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

Evolution of Pineal Nonvisual Opsins in Lizards and the Tuatara and Identification of Lepidopsin: A New Opsin Gene

Many lizards (Squamata), as well as the tuatara (Rhynchocephalia), are distinguished among vertebrate groups for the presence of the parietal eye, or "third eye", a structure derived from the pineal complex containing a simplified retina with photoreceptor cells. The parietal eye expresses nonvisual opsins that differ from the visual opsin repertoire of the lateral eyes. These are pinopsin (OPNP), parapinopsin (OPNPP), and parietopsin (OPNPT), all being evolutionary close to visual opsins. Here, we searched over 60 lepidosaurian genomes for pineal nonvisual opsins to check for the evolutionary trajectory of these genes in reptiles. Unexpectedly, we identified a novel opsin gene, which we termed "lepidopsin" (OPNLEP), that is present solely in the genomes of the tuatara and most lizard groups but absent from other vertebrates. Remnants of the gene are found in the coelacanth and some ray-finned fishes, implying that OPNLEP is an ancient opsin that has been repeatedly lost during vertebrate evolution. We found that the tuatara and most lizards of the Iguania, Anguimorpha, Scincoidea, and Lacertidae clades, which possess a parietal eye, harbor all pineal opsin genes. Lizards missing the parietal eye, like geckos, teiids, and a fossorial amphisbaenian, lack most or all pineal nonvisual opsins. In summary, our survey of pineal nonvisual opsins reveals (i) the persistence of a previously unknown ancient opsin gene-OPNLEP-in lepidosaurians; (ii) losses of nonvisual opsins in specific lizard clades; and (iii) a correlation between the presence of a parietal eye and the genomic repertoire of pineal nonvisual opsins.

Riverine Realities: Evaluating Climate Change Impacts on Habitat Dynamics of the Critically Endangered Gharial (Gavialis gangeticus) in the Indian Landscape

The endemic and critically endangered gharial, Gavialis gangeticus, experienced a severe population decline in its range. However, conservation efforts, notably through the implementation of "Project Crocodile" in India, have led to a significant recovery of its population. The present study employs an ensemble Species Distribution Model (SDM) to delineate suitable habitats for G. gangeticus under current and future climatic scenarios to understand the impact of climate change. The model estimates that 46.85% of the area of occupancy is suitable under the present scenario, with this suitable area projected to increase by 145.16% in future climatic conditions. States such as Madhya Pradesh, Uttar Pradesh, and Assam are projected to experience an increase in habitat suitability, whereas Odisha and Rajasthan are anticipated to face declines. The study recommends conducting ground-truthing ecological assessments using advanced technologies and genetic analyses to validate the viability of newly identified habitats in the Lower Ganges, Mahanadi, and Brahmaputra River systems. These areas should be prioritized within the Protected Area network for potential translocation sites allocation. Collaborative efforts between the IUCN-SSC Crocodile Specialist Group and stakeholders are vital for prioritizing conservation and implementing site-specific interventions to protect the highly threatened gharial population in the wild.

Habitat openness and squamate color evolution over deep time

While the ecological roles of colored integument have been extensively studied, what regulates global patterns of color variation remains poorly understood. Here, using a global dataset of 1249 squamates, we evaluate whether and how six key eco-environmental variables and their interactions shaped the evolutionary history of their coloration. We show that only habitat openness consistently associates with brightness evolution, with brighter integuments favored in open habitats, possibly for enhanced heat reflection. Furthermore, brightness evolution rates likely track δ18O (a temperature proxy) changes and increase during global aridification phases, such as those in the Miocene and Pliocene. This trend may be due to the establishment of an arid climate that promoted habitat openness shifts, ultimately inducing adaption to new niches. Our findings suggest that a single environmental variable is associated with color variation in the largest extant tetrapod order.

A new stem saurian reptile from the late Permian of South Africa and insights into saurian evolution

The evolutionary radiation of diapsid reptiles that includes all extant and most extinct reptiles is well-represented in the Mesozoic and Cenozoic fossil records, however, the earliest stages recorded in the Paleozoic Era are limited to comparatively few taxa. Consequently, the origins of Sauria, the crown-group of Diapsida, remains poorly understood and the phylogenetic positions of the few known taxa along the saurian stem are controversial. Here, we describe Akkedops bremneri sp. et gen. nov., a new early late Permian stem saurian from the Karoo of South Africa based on two skulls and show that the famous aggregation of "juvenile Youngina" SAM-PK-K7710 is also referrable to it, thereby making this one of the best-known stem saurians. The skull has a short rostrum, open lower temporal bar, large contribution of the postfrontal to the upper temporal fenestra, slender stapes, sliver-like supratemporal with a distinct lateral flange suturing to the postorbital, and lacks both postparietal and tabular bones. The saddle-shaped quadrate is rather saurian-like in being posteriorly emarginated with a tympanic crest and unique medial flange. The post cranial skeleton of Akkedops bremneri is lizard-like and notably shows a hook-shaped fifth metatarsal and thyroid fenestra. Phylogenetic analysis recovers Akkedops bremneri as sister to Sauria, which is especially surprising considering its rather small size and slender, lizard-like morphology prior to the split between the apparently similar lepidosauromorphs and many of the comparatively robust archosauromorph saurians. Our analysis also indicates that Youngina capensis falls outside the clade of Akkedops bremenri + Sauria and does not appear to form a clade with other "younginiform" reptiles. The available evidence indicates a surprising level of complexity related to the evolution of stem saurians and the origin of Sauria that occurred in the shadow of other Paleozoic amniotes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-025-00351-y.

Cranial osteology and neuroanatomy of the late Permian reptile Milleropsis pricei and implications for early reptile evolution

Millerettidae are a group of superficially lizard-like Permian stem reptiles originally hypothesized as relevant to the ancestry of the reptile crown group, and particularly to lepidosaurs and archosaurs. Since the advent of cladistics, millerettids have typically been considered to be more distant relatives of crown reptiles as the earliest-diverging parareptiles and therefore outside of 'Eureptilia'. Despite this cladistic consensus, some conspicuous features of millerettid anatomy invite reconsideration of their relationships. We provide a detailed description of the late Permian millerettid Milleropsis pricei using synchrotron X-ray phase-contrast micro-computed tomography focusing on the cranial anatomy of three individuals known from a burrow aggregation. Our data reveal a suite of neuroanatomical features Milleropsis shares with neodiapsids that are absent both in other 'parareptiles' and in early diverging groups of 'eureptiles'. Traits shared between Milleropsis and neodiapsids include: the presence of a tympanic emargination on the quadrate, quadratojugal and squamosal, the loss of epipterygoid contribution to the basicranial articulation suggesting a more kinetic palatoquadrate, the absence of a sphenethmoid and the pathway of the abducens nerve through the braincase. Our findings suggest that the early reptile neurocranium, a region poorly sampled in phylogenetic analyses due to relative visual inaccessibility and poor preservation, has the potential to inform the phylogenetic relationships of early reptiles.

Early-middle Permian Mediterranean gorgonopsian suggests an equatorial origin of therapsids

Therapsids were a dominant component of middle-late Permian terrestrial ecosystems worldwide, eventually giving rise to mammals during the early Mesozoic. However, little is currently known about the time and place of origin of Therapsida. Here we describe a definitive therapsid from the lower-?middle Permian palaeotropics, a partial skeleton of a gorgonopsian from the island of Mallorca, western Mediterranean. This specimen represents, to our knowledge, the oldest gorgonopsian record worldwide, and possibly the oldest known therapsid. Using emerging relaxed clock models, we provide a quantitative timeline for the origin and early diversification of therapsids, indicating a long ghost lineage leading to the evolutionary radiation of all major therapsid clades within less than 10 Myr, in the aftermath of Olson's Extinction. Our findings place this unambiguous early therapsid in an ancient summer wet biome of equatorial Pangaea, thus suggesting that the group originated in tropical rather than temperate regions.

Klastomycter conodentatus, gen et sp. nov., a small early Permian parareptile with conical teeth from Richards Spur, Oklahoma

A small, pristinely preserved specimen recently collected from the Dolese Brothers limestone quarry near Richards Spur, Oklahoma provides evidence for the presence of a new early Permian parareptile at this locality. The specimen includes an articulated, nearly complete skull roof, and with the right premaxilla, right quadratojugal, most of the right palate, as well as the right epipterygoid and the sphenethmoid preserved inside. Although similar in many respects to the other contemporary parareptiles Acleistorhinus, Delorhynchus and Colobomycter, it can be distinguished from other acleistorhinids by the presence of a number of autapomorphies related to its dentition. Phylogenetic analysis places it closer to Delorhynchus and Colobomycter within Acleistorhinidae than to Acleistorhinus pteroticus. Unique aspects of the present specimen include the pronounced anterior extension of the lacrimal bone, largely homodont dentition composed of simple conical crowns with slight recurvature in the premaxillary and anterior maxillary teeth, and simple conical crowns in posterior maxillary dentition. The discovery of this new parareptile along with the surprisingly large number of acleistorhinids at Richards Spur highlights the importance of the unique fissure and vertical cave system at this site. No other early Permian site has provided such a wide diversity of parareptilian taxa, part of a complex community of terrestrial vertebrates. The present specimen highlights the fine niche partitioning that appears to have been present among reptiles of this region.

Deep-time origin of tympanic hearing in crown reptiles

The invasion of terrestrial ecosystems by tetrapods (c. 375 million years [Ma]) represents one of the major evolutionary transitions in the history of life on Earth. The success of tetrapods on land is linked to evolutionary novelties. Among these, the evolution of a tympanic ear contributed to mitigating the problem of an impedance mismatch between the air and the fluid embedding sound-detecting hair cells in the inner ear.1,2,3 Pioneering studies advocated that similarities in the tympanic ear of tetrapods could only result from a single origin of this structure in the group,4,5 an idea later challenged by paleontological and developmental data.4,6,7,8 Current evidence suggests that this sensory structure evolved independently in amphibians, mammals, and reptiles,1,6 but it remains uncertain how many times tympanic hearing originated in crown reptiles.9,10 We combine developmental information with paleontological data to evaluate the evolution of the tympanic ear in reptiles from two complementary perspectives. Phylogenetically informed ancestral reconstruction analyses of a taxonomically broad sample of early reptiles point to the presence of a tympanic membrane as the ancestral condition of the crown group. Consistently, comparative analyses using embryos of lizards and crocodylians reveal similarities, including the formation of the tympanic membrane within the second pharyngeal arch, which has been previously reported for birds. Therefore, both our developmental and paleontological data suggest a single origin for the tympanic middle ear in the group, challenging the current paradigm of multiple acquisitions of tympanic hearing in living reptiles.

A systematic comparative description of extant turtle humeri, with comments on humerus disparity and evolution based on fossil comparisons

The humerus is central for locomotion in turtles as quadrupedal animals. Osteological variation across testudine clades remains poorly documented. Here, we systematically describe the humerus anatomy for all major extant turtle clades based on 38 species representing the phylogenetic and ecological diversity of crown turtles. Three Late Triassic species of shelled stem turtles (Testudindata) are included to establish the plesiomorphic humerus morphology. Our work is based on 3D models, establishing a publicly available digital database. Previously defined terms for anatomical sides of the humerus (e.g., dorsal, ventral) are often not aligned with the respective body sides in turtles and other quadrupedal animals with sprawling gait. We propose alternative anatomical directional terms to simplify communication: radial and ulnar (the sides articulating with the radius/ulna), capitular (the side bearing the humeral head), and intertubercular (opposite to capitular surface). Turtle humeri show low morphological variation with exceptions concentrated in locomotory specialists. We propose 15 discrete characters to summarize osteological variation for future phylogenetic studies. Disparity analyses comparing non-shelled and shelled turtles indicate that the presence of the shell constrains humerus variation. Flippered aquatic turtles are released from this constraint and significantly increase overall disparity. Ontogenetic changes of turtle humeri are related to increased ossification and pronunciation of the proximal processes, the distal articulation areas, and the closure of the ectepicondylar groove to a foramen. Some turtle species retain juvenile features into adulthood and provide evidence for paedomorphic evolution. We review major changes of turtle humerus morphology throughout the evolution of its stem group.

Thought for food: the endothermic brain hypothesis

The evolution of whole-body endothermy occurred independently in dinosaurs and mammals and was associated with some of the most significant neurocognitive shifts in life's history. These included a 20-fold increase in neurons and the evolution of new brain structures, supporting similar functions in both lineages. We propose the endothermic brain hypothesis, which holds that elaborations in endotherm brains were geared towards increasing caloric intake through efficient foraging. The hypothesis is grounded in the intrinsic coupling of cognition and organismic self-maintenance. We argue that coevolution of increased metabolism and new forms of cognition should be jointly investigated in comparative studies of behaviors and brain anatomy, along with studies of fossil species. We suggest avenues for such research and highlight critical open questions.

Thalattosauria in time and space: a review of thalattosaur spatiotemporal occurrences, presumed evolutionary relationships and current ecological hypotheses

In the wake of the greatest mass extinction in Earth's history, the End-Permian Mass Extinction, the Triassic was a time of recovery and innovation. Aided by warm climatic conditions and favorable ecological circumstances, many reptilian clades originated and rapidly diversified during this time. This set the stage for numerous independent invasions of the marine realm by several reptilian clades, such as Ichthyosauriformes and Sauropterygia, shaping the oceanic ecosystems for the entire Mesozoic. Although comparatively less speciose, and temporally and latitudinally more restricted, another marine reptile clade, the Thalattosauriformes, stands out because of their unusual and highly disparate cranial, dental and skeletal morphology. Research on Thalattosauriformes has been hampered by a historic dearth of material, with the exception of rare material from Lagerstätten and highly fossiliferous localities, such as that from the UNESCO world heritage site of Monte San Giorgio. Consequently, their evolutionary origins and paleobiology remain poorly understood. The recent influx of new material from southwestern China and North America has renewed interest in this enigmatic group prompting the need for a detailed review of historic work and current views. The earliest representatives of the group may have been present from the late Early Triassic onwards in British Columbia. By the Ladinian the group had achieved a wide distribution across the northern hemisphere, spanning the eastern Panthalassic as well as the eastern and western Tethyan provinces. Distinct morphological and likely ecological differences exist between the two major clades of Thalattosauriformes, the Askeptosauroidea and the Thalattosauroidea, with the latter showing a higher degree of cranial and skeletal morphological disparity. In-group relationships remain poorly resolved beyond this bipartition. Overall, thalattosaurs may be closely related to other marine reptile groups such as ichthyopterygians and sauropterygians. However, their exact position within Diapsida remains elusive. Future focal points should utilize modern digital paleontological approaches to explore the many fragmentary specimens of otherwise poorly sampled localities.

The topological organization of the turtle cranium is constrained and conserved over long evolutionary timescales

The cranium of turtles (Testudines) is characterized by the secondary reduction of temporal fenestrae and loss of cranial joints (i.e., characteristics of anapsid, akinetic skulls). Evolution and ontogeny of the turtle cranium are associated with shape changes. Cranial shape variation among Testudines can partially be explained by dietary and functional adaptations (neck retraction), but it is unclear if cranial topology shows similar ecomorphological signal, or if it is decoupled from shape evolution. We assess the topological arrangement of cranial bones (i.e., number, relative positioning, connections), using anatomical network analysis. Non-shelled stem turtles have similar cranial arrangements to archosauromorph outgroups. Shelled turtles (Testudinata) evolve a unique cranial organization that is associated with bone losses (e.g., supratemporal, lacrimal, ectopterygoid) and an increase in complexity (i.e., densely and highly interconnected skulls with low path lengths between bones), resulting from the closure of skull openings and establishment of unusual connections such as a parietal-pterygoid contact in the secondary braincase. Topological changes evolutionarily predate many shape changes. Topological variation and taxonomic morphospace discrimination among crown turtles are low, indicating that cranial topology may be constrained. Observed variation results from repeated losses of nonintegral bones (i.e., premaxilla, nasal, epipterygoid, quadratojugal), and changes in temporal emarginations and palate construction. We observe only minor ontogenetic changes. Topology is not influenced by diet and habitat, contrasting cranial shape. Our results indicate that turtles have a unique cranial topology among reptiles that is conserved after its initial establishment, and shows that cranial topology and shape have different evolutionary histories.

Cranial anatomy and phylogenetic affinities of Bolosaurus major, with new information on the unique bolosaurid feeding apparatus and evolution of the impedance-matching ear

Resolving the phylogenetic relationships of early amniotes, in particular stem reptiles, remains a difficult problem. Three-dimensional morphological analysis of well-preserved stem-reptile specimens can reveal important anatomical data and clarify regions of phylogeny. Here, we present the first thorough description of the unusual early Permian stem reptile Bolosaurus major, including the first comprehensive description of a bolosaurid braincase. We describe previously obscured details of the palate, allowing for insight into bolosaurid feeding mechanics. Aspects of the rostrum, palate, mandible, and neurocranium suggest that B. major had a particularly strong bite. We additionally found B. major has a surprisingly slender stapes, similar to that of the middle Permian stem reptile Macroleter poezicus, which may suggest enhanced hearing abilities compared to other Paleozoic amniotes (e.g., captorhinids). We incorporated our new anatomical information into a large phylogenetic matrix (150 OTUs, 590 characters) to explore the relationship of Bolosauridae among stem reptiles. Our analyses generally recovered a paraphyletic "Parareptilia," and found Bolosauridae to diverge after Captorhinidae + Araeoscelidia. We also included B. major within a smaller matrix (10 OTUs, 27 characters) designed to explore the interrelationships of Bolosauridae and found all species of Bolosaurus to be monophyletic. While reptile relationships still require further investigation, our phylogeny suggests repeated evolution of impedance-matching ears in Paleozoic stem reptiles.

A comprehensive phylogeny and revised taxonomy of Diadectomorpha with a discussion on the origin of tetrapod herbivory

Among terrestrial tetrapods, the origin of herbivory marked a key evolutionary event that allowed for the evolution of modern terrestrial ecosystems. A 100 Ma gap separates the oldest terrestrial tetrapods and the first undisputed herbivorous tetrapods. While four clades of early tetrapod herbivores are undisputed amniotes, the phylogenetic position of Diadectomorpha with respect to Amniota has long been controversial. Given that the origin of herbivory coincides with the oldest amniotes, and obligate herbivory is unknown within amphibians, this suggests that a key adaptation necessary to evolve obligate herbivory is unique to amniotes. Historically, phylogenetic analyses have found Diadectomorpha as the sister-group to amniotes, but recent analyses recover Diadectomorpha as sister-group to Synapsida, within Amniota. We tested whether diadectomorphs are amniotes by updating the most recent character-taxon matrix. Specifically, we added new characters from the lower jaw and added diadectomorph taxa, resulting in a dataset of 341 characters and 61 operational taxonomic units. We updated the description of five diadectomorph jaws using microcomputed tomography data. Our majority-rule consensus places Diadectomorpha as sister-group to Synapsida; other methods do not recover this relationship. We revise diadectomorph taxonomy, erecting a new species from the early Permian Bromacker locality, Germany, and a new genus to accommodate 'Diadectes' sanmiguelensis.

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

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

Size and shape heterodonty in the early Permian synapsid Mesenosaurus efremovi

Paleozoic synapsids represent the first chapter in the evolution of this large clade that includes mammals. These fascinating terrestrial vertebrates were the first amniotes to successfully adapt to a wide range of feeding strategies, reflected by their varied dental morphologies. Evolution of the marginal dentition on the mammalian side of amniotes is characterized by strong, size and shape heterodonty, with the late Permian therapsids showing heterodonty with the presence of incisiform, caniniform, and multicuspid molariform dentition. Rarity of available specimens has previously prevented detailed studies of dental anatomy and evolution in the initial chapter of synapsid evolution, when synapsids were able to evolve dentition for insectivory, herbivory, and carnivory. Numerous teeth, jaw elements, and skulls of the hypercarnivorous varanopid Mesenosaurus efremovi have been recently discovered in the cave systems near Richards Spur, Oklahoma, permitting the first detailed investigation of the dental anatomy of a Paleozoic tetrapod using multiple approaches, including morphometric and histological analyses. As a distant stem mammal, Mesenosaurus is the first member of this large and successful clade to exhibit a type of dental heterodonty that combines size and morphological (shape) variation of the tooth crowns. Here we present the first evidence of functional differentiation in the dentition of this early synapsid, with three distinct dental regions having diverse morphologies and functions. The quality and quantity of preserved materials has allowed us to identify the orientation and curvature of the carinae (cutting edges), and the variation and distribution of the ziphodonty (serrations) along the carinae. The shape-related heterodonty seen in this taxon may have contributed to this taxon's ability to be a successful mid-sized predator in the taxonomically diverse community of early Permian carnivores, but may have also extended the ecological resilience of this clade of mid-sized predators across major faunal and environmental transitions.

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.

The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part II-Hindlimb

This paper is the second in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the hindlimb. Although the hindlimb skeleton did not undergo as marked a transformation on the line to mammals as did the forelimb skeleton, the anatomy of extant tetrapods indicates that major changes to musculature have nonetheless occurred. To better understand these changes, this study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 80 character-state complexes covering all muscles crossing the hip, knee, and ankle joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. The evolutionary history of mammalian hindlimb musculature was complex, nonlinear, and protracted, with several instances of convergence and pulses of anatomical transformation that continued well into the crown group. Numerous traits typically regarded as characteristically "mammalian" have much greater antiquity than previously recognized, and for some traits, most synapsids are probably more reflective of the ancestral amniote condition than are extant saurians. More broadly, this study highlights the utility of the fossil record in interpreting the evolutionary appearance of distinctive anatomies.

The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part I-Forelimb

This paper is the first in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the forelimb. Understanding forelimb muscular anatomy in extinct synapsids, and how this changed on the line to mammals, can provide important perspective for interpreting skeletal and functional evolution in this lineage, and how the diversity of forelimb functions in extant mammals arose. This study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 73 character-state complexes covering all muscles crossing the shoulder, elbow, and wrist joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. In addition to producing a comprehensive documentation of osteological evidence for muscle attachments in extinct synapsids, this work has clarified homology hypotheses across disparate taxa and helped resolve competing hypotheses of muscular anatomy in extinct species. The evolutionary history of mammalian forelimb musculature was a complex and nonlinear narrative, punctuated by multiple instances of convergence and concentrated phases of anatomical transformation. More broadly, this study highlights the great insight that a fossil-based perspective can provide for understanding the assembly of novel body plans.

Cranial anatomy of Emeroleter levis and the phylogeny of Nycteroleteridae

Among the diverse basal reptile clade Parareptilia, the nycteroleters are among the most poorly understood. The interrelationships of nycteroleters are contentious, being recovered as both monophyletic and paraphyletic in different analyses, yet their anatomy has received little attention. We utilized x-ray computed tomography to investigate the skull of the nycteroleterid Emeroleter levis, revealing aspects of both the external and internal cranial anatomy that were previously unknown or undescribed, especially relating to the palate, braincase, and mandible. Our results reveal a greater diversity in nycteroleter cranial anatomy than was previously recognized, including variation in the contribution of the palatal elements to the orbitonasal ridge among nycteroleters. Of particular note are the unique dentition patterns in Emeroleter, including the presence of dentition on the ectopterygoid, an element which is typically edentulous in most parareptiles. We then incorporate the novel information gained from the computed tomography analysis into an updated phylogenetic analysis of parareptiles, producing a fully resolved Nycteroleteridae and further supporting previous suggestions that the genus 'Bashkyroleter' is paraphyletic.

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.

Evolution of the temporal skull openings in land vertebrates: A hypothetical framework on the basis of biomechanics

The complex constructions of land vertebrate skulls have inspired a number of functional analyses. In the present study, we provide a basic view on skull biomechanics and offer a framework for more general observations using advanced modeling approaches in the future. We concentrate our discussion on the cranial openings in the temporal skull region and work out two major, feeding-related factors that largely influence the shape of the skull. We argue that (1) the place where the most forceful biting is conducted and (2) the handling of resisting food (sideward movements) constitute the formation and shaping of either one or two temporal arcades surrounding these openings. Diversity in temporal skull anatomy among amniotes can be explained by specific modulations of these factors with different amounts of acting forces which inevitably lead to deposition or reduction of bone material. For example, forceful anterior bite favors an infratemporal bar, whereas forceful posterior bite favors formation of an upper temporal arcade. Transverse forces (inertia and resistance of seized objects) as well as neck posture also influence the shaping of the temporal region. Considering their individual skull morphotypes, we finally provide hypotheses on the feeding adaptation in a variety of major tetrapod groups. We did not consider ligaments, internal bone structure, or cranial kinesis in our considerations. Involving those in quantitative tests of our hypotheses, such as finite element system synthesis, will provide a comprehensive picture on cranial mechanics and evolution in the future.

Temporal fenestration in a Procolophon trigoniceps specimen (Procolophonoidea) from the Lower Triassic of Brazil

The parareptiles diversified widely during the Permian and persisted in Pangean ecosystems until the end of the Triassic. However, most parareptiles succumbed to the Permian-Triassic extinction, leading to the exclusive survival of procolophonoids. Procolophonoidea stands out as one of the most diverse parareptile clades, with about 40 species across Pangean land masses. The Early Triassic species Procolophon trigoniceps is known from South Africa, Antarctica, and Brazil. The majority of cranial materials of this procolophonoid are described as anapsid in temporal morphology, however, some skulls discovered in South Africa were found to exhibit temporal fenestration. Once thought to have systematic significance for the genus Procolophon, temporal fenestration was lately proposed to be an anomalous or pathological feature in P. trigoniceps. In this study, we describe new cranial material of P. trigoniceps from the Sanga do Cabral Formation of Brazil that clearly displays temporal fenestration. Aside from the fenestra, the specimen closely resembles more complete Brazilian P. trigoniceps skulls. The recurrent presence of the feature and the varying morphologies exhibited by the temporal fenestrae of P. trigoniceps may substantiate its characterization as an anomalous trait within the species. Furthermore, the occurrence of temporal fenestration in P. trigoniceps specimens from both South America and South Africa underscores parallels between these two Early Triassic ecosystems.

Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution

Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of 5 statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all 5 methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.

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.

Skeletal anatomy of the early Permian parareptile Delorhynchus with new information provided by neutron tomography

Detailed description of the holotype skeleton of Delorhynchus cifellii, made possible through the use of neutron tomography, has yielded important new information about the cranial and postcranial anatomy of this early Permian acleistorhinid parareptile. Hitherto unknown features of the skull include a sphenethmoid, paired epipterygoids and a complete neurocranium. In addition, the stapes has been exposed in three dimensions for the first time in an early parareptile. Postcranial material found in articulation with the skull in this holotype allows for the first detailed description of vertebrae, ribs, shoulder girdle and humerus of an acleistorhinid parareptile, allowing for a reevaluation of the phylogenetic relationships of this taxon with other acleistorhinids, and more broadly among parareptiles. Results show that Delorhynchus is recovered as the sister taxon of Colobomycter, and 'acleistorhinids' now include Lanthanosuchus.

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.

Rapid turnover of top predators in African terrestrial faunas around the Permian-Triassic mass extinction

Catastrophic ecosystem disruption in the late Permian period resulted in the greatest loss of biodiversity in Earth's history, the Permian-Triassic mass extinction (PTME).¹ The dominant terrestrial vertebrates of the Permian (synapsids) suffered major losses at this time, leading to their replacement by reptiles in the Triassic.² The dominant late Permian predatory synapsids, gorgonopsians, were completely extirpated by the PTME. The largest African gorgonopsians, the Rubidgeinae, have traditionally been assumed to go extinct at the Permo-Triassic boundary (PTB).^3,4,5 However, this apparent persistence through the sustained extinction interval characterizing the continental PTME⁶ is at odds with ecological theory indicating that top predators have high extinction risk.⁷ Here, we report the youngest known large-bodied gorgonopsians, gigantic specimens from the PTB site of Nooitgedacht 68 in South Africa. These specimens are not rubidgeine, and instead are referable to Inostrancevia, a taxon previously thought to be a Russian endemic.⁸ Based on comprehensive review of the South African gorgonopsian record, we show that rubidgeines were early victims of ecosystem disruption preceding the PTME and were replaced as top predators by Laurasian immigrant inostranceviines. The reign of this latter group was short-lived, however; by the PTB, gorgonopsians were extinct, and a different group (therocephalians) became the largest synapsid predators, before themselves going extinct. The extinction and replacement of top predators in rapid succession at the clade level underlines the extreme degree of ecosystem instability in the latest Permian and earliest Triassic, a phenomenon that was likely global in extent.

Single Copies of the 5S rRNA Inserted into 45S rDNA Intergenic Spacers in the Genomes of Nototheniidae (Perciformes, Actinopterygii)

In the vast majority of Animalia genomes, the 5S rRNA gene repeats are located on chromosomes outside of the 45S rDNA arrays of the nucleolar organiser (NOR). We analysed the genomic databases available and found that a 5S rDNA sequence is inserted into the intergenic spacer (IGS) between the 45S rDNA repeats in ten species of the family Nototheniidae (Perciformes, Actinopterigii). We call this sequence the NOR-5S rRNA gene. Along with Testudines and Crocodilia, this is the second case of a close association between four rRNA genes within one repetitive unit in deuterostomes. In both cases, NOR-5S is oriented opposite the 45S rDNA. None of the three nucleotide substitutions compared to the canonical 5S rRNA gene influenced the 5S rRNA secondary structure. In transcriptomes of the Patagonian toothfish, we only found NOR-5S rRNA reads in ovaries and early embryos, but not in testis or somatic tissues of adults. Thus, we consider the NOR-5S gene to be a maternal-type 5S rRNA template. The colocalization of the 5S and 45S ribosomal genes appears to be essential for the equimolar production of all four rRNAs in the species that show rDNA amplification during oogenesis. Most likely, the integration of 5S and NOR rRNA genes occurred prior to Nototheniidae lineage diversification.

Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation

The group Anguimorpha represents one of the most unified squamate clades in terms of body plan, ecomorphology, ecophysiology and evolution. On the other hand, the anguimorphs vary between different habitats and ecological niches. Therefore, we focused on the group Anguimorpha to test a possible correlation between heart morphology and ecological niche with respect to phylogenetic position in Squamata with Sphenodon, Salvator, and Pogona as the outgroups. The chosen lepidosaurian species were investigated by microCT. Generally, all lepidosaurs had two well-developed atria with complete interatrial septum and one ventricle divided by ventricular septa to three different areas. The ventricles of all lepidosaurians had a compact layer and abundant trabeculae. The compact layer and trabeculae were developed in accordance with particular ecological niche of the species, the trabeculae in nocturnal animals with low metabolism, such as Sphenodon, Heloderma or Lanthanotus were more massive. On the other hand athletic animals, such as varanids or Salvator, had ventricle compartmentalization divided by three incomplete septa. A difference between varanids and Salvator was found in compact layer thickness: thicker in monitor lizards and possibly linked to their mammalian-like high blood pressure, and the level of ventricular septation. In summary: heart morphology varied among clades in connection with the ecological niche of particular species and it reflects the phylogenetic position in model clade Anguimorpha. In the absence of fossil evidence, this is the closest approach how to understand heart evolution and septation in clade with different cardiac compartmentalization levels.