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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.

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The remarkable sensory, motor, and cognitive abilities of mammals mainly depend on the neocortex. Thus, the emergence of the six-layered neocortex in reptilian ancestors of mammals constitutes a fundamental evolutionary landmark. The mammalian cortex is a columnar epithelium of densely packed cells organized in layers where neurons are generated mainly in the subventricular zone in successive waves throughout development. Newborn cells move away from their site of neurogenesis through radial or tangential migration to reach their specific destination closer to the pial surface of the same or different cortical area. Interestingly, the genetic programs underlying neocortical development diversified in different mammalian lineages. In this work, I will review several recent studies that characterized how distinct transcriptional programs relate to the development and functional organization of the neocortex across diverse mammalian lineages. In some primates such as the anthropoids, the neocortex became extremely large, especially in humans where it comprises around 80% of the brain. It has been hypothesized that the massive expansion of the cortical surface and elaboration of its connections in the human lineage, has enabled our unique cognitive capacities including abstract thinking, long-term planning, verbal language and elaborated tool making capabilities. I will also analyze the lineage-specific genetic changes that could have led to the modification of key neurodevelopmental events, including regulation of cell number, neuronal migration, and differentiation into specific phenotypes, in order to shed light on the evolutionary mechanisms underlying the diversity of mammalian brains including the human brain.

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Here we describe the histology and microanatomy of vertebral centra of the iconic pelycosaur-grade synapsids Edaphosaurus boanerges and Dimetrodon spp. Vertebrae from different axial positions and, in the case of Dimetrodon, from different ontogenetic stages were selected. For the histological description, we produced histological petrographic thin sections ground to a thickness of 50-80 µm of the vertebrae in the sagittal and transversal cutting planes. After the preparation process, the thin sections were examined under transmitted and cross-polarized light in a polarized microscope. The analyzed vertebrae reveal similar bone tissues, where both taxa have cortical parallel-fibered bone (PFB). PFB and lamellar bone (LB) forms in the cancellous part. However, in juvenile Dimetrodon, woven-fibered bone (WFB) is also deposited and shows a high degree of vascularity. This suggests that Dimetrodon had slightly faster bone growth than Edaphosaurus, which is mainly made of PFB and LB and shows poorly developed vascular canals. In addition, one specimen of Dimetrodon displays the preservation of an ossified notochord, which can be assumed to be indicative of how the intervertebral tissues were developed. Historically, evidence of how the joint between Dimetrodon vertebral centra was built was lacking until this specimen appeared. If the notochord ran persistently through the vertebrae, it would have possibly increased the stiffness of the vertebral column and would have affected the limbs and locomotion. Furthermore, the organization of trabeculae and relative thickness of the vertebral cortex gives insights into how the animals were adapted to their habitat.

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The acquisition of mammalian endothermy is poorly constrained both phylogenetically and temporally. Here, we inferred the resting metabolic rates (RMRs) and the thermometabolic regimes (endothermy or ectothermy) of a sample of eight extinct synapsids using palaeohistology, phylogenetic eigenvector maps (PEMs), and a sample of 17 extant tetrapods of known RMR (quantified using respirometry). We inferred high RMR values and an endothermic metabolism for the anomodonts (Lystrosaurus sp., Oudenodon bainii) and low RMR values and an ectothermic metabolism for Clepsydrops collettii, Dimetrodon sp., Edaphosaurus boanerges, Mycterosaurus sp., Ophiacodon uniformis and Sphenacodon sp. A maximum-likelihood ancestral states reconstruction of RMRs performed using the values inferred for extinct synapsids, and the values measured using respirometry in extant tetrapods, shows that the nodes Anomodontia and Mammalia were primitively endotherms. Finally, we performed a parsimony optimization of the presence of endothermy using the results obtained in the present study and those obtained in previous studies that used PEMs. For this, we assigned to each extinct taxon a thermometabolic regime (ectothermy or endothermy) depending on whether the inferred values were significantly higher, lower or not significantly different from the RMR value separating ectotherms from endotherms (1.5 ml O2 h-1 g-0.67). According to this optimization, endothermy arose independently in Archosauromorpha, Sauropterygia and Therapsida. This article is part of the theme issue 'Vertebrate palaeophysiology'.

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The cranial anatomy of the early non-mammalian cynodont Galesaurus planiceps from the South African Karoo Basin is redescribed on the basis of a computed tomographic reconstruction of the skull. Previously, little was known about internal skull morphology and the nervous and sensory system of this taxon. The endocranial anatomy of various cynodonts has been intensively studied in recent years to understand the origin of mammalian characters in the nasal capsule, brain and ear. However, these studies have focused on only a few taxa, the earliest of which is another Early Triassic cynodont, Thrinaxodon liorhinus. Galesaurus is phylogenetically stemward of Thrinaxodon and thus provides a useful test of whether the mammal-like features observed in Thrinaxodon were present even more basally in cynodont evolution. The cranial anatomy of G. planiceps is characterized by an intriguing mosaic of primitive and derived features within cynodonts. In contrast to the very similar internal nasal and braincase morphology of Galesaurus and Thrinaxodon, parts of the skull that seem to be fairly conservative in non-prozostrodont cynodonts, the morphology of the maxillary canal differs markedly between these taxa. Unusually, the maxillary canal of Galesaurus has relatively few ramifications, more similar to those of probainognathian cynodonts than that of Thrinaxodon. However, its caudal section is very short, a primitive feature shared with gorgonopsians and therocephalians. The otic labyrinth of Galesaurus is generally similar to that of Thrinaxodon, but differs in some notable features (e.g. proportional size of the anterior semicircular canal). An extremely large, protruding paraflocculus of the brain and a distinct medioventrally located notch on the anterior surface of the tabular, which forms the dorsal border of the large parafloccular lobe, are unique to Galesaurus among therapsids with reconstructed endocasts. These features may represent autapomorphies of Galesaurus, but additional sampling is needed at the base of Cynodontia to test this.

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The musculoskeletal configuration of the mammalian pectoral limb has been heralded as a key anatomical feature leading to the adaptive radiation of mammals, but limb function in the non-mammaliaform cynodont outgroup remains unresolved. Conflicting reconstructions of abducted and adducted posture are based on mutually incompatible interpretations of ambiguous osteology. We reconstruct the pectoral limb of the Triassic non-mammaliaform cynodont Massetognathus pascuali in three dimensions, by combining skeletal morphology from micro-computed tomography with muscle anatomy from an extended extant phylogenetic bracket. Conservative tests of maximum range of motion suggest a degree of girdle mobility, as well as substantial freedom at the shoulder and the elbow joints. The glenoid fossa supports a neutral pose in which the distal end of the humerus points 45° posterolaterally from the body wall, intermediate between classically 'sprawling' and 'parasagittal' limb postures. Massetognathus pascuali is reconstructed as having a near-mammalian complement of shoulder muscles, including an incipient rotator cuff (m. subscapularis, m. infraspinatus, m. supraspinatus, and m. teres minor). Based on close inspection of the morphology of the glenoid fossa, we hypothesize a posture-driven scenario for the evolution of the therian ball-and-socket shoulder joint. The musculoskeletal reconstruction presented here provides the anatomical scaffolding for more detailed examination of locomotor evolution in the precursors to mammals.

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Recent palaeontological data and novel physiological hypotheses now allow a timescaled reconstruction of the evolution of endothermy in birds and mammals. A three-phase iterative model describing how endothermy evolved from Permian ectothermic ancestors is presented. In Phase One I propose that the elevation of endothermy - increased metabolism and body temperature (Tb ) - complemented large-body-size homeothermy during the Permian and Triassic in response to the fitness benefits of enhanced embryo development (parental care) and the activity demands of conquering dry land. I propose that Phase Two commenced in the Late Triassic and Jurassic and was marked by extreme body-size miniaturization, the evolution of enhanced body insulation (fur and feathers), increased brain size, thermoregulatory control, and increased ecomorphological diversity. I suggest that Phase Three occurred during the Cretaceous and Cenozoic and involved endothermic pulses associated with the evolution of muscle-powered flapping flight in birds, terrestrial cursoriality in mammals, and climate adaptation in response to Late Cenozoic cooling in both birds and mammals. Although the triphasic model argues for an iterative evolution of endothermy in pulses throughout the Mesozoic and Cenozoic, it is also argued that endothermy was potentially abandoned at any time that a bird or mammal did not rely upon its thermal benefits for parental care or breeding success. The abandonment would have taken the form of either hibernation or daily torpor as observed in extant endotherms. Thus torpor and hibernation are argued to be as ancient as the origins of endothermy itself, a plesiomorphic characteristic observed today in many small birds and mammals.

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Unravelling the evolutionary and developmental mechanisms that have impacted the mammalian dentition, since more than 200 Ma, is an intricate issue. Interestingly, a few mammal species, including the silvery mole-rat Heliophobius argenteocinereus, are able to replace their dentition by the addition of supernumerary molars at the back of jaw migrating then toward the front. The aim here was to demonstrate the potential interest of further studying this rodent in order to better understand the origins of continuous dental replacement in mammals, which could also provide interesting data concerning the evolution of limited dental generation occurring in first mammals. In the present study, we described the main stages of the dental eruptive sequence in the silvery mole-rat and the associated characteristics of horizontal replacement using X-ray microtomography. This was coupled to the investigation of other African mole-rats which have no dental replacement. This method permitted to establish evidence that the initial development of the dentition in Heliophobius is comparable to what it is observed in most of African mole-rats. This rodent first has premolars, but then identical additional molars, a mechanism convergent to manatees and the pygmy rock-wallaby. Evidence of continuous replacement and strong dental dynamics were also illustrated in Heliophobius, and stressed the need to deeply investigate these aspects for evolutionary, functional and developmental purposes. We also noticed that two groups of extinct non-mammalian synapsids convergently acquired this dental mechanism, but in a way differing from extant mammals. The discussion on the diverse evolutionary origins of horizontal dental replacement put emphasis on the necessity of focusing on biological parameters potentially involved in both continuous and limited developments of teeth in mammals. In that context, the silvery mole-rat could appear as the most appropriate candidate to do so.

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Therocephalians were a speciose clade of nonmammalian therapsids whose ecological diversity and survivorship of the end-Permian mass extinction offer the potential to investigate the evolution of growth patterns across the clade and their underlying influences on post-extinction body size reductions, or 'Lilliput effects'. We present a phylogenetic survey of limb bone histology and growth patterns in therocephalians from the Middle Permian through Middle Triassic of the Karoo Basin, South Africa. Histologic sections were prepared from 80 limb bones representing 11 genera of therocephalians. Histologic indicators of skeletal growth, including cortical vascularity (%CV) and mean primary osteon diameters (POD), were evaluated in a phylogenetic framework and assessed for correlations with other biologically significant variables (e.g., size and robusticity). Changes in %CV and POD correlated strongly with evolutionary changes in body size (i.e., smaller-bodied descendants tended to have lower %CV than their larger-bodied ancestors across the tree). Bone wall thickness tended to be high in early therocephalians and lower in the gracile-limbed baurioids, but showed no general correlation with cross-sectional area or degree of vascularity (and, thus, growth). Clade-level patterns, however, deviated from previously studied within-lineage patterns. For example, Moschorhinus, one of few therapsid genera to have survived the extinction boundary, demonstrated higher %CV in the Triassic than in the Permian despite its smaller size in the extinction aftermath. Results support a synergistic model of size reductions for Triassic therocephalians, influenced both by within-lineage heterochronic shifts in survivor taxa (as reported in Moschorhinus and the dicynodont Lystrosaurus) and phylogenetically inferred survival of small-bodied taxa that had evolved short growth durations (e.g., baurioids). These findings mirror the multi-causal Lilliput patterns described in marine faunas, but contrast with skeletochronologic studies that suggest slow, prolonged shell secretion over several years in marine benthos. Applications of phylogenetic comparative methods to new histologic data will continue to improve our understanding of the evolutionary dynamics of growth and body size shifts during mass extinctions and recoveries.