Interrelationships among Early Triassic faunas of Western Gondwana and Laurasia as illuminated by a new South American benthosuchid temnospondyl.

The End-Permian Mass Extinction marked a critical turning point in Earth's history, and the biological recovery that followed the crisis led to the emergence of several modern vertebrate and invertebrate taxa. Even considering the importance of the Early Triassic biotic recovery for the evolution of modern faunas and floras, our knowledge of this event is still hindered by the sparse sampling of crucial geological formations. This leaves our understanding of Early Triassic ecosystems fundamentally biased toward productive and historically well-explored geological units. Recent surveys in poorly known Gondwanan localities, such as those within the Sanga do Cabral Formation in southern Brazil, have unveiled insights into Early Triassic terrestrial ecosystems, shedding light on a diverse and previously unknown tetrapod fauna. Here, we report the discovery of a new temnospondyl genus and species in the Lower Triassic Sanga do Cabral Formation. The new taxon can be confidently assigned to the Benthosuchidae, a stereospondyl clade with a distribution previously restricted to the East European Platform. Phylogenetic analysis confirms the relationship of the new genus to the trematosaurian lineage, being closely related to the genus Benthosuchus. Our results raise questions about the biogeographical history of stereospondyls after the End-Permian Mass Extinction and suggest a potential connection between Russian and South American Early Triassic faunas. Further investigations are needed to thoroughly explore the potential dispersal routes that may explain this seemingly unusual biogeographical pattern.

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.

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.].

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.

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.

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.

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 Europe1-3. 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.

Sustained high rates of morphological evolution during the rise of tetrapods.

The fish-to-tetrapod transition is one of the most iconic events in vertebrate evolution, yet fundamental questions regarding the dynamics of this transition remain unresolved. Here, we use advances in Bayesian morphological clock modelling to reveal the evolutionary dynamics of early tetrapodomorphs (tetrapods and their closest fish relatives). We show that combining osteological and ichnological calibration data results in major shifts on the time of origin of all major groups of tetrapodomorphs (up to 25 million years) and that low rates of net diversification, not fossilization, explain long ghost lineages in the early tetrapodomorph fossil record. Further, our findings reveal extremely low rates of morphological change for most early tetrapodomorphs, indicating widespread stabilizing selection upon their 'fish' morphotype. This pattern was broken only by elpistostegalians (including early tetrapods), which underwent sustained high rates of morphological evolution for ~30 Myr during the deployment of the tetrapod body plan.

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates.

BACKGROUND: The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. RESULTS: Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. CONCLUSIONS: We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles.

The origin of phenotypic diversity among higher clades is one of the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates of evolution and phenotypic disparity across broad scales of time to understand the evolutionary dynamics behind the origin and early evolution of new clades. Here, we provide a total-evidence dating approach to this problem in diapsid reptiles. We find major chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expansion in phenotypic disparity in reptile evolution. Importantly, many instances of accelerated phenotypic evolution are detected at the origin of major clades and body plans, but not concurrent with previously proposed periods of adaptive radiation. Furthermore, strongly heterogenic rates of evolution mark the acquisition of similarly adapted functional types, and the origin of snakes is marked by the highest rates of phenotypic evolution in diapsid history.

Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study.

Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.

A tiny new Middle Triassic stem-lepidosauromorph from Germany: implications for the early evolution of lepidosauromorphs and the Vellberg fauna.

The Middle Triassic was a time of major changes in tetrapod faunas worldwide, but the fossil record for this interval is largely obscure for terrestrial faunas. This poses a severe limitation to our understanding on the earliest stages of diversification of lineages representing some of the most diverse faunas in the world today, such as lepidosauromorphs (e.g., lizards and tuataras). Here, we report a tiny new lepidosauromorph from the Middle Triassic from Vellberg (Germany), which combines a mosaic of features from both early evolving squamates and rhynchocephalians, such as the simultaneous occurrence of a splenial bone and partial development of acrodonty. Phylogenetic analyses applying different optimality criteria, and combined morphological and molecular data, consistently recover the new taxon as a stem-lepidosauromorph, implying stem-lepidosauromorph species coinhabited areas comprising today's central Europe at the same time as the earliest known rhynchocephalians and squamates. It further demonstrates a more complex evolutionary scenario for dental evolution in early lepidosauromorphs, with independent acquisitions of acrodonty early in their evolutionary history. The small size of most terrestrial vertebrates from Vellberg is conspicuous, contrasting to younger Triassic deposits worldwide, but comparable to Early Triassic faunas, suggesting a potential long-lasting Lilliput effect in this fauna.

New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake body plan.

Snakes represent one of the most dramatic examples of the evolutionary versatility of the vertebrate body plan, including body elongation, limb loss, and skull kinesis. However, understanding the earliest steps toward the acquisition of these remarkable adaptations is hampered by the very limited fossil record of early snakes. Here, we shed light on the acquisition of the snake body plan using micro-computed tomography scans of the first three-dimensionally preserved skulls of the legged snake Najash and a new phylogenetic hypothesis. These findings elucidate the initial sequence of bone loss that gave origin to the modern snake skull. Morphological and molecular analyses including the new cranial data provide robust support for an extensive basal radiation of early snakes with hindlimbs and pelves, demonstrating that this intermediate morphology was not merely a transient phase between limbed and limbless body plans.

Cranial ontogeny of Thamnophis radix (Serpentes: Colubroidea) with a re-evaluation of current paradigms of snake skull evolution.

Accurate knowledge of skeletal ontogeny in extant organisms is crucial in understanding important morpho-functional systems and in enabling inferences of the ontogenetic stage of fossil specimens. However, detailed knowledge of skeletal ontogeny is lacking for most squamates, including snakes. Very few studies have discussed postnatal development in snakes, with none incorporating data from all three major ontogenetic stages-embryonic, juvenile and adult. Here, we provide the first analysis encompassing these three ontogenetic stages for any squamate, using the first complete micro-computed tomography (micro-CT)-based segmentations of any non-adult snake, based on fresh specimens of Thamnophis radix. The most significant ontogenetic changes involve the feeding apparatus, with major elongation of the tooth-bearing elements and jaw suspensorium causing a posterior shift in the jaw articulation. This shift enables macrostomy (large-gaped feeding in snakes) and occurs in T. radix via a different developmental trajectory than in most other macrostomatans, indicating that the evolution of macrostomy is more complex than previously thought. The braincase of T. radix is also evolutionarily unique among derived snakes in lacking a crista circumfenestralis, a phenomenon considered herein to represent paedomorphic retention of the embryonic condition. We thus present numerous important challenges to current paradigms regarding snake cranial evolution.

A New Clevosaurid from the Triassic (Carnian) of Brazil and the Rise of Sphenodontians in Gondwana.

The early evolution of lepidosaurs is marked by an extremely scarce fossil record during the Triassic. Importantly, most Triassic lepidosaur specimens are represented by disarticulated individuals from high energy accretion deposits in Laurasia, thus greatly hampering our understanding of the initial stages of lepidosaur evolution. Here, we describe the fragmentary remains of an associated skull and mandible of Clevosaurus hadroprodon sp. nov., a new taxon of sphenodontian lepidosaur from the Late Triassic (Carnian; 237-228 Mya) of Brazil. Referral to Sphenodontia is supported by the combined presence of a marginal dentition ankylosed to the apex of the dentary, maxilla, and premaxilla; the presence of 'secondary bone' at the bases of the marginal dentition; and a ventrally directed mental process at the symphysis of the dentary. Our phylogenetic analyses recover Clevosaurus hadroprodon as a clevosaurid, either in a polytomy with the Late Triassic to Early Jurassic Clevosaurus and Brachyrhinodon (under Bayesian inference), or nested among different species of Clevosaurus (under maximum parsimony). Clevosaurus hadroprodon represents the oldest known sphenodontian from Gondwana, and its clevosaurid relationships indicates that these sphenodontians achieved a widespread biogeographic distribution much earlier than previously thought.

The evolution of the axial skeleton intercentrum system in snakes revealed by new data from the Cretaceous snakes Dinilysia and Najash.

Snakes are an extremely modified and long-lived clade of lizards that have either lost or highly altered many of the synapomorphies that would clearly link them to their closest sister-group among squamates. We focus here on one postcranial morphological complex, the intercentrum system which in most non-ophidian squamates is limited to the cervical and caudal regions. The Cervical Intercentrum System (CeIS) is composed of a single intercentral element that sometimes articulates with a ventral projection (hypapophyses) of the centrum; the Caudal Intercentrum System (CaIS) is formed by an intercentral element, the haemal arch/chevron bone, and paired ventral projections of the centrum, the haemapophyses. In modern snakes, the intercentrum element of the CeIS is considered lost or fused to the hypaphophysis, and the chevron bone in CaIS is considered lost. Here, we describe new specimens of the early snake Dinilysia patagonica, and reinterpret previously known specimens of Dinilysia and Najash rionegrina, that do not show the expected snake morphology. The anatomy of these fossil taxa unambiguously shows that free cervical and caudal intercentra attached to distinct downgrowths (hypapophyses and haemapophyses) of the centra, are present in basal fossil snakes, and agrees with the proposed loss of post atlas-axis intercentra in later evolving snakes.

X-ray computed microtomography of Megachirella wachtleri.

Understanding the origin and early evolution of squamates has been a considerable challenge given the extremely scarce fossil record of early squamates and their poor degree of preservation. In order to overcome those limitations, we conducted high-resolution X-ray computed tomography (CT) studies on the fossil reptile Megachirella wachtleri (Middle Triassic, northern Italy), which revealed an important set of features indicating this is the oldest known fossil squamate in the world, predating the previous oldest record by ca. 75 million years. We also compiled a new phylogenetic data set comprising a large sample of diapsid reptiles (including morphological and molecular data) to investigate the phylogenetic relationships of early squamates and other reptile groups along with the divergence time of those lineages. The re-description of Megachirella and a new phylogenetic hypothesis of diapsid relationships are presented in a separate study. Here we present the data descriptors for the tomographic scans of Megachirella, which holds fundamental information to our understanding on the early evolution of one of the largest vertebrate groups on Earth today.

A mid-Cretaceous embryonic-to-neonate snake in amber from Myanmar.

We present the first known fossilized snake embryo/neonate preserved in early Late Cretaceous (Early Cenomanian) amber from Myanmar, which at the time, was an island arc including terranes from Austral Gondwana. This unique and very tiny snake fossil is an articulated postcranial skeleton, which includes posterior precloacal, cloacal, and caudal vertebrae, and details of squamation and body shape; a second specimen preserves a fragment of shed skin interpreted as a snake. Important details of skeletal ontogeny, including the stage at which snake zygosphene-zygantral joints began to form along with the neural arch lamina, are preserved. The vertebrae show similarities to those of fossil Gondwanan snakes, suggesting a dispersal route of Gondwanan faunas to Laurasia. Finally, the new species is the first Mesozoic snake to be found in a forested environment, indicating greater ecological diversity among early snakes than previously thought.

New data on the Late Cretaceous lizard Dicothodon bajaensis (Squamata, Borioteiioidea) from Baja California, Mexico reveals an unusual tooth replacement pattern in squamates.

Borioteiioids comprise an extinct family of squamates that inhabited the Northern Hemisphere during the Cretaceous and were characterized by varying patterns of tooth replacement and dental morphology. Understanding the evolution of these tooth replacement patterns has, however, been largely hampered by an extremely fragmentary fossil record. Here we present new information on Dicothodon bajaensisfrom the Campanian of Baja California (Mexico), so far known only from isolated teeth and jaw fragments. Among abundant new materials there are ten maxillae and five dentaries belonging to distinct ontogenetic stages. Whereas juveniles display active tooth replacement, older specimens show no evidence of replacement. Dicothodon bajaensis is therefore inferred to have had arrested tooth replacement later in ontogeny. This provides the first evidence of cessation of tooth replacement during late ontogeny in lizards (living or extinct). This replacement type is also an evolutionary intermediate between the typical lizard replacement pattern, observed in some borioteiioids (e.g., Bicuspidon) and the complete absence of tooth replacement since early ontogeny as observed in other borioteiioids (e.g., Polyglyphanodon).