functional anatomy, including descriptions of novel taxa, comprehensive anatomical reviews, systematic investigations, phylogenetic analyses, paleoneurological studies, biomechanical assessments, and detailed examinations of histology and ontogeny. Collectively, this Special Issue offers an extensive exploration of Triassic tetrapods from anatomical, ecological, and evolutionary perspectives, unveiling fresh insights into this intriguing moment in vertebrate evolutionary history.

The macroevolutionary singularity of snakes

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

Quantifying the effects of exceptional fossil preservation on the global availability of phylogenetic data in deep time

Fossil deposits with exceptional preservation ("lagerstätten") provide important details not typically preserved in the fossil record, such that they hold an outsized influence on our understanding of biodiversity and evolution. In particular, the potential bias imparted by this so-called "lagerstätten effect" remains a critical, but underexplored aspect of reconstructing evolutionary relationships. Here, we quantify the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards, snakes, mosasaurs), and then compare the influence of lagerstätten deposits on phylogenetic information content and taxon selection in phylogenetic analyses to other fossil-bearing deposits. We find that groups that preserve a high amount of phylogenetic information in their global fossil record (e.g., non-avian theropods) are less vulnerable to a "lagerstätten effect" that leads to disproportionate representation of fossil taxa from one geologic unit in an evolutionary tree. Additionally, for each taxonomic group, we find comparable amounts of phylogenetic information in lagerstätten deposits, even though corresponding morphological character datasets vary greatly. Finally, we unexpectedly find that ancient sand dune deposits of the Late Cretaceous Gobi Desert of Mongolia and China exert an anomalously large influence on the phylogenetic information available in the squamate fossil record, suggesting a "lagerstätten effect" can be present in units not traditionally considered lagerstätten. These results offer a phylogenetics-based lens through which to examine the effects of exceptional fossil preservation on biological patterns through time and space, and invites further quantification of evolutionary information in the rock record.

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

Exceptionally rapid tooth development and ontogenetic changes in the feeding apparatus of the Komodo dragon

Dental developmental and replacement patterns in extinct amniotes have attracted a lot of attention. Notable among these are Paleozoic predatory synapsids, but also Mesozoic theropod dinosaurs, well known for having true ziphodonty, strongly serrated carinae with dentine cores within an enamel cap. The Komodo dragon, Varanus komodoensis, is the only extant terrestrial vertebrate to exhibit true ziphodonty, making it an ideal model organism for gaining new insights into the life history and feeding behaviours of theropod dinosaurs and early synapsids. We undertook a comparative dental histological analysis of this extant apex predator in combination with computed tomography of intact skulls. This study allowed us to reconstruct the dental morphology, ontogeny, and replacement patterns in the largest living lizard with known feeding behaviour, and apply our findings to extinct taxa where the behaviour is largely unknown. We discovered through computed tomography that V. komodoensis maintains up to five replacement teeth per tooth position, while histological analysis showed an exceptionally rapid formation of new teeth, every 40 days. Additionally, a dramatic ontogenetic shift in the dental morphology of V. komodoensis was also discovered, likely related to changes in feeding preferences and habitat. The juveniles have fewer dental specializations, lack true ziphodonty, are arboreal and feed mostly on insects, whereas the adults have strongly developed ziphodonty and are terrestrial apex predators with defleshing feeding behaviour. In addition, we found evidence that the ziphodont teeth of V. komodoensis have true ampullae (interdental folds for strengthening the serrations), similar to those found only in theropod dinosaurs. Comparisons with other species of Varanus and successive outgroup taxa reveal a complex pattern of dental features and adaptations, including the evolution of snake-like tongue flicking used for foraging for prey. However, only the Komodo dragon exhibits this remarkable set of dental innovations and specializations among squamates.

A Palaeogene stem crotaphytid (Aciprion formosum) and the phylogenetic affinities of early fossil pleurodontan iguanians

Pleurodonta is an ancient, diverse clade of iguanian lizard distributed primarily in the Western Hemisphere. Although the clade is a frequent subject of systematic research, phylogenetic resolution among the major pleurodontan clades is elusive. That uncertainty has complicated the interpretations of many fossil pleurodontans. I describe a fossil skull of a pleurodontan lizard from the Palaeogene of Wyoming that was previously allocated to the puzzling taxon Aciprion formosum, and provide an updated morphological matrix for iguanian lizards. Phylogenetic analyses using Bayesian inference demonstrate that the fossil skull is the oldest and first definitive stem member of Crotaphytidae (collared and leopard lizards), establishing the presence of that clade in North America during the Palaeogene. I also discuss new or revised hypotheses for the relationships of several early pleurodontans. In particular, I examine potential evidence for crown-Pleurodonta in the Cretaceous of Mongolia (Polrussia), stem Pleurodonta in the Cretaceous of North America (Magnuviator) and a stem anole in the Eocene of North America (Afairiguana). I suggest that the placement of the fossil crotaphytid is stable to the uncertain phylogeny of Pleurodonta, but recognize the dynamic nature of fossil diagnosis and the potential for updated systematic hypotheses for the other fossils analysed here.

A Morrison stem gekkotan reveals gecko evolution and Jurassic biogeography

Geckos are a speciose and globally distributed clade of Squamata (lizards, including snakes and amphisbaenians) that are characterized by a host of modifications for nocturnal, scansorial and insectivorous ecologies. They are among the oldest divergences in the lizard crown, so understanding the origin of geckoes (Gekkota) is essential to understanding the origin of Squamata, the most species-rich extant tetrapod clade. However, the poor fossil record of gekkotans has obscured the sequence and timing of the assembly of their distinctive morphology. Here, we describe the first North American stem gekkotan based on a three-dimensionally preserved skull from the Morrison Formation of western North America. Despite its Late Jurassic age, the new species already possesses several key characteristics of the gekkotan skull along with retained ancestral features. We show that this new stem gekkotan, and several previously named species of uncertain phylogenetic relationships, comprise a widespread clade of early crown lizards, substantiating faunal homogeneity in Laurasia during the Late Jurassic that extended across disparate ecological, body-size and physiological classes.

The affinities of the Late Triassic Cryptovaranoides and the age of crown squamates

Most living reptile diversity is concentrated in Squamata (lizards, including snakes), which have poorly known origins in space and time. Recently, †Cryptovaranoides microlanius from the Late Triassic of the United Kingdom was described as the oldest crown squamate. If true, this result would push back the origin of all major lizard clades by 30-65 Myr and suggest that divergence times for reptile clades estimated using genomic and morphological data are grossly inaccurate. Here, we use computed tomography scans and expanded phylogenetic datasets to re-evaluate the phylogenetic affinities of †Cryptovaranoides and other putative early squamates. We robustly reject the crown squamate affinities of †Cryptovaranoides, and instead resolve †Cryptovaranoides as a potential member of the bird and crocodylian total clade, Archosauromorpha. Bayesian total evidence dating supports a Jurassic origin of crown squamates, not Triassic as recently suggested. We highlight how features traditionally linked to lepidosaurs are in fact widespread across Triassic reptiles. Our study reaffirms the importance of critically choosing and constructing morphological datasets and appropriate taxon sampling to test the phylogenetic affinities of problematic fossils and calibrate the Tree of Life.

Reconstructing the origin and early evolution of the snake brain

Snakes represent one-eighth of terrestrial vertebrate diversity, encompassing various lifestyles, ecologies, and morphologies. However, the ecological origins and early evolution of snakes are controversial topics in biology. To address the paucity of well-preserved fossils and the caveats of osteological traits for reconstructing snake evolution, we applied a different ecomorphological hypothesis based on high-definition brain reconstructions of extant Squamata. Our predictive models revealed a burrowing lifestyle with opportunistic behavior at the origin of crown snakes, reflecting a complex ancestral mosaic brain pattern. These findings emphasize the importance of quantitatively tracking the phenotypic diversification of soft tissues-including the accurate definition of intact brain morphological traits such as the cerebellum-in understanding snake evolution and vertebrate paleobiology. Furthermore, our study highlights the power of combining extant and extinct species, soft tissue reconstructions, and osteological traits in tracing the deep evolution of not only snakes but also other groups where fossil data are scarce.

An armoured marine reptile from the Early Triassic of South China and its phylogenetic and evolutionary implications

Sauropterygia was a taxonomically and ecomorphologically diverse clade of Mesozoic marine reptiles spanning the Early Triassic to the Late Cretaceous. Sauropterygians are traditionally divided into two groups representing two markedly different body plans - the short-necked, durophagous Placodontia and the long-necked Eosauropterygia - whereas Saurosphargidae, a small clade of armoured marine reptiles, is generally considered as the sauropterygian sister-group. However, the early evolutionary history of sauropterygians and their phylogenetic relationships with other groups within Diapsida are still incompletely understood. Here, we report a new saurosphargid from the Early Triassic (Olenekian) of South China - Prosaurosphargis yingzishanensis gen. et sp. nov. - representing the earliest known occurrence of the clade. An updated phylogenetic analysis focussing on the interrelationships among diapsid reptiles recovers saurosphargids as nested within sauropterygians, forming a clade with eosauropterygians to the exclusion of placodonts. Furthermore, a clade comprising Eusaurosphargis and Palatodonta is recovered as the sauropterygian sister-group within Sauropterygomorpha tax. nov. The phylogenetic position of several Early and Middle Triassic sauropterygians of previously uncertain phylogenetic affinity, such as Atopodentatus, Hanosaurus, Majiashanosaurus, and Corosaurus, is also clarified, elucidating the early evolutionary assembly of the sauropterygian body plan. Finally, our phylogenetic analysis supports the placement of Testudines and Archosauromorpha within Archelosauria, a result strongly corroborated by molecular data, but only recently recovered in a phylogenetic analysis using a morphology-only dataset. Our study provides evidence for the rapid diversification of sauropterygians in the aftermath of the Permo-Triassic mass extinction event and emphasises the importance of broad taxonomic sampling in reconstructing phylogenetic relationships among extinct taxa.

A late-surviving phytosaur from the northern Atlantic rift reveals climate constraints on Triassic reptile biogeography

BACKGROUND

The origins of all major living reptile clades, including the one leading to birds, lie in the Triassic. Following the largest mass extinction in Earth's history at the end of the Permian, the earliest definite members of the three major living reptile clades, the turtles (Testudines), crocodylians and birds (Archosauria), and lizards, snakes, amphisbaenians, and Tuatara (Lepidosauria) appeared. Recent analyses of the Triassic reptile fossil record suggest that the earliest diversifications in all three of these clades were tightly controlled by abrupt paleoclimate fluctuations and concordant environmental changes. Yet, this has only been preliminarily tested using information from evolutionary trees. Phytosauria consists of superficially crocodylian-like archosaurs that either form the sister to the crown or are the earliest divergence on the crocodylian stem and are present throughout the Triassic, making this clade an excellent test case for examining this biogeographic hypothesis.

RESULTS

Here, I describe a new phytosaur, Jupijkam paleofluvialis gen. et sp. nov., from the Late Triassic of Nova Scotia, Canada, which at that time sat in northern Pangaea near the northern terminus of the great central Pangean rift. As one of the northernmost occurrences of Phytosauria, J. paleofluvialis provides critical new biogeographic data that enables revised estimations of phytosaur historical biogeography along phylogenies of this clade built under multiple methodologies. Reconstructions of phytosaur historical biogeography based on different phylogenies and biogeographic models suggest that phytosaurs originated in northern Pangaea, spread southward, and then dispersed back northward at least once more during the Late Triassic.

CONCLUSIONS

The results presented in this study link phytosaur biogeography to major changes to Triassic global climate and aridity. Together with the earliest dinosaurs and several other reptile lineages, phytosaur diversification and migration appear to have been restricted by the formation and loss of arid belts across the Pangean supercontinent.

The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order

Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.

Extended embryo retention and viviparity in the first amniotes

The amniotic egg with its complex fetal membranes was a key innovation in vertebrate evolution that enabled the great diversification of reptiles, birds and mammals. It is debated whether these fetal membranes evolved in eggs on land as an adaptation to the terrestrial environment or to control antagonistic fetal-maternal interaction in association with extended embryo retention (EER). Here we report an oviparous choristodere from the Lower Cretaceous period of northeast China. The ossification sequence of the embryo confirms that choristoderes are basal archosauromorphs. The discovery of oviparity in this assumed viviparous extinct clade, together with existing evidence, suggests that EER was the primitive reproductive mode in basal archosauromorphs. Phylogenetic comparative analyses on extant and extinct amniotes suggest that the first amniote displayed EER (including viviparity).

Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].

The build-up of the present-day tropical diversity of tetrapods

The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction, and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatiotemporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy, or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.

The femora of Drepanosauromorpha (Reptilia: Diapsida): Implications for the functional evolution of the thigh of Sauropsida

The femora of diapsids have undergone morphological changes related to shifts in postural and locomotor modes, such as the transition from plesiomorphic amniote and diapsid taxa to the apomorphic conditions related to a more erect posture within Archosauriformes. One remarkable clade of Triassic diapsids is the chameleon-like Drepanosauromorpha. This group is known from numerous articulated but heavily compressed skeletons that have the potential to further inform early reptile femoral evolution. For the first time, we describe the three-dimensional osteology of the femora of Drepanosauromorpha, based on undistorted fossils from the Upper Triassic Chinle Formation and Dockum Group of North America. We identify apomorphies and a combination of character states that link these femora to those in crushed specimens of drepanosauromorphs and compare our sample with a range of amniote taxa. Several characteristics of drepanosauromorph femora, including a hemispherical proximal articular surface, prominent asymmetry in the proximodistal length of the tibial condyles, and a deep intercondylar sulcus, are plesiomorphies shared with early diapsids. The femora contrast with those of most diapsids in lacking a crest-like, distally tapering internal trochanter. They bear a ventrolaterally positioned tuberosity on the femoral shaft, resembling the fourth trochanter in Archosauriformes. The reduction of an internal trochanter parallels independent reductions in therapsids and archosauriforms. The presence of a ventrolaterally positioned trochanter is also similar to that of chameleonid squamates. Collectively, these features demonstrate a unique femoral morphology for drepanosauromorphs, and suggest an increased capacity for femoral adduction and protraction relative to most other Permo-Triassic diapsids.

Dental form and function in the early feeding diversification of dinosaurs

Dinosaurs evolved a remarkable diversity of dietary adaptations throughout the Mesozoic, but the origins of different feeding modes are uncertain, especially the multiple origins of herbivory. Feeding habits of early dinosaurs have mostly been inferred from qualitative comparisons of dental morphology with extant analogs. Here, we use biomechanical and morphometric methods to investigate the dental morphofunctional diversity of early dinosaurs in comparison with extant squamates and crocodylians and predict their diets using machine learning classification models. Early saurischians/theropods are consistently classified as carnivores. Sauropodomorphs underwent a dietary shift from faunivory to herbivory, experimenting with diverse diets during the Triassic and Early Jurassic, and early ornithischians were likely omnivores. Obligate herbivory was a late evolutionary innovation in both clades. Carnivory is the most plausible ancestral diet of dinosaurs, but omnivory is equally likely under certain phylogenetic scenarios. This early dietary diversity was fundamental in the rise of dinosaurs to ecological dominance.

A Triassic crown squamate

Mammals, birds, and squamates (lizards, snakes, and relatives) are key living vertebrates, and thus understanding their evolution underpins important questions in biodiversity science. Whereas the origins of mammals and birds are relatively well understood, the roots of squamates have been obscure. Here, we report a modern-type lizard from the Late Triassic of England [202 million years (Ma)], comprising a partial skeleton, skull, and mandibles. It displays at least 15 unique squamate traits and further shares unidentatan and anguimorph apomorphies. The new discovery fixes the origin of crown Squamata as much older than had been thought, and the revised dating shows substantial diversification of modern-type squamates following the Carnian Pluvial Episode, 232 Ma ago.

Evolutionary origins of the prolonged extant squamate radiation

Squamata is the most diverse clade of terrestrial vertebrates. Although the origin of pan-squamates lies in the Triassic, the oldest undisputed members of extant clades known from nearly complete, uncrushed material come from the Cretaceous. Here, we describe three-dimensionally preserved partial skulls of two new crown lizards from the Late Jurassic of North America. Both species are placed at the base of the skink, girdled, and night lizard clade Pan-Scincoidea, which consistently occupies a position deep inside the squamate crown in both morphological and molecular phylogenies. The new lizards show that several features uniting pan-scincoids with another major lizard clade, the pan-lacertoids, in trees using morphology were convergently acquired as predicted by molecular analyses. Further, the palate of one new lizard bears a handful of ancestral saurian characteristics lost in nearly all extant squamates, revealing an underappreciated degree of complex morphological evolution in the early squamate crown. We find strong evidence for close relationships between the two new species and Cretaceous taxa from Eurasia. Together, these results suggest that early crown squamates had a wide geographic distribution and experienced complicated morphological evolution even while the Rhynchocephalia, now solely represented by the tuatara, was the dominant clade of lepidosaurs.

Africa's oldest dinosaurs reveal early suppression of dinosaur distribution

The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated across Triassic Pangaea^1-11. By the Late Triassic (Carnian stage, ~235 million years ago), cosmopolitan 'disaster faunas' (refs. ^12-14) had given way to highly endemic assemblages^12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging-there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are proposed to have controlled distribution^15-18. During this time of high endemism, dinosaurs began to disperse and thus offer an opportunity to test the timing and drivers of this biogeographic pattern. Increased sampling can test this prediction: if dinosaurs initially dispersed under palaeolatitudinal-driven endemism, then an assemblage similar to those of South America^4,19-21 and India^19,22-including the earliest dinosaurs-should be present in Carnian deposits in south-central Africa. Here we report a new Carnian assemblage from Zimbabwe that includes Africa's oldest definitive dinosaurs, including a nearly complete skeleton of the sauropodomorph Mbiresaurus raathi gen. et sp. nov. This assemblage resembles other dinosaur-bearing Carnian assemblages, suggesting that a similar vertebrate fauna ranged high-latitude austral Pangaea. The distribution of the first dinosaurs is correlated with palaeolatitude-linked climatic barriers, and dinosaurian dispersal to the rest of the supercontinent was delayed until these barriers relaxed, suggesting that climatic controls influenced the initial composition of the terrestrial faunas that persist to this day.

Convergence, divergence, and macroevolutionary constraint as revealed by anatomical network analysis of the squamate skull, with an emphasis on snakes

Traditionally considered the earliest-diverging group of snakes, scolecophidians are central to major evolutionary paradigms regarding squamate feeding mechanisms and the ecological origins of snakes. However, quantitative analyses of these phenomena remain scarce. Herein, we therefore assess skull modularity in squamates via anatomical network analysis, focusing on the interplay between ‘microstomy’ (small-gaped feeding), fossoriality, and miniaturization in scolecophidians. Our analyses reveal distinctive patterns of jaw connectivity across purported ‘microstomatans’, thus supporting a more complex scenario of jaw evolution than traditionally portrayed. We also find that fossoriality and miniaturization each define a similar region of topospace (i.e., connectivity-based morphospace), with their combined influence imposing further evolutionary constraint on skull architecture. These results ultimately indicate convergence among scolecophidians, refuting widespread perspectives of these snakes as fundamentally plesiomorphic and morphologically homogeneous. This network-based examination of skull modularity—the first of its kind for snakes, and one of the first to analyze squamates—thus provides key insights into macroevolutionary trends among squamates, with particular implications for snake origins and evolution.

Successive climate crises in the deep past drove the early evolution and radiation of reptiles

Climate change-induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.

Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.

The Jurassic rise of squamates as supported by lepidosaur disparity and evolutionary rates

The squamates (lizards, snakes, and relatives) today comprise more than 10,000 species, and yet their sister group, the Rhynchocephalia, is represented by a single species today, the tuatara. The explosion in squamate diversity has been tracked back to the Cretaceous Terrestrial Revolution, 100 million years ago (Ma), the time when flowering plants began their takeover of terrestrial ecosystems, associated with diversification of coevolving insects and insect-eating predators such as lizards, birds, and mammals. Squamates arose much earlier, but their long pre-Cretaceous history of some 150 million years (Myr) is documented by sparse fossils. Here, we provide evidence for an initial radiation of squamate morphology in the Middle and Late Jurassic (174-145 Ma), and show that they established their key ecological roles much earlier than had been assumed, and they have not changed them much since.

High morphological disparity in a bizarre Paleocene fauna of predatory freshwater reptiles

BACKGROUND

The consequences of the K-Pg mass extinction are reflected across present biodiversity, but many faunas that appeared immediately after the extinction event were very different from current ones. Choristodera is a clade of reptiles of uncertain phylogenetic placement that have an extremely poor fossil record throughout their 150-million-year history. Yet, choristoderes survived the K-Pg event and persisted until the Miocene.

RESULTS

I describe the skulls and skeletons of two new choristoderes from a single Paleocene ecosystem in western North America that reveal the hidden Cenozoic diversity of this reptile clade. Despite their similar size, the new species deviate dramatically in morphology. Kosmodraco magnicornis gen. et sp. nov. possesses an extremely short snout and extensive cranial ornamentation. The sacrum of K. magnicornis bears enlarged muscle attachment sites and other modifications reminiscent of some giant crocodylians. In contrast, Champsosaurus norelli sp. nov. is a longirostrine species with an uninflated and ventrally divergent postorbital skull. Together with a North American choristodere previously classified in the European genus Simoedosaurus, K. magnicornis substantiates a new clade of giant, short-snouted taxa endemic to the Americas. C. norelli is found to be an early-diverging member of the genus Champsosaurus from the Cretaceous-Paleogene of the northern hemisphere. This suggests the presence of several ghost lineages of champsosaurid that crossed the K-Pg boundary.

CONCLUSIONS

The new taxa greatly increase Cenozoic choristodere richness and strengthen the evidence for the existence of distinctive freshwater faunas in Paleogene Eurasia and North America, where this clade diversified to exploit newly available macropredatory niches in the aftermath of the asteroid impact. The new choristoderes also reveal the distinct ecological context in which extant freshwater predators of the Americas like alligatoroids and gars have their origins: Paleocene fluviolacustrine ecosystems in North America displayed high large predator diversity and morphological disparity relative to modern ones.

An exceptionally preserved Sphenodon-like sphenodontian reveals deep time conservation of the tuatara skeleton and ontogeny

Sphenodontian reptiles are an extremely old evolutionary lineage forming the closest relatives to squamates (lizards and snakes) and were globally distributed and more diverse than squamates during the first half of their evolutionary history. However, the majority of their fossils are highly fragmentary, especially within sphenodontines-the group including its single surviving species, Sphenodon punctatus (the tuatara of New Zealand)-thus severely hampering our understanding on the origins of the tuatara. Here, we present a new sphenodontian species from the Early Jurassic of North America (Arizona, USA) represented by a nearly complete articulated skeleton and dozens of upper and lower jaws forming the most complete ontogenetic series in the sphenodontian fossil record. CT-scanning provides plentitude of data that unambiguously place this new taxon as one of the earliest evolving and oldest known sphenodontines. Comparisons with Sphenodon reveal that fundamental patterns of mandibular ontogeny and skeletal architecture in Sphenodon may have originated at least ~190Mya. In combination with recent findings, our results suggest strong morphological stability and an ancient origin of the modern tuatara morphotype.

Subaqueous foraging among carnivorous dinosaurs

Secondary aquatic adaptations evolved independently more than 30 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 to be partly or predominantly aquatic^3-11. However, these hypotheses remain controversial^12,13, largely owing to the difficulty of identifying unambiguous anatomical adaptations for aquatic habits in extinct animals. Here 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 marked increase in bone density, which precedes the evolution of more conspicuous anatomical modifications, a pattern also observed in other aquatic reptiles and mammals^14-16. Spinosaurids are revealed to be aquatic specialists with surprising ecological disparity, including subaqueous foraging behaviour in Spinosaurus and Baryonyx, and non-diving habits in Suchomimus. Adaptation to aquatic environments appeared in spinosaurids during the Early Cretaceous, following their divergence from other tetanuran theropods during the Early Jurassic¹⁷.

A new Early Cretaceous lizard in Myanmar amber with exceptionally preserved integument

We here report on a well-preserved juvenile lizard specimen in Albian amber (ca. 110 mya) from the Hkamti site (Myanmar). This new taxon is represented by an articulated skull and the anterior portion of the trunk, including the pectoral girdle and forelimbs. The scleral ossicles and eyelid are also visible, and the specimen exhibits pristine detail of the integument (of both head and body). In a combined molecular and morphological analysis, it was consistently recovered as a scincoid lizard (Scinciformata), as sister to Tepexisaurus + Xantusiidae. However, the phylogenetic position of the new taxon should be interpreted with caution as the holotype is an immature individual. We explored the possibility of miscoding ontogenetically variable characters by running alternative analyses in which these characters were scored as missing data for our taxon. With the exception of one tree, in which it was sister to Amphisbaenia, the specimen was recovered as a Pan-xantusiid. Moreover, we cannot rule out the possibility that it represents a separate lineage of uncertain phylogenetic position, as it is the case for many Jurassic and Cretaceous taxa. Nonetheless, this fossil offers a rare opportunity to glimpse the external appearance of one group of lizards during the Early Cretaceous.

Ticks on reptiles and amphibians in Central Amazonia, with notes on rickettsial infections

Reptiles and amphibians are exceptional hosts for different ectoparasites, including mites and ticks. In this study, we investigated tick infestations on reptiles and amphibians trapped in Central Amazonia, and also assessed the presence of rickettsial infections in the collected ticks. From September 2016 to September 2019, 385 reptiles (350 lizards, 20 snakes, 12 tortoises, and three caimans) and 120 amphibians (119 anurans and one caecilian) were captured and examined for ectoparasites. Overall, 35 (10%) lizards, three (25%) tortoises and one (0.8%) toad were parasitized by ticks (124 larvae, 32 nymphs, and 22 adults). In lizards, tick infestation varied significantly according to landscape category and age group. Based on combined morphological and molecular analyses, these ticks were identified as Amblyomma humerale (14 larvae, 12 nymphs, 19 males, and one female), Amblyomma nodosum (three larvae, one nymph, and one female), and Amblyomma rotundatum (four larvae, three nymphs, and one female), and Amblyomma spp. (103 larvae and 16 nymphs). Our study presents the first records of A. nodosum in the Amazonas state and suggests that teiid lizards are important hosts for larvae and nymphs of A. humerale in Central Amazonia. Moreover, a nymph of A. humerale collected from a common tegu (Tupinambis teguixin) was found positive for Rickettsia amblyommatis, which agrees with previous reports, suggesting that the A. humerale-R. amblyommatis relationship may be more common than currently recognized.

Phylogenetic value of jaw elements of lacertid lizards (Squamata: Lacertoidea): a case study with Oligocene material from France

Several extinct species are known from the family Lacertidae, but due to poor preservation, many of them are based on single bones. Here, we compare phylogenetic signals of disarticulated premaxillae, maxillae and dentaries of lacertids from four French Oligocene localities (Coderet, La Colombière, Roqueprune 2, Mas de Got B). We identified five morphotypes among the premaxillae, six among the maxillae, and ten among the dentaries. These morphotypes were scored as individual taxa per locality into three separate character matrices with the same 246 characters, one matrix for each jaw element. Subsequently, the phylogenetic position of the morphotypes was tested using maximum parsimony. The consensus trees with the dentaries and the maxillae found a large polytomy including all taxa except the outgroup taxon Gekko gecko. The consensus tree with the premaxillae showed a considerably more resolved topology but found all morphotype taxa outside Lacertidae. In a second step, we compared the constitution of our three datasets and the morphotype taxa. Our results suggest that a combination of convergent characters and missing data led to the outgroup position of the premaxilla morphotype taxa. The poor resolution of the maxillae strict consensus is likely a consequence of their fragmentary preservation. For the dentaries, a high amount of missing data due to the high number of morphotype taxa most likely caused the poor tree resolution. Indeed, tests with fewer morphotypes found tree resolutions comparable to the premaxilla data. When linking the morphotypes, five possible lacertid "species" were found. Comparison with already known French Oligocene lacertid species points to a slightly higher species richness of Lacertidae at that time than known before. Reliable species classification based on phylogeny only seems possible when combining the jaw elements or in association with other cranial and postcranial material, putting some doubt on species identifications based on single bones.

Multiple evolutionary origins and losses of tooth complexity in squamates

Teeth act as tools for acquiring and processing food, thus holding a prominent role in vertebrate evolution. In mammals, dental-dietary adaptations rely on tooth complexity variations controlled by cusp number and pattern. Complexity increase through cusp addition has dominated the diversification of mammals. However, studies of Mammalia alone cannot reveal patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, multiple-cusped teeth evolved over 20 times independently from a single-cusped common ancestor. Squamates frequently lost cusps and evolved varied multiple-cusped morphologies at heterogeneous rates. Tooth complexity evolved in correlation with changes in plant consumption, resulting in several major increases in speciation. Complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental-dietary evolution.

A new extinct species of alligator lizard (Squamata: Elgaria) and an expanded perspective on the osteology and phylogeny of Gerrhonotinae

BACKGROUND

Alligator lizards (Gerrhonotinae) are a well-known group of extant North American lizard. Although many fossils were previously referred to Gerrhonotinae, most of those fossils are isolated and fragmentary cranial elements that could not be placed in a precise phylogenetic context, and only a handful of known fossils are articulated skulls. The fossil record has provided limited information on the biogeography and phylogeny of Gerrhonotinae.

RESULTS

We redescribe a nearly complete articulated fossil skull from the Pliocene sediments of the Anza-Borrego Desert in southern California, and refer the specimen to the alligator lizard genus Elgaria. The fossil is a representative of a newly described species, Elgaria peludoverde. We created a morphological matrix to assess the phylogeny of alligator lizards and facilitate identifications of fossil gerrhonotines. The matrix contains a considerably expanded taxonomic sample relative to previous morphological studies of gerrhonotines, and we sampled two specimens for many species to partially account for intraspecific variation. Specimen-based phylogenetic analyses of our dataset using Bayesian inference and parsimony inferred that Elgaria peludoverde is part of crown Elgaria. The new species is potentially related to the extant species Elgaria kingii and Elgaria paucicarinata, but that relationship was not strongly supported, probably because of extensive variation among Elgaria. We explored several alternative biogeographic scenarios implied by the geographic and temporal occurrence of the new species and its potential phylogenetic placements.

CONCLUSIONS

Elgaria peludoverde is the first described extinct species of Elgaria and provides new information on the biogeographic history and diversification of Elgaria. Our research expands the understanding of phylogenetic relationships and biogeography of alligator lizards and strengthens the foundation of future investigations. The osteological data and phylogenetic matrix that we provided will be critical for future efforts to place fossil gerrhonotines. Despite limited intraspecific sampled sizes, we encountered substantial variation among gerrhonotines, demonstrating the value of exploring patterns of variation for morphological phylogenetics and for the phylogenetic placement of fossils. Future osteological investigations on the species we examined and on species we did not examine will continue to augment our knowledge of patterns of variation in alligator lizards and aid in phylogenetics and fossil placement.

A Triassic stem lepidosaur illuminates the origin of lizard-like reptiles

The early evolution of diapsid reptiles is marked by a deep contrast between our knowledge of the origin and early evolution of archosauromorphs (crocodiles, avian and non-avian dinosaurs) to that of lepidosauromorphs (squamates (lizards, snakes) and sphenodontians (tuataras)). Whereas the former include hundreds of fossil species across various lineages during the Triassic period¹, the latter are represented by an extremely patchy early fossil record comprising only a handful of fragmentary fossils, most of which have uncertain phylogenetic affinities and are confined to Europe^1-3. Here we report the discovery of a three-dimensionally preserved reptile skull, assigned as Taytalura alcoberi gen. et sp. nov., from the Late Triassic epoch of Argentina that is robustly inferred phylogenetically as the earliest evolving lepidosauromorph, using various data types and optimality criteria. Micro-computed tomography scans of this skull reveal details about the origin of the lepidosaurian skull from early diapsids, suggesting that several traits traditionally associated with sphenodontians in fact originated much earlier in lepidosauromorph evolution. Taytalura suggests that the strongly evolutionarily conserved skull architecture of sphenodontians represents the plesiomorphic condition for all lepidosaurs, that stem and crown lepidosaurs were contemporaries for at least ten million years during the Triassic, and that early lepidosauromorphs had a much broader geographical distribution than has previously been thought.

A reassessment of the enigmatic diapsid Paliguana whitei and the early history of Lepidosauromorpha

Lepidosaurs include lizards, snakes, amphisbaenians and the tuatara, comprising a highly speciose evolutionary radiation with widely varying anatomical traits. Their stem-lineage originated by the late middle Permian 259 million years ago, but its early fossil record is poorly documented, obscuring the origins of key anatomical and functional traits of the group. Paliguana whitei, from the Early Triassic of South Africa, is an enigmatic fossil species with the potential to provide information on this. However, its anatomy and phylogenetic affinities remain highly uncertain, and have been debated since its discovery more than 100 years ago. We present microtomographic three-dimensional imaging of the cranial anatomy of P. whitei that clarifies these uncertainties, providing strong evidence for lepidosauromorph affinities based on the structure of the temporal region and the implantation of marginal dentition. Phylogenetic analysis including these new data recovers Paliguana as the earliest known stem-lepidosaur, within a long-lived group of early diverging lepidosauromorphs that persisted to at least the Middle Jurassic. Our results provide insights into cranial evolution on the lepidosaur stem-lineage, confirming that characteristics of pleurodont dental implantation evolved early on the lepidosaur stem-lineage. By contrast, key functional traits related to hearing (quadrate conch) and feeding (streptostyly) evolved later in the lepidosaur crown-group.

Bayesian Morphological Clock versus Parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia)

Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein, we present a morphological dataset for a group of cricetid rodents to which we apply an array of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated and non-calibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids.

Osteology, relationships and functional morphology of Weigeltisaurus jaekeli (Diapsida, Weigeltisauridae) based on a complete skeleton from the Upper Permian Kupferschiefer of Germany

BACKGROUND

Weigeltisauridae is a clade of small-bodied diapsids characterized by a horned cranial frill, slender trunk and limbs, and a patagium supported by elongated bony rods. Partial skeletons and fragments are definitively known only from upper Permian (Lopingian) rocks in England, Germany, Madagascar and Russia. Despite these discoveries, there have been few detailed descriptions of weigeltisaurid skeletons, and the homologies of many skeletal elements-especially the rods supporting the patagium-remain the subject of controversy.

MATERIALS & METHODS

Here, we provide a detailed description of a nearly complete skeleton of Weigeltisaurus jaekeli from the upper Permian (Lopingian: Wuchiapingian) Kupferschiefer of Lower Saxony, Germany. Briefly addressed by past authors, the skeleton preserves a nearly complete skull, postcranial axial skeleton, appendicular skeleton, and patagial supports. Through comparisons with extant and fossil diapsids, we examine the hypotheses for the homologies of the patagial rods. To examine the phylogenetic position of Weigeltisauridae and characterize the morphology of the clade, we integrate the material and other weigeltisaurids into a parsimony-based phylogenetic analysis focused on Permo-Triassic non-saurian Diapsida and early Sauria (61 taxa, 339 characters).

RESULTS

We recognize a number of intriguing anatomical features in the weigeltisaurid skeleton described here, including hollow horns on the post-temporal arch, lanceolate teeth in the posterior portion of the maxilla, the absence of a bony arch connecting the postorbital and squamosal bones, elongate and slender phalanges that resemble those of extant arboreal squamates, and patagial rods that are positioned superficial to the lateral one third of the gastral basket. Our phylogenetic study recovers a monophyletic Weigeltisauridae including Coelurosauravus elivensis, Weigeltisaurus jaekeli, and Rautiania spp. The clade is recovered as the sister taxon to Drepanosauromorpha outside of Sauria (=Lepidosauria + Archosauria).

CONCLUSIONS

Our anatomical observations and phylogenetic analysis show variety of plesiomorphic diapsid characters and apomorphies of Weigeltisauridae in the specimen described here. We corroborate the hypothesis that the patagial ossifications are dermal bones unrelated to the axial skeleton. The gliding apparatus of weigeltisaurids was constructed from dermal elements unknown in other known gliding diapsids. SMNK-PAL 2882 and other weigeltisaurid specimens highlight the high morphological disparity of Paleozoic diapsids already prior to their radiation in the early Mesozoic.

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.

Fossils improve phylogenetic analyses of morphological characters

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth-death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.

A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other "protorosaurs", and its implications for the early evolution of stem archosaurs

The historical clade "Protorosauria" represents an important group of archosauromorph reptiles that had a wide geographic distribution between the Late Permian and Late Triassic. "Protorosaurs" are characterized by their long necks, which are epitomized in the genus Tanystropheus and in Dinocephalosaurus orientalis. Recent phylogenetic analyses have indicated that "Protorosauria" is a polyphyletic clade, but the exact relationships of the various "protorosaur" taxa within the archosauromorph lineage is currently uncertain. Several taxa, although represented by relatively complete material, have previously not been assessed phylogenetically. We present a new phylogenetic hypothesis that comprises a wide range of archosauromorphs, including the most exhaustive sample of "protorosaurs" to date and several "protorosaur" taxa from the eastern Tethys margin that have not been included in any previous analysis. The polyphyly of "Protorosauria" is confirmed and therefore we suggest the usage of this term should be abandoned. Tanystropheidae is recovered as a monophyletic group and the Chinese taxa Dinocephalosaurus orientalis and Pectodens zhenyuensis form a new archosauromorph clade, Dinocephalosauridae, which is closely related to Tanystropheidae. The well-known crocopod and former "protorosaur" Prolacerta broomi is considerably less closely related to Archosauriformes than was previously considered.