AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS

Turbinal bones are still one of the last frontiers of the tetrapod skull: hypotheses, challenges and perspectives

Turbinals are bony or cartilaginous structures that are present in the nasal cavity of most tetrapods. They are involved in key functions such as olfaction, heat, and moisture conservation, as well as protection of the respiratory tract. Despite recent studies that challenged long-standing hypotheses about their physiological and genomic correlation, turbinals remain largely unexplored, particularly for non-mammalian species. Herein, we review and synthesise the current knowledge of turbinals using an integrative approach that includes comparative anatomy, physiology, histology and genomics. In addition, we provide synonyms and correspondences of tetrapod turbinals from about 80 publications. This work represents a first step towards drawing hypotheses of homology for the whole clade, and provides a strong basis to develop new research avenues.

Early Eocene infructescences from Argentine Patagonia expand the biogeography of Malvoideae

PREMISE

Fossil infructescences and isolated fruits with characters of Malvoideae, a subfamily of Malvaceae (mallow family), were collected from early Eocene sediments in Chubut, Argentina. The main goals of this research are to describe and place these fossils systematically, and to explore their biogeographical implications.

METHODS

Fossils were collected at the Laguna del Hunco site, Huitrera Formation, Chubut, Patagonia, Argentina. They were prepared, photographed, and compared with extant and fossil infructescences and fruits of various families using herbarium material and literature.

RESULTS

The infructescences are panicles with alternate arrangement of fruits. They bear the fruits on short pedicels that are subtended by a bract; the fruits display an infracarpelar disk and split to the base into five ovate sections interpreted as mericarps. Each mericarp is characterized by an acute apex and the presence of a longitudinal ridge. The isolated fruits show the same features as those on the infructescences. The fossils share unique features with members of the cosmopolitan family Malvaceae, subfamily Malvoideae.

CONCLUSIONS

The fossils have a unique combination of characters that does not conform to any previously described genus, justifying the erection of a new genus and species, Uiher karuen. This new taxon constitutes the first known Malvoideae reproductive fossils of the Southern Hemisphere, expanding the distribution of Malvoideae during the early Eocene.

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.

Assessing the adductor musculature and jaw mechanics of Proterochampsa nodosa (Archosauriformes: Proterochampsidae) through finite element analysis

Proterochampsids are a group of South American nonarchosaurian archosauromorphs whose general morphology has been historically likened to that of the extant Crocodylia, which purportedly exhibited similar habits by convergence. Taxa from the genus Proterochampsa, for example, show platyrostral skulls with dorsally faced orbits and external nares and elongated snouts that might indicate a feeding habit similar to that of crocodilians. Nonetheless, some aspects of their craniomandibular anatomy are distinct. Proterochampsa has comparatively larger skull temporal fenestrae, and a unique morphology of the mandibular adductor chamber, with a remarkably large surangular shelf and a fainter retroarticular region in the mandible. In light of this, we conducted biomechanical tests on a 3-dimensional model of Proterochampsa nodosa including the first Finite Element Analysis for proterochampsians and compared it with models of the extant crocodylians Tomistoma schlegelii and Alligator mississippiensis. Our analyses suggested that, despite the differences in adductor chamber, Proterochampsa was able to perform bite forces comparable to those modeled for Alligator and significantly higher than Tomistoma. However, the morphology of the surangular shelf and the adductor chamber of Proterochampsa renders it more prone to accumulate stresses resulting from muscle contraction, when compared with both analogs. The elongated lower jaw of Proterochampsa, like that of Tomistoma, is more susceptible to bending, when compared with Alligator. As a result, we suggest that Proterochampsa might employ anteriorly directed bites only when handling small and soft-bodied prey. In addition, Proterochampsa exemplifies the diversity of arrangements that the adductor musculature adopted in different diverging archosauromorph groups.

Cranial osteology and paleoneurology of Tarjadia ruthae: An erpetosuchid pseudosuchian from the Triassic Chañares Formation (late Ladinian-?early Carnian) of Argentina

Tarjadia ruthae is a quadrupedal terrestrial pseudosuchian from the Middle-early Upper Triassic of the Chañares Formation, La Rioja Province, Argentina. Originally, this species was identified as an indeterminate archosaur and later as a doswelliid archosauriform based on very fragmentary specimens characterized by the ornamentation of the skull roof and osteoderms. Additional specimens (including skulls and postcrania) recovered in the last decade show that Tarjadia is an erpetosuchid, an enigmatic pseudosuchian group composed of six species registered in Middle-Upper Triassic continental units of Tanzania, Germany, Scotland, North America, Brazil, and Argentina. Tarjadia ruthae from Argentina and Parringtonia gracilis from Tanzania are the best preserved and more abundant species. Although the monophyly of Erpetosuchidae is well supported, alternative high-level positions within Archosauria have been suggested, such as sister taxon to Crocodylomorpha, Aetosauria, or Ornithosuchidae. In order to improve the knowledge about the erpetosuchids, we performed a detailed description and paleoneurological reconstruction of the skull of Tarjadia ruthae, based on two articulated partial skulls (CRILAR-Pv 478 and CRILAR-Pv 495) and other fragmentary specimens. We analyzed the stratigraphic and geographic occurrence of historical and new specimens of Tarjadia and provided a new emended diagnosis (the same for the genus as for the species, due to monotypy) along with a comparative description of the cranial endocast. The skull of Tarjadia is robust, with a thick and strongly ornamented skull roof, triangular in dorsal view, with concave lateral margins at mid-length that form an abrupt widened posterior region. The external nares are the smallest openings of the skull. The antorbital fossa is deeply excavated and has a small heart-shaped fenestra with both lobes pointing anteriorly. The supratemporal fenestrae are as large and rounded as the orbits, and the infratemporal fenestrae are L-shaped with an extensive excavation along the jugal, quadratojugal and quadrate. The hemimandibles are low, slightly concave on the dentigerous region and strongly convex on the posterior region, conferring them a S-shaped profile in dorsal view. The external mandibular fenestra is small and elliptic, being twice longer than high. The maxillary dentition is restricted to the anterior to mid region of the rostrum. Since the braincase of both specimens is partially damaged, the dorsal surface of the brain could not be entirely reconstructed. As a result, the endocast is anteroposteriorly elongated and seemingly flat, and the cephalic flexure seems to be lower than expected for a suchian. The labyrinth is twice wider than high, the semicircular canals are remarkably straight, and the anterior canal is longer than the posterior one.

New rhadinosuchine proterochampsids from the late Middle-early Late Triassic of southern Brazil enhance the diversity of archosauriforms

Proterochampsidae is a clade of non-archosaurian archosauriforms restricted to the Middle to the Late Triassic of the Ischigualasto-Villa Unión Basin of Argentina and the Santa Maria Supersequence of Brazil. A reappraisal of proterochampsid specimens from the Brazilian Dinodontosaurus Assemblage Zone (AZ) of the Pinheiros-Chiniquá Sequence (late Ladinian-early Carnian) is presented here. One of the specimens was preliminary assigned to Chanaresuchus sp., whose type species comes from the Massetognathus-Chanaresuchus AZ of the Chañares Formation of Argentina. However, our revision indicates that it differs from Chanaresuchus, being more closely related to the middle-late Carnian Rhadinosuchus gracilis. We therefore propose the new taxon, Pinheirochampsa rodriguesi, to reallocate this specimen. Additionally, we present a revision of other putative Chanaresuchus occurrences in Brazil, including the only known specimen described for the Santacruzodon AZ (Santa Cruz do Sul Sequence; early Carnian), also proposing it as a new taxon: Kuruxuchampsa dornellesi. Both new species are characterized, among other features, by transverse expansion of the anterior end of the rostrum, similar to the condition present in Rhadinosuchus, but absent in Chanaresuchus, Gualosuchus, Pseudochampsa, and non-rhadinosuchine proterochampsids. These two new species expand the growing knowledge of the non-archosaurian archosauriform diversity during the Middle-Late Triassic in South America and enhance faunal and chronological comparisons between approximately coeval geological units between Argentina and Brazil.

The osteology of the Late Triassic reptile Scleromochlus taylori from μCT data

Scleromochlus taylori is one of the most enigmatic members of the herpetofauna from the Lossiemouth Sandstone Formation (Upper Triassic) of Elgin (Moray, Scotland). For many years it was thought to be closely related to pterosaurs and dinosaurs, but the anatomy of this animal is difficult to interpret because of the notoriously poor preservation of the six available specimens, which comprise void space in the sandstone after the bones were destroyed by diagenesis. Historically, these fossils have been studied using physical molds, which provide only incomplete, and potentially distorted, information. Due to these uncertainties, interpretations of the anatomy, phylogenetic relationships, and paleobiology of Scleromochlus taylori have remained contentious. Here, we use microcomputed tomographic (μCT) techniques to redescribe and illustrate the osteology of Scleromochlus in detail, building upon a short redescription of keystone features of the anatomy that we recently published. We digitally visualize, describe, and figure previously inaccessible-and thus unaltered-portions of its skeleton, as well as providing new observations on the exposed parts of each specimen. This work reveals many novel features of the skull, mandible, trunk, tail, girdles, forelimb, and hindlimb (particularly of the manus, femur, and pes), demonstrating that historic molding techniques failed, in some cases, to accurately capture the anatomy of Scleromochlus. Our review sheds light on some of the most controversial aspects of Scleromochlus morphology showing that this taxon retains plesiomorphic features of Avemetatarsalia in the postcranial skeleton, alongside a suite of synapomorphies diagnostic of pterosauromorphs (the broad clade of pterosaurs and taxa more closely related to them than dinosaurs), particularly one subgroup, the lagerpetids. Consistent with recent work, our updated phylogenetic analyses (Maximum Parsimony and Bayesian Inference) demonstrate that Scleromochlus taylori is an avemetatarsalian archosaur that is recovered firmly in an early diverging position within Pterosauromorpha, as a member of Lagerpetidae, thus shedding important information on the origin of pterosaurs, the first group of vertebrates to evolve powered flight.

Cranial anatomy of the "round-headed" Amphisbaenian Zygaspis quadrifrons (Squamata, Amphisbaenia) based on high-resolution x-ray computed tomography

Amphisbaenians are a poorly understood clade of fossorial lizards. Because of their derived anatomy and relative scarcity, the systematics of the clade and its placement within squamates has long been controversial. Traditional approaches grouped species into four assemblages according to burrowing behavior and cranial morphology, resulting in the recognition of "shovel-headed," "round-headed," "keel-headed," and "spade-headed" morphotypes. Recent phylogenetic analyses do not support the monophyly of the taxa that share those morphotypes. Detailed analyses of cranial osteology were previously accomplished using high-resolution x-ray computed tomography (HRXCT) for the "shovel-headed" Rhineura hatcherii (Rhineruidae) and the "spade-headed" Diplometopon zarudnyi (Trogonophidae). A detailed description of the "round-headed" Amphisbaena alba was previously completed based upon traditional "dry" skeletal specimens. Seven species of the "round-headed" Blanus (Blanidae) were also analyzed using HRXCT. The goal of that project was a comparative analysis of all extant species of Blanus rather than a detailed, bone-by-bone description of one species, but certainly is useful for comparison with another "round-headed" taxon. The "round-headed" morphotype is by far the most common among amphisbaenians and is much in need of further documentation. We use HRXCT imagery to provide additional data about the disparity in cranial morphology among amphisbaenians. Those data allow us to provide another detailed description of a "round-headed" amphisbaenian, the poorly known southern African species Zygaspis quadrifrons. HRXCT is ideal for this relatively rare and diminutive species. We are able to visualize and describe a detailed reconstruction of the entire skull as well as individual cranial elements. Comparisons with other species that were described in similar detail-D. zarudnyi, Spathorhynchus fossorium, R. hatcherii, and A. alba-and to a lesser degree with Blanus, reveal a complex mosaic of morphological features of the skull in Zygaspis. Preliminary data suggest that intraspecific variation is present within Z. quadrifrons, and interspecific variation among other species of Zygaspis may be sufficient for species-level recognition based on cranial osteology. Our description is, therefore, also intended to serve as a baseline for comparative analysis of other specimens of Z. quadrifrons and of other species within the genus.

Novel symmetry-preserving neural network model for phylogenetic inference

Motivation

Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of Life. Low sampling rates and high heterogeneity in the rate of evolution across sites and lineages produce a phenomenon denoted "long branch attraction" (LBA) in which long nonsister lineages are estimated to be sisters regardless of their true evolutionary relationship. LBA has been a pervasive problem in phylogenetic inference affecting different types of methodologies from distance-based to likelihood-based.

Results

Here, we present a novel neural network model that outperforms standard phylogenetic methods and other neural network implementations under LBA settings. Furthermore, unlike existing neural network models in phylogenetics, our model naturally accounts for the tree isomorphisms via permutation invariant functions which ultimately result in lower memory and allows the seamless extension to larger trees.

Availability and implementation

We implement our novel theory on an open-source publicly available GitHub repository: https://github.com/crsl4/nn-phylogenetics.

Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total-evidence dating analysis supports a Late Silurian-Early Devonian origin and post-Mesozoic morphological stasis

Divergence times based on molecular clock analyses often differ from those derived from total-evidence dating (TED) approaches. For bryophytes, fossils have been excluded from previous assessments of divergence times, and thus, their utility in dating analyses remains unexplored. Here, we conduct the first TED analyses of the complex thalloid liverworts (Marchantiopsida) that include fossils and evaluate macroevolutionary trends in morphological 'diversity' (disparity) and rates. Phylogenetic analyses were performed on a combined dataset of 130 discrete characters and 11 molecular markers (sampled from nuclear, plastid and mitochondrial genomes). Taxon sampling spanned 56 extant species - representing all the orders within Marchantiophyta and extant genera within Marchantiales - and eight fossil taxa. Total-evidence dating analyses support the radiation of Marchantiopsida during Late Silurian-Early Devonian (or Middle Ordovician when the outgroup is excluded) and that of Ricciaceae in the Middle Jurassic. Morphological change rate was high early in the history of the group, but it barely increased after Late Cretaceous. Disparity-through-time analyses support a fast increase in diversity until the Middle Triassic (c. 250 Ma), after which phenotypic evolution slows down considerably. Incorporating fossils in analyses challenges previous assumptions on the affinities of extinct taxa and indicates that complex thalloid liverworts radiated c. 125 Ma earlier than previously inferred.

Implications of outgroup selection in the phylogenetic inference of hominoids and fossil hominins

Understanding the phylogenetic relationships among hominins and other hominoid species is critical to the study of human origins. However, phylogenetic inferences are dependent on both the character data and taxon sampling used. Previous studies of hominin phylogenetics have used Papio and Colobus as outgroups in their analyses; however, these extant monkeys possess many derived traits that may confound the polarities of morphological changes among living apes and hominins. Here, we consider Victoriapithecus and Ekembo as more suitable outgroups. Both Victoriapithecus and Ekembo are anatomically well known and are widely accepted as morphologically primitive stem cercopithecoid and hominoid taxa, respectively, making them more appropriate for inferring polarity for later-occurring hominoid- and hominin-focused analyses. Craniodental characters for both taxa were scored and then added to a previously published matrix of fossil hominin and extant hominoid taxa, replacing outgroups Papio and Colobus over a series of iterative analyses using both parsimony and Bayesian inference methods. Neither the addition nor replacement of outgroup taxa changed tree topology in any analysis. Importantly, however, bootstrap support values and posterior probabilities for nodes supporting their relationships generally increased compared to previous analyses. These increases were the highest at extant hominoid and basal hominin nodes, recovering the molecular ape phylogeny with considerably higher support and strengthening the inferred relationships among basal hominins. Interestingly, however, the inclusion of both extant and fossil outgroups reduced support for the crown hominid node. Our findings suggest that, in addition to improving character polarity estimation, including fossil outgroups generally strengthens confidence in relationships among extant hominoid and basal hominins.

A new archosauriform species from the Panchet Formation of India and the diversification of Proterosuchidae after the end-Permian mass extinction

Proterosuchidae represents the oldest substantial diversification of Archosauromorpha and plays a key role in understanding the biotic recovery after the end-Permian mass extinction. Proterosuchidae was long treated as a wastebasket taxon, but recent revisions have reduced its taxonomic content to five valid species from the latest Permian of Russia and the earliest Triassic (Induan) of South Africa and China. In addition to these occurrences, several isolated proterosuchid bones have been reported from the Induan Panchet Formation of India for over 150 years. Following the re-study of historical specimens and newly collected material from this unit, we erect the new proterosuchid species Samsarasuchus pamelae, which is represented by most of the presacral vertebral column. We also describe cf. proterosuchid and proterosuchid cranial, girdle and limb bones that are not referred to Samsarasuchus pamelae. Phylogenetic analyses recovered Samsarasuchus pamelae within the new proterosuchid clade Chasmatosuchinae. The taxonomic diversity of Proterosuchidae is substantially expanded here, with at least 11 nominal species and several currently unnamed specimens, and a biogeographical range encompassing present-day South Africa, China, Russia, India, Brazil, Uruguay and Australia. This indicates a broader taxonomic, phylogenetic and biogeographic diversification of Proterosuchidae than previously thought in the aftermath of the end-Permian mass extinction.

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 influence of fossils in macroevolutionary analyses of 3D geometric morphometric data: A case study of galloanseran quadrates

In birds and other reptiles, the quadrate acts as a hinge between the lower jaw and the skull and plays an important role in avian cranial kinesis. Though previous studies have qualitatively described substantial variation in quadrate morphology among birds, none have attempted to quantify evolutionary changes in quadrate shape. Here, we investigate geometric evolution of the quadrate in Galloanserae, a major clade of extant birds uniting chicken-like (Galliformes) and duck-like (Anseriformes) fowl. We quantified morphological variation in the quadrate across 50 extant galloanseran species covering all major extant subclades using three-dimensional geometric morphometrics, and performed ancestral shape reconstructions in the context of an up-to-date neornithine phylogeny. We find that our results based only on extant quadrates may overlook plesiomorphic features captured by fossil taxa, resulting in an ancestral state reconstruction for Galloanserae that is seemingly an approximation of the average shape of the extant data set. By contrast, analyses incorporating early fossil galloanseran quadrates (from taxa such as Asteriornis, Presbyornis, and Conflicto) result in ancestral geometric reconstructions more similar to the morphology of extant galliforms, indicating that the quadrate of the last common ancestor of galloanserans may have been more morphologically and functionally similar to those of extant galliforms than to extant anseriforms. These results generally corroborate previous inferences of galloanseran quadrate plesiomorphies and identify several additional plesiomorphic features of the galloanseran quadrate for the first time. Our results illustrate the importance of incorporating fossil taxa into ancestral shape reconstructions and help elucidate important aspects of the morphology and function of the avian feeding apparatus early in crown bird evolutionary history.

Morphologic aspects of the cervical (C3 to C7) annular epiphysis: a skeletal study

BACKGROUND CONTEXT

The annular epiphysis (AE) is a peripheral ring of cortical bone that forms a secondary ossification center in the superior and inferior surfaces of vertebral bodies (VBs). The AE is the last ossification site in the skeleton, typically forming at about the 25th year of life. The AE functions jointly with vertebral endplates to anchor the intervertebral discs to the VBs.

PURPOSE

To establish accurate data on the sizes of the AE of the cervical spine (C3-C7); to compare the ratios between areas and the ratios of the AE to VBs; to compare the ratios between the superior and inferior VB surface areas; and to compare AE lengths between the posterior and anterior midsagittal areas.

STUDY DESIGN

Measurement of 424 cervical spines (C3-C7) obtained from the skeletal collection of the Natural History Museum, Cleveland, Ohio (USA).

METHODS

The sample was characterized by sex, age, and ethnic origin. The following measurements were recorded for each vertebra: (1) the surface area of the VBs and the AE, (2) the midsagittal anterior and posterior length of the AE, (3) the ratios between the AE and VB surface areas, and (4) the ratios between the superior and inferior disc surface areas.

RESULTS

The study revealed that the AE and VBs in men were larger than in women. With age, the AE and VBs became larger; the ratio between the AE and VB surface was ∼0.5 throughout the middle to lower cervical spine. The ratio of superior to inferior VBs was ∼0.8. We found no differences between African Americans versus European Americans or between the anterior versus the posterior midsagittal length of the AE of the superior and inferior VBs.

CONCLUSION

The ratios between the superior and inferior VBs is ≥0.8, and the ratio is the same for the entire middle to lower spine. Thus, the ratio between the superior and inferior VBs to the AE is ≥ 0.5. Men had larger AEs and VBs than women did, with both VBs and AEs becoming larger with age. Knowing these relationships are important so that orthopedic surgeons can best correct these issues in young patients (<25 years old) during spine surgery. The data reported here provide, for the first time, all the relevant sizes of the AE and VB. In future studies, AEs and VBs of living patients can be measured with computed tomography.

CLINICAL SIGNIFICANCE

The ER location and function are clinically significant showing any changes during life that might lead to clinical issues related to intervertebral discs such as intervertebral disc asymmetry, disc herniation, nerve pressure, cervical osteophytes and neck pain.

Systematics of Miocene apes: State of the art of a neverending controversy

Hominoids diverged from cercopithecoids during the Oligocene in Afro-Arabia, initially radiating in that continent and subsequently dispersing into Eurasia. From the Late Miocene onward, the geographic range of hominoids progressively shrank, except for hominins, which dispersed out of Africa during the Pleistocene. Although the overall picture of hominoid evolution is clear based on available fossil evidence, many uncertainties persist regarding the phylogeny and paleobiogeography of Miocene apes (nonhominin hominoids), owing to their sparse record, pervasive homoplasy, and the decimated current diversity of this group. We review Miocene ape systematics and evolution by focusing on the most parsimonious cladograms published during the last decade. First, we provide a historical account of the progress made in Miocene ape phylogeny and paleobiogeography, report an updated classification of Miocene apes, and provide a list of Miocene ape species-locality occurrences together with an analysis of their paleobiodiversity dynamics. Second, we discuss various critical issues of Miocene ape phylogeny and paleobiogeography (hylobatid and crown hominid origins, plus the relationships of Oreopithecus) in the light of the highly divergent results obtained from cladistic analyses of craniodental and postcranial characters separately. We conclude that cladistic efforts to disentangle Miocene ape phylogeny are potentially biased by a long-branch attraction problem caused by the numerous postcranial similarities shared between hylobatids and hominids-despite the increasingly held view that they are likely homoplastic to a large extent, as illustrated by Sivapithecus and Pierolapithecus-and further aggravated by abundant missing data owing to incomplete preservation. Finally, we argue that-besides the recovery of additional fossils, the retrieval of paleoproteomic data, and a better integration between cladistics and geometric morphometrics-Miocene ape phylogenetics should take advantage of total-evidence (tip-dating) Bayesian methods of phylogenetic inference combining morphologic, molecular, and chronostratigraphic data. This would hopefully help ascertain whether hylobatid divergence was more basal than currently supported.

A late Permian archosauriform from Xinjiang shows evidence of parasagittal posture

Archosaurs diversified and became dominant during the Mesozoic Era, but their earliest relatives (non-archosaurian archosauromorphs) were already scarcely present in the late Permian. Here we describe a new species of non-archosaurian archosauriform from the upper Permian of Xinjiang, China. Preserved as a partial hindlimb, it possesses a few derived features shared with other archosauriforms, including a much stouter tibia than fibula, a longer metatarsal III than metatarsal IV, and a hooked metatarsal V. Phylogenetic analysis confirmed the new taxon to be a non-archosaurian archosauriform. The morphology of the knee, crus, and pes shows traits that are commonly related with a parasagittal posture, including an entirely proximo-distal articulation of the femur and fibula, the slender and closely spaced tibia and fibula, and a mesaxonic foot with a reduced fifth toe. The new taxon shows that the parasagittal posture evolved before the end-Permian Mass Extinction.

Functional complexity in the chorioallantoic membrane of an oviparous snake: Specializations for calcium uptake from the eggshell

The chorioallantoic membrane of oviparous reptiles forms a vascular interface with the eggshell. The eggshell contains calcium, primarily as calcium carbonate. Extraction and mobilization of this calcium by the chorioallantoic membrane contributes importantly to embryonic nutrition. Development of the chorioallantoic membrane is primarily known from studies of squamates and birds. Although there are pronounced differences in eggshell structure, squamate and bird embryos each mobilize calcium from eggshells. Specialized cells in the chicken chorionic epithelium transport calcium from the eggshell aided by a second population of cells that secrete protons generated by the enzyme carbonic anhydrase. Calcium transporting cells also are present in the chorioallantoic membrane of corn snakes, although these cells function differently than those of chickens. We used histology and immunohistology to characterize the morphology and functional attributes of the chorioallantoic membrane of corn snakes. We identified two populations of cells in the outer layer of the chorionic epithelium. Calbindin-D_28K , a cellular marker for calcium transport expressed in squamate chorioallantoic membranes, is localized in large, flattened cells that predominate in the chorionic epithelium. Smaller cells, interspersed among the large cells, express carbonic anhydrase 2, an enzyme not previously localized in the chorionic epithelium of an oviparous squamate. These findings indicate that differentiation of chorionic epithelial cells contributes to extraction and transport of calcium from the eggshell. The presence of specializations of chorioallantoic membranes for calcium uptake from eggshells in chickens and corn snakes suggests that eggshell calcium was a source of embryonic nutrition early in the evolution of Sauropsida.

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.

Functional and ecomorphological evolution of orbit shape in mesozoic archosaurs is driven by body size and diet

The orbit is one of several skull openings in the archosauromorph skull. Intuitively, it could be assumed that orbit shape would closely approximate the shape and size of the eyeball resulting in a predominantly circular morphology. However, a quantification of orbit shape across Archosauromorpha using a geometric morphometric approach demonstrates a large morphological diversity despite the fact that the majority of species retained a circular orbit. This morphological diversity is nearly exclusively driven by large (skull length > 1000 mm) and carnivorous species in all studied archosauromorph groups, but particularly prominently in theropod dinosaurs. While circular orbit shapes are retained in most herbivores and smaller species, as well as in juveniles and early ontogenetic stages, large carnivores adopted elliptical and keyhole-shaped orbits. Biomechanical modelling using finite element analysis reveals that these morphologies are beneficial in mitigating and dissipating feeding-induced stresses without additional reinforcement of the bony structure of the skull.

The role of paleontological data in bryophyte systematics

Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products-phenotypes and genotypes-to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils-age, phenotypes, and systematic affinities-and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology.

Redescription, taxonomic revaluation and phylogenetic affinities of Proterochampsa nodosa (Archosauriformes: Proterochampsidae) from the early Late Triassic of the Candelaria Sequence (Santa Maria Supersequence)

Proterochampsidae are a group of predatory, putatively semi-aquatic, archosauriforms endemic to the Middle and Upper Triassic strata of Argentina and Brazil (Ischigualasto Formation and Santa Maria Supersequence). Here, the Brazilian species Proterochampsa nodosa from the Candelária Sequence (Santa Maria Supersequence of the Paraná Basin) is revisited with a detailed description, phylogenetic analysis and taxonomic revaluation. Through the application of computed tomographic scans, we were able to reveal part of the previously hidden morphology of its mandible and palate. We also discuss further differences between P. nodosa and P. barrionuevoi. The new phylogenetic analysis bolsters the monophyly of Proterochampsidae, the genus Proterochampsa and its position as the basalmost proterochampsid taxon in the clade.

A novel cupulate seed plant, Xadzigacalix quatsinoensis gen. et sp. nov., provides new insight into the Mesozoic radiation of gymnosperms

PREMISE

Anatomically preserved evidence for a novel clade of gymnosperms emphasizes diversity of seed plants immediately prior to the appearance of angiosperm fossils in the paleontological record.

METHODS

Cupulate seeds from the Early Cretaceous Apple Bay locality (Vancouver Island) are described from serial cellulose acetate peels and three-dimensional reconstruction. Phylogenetic context is assessed through the comparative analysis of gymnosperm seed producing fructifications and maximum parsimony analysis of a revised morphological data set for seed plant phylogeny.

RESULTS

Xadzigacalix quatsinoensis gen. et sp. nov. is characterized by an orthotropous ovule with an elongated micropyle and complex integument, enclosed within a radial cupule. The micropylar canal is elongated; and the nucellus extends into the micropyle to seal the post pollination ovule. Except at the apex of the micropyle, the seed is completely enclosed by a parenchymatous cupule with ca. 20 axially elongated secretory ducts. The cupulate seed is produced upon a triangular woody stele, consisting of a parenchymatous pith surrounded by radially aligned tracheids. The stele produces three short terete traces that terminate within the base of the cupule as transfusion tissue at the seed chalaza.

CONCLUSIONS

Organography, vascularization, nature of the integument and nucellus, and configuration of the micropylar canal distinguish Xadzigacalix quatsinoensis from all other gymnosperm clades. Cladistic analyses suggest the new plant may have affinities with gnetophytes or angiosperms. These results are complemented with a critical re-evaluation of ovulate structures for Mesozoic gymnosperms, providing new insight into plant diversity immediately antecedent to the explosive diversification of flowering plants.

Reassessment of Faxinalipterus minimus, a purported Triassic pterosaur from southern Brazil with the description of a new taxon

Faxinalipterus minimus was originally described as a purported pterosaur from the Late Triassic (early Norian) Caturrita Formation of southern Brazil. Its holotype comprises fragmentary postcranial elements, whereas a partial maxilla was referred to the species. The assignment of Faxinalipterus minimus to Pterosauria has been questioned by some studies, but the specimen has never been accessed in detail after its original description. Here we provide a reassessment of Faxinalipterus minimus after additional mechanical preparation of the holotype. Our interpretations on the identity of several bones differ from those of the original description, and we found no support favoring pterosaur affinities for the taxon. The maxilla previously referred to Faxinalipterus minimus is disassociated from this taxon and referred to a new putative pterosauromorph described here from a partial skull and fragmentary postcranial elements. Maehary bonapartei gen. et sp. nov. comes from the same fossiliferous site that yielded Faxinalipterus minimus, but the lack of overlapping bones hampers comparisons between the two taxa. Our phylogenetic analysis places Faxinalipterus minimus within Lagerpetidae and Maehary bonapartei gen. et sp. nov. as the earliest-diverging member of Pterosauromorpha. Furthermore, the peculiar morphology of the new taxon reveals a new dental morphotype for archosaurs, characterized by conical, unserrated crowns, with a pair of apicobasally oriented grooves. These two enigmatic archosaurs expand our knowledge on the Caturrita Formation fauna and reinforce the importance of its beds on the understanding of Late Triassic ecosystems.

Topology-Based Three-Dimensional Reconstruction of Delicate Skeletal Fossil Remains and the Quantification of Their Taphonomic Deformation

Taphonomic and diagenetic processes inevitably distort the original skeletal morphology of fossil vertebrate remains. Key aspects of palaeobiological datasets may be directly impacted by such morphological deformation, such as taxonomic diagnoses and phylogenetic hypotheses, interpretations of the shape and orientation of anatomical structures, and assessments of interspecific and intraspecific variation. In order to overcome these ubiquitous challenges we present a novel reconstruction workflow combining retopology and retrodeformation, allowing the original morphology of both symmetrically and asymmetrically damaged areas of fossils to be reconstructed. As case studies, we present idealised three-dimensional reconstructions of the sternum of the crownward stem-bird Ichthyornis dispar, and cervical vertebrae of the diplodocid sauropod Galeamopus pabsti. Multiple Ichthyornis sterna were combined into a single, idealised composite representation through superimposition and alignment of retopologised models, and this composite was subsequently retrodeformed. The Galeamopus vertebrae were individually retrodeformed and symmetrised. Our workflow enabled us to quantify deformation of individual specimens with respect to our reconstructions, and to characterise global and local taphonomic deformation. Our workflow can be integrated with geometric morphometric approaches to enable quantitative morphological comparisons among multiple specimens, as well as quantitative interpolation of “mediotypes” of serially homologous elements such as missing vertebrae, haemal arches, or ribs.

On the homology of crocodylian post-dentary bones and their macroevolution throughout Pseudosuchia

The lower jaw of early tetrapods is composed of several intramembranous ossifications. However, a tendency toward the independent reduction of the number of bones has been observed in the mandible of mammals, lepidosaurs, turtles, crocodiles, and birds. Regarding archosaurs, the coronoid and prearticular bones are interpreted to be lost during the evolution of stem-birds and stem-crocodiles, respectively, but the homology of the post-dentary bones retained in living pseudosuchians remains unclear. Here, we combine paleontological and embryological evidence to explore in detail the homology of the crocodylian post-dentary bones. We study the mandible embryogenesis on a sample of 71 embryos of Caiman and compare this pattern with the mandibular transformations observed across pseudosuchian evolution. In the pre-hatching ontogeny of caimans, at least five intramembranous ossification centers are formed along the margins of the internal mandibular fenestra (perifenestral centers) and, subsequently, merge to form the coronoid (three intramembranous centers), angular (one intramembranous center), and articular (one intramembranous and one chondral center). In the fossil record, an independent prearticular is lost around the base of Mesoeucrocodylia (optimized as reappearing in Thalattosuchia if they are placed within Neosuchia), and the coronoid is apomorphically lost in notosuchians. The integration of embryological and paleontological data indicates that most perifenestral centers are involved in the origin of the prearticular of non-mesoeucrocodylian pseudosuchians. These centers are rearranged during the evolution to contribute to different post-dentary bones in mesoeucrocodylians bolstering the idea that the coronoid and the articular of Crocodylia are not completely homologous to those of other diapsids.

A proposed standard for quantifying 3-D hindlimb joint poses in living and extinct archosaurs

The last common ancestor of birds and crocodylians plus all of its descendants (clade Archosauria) dominated terrestrial Mesozoic ecosystems, giving rise to disparate body plans, sizes, and modes of locomotion. As in the fields of vertebrate morphology and paleontology more generally, studies of archosaur skeletal structure have come to depend on tools for acquiring, measuring, and exploring three‐dimensional (3‐D) digital models. Such models, in turn, form the basis for many analyses of musculoskeletal function. A set of shared conventions for describing 3‐D pose (joint or limb configuration) and 3‐D kinematics (change in pose through time) is essential for fostering comparison of posture/movement among such varied species, as well as for maximizing communication among scientists. Following researchers in human biomechanics, we propose a standard methodological approach for measuring the relative position and orientation of the major segments of the archosaur pelvis and hindlimb in 3‐D. We describe the construction of anatomical and joint coordinate systems using the extant guineafowl and alligator as examples. Our new standards are then applied to three extinct taxa sampled from the wider range of morphological, postural, and kinematic variation that has arisen across >250 million years of archosaur evolution. These proposed conventions, and the founding principles upon which they are based, can also serve as starting points for measuring poses between elements within a hindlimb segment, for establishing coordinate systems in the forelimb and axial skeleton, or for applying our archosaurian system more broadly to different vertebrate clades.

Developmental evolution of the distal ankle in the dinosaur-bird transition

The adult ankle of early reptiles had five distal tarsal (dt) bones, but in Dinosauria, these were reduced to only two: dt3 and dt4, articulated to metatarsals (mt) mt3 and mt4. Birds have a single distal tarsal ossification center that fuses to the proximal metatarsals to form a new adult skeletal structure: the composite tarsometatarsus. This ossification center develops within a single large embryonic cartilage, but it is unclear if this cartilage results from fusion of earlier cartilages. We studied embryos in species from four different bird orders, an alligatorid, and an iguanid. In all embryos, cartilages dt2, dt3, and dt4 are formed. In the alligatorid and the iguanid, dt2 failed to ossify: only dt3 and dt4 develop into adult bones. In birds, dt2, dt3, and dt4 fuse to form the large distal tarsal cartilage; the ossification center then develops above mt3, in cartilage presumably derived from dt3. During the entire dinosaur-bird transition, a dt2 embryonic cartilage was always formed, as inferred from the embryology of extant birds and crocodilians. We propose that in the evolution of the avian ankle, fusion of cartilages dt3 and dt2 allowed ossification from dt3 to progress into dt2, which began to contribute bone medially, while fusion of dt3 to dt4 enabled the evolutionary loss of the dt4 ossification center. As a result, a single ossification center expands into a plate-like unit covering the proximal ends of the metatarsals, that is key to the development of an integrated tarsometatarsus.

Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.

Femoral specializations to locomotor habits in early archosauriforms

The evolutionary history of archosaurs and their closest relatives is characterized by a wide diversity of locomotor modes, which has even been suggested as a pivotal aspect underlying the evolutionary success of dinosaurs vs. pseudosuchians across the Triassic–Jurassic transition. This locomotor diversity (e.g., more sprawling/erect; crouched/upright; quadrupedal/bipedal) led to several morphofunctional specializations of archosauriform limb bones that have been studied qualitatively as well as quantitatively through various linear morphometric studies. However, differences in locomotor habits have never been studied across the Triassic–Jurassic transition using 3D geometric morphometrics, which can relate how morphological features vary according to biological factors such as locomotor habit and body mass. Herein, we investigate morphological variation across a dataset of 72 femora from 36 different species of archosauriforms. First, we identify femoral head rotation, distal slope of the fourth trochanter, femoral curvature, and the angle between the lateral condyle and crista tibiofibularis as the main features varying between bipedal and quadrupedal taxa, all of these traits having a stronger locomotor signal than the lesser trochanter's proximal extent. We show a significant association between locomotor mode and phylogeny, but with the locomotor signal being stronger than the phylogenetic signal. This enables us to predict locomotor modes of some of the more ambiguous early archosauriforms without relying on the relationships between hindlimb and forelimb linear bone dimensions as in prior studies. Second, we highlight that the most important morphological variation is linked to the increase of body size, which impacts the width of the epiphyses and the roundness and proximodistal position of the fourth trochanter. Furthermore, we show that bipedal and quadrupedal archosauriforms have different allometric trajectories along the morphological variation in relation to body size. Finally, we demonstrate a covariation between locomotor mode and body size, with variations in femoral bowing (anteroposterior curvature) being more distinct among robust femora than gracile ones. We also identify a decoupling in fourth trochanter variation between locomotor mode (symmetrical to semi‐pendant) and body size (sharp to rounded). Our results indicate a similar level of morphological disparity linked to a clear convergence in femoral robusticity between the two clades of archosauriforms (Pseudosuchia and Avemetatarsalia), emphasizing the importance of accounting for body size when studying their evolutionary history, as well as when studying the functional morphology of appendicular features. Determining how early archosauriform skeletal features were impacted by locomotor habits and body size also enables us to discuss the potential homoplasy of some phylogenetic characters used previously in cladistic analyses as well as when bipedalism evolved in the avemetatarsalian lineage. This study illuminates how the evolution of femoral morphology in early archosauriforms was functionally constrained by locomotor habit and body size, which should aid ongoing discussions about the early evolution of dinosaurs and the nature of their evolutionary “success” over pseudosuchians.

Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ${\sim}$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth-death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.].

The First Age of Reptiles? Comparing Reptile and Synapsid Diversity, and the Influence of Lagerstätten, During the Carboniferous and Early Permian

Terrestrial ecosystems during the Pennsylvanian (late Carboniferous) and Cisuralian (early Permian) are usually described in the literature as being dominated by synapsids, the mammal-line amniotes. The pelycosaurs (a paraphyletic grouping of synapsid families) have been considered more speciose, abundant, and ecologically diverse than contemporary reptile-line amniotes. However, this dominance has never been subjected to quantitative testing accounting for sampling bias. Moreover, in recent years the amniote phylogeny has undergone numerous revisions, with suggestions that varanopids and recumbirostran microsaurs fall within reptiles, and that diadectomorphs may be pelycosaurian-grade synapsids. An examination of local species richness (alpha diversity) of synapsids and reptiles during the Pennsylvanian and Cisuralian at different spatial scales shows that these taxonomic revisions have substantial impacts on relative diversity patterns of synapsids and reptiles. Synapsids are only found to be consistently more diverse through the early Permian when using the “traditional” taxonomy. The recent taxonomic updates produce diversity estimates where reptile diversity is consistent with, or in some cases higher than that of synapsids. Moreover, biases in preservation may affect patterns. Where preservation favors smaller vertebrates, e.g., Richards Spur, South Grandfield, reptiles overwhelmingly dominate. If smaller vertebrates are expected to make up the bulk of amniote diversity, as they do in the present day, such lagerstätten may be more representative of true diversity patterns. Therefore, the dominance of pelycosaurs during this interval should be reconsidered, and this interval may be considered the First Age of Reptiles.

A new short-faced archosauriform from the Upper Triassic Placerias/Downs' quarry complex, Arizona, USA, expands the morphological diversity of the Triassic archosauriform radiation

The Placerias/Downs' Quarry complex in eastern Arizona, USA, is the most diverse Upper Triassic vertebrate locality known. We report a new short-faced archosauriform, Syntomiprosopus sucherorum gen. et sp. nov., represented by four incomplete mandibles, that expands that diversity with a morphology unique among Late Triassic archosauriforms. The most distinctive feature of Syntomiprosopus gen. nov. is its anteroposteriorly short, robust mandible with 3-4 anterior, a larger caniniform, and 1-3 "postcanine" alveoli. The size and shape of the alveoli and the preserved tips of replacement teeth preclude assignment to any taxon known only from teeth. Additional autapomorphies of S. sucherorum gen. et sp. nov. include a large fossa associated with the mandibular fenestra, an interdigitating suture of the surangular with the dentary, fine texture ornamenting the medial surface of the splenial, and a surangular ridge that completes a 90° arc. The external surfaces of the mandibles bear shallow, densely packed, irregular, fine pits and narrow, arcuate grooves. This combination of character states allows an archosauriform assignment; however, an associated and similarly sized braincase indicates that Syntomiprosopus n. gen. may represent previously unsampled disparity in early-diverging crocodylomorphs. The Placerias Quarry is Adamanian (Norian, maximum depositional age ~219 Ma), and this specimen appears to be an early example of shortening of the skull, which occurs later in diverse archosaur lineages, including the Late Cretaceous crocodyliform Simosuchus. This is another case where Triassic archosauriforms occupied morphospace converged upon by other archosaurs later in the Mesozoic and further demonstrates that even well-sampled localities can yield new taxa.

A remarkable group of thick-headed Triassic Period archosauromorphs with a wide, possibly Pangean distribution

The radiation of archosauromorph reptiles in the Triassic Period produced an unprecedented collection of diverse and disparate forms with a mix of varied ecologies and body sizes. Some of these forms were completely unique to the Triassic, whereas others were converged on by later members of Archosauromorpha. One of the most striking examples of this is with Triopticus primus, the early dome-headed form later mimicked by pachycephalosaurid dinosaurs. Here we fully describe the cranial anatomy of Triopticus primus, but also recognize a second dome-headed form from a Upper Triassic deposit in present-day India. The new taxon, Kranosaura kuttyi gen. et sp. nov., is likely the sister taxon of Triopticus primus based on the presence of a greatly expanded skull roof with a deep dorsal opening (possibly the pineal opening) through the dome, similar cranial sculpturing, and a skull table that is expanded more posterior than the posterior extent of the basioccipital. However, the dome of Kranosaura kuttyi gen. et sp. nov. extends anterodorsally, unlike that of any other archosauromorph. Histological sections and computed tomographic reconstructions through the skull of Kranosaura kuttyi gen. et sp. nov. further reveal the uniqueness of the dome of these early archosauromorphs. Moreover, our integrated analysis further demonstrates that there are many ways to create a dome in Amniota. The presence of 'dome-headed' archosauromorphs at two localities on the western and eastern portions of Pangea suggests that these archosauromorphs were widespread and are likely part of more assemblages than currently recognized.

Unusual morphology in the mid-Cretaceous lizard Oculudentavis

Oculudentavis khaungraae was described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted narial openings, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance, Oculudentavis showed several features inconsistent with its original phylogenetic placement. Here, we describe a more complete specimen that demonstrates Oculudentavis is actually a bizarre lizard of uncertain position. The new specimen is described as a new species within the genus Oculudentavis. The new interpretation and phylogenetic placement highlight a rare case of convergent evolution in skull proportions but apparently not in morphological characters. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record.

The evolutionary biomechanics of locomotor function in giant land animals

Giant land vertebrates have evolved more than 30 times, notably in dinosaurs and mammals. The evolutionary and biomechanical perspectives considered here unify data from extant and extinct species, assessing current theory regarding how the locomotor biomechanics of giants has evolved. In terrestrial tetrapods, isometric and allometric scaling patterns of bones are evident throughout evolutionary history, reflecting general trends and lineage-specific divergences as animals evolve giant size. Added to data on the scaling of other supportive tissues and neuromuscular control, these patterns illuminate how lineages of giant tetrapods each evolved into robust forms adapted to the constraints of gigantism, but with some morphological variation. Insights from scaling of the leverage of limbs and trends in maximal speed reinforce the idea that, beyond 100-300 kg of body mass, tetrapods reduce their locomotor abilities, and eventually may lose entire behaviours such as galloping or even running. Compared with prehistory, extant megafaunas are depauperate in diversity and morphological disparity; therefore, turning to the fossil record can tell us more about the evolutionary biomechanics of giant tetrapods. Interspecific variation and uncertainty about unknown aspects of form and function in living and extinct taxa still render it impossible to use first principles of theoretical biomechanics to tightly bound the limits of gigantism. Yet sauropod dinosaurs demonstrate that >50 tonne masses repeatedly evolved, with body plans quite different from those of mammalian giants. Considering the largest bipedal dinosaurs, and the disparity in locomotor function of modern megafauna, this shows that even in terrestrial giants there is flexibility allowing divergent locomotor specialisations.

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

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

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.

An Evolutionary Microcircuit Approach to the Neural Basis of High Dimensional Sensory Processing in Olfaction

Odor stimuli consist of thousands of possible molecules, each molecule with many different properties, each property a dimension of the stimulus. Processing these high dimensional stimuli would appear to require many stages in the brain to reach odor perception, yet, in mammals, after the sensory receptors this is accomplished through only two regions, the olfactory bulb and olfactory cortex. We take a first step toward a fundamental understanding by identifying the sequence of local operations carried out by microcircuits in the pathway. Parallel research provided strong evidence that processed odor information is spatial representations of odor molecules that constitute odor images in the olfactory bulb and odor objects in olfactory cortex. Paleontology provides a unique advantage with evolutionary insights providing evidence that the basic architecture of the olfactory pathway almost from the start ∼330 million years ago (mya) has included an overwhelming input from olfactory sensory neurons combined with a large olfactory bulb and olfactory cortex to process that input, driven by olfactory receptor gene duplications. We identify a sequence of over 20 microcircuits that are involved, and expand on results of research on several microcircuits that give the best insights thus far into the nature of the high dimensional processing.

Deep evolutionary diversification of semicircular canals in archosaurs

Living archosaurs (birds and crocodylians) have disparate locomotor strategies that evolved since their divergence ∼250 mya. Little is known about the early evolution of the sensory structures that are coupled with these changes, mostly due to limited sampling of early fossils on key stem lineages. In particular, the morphology of the semicircular canals (SCCs) of the endosseous labyrinth has a long-hypothesized relationship with locomotion. Here, we analyze SCC shapes and sizes of living and extinct archosaurs encompassing diverse locomotor habits, including bipedal, semi-aquatic, and flying taxa. We test form-function hypotheses of the SCCs and chronicle their evolution during deep archosaurian divergences. We find that SCC shape is statistically associated with both flight and bipedalism. However, this shape variation is small and is more likely explained by changes in braincase geometry than by locomotor changes. We demonstrate high disparity of both shape and size among stem-archosaurs and a deep divergence of SCC morphologies at the bird-crocodylian split. Stem-crocodylians exhibit diverse morphologies, including aspects also present in birds and distinct from other reptiles. Therefore, extant crocodylian SCC morphologies do not reflect retention of a "primitive" reptilian condition. Key aspects of bird SCC morphology that hitherto were interpreted as flight related, including large SCC size and enhanced sensitivity, appeared early on the bird stem-lineage in non-flying dinosaur precursors. Taken together, our results indicate a deep divergence of SCC traits at the bird-crocodylian split and that living archosaurs evolved from an early radiation with high sensory diversity. VIDEO ABSTRACT.

Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus

Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.

Heading for higher ground: Developmental origins and evolutionary diversification of the amniote face

Amniotes, a clade of terrestrial vertebrates, which includes all of the descendants of the last common ancestor of the reptiles (including dinosaurs and birds) and mammals, is one of the most successful group of animals on our planet. In addition to having an egg equipped with an amnion, an adaptation to lay eggs on land, amniotes possess a number of other major morphological characteristics. Chief among them is the amniote skull, which can be classified into several major types distinguished by the presence and number of temporal fenestrae (windows) in the posterior part. Amniotes evolved from ancestors who possessed a skull composed of a complex mosaic of small bones separated by sutures. Changes in skull composition underlie much of the large-scale evolution of amniotes with many lineages showing a trend in reduction of cranial elements known as the "Williston's Law." The skull of amniotes is also arranged into a set of modules of closely co-evolving bones as revealed by modularity and integration tests. One of the most consistently recovered and at the same time most versatile modules is the "face," anatomically defined as the anterior portion of the head. The faces of amniotes display extraordinary amount of variation, with many adaptive radiations showing parallel tendencies in facial scaling, e.g., changes in length or width. This review explores the natural history of the amniote face and discusses how a better understanding of its anatomy and developmental biology helps to explain the outstanding scale of adaptive facial diversity. We propose a model for facial evolution in the amniotes, based on the differential rate of cranial neural crest cell proliferation and the timing of their skeletal differentiation.

Molecular cloning, characterization, and gene expression behavior of glucocorticoid and mineralocorticoid receptors from the Chinese alligator (Alligator sinensis)

The Chinese alligator is an endemic crocodilian species in China. We isolated and obtained the glucocorticoid and mineralocorticoid receptor genes coding from the kidney of Alligator sinensis by nested polymerase chain reaction (PCR) and rapid amplification of cDNA ends (RACE). The glucocorticoid receptor (GR) gene has 2343 base pairs encoding 780 amino acids, while the mineralocorticoid receptor (MR) gene is 2958 bp in length encoding 985 amino acids. Quantitative real-time PCR was used to detect the distribution of messenger RNA (mRNA) levels. The maximum mRNA expressions were observed in the ovary and kidney, suggesting that these receptors may be involved in basic cellular functions or stress response of alligators. Besides this, RT-qPCR was performed to analyze the abundance of GR and MR mRNA transcripts in early embryonic development of the Chinese alligator in the kidney, liver, and heart. The mRNA levels of GR and MR at earlier stages in kidney, liver, and heart indicates that they might involve in the transcriptional regulation of early embryos and activate many precise developmental effects in fetal tissues. We also measured the protein expression in the liver embryonic developmental stages and found that the GR and MR proteins were restricted to both the nuclei and cytoplasm. The protein expression levels in the liver at different embryonic developmental stages have extremely prominent differences. Taken together, our results showed the full coding regions of GR and MR, their characteristics, and embryonic developmental mRNA and protein expressions of both genes in A. sinensis. This study could provide the necessary information for further investigating the diverse functions of GR and MR in A. sinensis.

The postcranial skeleton of the erythrosuchid archosauriform Garjainia prima from the Early Triassic of European Russia

Erythrosuchidae were large-bodied, quadrupedal, predatory archosauriforms that dominated the hypercarnivorous niche in the aftermath of the Permo-Triassic mass extinction. Garjainia, one of the oldest members of the clade, is known from the late Olenekian of European Russia. The holotype of Garjainia prima comprises a well-preserved skull, but highly incomplete postcranium. Recent taxonomic reappraisal demonstrates that material from a bone bed found close to the type locality, previously referred to as 'Vjushkovia triplicostata', is referable to G. prima. At least, seven individuals comprising cranial remains and virtually the entire postcranium are represented, and we describe this material in detail for the first time. An updated phylogenetic analysis confirms previous results that a monophyletic Garjainia is the sister taxon to a clade containing Erythrosuchus, Shansisuchus and Chalishevia. Muscle scars on many limb elements are clear, allowing reconstruction of the proximal locomotor musculature. We calculate the body mass of G. prima to have been 147-248 kg, similar to that of an adult male lion. Large body size in erythrosuchids may have been attained as part of a trend of increasing body size after the Permo-Triassic mass extinction and allowed erythrosuchids to become the dominant carnivores of the Early and Middle Triassic.

Origin and Evolution of the Turtle Body Plan

The origin of turtles and their uniquely shelled body plan is one of the longest standing problems in vertebrate biology. The unfulfilled need for a hypothesis that both explains the derived nature of turtle anatomy and resolves their unclear phylogenetic position among reptiles largely reflects the absence of a transitional fossil record. Recent discoveries have dramatically improved this situation, providing an integrated, time-calibrated model of the morphological, developmental, and ecological transformations responsible for the modern turtle body plan. This evolutionary trajectory was initiated in the Permian (>260 million years ago) when a turtle ancestor with a diapsid skull evolved a novel mechanism for lung ventilation. This key innovation permitted the torso to become apomorphically stiff, most likely as an adaption for digging and a fossorial ecology. The construction of the modern turtle body plan then proceeded over the next 100 million years following a largely stepwise model of osteological innovation.

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

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

Evolutionary and ontogenetic changes of the anatomical organization and modularity in the skull of archosaurs

Comparative anatomy studies of the skull of archosaurs provide insights on the mechanisms of evolution for the morphologically and functionally diverse species of crocodiles and birds. One of the key attributes of skull evolution is the anatomical changes associated with the physical arrangement of cranial bones. Here, we compare the changes in anatomical organization and modularity of the skull of extinct and extant archosaurs using an Anatomical Network Analysis approach. We show that the number of bones, their topological arrangement, and modular organization can discriminate birds from non-avian dinosaurs, and crurotarsans. We could also discriminate extant taxa from extinct species when adult birds were included. By comparing within the same framework, juveniles and adults for crown birds and alligator (Alligator mississippiensis), we find that adult and juvenile alligator skulls are topologically similar, whereas juvenile bird skulls have a morphological complexity and anisomerism more similar to those of non-avian dinosaurs and crurotarsans than of their own adult forms. Clade-specific ontogenetic differences in skull organization, such as extensive postnatal fusion of cranial bones in crown birds, can explain this pattern. The fact that juvenile and adult skulls in birds do share a similar anatomical integration suggests the presence of a specific constraint to their ontogenetic growth.