Nocturnality in synapsids predates the origin of mammals by over 100 million years

Predatory synapsid ecomorphology signals growing dynamism of late Palaeozoic terrestrial ecosystems

Terrestrial ecosystems evolved substantially through the Palaeozoic, especially the Permian, gaining much new complexity, especially among predators. Key among these predators were non-mammalian synapsids. Predator ecomorphology reflect interactions with prey and competitors, which are key controls on carnivore diversity and ecology. Therefore, carnivorous synapsids may offer insight on wider ecological evolution as the first complex, tetrapod-dominated, terrestrial ecosystems formed through the late Palaeozoic. Using morphometric and phylogenetic comparative methods, we chart carnivorous synapsid trophic morphology from the latest Carboniferous to the earliest Triassic (307-251.2 Ma). We find a major morphofunctional shift in synapsid carnivory between the early and middle Permian, via the addition of new feeding modes increasingly specialised for greater biting power or speed that captures the growing antagonism and dynamism of terrestrial tetrapod predator-prey interactions. The further evolution of new hypo- and hypercarnivorous synapsids highlight the nascent intrinsic pressures and complexification of terrestrial ecosystems across the mid-late Permian.

Nasal turbinates of the dicynodont Kawingasaurus fossilis and the possible impact of the fossorial habitat on the evolution of endothermy

The nasal region of the fossorial anomodont Kawingasaurus fossilis was virtually reconstructed from neutron-computed tomographic data and compared with the terrestrial species Pristerodon mackayi and other nonmammalian synapsids. The tomography of the Kawingasaurus skull reveals a pattern of maxillo-, naso-, fronto- and ethmoturbinal ridges that strongly resemble the mammalian condition. On both sides of the nasal cavity, remains of scrolled maxilloturbinals were preserved that were still partially articulated with maxilloturbinal ridges. Furthermore, possible remains of the lamina semicircularis as well as fronto- or ethmoturbinals were found. In Kawingasaurus, the maxilloturbinal ridges were longer and stronger than in Pristerodon. Except for the nasoturbinal ridges, no other ridges in the olfactory region and no remains of turbinates were recognized. This supports the hypothesis that naso-, fronto-, ethmo- and maxilloturbinals were a plesiomorphic feature of synapsids, but due to their cartilaginous nature in most taxa were, in almost all cases, not preserved. The well-developed maxilloturbinals in Kawingasaurus were probably an adaptation to hypoxia-induced hyperventilation in the fossorial habitat, maintaining the high oxygen demands of Kawingasaurus' large brain. The surface area of the respiratory turbinates in Kawingasaurus falls into the mammalian range, which suggests that they functioned as a countercurrent exchange system for thermoregulation and conditioning of the respiratory airflow. Our results suggest that the environmental conditions of the fossorial habitat led to specific sensory adaptations, accompanied by a pulse in brain evolution and of endothermy in cistecephalids, ~50 million years before the origin of endothermy in the mammalian stem line. This supports the Nocturnal Bottleneck Theory, in that we found evidence for a similar evolutionary scenario in cistecephalids as proposed for early mammals.

Craniodental anatomy in Permian-Jurassic Cynodontia and Mammaliaformes (Synapsida, Therapsida) as a gateway to defining mammalian soft tissue and behavioural traits

Mammals are diagnosed by more than 30 osteological characters (e.g. squamosal-dentary jaw joint, three inner ear ossicles, etc.) that are readily preserved in the fossil record. However, it is the suite of physiological, soft tissue and behavioural characters (e.g. endothermy, hair, lactation, isocortex and parental care), the evolutionary origins of which have eluded scholars for decades, that most prominently distinguishes living mammals from other amniotes. Here, we review recent works that illustrate how evolutionary changes concentrated in the cranial and dental morphology of mammalian ancestors, the Permian-Jurassic Cynodontia and Mammaliaformes, can potentially be used to document the origin of some of the most crucial defining features of mammals. We discuss how these soft tissue and behavioural traits are highly integrated, and how their evolution is intermingled with that of craniodental traits, thus enabling the tracing of their previously out-of-reach phylogenetic history. Most of these osteological and dental proxies, such as the maxillary canal, bony labyrinth and dental replacement only recently became more easily accessible-thanks, in large part, to the widespread use of X-ray microtomography scanning in palaeontology-because they are linked to internal cranial characters. This article is part of the theme issue 'The mammalian skull: development, structure and function'.

Revisiting the evolutionary trend toward the mammalian lower jaw in non-mammalian synapsids in a phylogenetic context

The mammalian lower jaw comprises a single bone, the dentary, which is a unique feature among vertebrates. The lower jaws of extinct non-mammalian synapsids were composed of the dentary and several postdentary bones. Synapsid fossils exhibit variation in the dentary size relative to the overall lower jaw. An evolutionary trend toward dentary enlargement and postdentary reduction in non-mammalian synapsids has long been documented but has not been established using modern phylogenetic comparative methods. In this study, we examine the evolutionary pattern of dentary size relative to the lower jaw through phylogenetic analyses of measurements in a broad range of non-mammalian synapsid taxa. Our analyses revealed an evolutionary trend toward dentary area enlargement relative to the overall lower jaw in the lateral view across all non-mammalian synapsids. This trend is likely due to vertical expansion of the dentary given that the same trend is not evident when looking at anterior to posterior measurements of the dentary relative to the lower jaw as a whole in lateral view. Ancestral character reconstructions revealed that the evolution of the measurements was not unidirectional in non-mammalian synapsids. Our results provide no evidence of an evolutionary trend toward the dentary enlargement at the expense of postdentary bones across non-mammalian synapsids. This implies that the evolutionary origin of the mammalian lower jaw is not adequately explained by the evolutionary trend of dentary enlargement throughout non-mammalian synapsids. Instead, selection that occurred during the transition from non-mammalian cynodonts to early mammals may have produced the mammalian lower jaw.

Ecomorphological patterns in trigeminal canal branching among sauropsids reveal sensory shift in suchians

The vertebrate trigeminal nerve is the primary mediator of somatosensory information from nerve endings across the face, extending nerve branches through bony canals in the face and mandibles, terminating in sensory receptors. Reptiles evolved several extreme forms of cranial somatosensation in which enhanced trigeminal tissues are present in species engaging in unique mechanosensory behaviors. However, morphology varies by clade and ecology among reptiles. Few lineages approach the extreme degree of tactile somatosensation possessed by crocodylians, the only remaining members of a clade that underwent an ecological transition from the terrestrial to semiaquatic habitat, also evolving a specialized trigeminal system. It remains to be understood how trigeminal osteological correlates inform how adaptations for enhanced cranial sensation evolved in crocodylians. Here we identify an increase in sensory abilities in Early Jurassic crocodylomorphs, preceding the transitions to a semiaquatic habitat. Through quantification of trigeminal neurovascular canal branching patterns in an extant phylogenetic bracket we quantify and identify morphologies associated with sensory behaviors in representative fossil taxa, we find stepwise progression of increasing neurovascular canal density, complexity, and distribution from the primitive archosaurian to the derived crocodilian condition. Model-based inferences of sensory ecologies tested on quantified morphologies of extant taxa with known sensory behaviors indicate a parallel increase in sensory abilities among pseudosuchians. These findings establish patterns of reptile trigeminal ecomorphology, revealing evolutionary patterns of somatosensory ecology.

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.

Inner ear biomechanics reveals a Late Triassic origin for mammalian endothermy

Endothermy underpins the ecological dominance of mammals and birds in diverse environmental settings^1,2. However, it is unclear when this crucial feature emerged during mammalian evolutionary history, as most of the fossil evidence is ambiguous^3-17. Here we show that this key evolutionary transition can be investigated using the morphology of the endolymph-filled semicircular ducts of the inner ear, which monitor head rotations and are essential for motor coordination, navigation and spatial awareness^18-22. Increased body temperatures during the ectotherm-endotherm transition of mammal ancestors would decrease endolymph viscosity, negatively affecting semicircular duct biomechanics^23,24, while simultaneously increasing behavioural activity^25,26 probably required improved performance²⁷. Morphological changes to the membranous ducts and enclosing bony canals would have been necessary to maintain optimal functionality during this transition. To track these morphofunctional changes in 56 extinct synapsid species, we developed the thermo-motility index, a proxy based on bony canal morphology. The results suggest that endothermy evolved abruptly during the Late Triassic period in Mammaliamorpha, correlated with a sharp increase in body temperature (5-9 °C) and an expansion of aerobic and anaerobic capacities. Contrary to previous suggestions^3-14, all stem mammaliamorphs were most probably ectotherms. Endothermy, as a crucial physiological characteristic, joins other distinctive mammalian features that arose during this period of climatic instability²⁸.

Temporal activity patterns of North China leopards and their prey in response to moonlight and habitat factors

The nocturnal activities of predators and prey are influenced by several factors, including physiological adaptations, habitat quality and, we suspect, corresponds to changes in brightness of moonlight according to moon phase. In this study, we used a dataset from 102 camera traps to explore which factors are related to the activity pattern of North China leopards (Panthera pardus japonensis) in Shanxi Tieqiaoshan Provincial Nature Reserve (TPNR), China. We found that nocturnal activities of leopards were irregular during four different lunar phases, and while not strictly lunar philic or lunar phobic, their temporal activity was highest during the brighter moon phases (especially the last quarter) and lower during the new moon phase. On the contrary, roe deer (Capreolus pygargus) exhibited lunar philic activity, while wild boar (Sus scrofa) and tolai hare (Lepus tolai) were evidently lunar phobic, with high and low temporal activity during the full moon, respectively. In terms of temporal overlap, there was positive overlap between leopards and their prey species, including roe deer and tolai hare, while leopard activity did not dip to the same low level of wild boar during the full moon phase. Human activities also more influenced the temporal activity of leopards and wild boar than other species investigated. Generally, our results suggested that besides moonlight risk index (MRI), cloud cover and season have diverse effects on leopard and prey nocturnal activity. Finally, distinct daytime and nighttime habitats were identified, with leopards, wild boar, and tolai hare all using lower elevations at night and higher elevations during the day, while leopards and roe deer were closer to secondary roads during the day than at night.

Early evolution of diurnal habits in owls (Aves, Strigiformes) documented by a new and exquisitely preserved Miocene owl fossil from China

SignificanceOwls, with their largely nocturnal habits, contrast strikingly with the vast majority of diurnal birds. A new spectacular late Miocene owl skeleton from China unexpectedly preserves the oldest evidence for daytime behavior in owls. The extinct owl is a member of the clade Surniini, which contains most living diurnal owl species. Analysis of the preserved eye bones documents them as consistent with diurnal birds, and phylogenetically constrained character mapping coincides with a reconstruction of an early evolutionary reversal away from nocturnal habits in this owl group. These results support a potential Miocene origin of nonnocturnal habits in a globally distributed owl group, which may be linked to steppe habitat expansion and climatic cooling in the late Miocene.

Early origins of divergent patterns of morphological evolution on the mammal and reptile stem-lineages

The origin of amniotes 320 million years ago signaled independence from water in vertebrates and was closely followed by divergences within the mammal and reptile stem lineages (Synapsida and Reptilia). Early members of both groups had highly similar morphologies, being superficially “lizard-like” forms with many plesiomorphies. However, the extent to which they might have exhibited divergent patterns of evolutionary change, with the potential to explain the large biological differences between their living members, is unresolved. We use a new, comprehensive phylogenetic dataset to quantify variation in rates and constraints of morphological evolution among Carboniferous–early Permian amniotes. We find evidence for an early burst of evolutionary rates, resulting in the early origins of morphologically distinctive subgroups that mostly persisted through the Cisuralian. Rates declined substantially through time, especially in reptiles. Early reptile evolution was also more constrained compared with early synapsids, exploring a more limited character state space. Postcranial innovation in particular was important in early synapsids, potentially related to their early origins of large body size. In contrast, early reptiles predominantly varied the temporal region, suggesting disparity in skull and jaw kinematics, and foreshadowing the variability of cranial biomechanics seen in reptiles today. Our results demonstrate that synapsids and reptiles underwent an early divergence of macroevolutionary patterns. This laid the foundation for subsequent evolutionary events and may be critical in understanding the substantial differences between mammals and reptiles today. Potential explanations include an early divergence of developmental processes or of ecological factors, warranting cross-disciplinary investigation. [Amniote; body size; constraint; phylogeny; rate.]

New tools suggest a middle Jurassic origin for mammalian endothermy: Advances in state-of-the-art techniques uncover new insights on the evolutionary patterns of mammalian endothermy through time: Advances in state-of-the-art techniques uncover new insights on the evolutionary patterns of mammalian endothermy through time

We suggest that mammalian endothermy was established amongst Middle Jurassic crown mammals, through reviewing state-of-the-art fossil and living mammal studies. This is considerably later than the prevailing paradigm, and has important ramifications for the causes, pattern, and pace of physiological evolution amongst synapsids. Most hypotheses argue that selection for either enhanced aerobic activity, or thermoregulation was the primary driver for synapsid physiological evolution, based on a range of fossil characters that have been linked to endothermy. We argue that, rather than either alternative being the primary selective force for the entirety of endothermic evolution, these characters evolved quite independently through time, and across the mammal family tree, principally as a response to shifting environmental pressures and ecological opportunities. Our interpretations can be tested using closely linked proxies for both factors, derived from study of fossils of a range of Jurassic and Cretaceous mammaliaforms and early mammals.

Escaping the nocturnal bottleneck, and the evolution of the dorsal and ventral streams of visual processing in primates

Early mammals were small and nocturnal. Their visual systems had regressed and they had poor vision. After the extinction of the dinosaurs 66 mya, some but not all escaped the 'nocturnal bottleneck' by recovering high-acuity vision. By contrast, early primates escaped the bottleneck within the age of dinosaurs by having large forward-facing eyes and acute vision while remaining nocturnal. We propose that these primates differed from other mammals by changing the balance between two sources of visual information to cortex. Thus, cortical processing became less dependent on a relay of information from the superior colliculus (SC) to temporal cortex and more dependent on information distributed from primary visual cortex (V1). In addition, the two major classes of visual information from the retina became highly segregated into magnocellular (M cell) projections from V1 to the primate-specific temporal visual area (MT), and parvocellular-dominated projections to the dorsolateral visual area (DL or V4). The greatly expanded P cell inputs from V1 informed the ventral stream of cortical processing involving temporal and frontal cortex. The M cell pathways from V1 and the SC informed the dorsal stream of cortical processing involving MT, surrounding temporal cortex, and parietal-frontal sensorimotor domains. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'.

Ecomorphology of the tarsometatarsus of waterfowl (Anseriformes) based on geometric morphometrics and its application to fossils

Anseriformes is a diverse group of birds that comprises screamers, the Magpie Goose, and swans ducks and geese, with a relatively rich fossil record. Waterfowl live in close relation to water bodies, but show a diversity of locomotory habits, being typically categorized as walkers, dabblers, and divers. Owing to its functional significance and high preservation potential, the tarsometatarsus has been considered to be a "key" element upon which to base ecomorphological inferences in fossil waterfowl. For instance, based on features of the tarsometatarsus the Miocene flightless duck Cayaoa bruneti and the Oligocene-Miocene large waterfowl Paranyroca have been inferred as divers. Herein, we use a geometric morphometric approach and comparative methods to assess the phylogenetic and ecomorphological signals in the shape and size of waterfowl tarsometatarsi in relation to their locomotory habits. We also apply phylogenetic flexible discriminant analysis (pFDA) to test the inferred diving habits in the extinct waterfowl Cayaoa and Paranyroca. Extant waterfowl species are largely distributed according to their locomotory habit along the main axis of variation in the shape space, a pattern mirrored by the phylogenetic generalized least squares model, which shows that a third of the shape variation is significantly explained by the habit. The pFDA reclassifies correctly almost all extant species and classified with high posterior probabilities the fossil Cayaoa and Paranyroca as a diver and as a dabbler, respectively. Our quantitative multivariate approach confirms the tarsometatarsus as a useful source of data upon which reliably assesses locomotory habits of fossil waterfowl.

The functional diversity of marsupial limbs is influenced by both ecology and developmental constraint

Extant marsupials are less ecologically diverse than placentals, and this is reflected by placentals exhibiting a greater diversity of locomotor modes, including powered flight and fully aquatic swimming. One proposed explanation for this discrepancy is that the development of more disparate marsupial forelimbs is prevented by the neonate’s crawl to the pouch, which requires precocious forelimb development for climbing adaptations. To test predictions of this Developmental Constraint Hypothesis (DCH), we pursue a comparative morphometric study on osteological traits of mammalian limbs, with an emphasis on functional differentiation of marsupial limbs among locomotor modes. We apply multivariate analyses to a large dataset of limb metrics and a diverse sample of mammals, with the placental sample limited to taxa whose locomotor modes are exhibited in marsupials. Overall, we do not find consistent evidence in support of the DCH. Diprotodontia serves as an exception, with comparisons of their forelimbs to hind limbs supporting the DCH. Our results suggest that developmental constraints on marsupial forelimbs may have limited marsupial diversity to some degree. Despite this, the marsupial locomotor groups show unexpectedly high levels of morphological differentiation relative to placentals of the same locomotor modes, indicating that ecological functions may overcome developmental constraints on a macroevolutionary scale.

Computed Tomography elucidates ontogeny within the basal therapsid clade Biarmosuchia

Biarmosuchia is a clade of basal therapsids that includes forms possessing plesiomorphic ‘pelycosaurian’ cranial characters as well as the highly derived Burnetiamorpha which are characterised by cranial pachyostosis and a variety of cranial bosses. Potential ontogenetic variation in these structures has been suggested based on growth series of other therapsids with pachyostosed crania, which complicates burnetiamorph taxonomic distinction and thus it is essential to better understand cranial ontogeny of the Burnetiamorpha. Here, three new juvenile biarmosuchian skulls from the late Permian of South Africa are described using X-ray micro computed tomography (CT). We found that juvenile biarmosuchians are distinguished from adults by their relatively large orbits, open cranial sutures, and incomplete ossification of the braincase and bony labyrinth. Also, they manifest multiple centres of ossification within the parietal and preparietal bones. CT examination reveals that the holotype of Lemurosaurus pricei (BP/1/816), previously alleged to be a juvenile, shows no evidence of juvenility and is thus probably an adult. This suggests that the larger skull NMQR 1702, previously considered to be an adult L. pricei, may represent a new taxon. This study provides, for the first time, a list of characters by which to recognise juvenile biarmosuchians.

The lacrimal/ectethmoid region of waterfowl (Aves, Anseriformes): Phylogenetic signal and major evolutionary patterns

Waterfowl (Aves, Anseriformes) constitute an ancient global radiation, and understanding the pattern and timing of their evolution requires a well-corroborated phylogeny including extant species and fossils. Following the molecular advances in avian systematics, however, morphology has often been held as misleading, yet congruence with molecular data has been shown to vary considerably among different skeletal parts. Here, we explore phylogenetic signal in discrete characters of the lacrimal/ectethmoid region of waterfowl, which is highly variable among species and constitutes a rich source of data. We do so by combining cladistic and multivariate approaches, and using phylogenetic comparative methods. We quantitatively recognize three major morphological types among lacrimal bones, and discuss homoplasy and potential synapomorphies of major clades using a molecular backbone tree. Our results clearly indicate that the lacrimal bone carries substantial phylogenetic signal and could be of systematic value at different levels of the phylogeny of waterfowl, feeding the exploration of other regions of the skull with this combined approach.

Convergent evolution of bird-mammal shared characteristics for adapting to nocturnality

The diapsid lineage (birds) and synapsid lineage (mammals), share a suite of functionally similar characteristics (e.g. endothermy) that are considered to be a result of their convergent evolution, but the candidate selections leading to this convergent evolution are still under debate. Here, we used a newly developed molecular phyloecological approach to reconstruct the diel activity pattern of the common ancestors of living birds. Our results strongly suggest that they had adaptations to nocturnality during their early evolution, which is remarkably similar to that of ancestral mammals. Given their similar adaptation to nocturnality, we propose that the shared traits in birds and mammals may have partly evolved as a result of the convergent evolution of their early ancestors adapting to ecological factors (e.g. low ambient temperature) associated with nocturnality. Finally, a conceptually unifying ecological model on the evolution of endothermy in diverse organisms with an emphasis on low ambient temperature is proposed. We reason that endothermy may evolve as an adaptive strategy to enable organisms to effectively implement various life-cycle activities under relatively low-temperature environments. In particular, a habitat shift from high-temperature to relatively low-temperature environments is identified as a common factor underlying the evolution of endothermy.

Scotopic rod vision in tetrapods arose from multiple early adaptive shifts in the rate of retinal release

The ability of vertebrates to occupy diverse niches has been linked to the spectral properties of rhodopsin, conferring rod-based vision in low-light conditions. More recent insights have come from nonspectral kinetics, including the retinal release rate of the active state of rhodopsin, a key aspect of scotopic vision that shows strong associations with light environments in diverse taxa. We examined the retinal release rates in resurrected proteins across early vertebrates and show that the earliest forms were characterized by much faster rates of retinal release than more recent ancestors. We also show that scotopic vision at the origin of tetrapods is a derived state that arose via at least 4 major shifts in retinal release rate. Our results suggest that early rhodopsin had a function intermediate to that of modern rod and cone pigments and that its well-developed adaptation to low light is a relatively recent innovation since the origin of tetrapods.

Interference competition pressure predicts the number of avian predators that shifted their timing of activity

Being active at different times facilitates the coexistence of functionally similar species. Hence, time partitioning might be induced by competition. However, the relative importance of direct interference and indirect exploitation competition on time partitioning remains unclear. The aim of this study was to investigate the relative importance of these two forms of competition on the occurrence of time-shifting among avian predator species. As a measure of interference competition pressure, we used the species richness of day-active avian predator species or of night-active avian predator species (i.e. species of Accipitriformes, Falconiformes and Strigiformes) in a particular geographical area (assemblage). As an estimate of exploitation competition pressure, we used the total species richness of avian predators in each assemblage. Estimates of the intensity of interference competition robustly predicted the number of Accipitriformes species that became crepuscular and the number of Strigiformes species that became day-active or strictly crepuscular. Interference competition pressure may depend on body size and on the total duration of the typical active period (day or night length). Our results support-to some extent-that smaller species are more likely to become time-shifters. Day length did not have an effect on the number of time-shifter species in the Accipitriformes. Among the large Strigiformes, more time-shifter species occur in areas where nights are shorter (i.e. where less of the typical time resource is available). However, in the small Strigiformes, we found the opposite, counterintuitive effect: more time-shifters where nights are longer. Exploitation competition may have had an additional positive effect on the number of time-shifters, but only in Accipitriformes, and the effect was not as robust. Our results thus support the interference competition hypothesis, suggesting that animals may have shifted their time of activity, despite phylogenetic constraints on the ability to do so, to reduce the costs of direct interactions. Our findings also highlight the influence of body size as a surrogate of competitive ability during encounters on time partitioning, at least among avian predators.

Taking a look into the orbit of mammalian carnivorans

In this study, we explore the relationship between orbit anatomy and different ecological factors in carnivorous mammals from a phylogenetic perspective. We calculated the frontation (α), convergence (β), and orbitotemporal (Ω) angles of the orbit from 3D coordinates of anatomical landmarks in a wide sample of carnivores with different kinds of visual strategy (i.e. photopic, scotopic, and mesopic), habitat (i.e. open, mixed, and closed), and substrate use (i.e. arboreal, terrestrial, and aquatic). We used Bloomberg's K and Pagel's λ to assess phylogenetic signal in frontation, convergence, and orbitotemporal angles. The association of orbit orientation with skull length and ecology was explored using phylogenetic generalized least squares and phylogenetic manova, respectively. Moreover, we also computed phylomorphospaces from orbit orientation. Our results indicate that there is not a clear association between orbit orientation and the ecology of living carnivorans. We hypothesize that the evolution of the orbit in mammalian carnivores represents a new case of an ecological bottleneck specific to carnivorans. New directions for future research are discussed in light of this new evidence.

Skeletons of the Eye: An Evolutionary and Developmental Perspective

The ocular skeleton, composed of the scleral cartilage and scleral ossicles, is present in many vertebrates. The morphology of the scleral cartilage and ossicles varies within different extant reptiles (including birds) and also varies dramatically from the morphology in extant teleosts. This incredible range of diverse morphologies is the result of millions of years of evolution. Both the position of these elements within the eye and the timing of development vary amongst different vertebrates. While the development of both the scleral cartilage and scleral ossicles is somewhat understood in reptiles and in teleosts, the functional advantage of these elements is still debated. Most reptiles have a multi-component scleral ossicle ring composed of a series of flat bone plates and a scleral cartilage cup lining the retina, some sharks have calcified cartilage plates, and some teleosts have two bones while most others only have a ring of scleral cartilage. The data presented shows that different vertebrates have adapted to similar selective pressures in different ways. However, the reason why sarcopterygians have a series of overlapping bones in the sclera remains unclear. A better understanding of the ocular skeletal diversity in Reptilia as well as a better understanding of the mechanisms of vision within different environments (i.e., air vs. water) and that used by secondarily aquatic organisms is needed. This review discusses the observed variation in morphology and development of the ocular skeleton in the context of evolution and highlights our knowledge gaps in these areas. Anat Rec, 2018. © 2018 American Association for Anatomy.

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.

Gorgonopsian therapsids (Nochnitsa gen. nov. and Viatkogorgon) from the Permian Kotelnich locality of Russia

The early evolution of gorgonopsians is poorly understood. New material from the Kotelnich locality in Russia expands our knowledge of middle/earliest late Permian gorgonopsians from Laurasia. Two gorgonopsian taxa are recognized from Kotelnich: Viatkogorgon ivakhnenkoi Tatarinov, 1999 and Nochnitsa geminidens gen. et sp. nov. Nochnitsa can be distinguished from all known gorgonopsians by its unique upper postcanine tooth row, composed of pairs of teeth (a small anterior and larger posterior) separated by diastemata. Both Viatkogorgon and Nochnitsa are relatively small gorgonopsians, comparable in size to the South African middle Permian taxon Eriphostoma. Inclusion of Viatkogorgon and Nochnitsa in a phylogenetic analysis of gorgonopsians recovers them in basal positions, with Nochnitsa representing the earliest-diverging gorgonopsian genus. All other sampled gorgonopsians fall into two major subclades: one made up entirely of Russian taxa (Inostrancevia, Pravoslavlevia, Sauroctonus, and Suchogorgon) and the other containing only African gorgonopsians. The high degree of endemism indicated in this analysis for gorgonopsians is remarkable, especially given the extensive intercontinental dispersal inferred for coeval therapsid groups.

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

BACKGROUND

Based on evolutionary patterns of the vertebrate eye, Walls (1942) hypothesized that early placental mammals evolved primarily in nocturnal habitats. However, not only Eutheria, but all mammals show photic characteristics (i.e. dichromatic vision, rod-dominated retina) suggestive of a scotopic eye design.

RESULTS

Here, we used integrative comparative genomic and phylogenetic methodologies employing the photoreceptive opsin gene family in 154 mammals to test the likelihood of a nocturnal period in the emergence of all mammals. We showed that mammals possess genomic patterns concordant with a nocturnal ancestry. The loss of the RH2, VA, PARA, PARIE and OPN4x opsins in all mammals led us to advance a probable and most-parsimonious hypothesis of a global nocturnal bottleneck that explains the loss of these genes in the emerging lineage (> > 215.5 million years ago). In addition, ancestral character reconstruction analyses provided strong evidence that ancestral mammals possessed a nocturnal lifestyle, ultra-violet-sensitive vision, low visual acuity and low orbit convergence (i.e. panoramic vision).

CONCLUSIONS

Overall, this study provides insight into the evolutionary history of the mammalian eye while discussing important ecological aspects of the photic paleo-environments ancestral mammals have occupied.

Two sides of a coin: ecological and chronobiological perspectives of timing in the wild

Most processes within organisms, and most interactions between organisms and their environment, have distinct time profiles. The temporal coordination of such processes is crucial across levels of biological organization, but disciplines differ widely in their approaches to study timing. Such differences are accentuated between ecologists, who are centrally concerned with a holistic view of an organism in relation to its external environment, and chronobiologists, who emphasize internal timekeeping within an organism and the mechanisms of its adjustment to the environment. We argue that ecological and chronobiological perspectives are complementary, and that studies at the intersection will enable both fields to jointly overcome obstacles that currently hinder progress. However, to achieve this integration, we first have to cross some conceptual barriers, clarifying prohibitively inaccessible terminologies. We critically assess main assumptions and concepts in either field, as well as their common interests. Both approaches intersect in their need to understand the extent and regulation of temporal plasticity, and in the concept of 'chronotype', i.e. the characteristic temporal properties of individuals which are the targets of natural and sexual selection. We then highlight promising developments, point out open questions, acknowledge difficulties and propose directions for further integration of ecological and chronobiological perspectives through Wild Clock research.This article is part of the themed issue 'Wild Clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.

Exceptional preservation and the fossil record of tetrapod integument

The fossil record of exceptionally preserved soft tissues in Konservat-Lagerstätten provides rare yet significant insight into past behaviours and ecologies. Such deposits are known to occur in bursts rather than evenly through time, but reasons for this pattern and implications for the origins of novel structures remain unclear. Previous assessments of these records focused on marine environments preserving chemically heterogeneous tissues from across animals. Here, we investigate the preservation of skin and keratinous integumentary structures in land-dwelling vertebrates (tetrapods) through time, and in distinct terrestrial and marine depositional environments. We also evaluate previously proposed biotic and abiotic controls on the distribution of 143 tetrapod Konservat-Lagerstätten from the Permian to the Pleistocene in a multivariate framework. Gap analyses taking into account sampling intensity and distribution indicate that feathers probably evolved close to their first appearance in the fossil record. By contrast, hair and archosaur filaments are weakly sampled (five times less common than feathers), and their origins may significantly pre-date earliest known occurrences in the fossil record. This work suggests that among-integument variation in preservation can bias the reconstructed first origins of integumentary novelties and has implications for predicting where, and in what depositional environments, to expect further discoveries of exquisitely preserved tetrapod integument.

Seasonal changes in activity patterns of Japanese flying squirrel Pteromys momonga

Seasonal changes of activity patterns are an important survival strategy for several species. Seasonal changes in the activity patterns of Japanese flying squirrels (Pteromys momonga) were studied at Daibosatsu Mountain on Honshu Island, Japan from 2 June to 20 November 2007 and 11 April to 14 November 2008, to discuss their survival strategy based on the change. Activity patterns were assessed using long-term sensor camera traps at 214 sites for 14 months of a 2-year period. The cameras were placed for a total of 7317 camera trap nights over which total of 90 photographs of this species were collected from 22 of the 214 sites. Although distinct nocturnal activity was detected throughout the study period, activity patterns differed between temperate (June-September) and cold (April, May, October, and November) seasons. So, activity peaks were found to be bimodal during the temperate seasons and trimodal during the cold seasons. It is possible that the squirrels reduce their activity times per bout during the cold seasons to reduce energy loss arising from prolonged exposure to cold temperatures, as a survival strategy.

Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates

Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e.g., amphibians, mammals). Remarkably, nocturnal activity appears to have been maintained continuously in some lineages for ∼350 million years. Thus, we show that traits involved in local-scale resource partitioning can be conserved over strikingly deep evolutionary time scales. We also demonstrate a potentially important (but often overlooked) metric of niche conservatism. Finally, we show that diurnal lineages appear to have faster speciation and diversification rates than nocturnal lineages, which may explain why there are presently more diurnal tetrapod species even though diurnality appears to have evolved more recently. Overall, our results may have implications for studies of community ecology, species richness, and the evolution of diet and communication systems.

Evidence for convergent evolution of a neocortex-like structure in a late Permian therapsid

The special sensory, motor, and cognitive capabilities of mammals mainly depend upon the neocortex, which is the six-layered cover of the mammalian forebrain. The origin of the neocortex is still controversial and the current view is that larger brains with neocortex first evolved in late Triassic Mammaliaformes. Here, we report the earliest evidence of a structure analogous to the mammalian neocortex in a forerunner of mammals, the fossorial anomodont Kawingasaurus fossilis from the late Permian of Tanzania. The endocranial cavity of Kawingasaurus is almost completely ossified, which allowed a less hypothetical virtual reconstruction of the brain endocast to be generated. A parietal foramen is absent. A small pit between the cerebral hemispheres is interpreted as a pineal body. The inflated cerebral hemispheres are demarcated from each other by a median sulcus and by a possible rhinal fissure from the rest of the endocast. The encephalization quotient estimated by using the method of Eisenberg is 0.52, which is 2-3 times larger than in other nonmammalian synapsids. Another remarkable feature are the extremely ramified infraorbital canals in the snout. The shape of the brain endocast, the extremely ramified maxillary canals as well as the small frontally placed eyes suggest that special sensory adaptations to the subterranean habitat such as a well developed sense of touch and binocular vision may have driven the parallel evolution of an equivalent of the mammalian neocortex and a mammal-like lemnothalamic visual system in Kawingasaurus. The gross anatomy of the brain endocast of Kawingasaurus supports the Outgroup Hypothesis, according to which the neocortex evolved from the dorsal pallium of an amphibian-like ancestor, which receives sensory projections from the lemnothalamic pathway. The enlarged brain as well as the absence of a parietal foramen may be an indication for a higher metabolic rate of Kawingasaurus compared to other nonmammalian synapsids.

An experimental comparison of human and bovine rhodopsin provides insight into the molecular basis of retinal disease

Rhodopsin is the visual pigment that mediates dim-light vision in vertebrates and is a model system for the study of retinal disease. The majority of rhodopsin experiments are performed using bovine rhodopsin; however, recent evidence suggests that significant functional differences exist among mammalian rhodopsins. In this study, we identify differences in both thermal decay and light-activated retinal release rates between bovine and human rhodopsin and perform mutagenesis studies to highlight two clusters of substitutions that contribute to these differences. We also demonstrate that the retinitis pigmentosa-associated mutation G51A behaves differently in human rhodopsin compared to bovine rhodopsin and determine that the thermal decay rate of an ancestrally reconstructed mammalian rhodopsin displays an intermediate phenotype compared to the two extant pigments.

Floccular fossa size is not a reliable proxy of ecology and behaviour in vertebrates

The cerebellar floccular and parafloccular lobes are housed in fossae of the periotic region of the skull of different vertebrates. Experimental evidence indicates that the lobes integrate visual and vestibular information and control the vestibulo-ocular reflex, vestibulo-collic reflex, smooth pursuit and gaze holding. Multiple paleoneuroanatomy studies have deduced the behaviour of fossil vertebrates by measuring the floccular fossae (FF). These studies assumed that there are correlations between FF volume and behaviour. However, these assumptions have not been fully tested. Here, we used micro-CT scans of extant mammals (47 species) and birds (59 species) to test six possible morphological-functional associations between FF volume and ecological/behavioural traits of extant animals. Behaviour and ecology do not explain FF volume variability in four out of six variables tested. Two variables with significant results require further empirical testing. Cerebellum plasticity may explain the lack of statistical evidence for the hypotheses tested. Therefore, variation in FF volume seems to be better explained by a combination of factors such as anatomical and phylogenetic evolutionary constraints, and further empirical testing is required.

Selection towards larger body size in both herbivorous and carnivorous synapsids during the Carboniferous

Body size is one of the most important characteristics of an organism, impacting a great variety of ecological characteristics. The influence of diet on body size has received considerable attention, with previous studies suggesting a greater tendency towards increased body size in herbivores than macro-carnivores. The earliest known herbivorous and macro-carnivorous synapsids provide an ideal case study for examining body size evolution in different dietary regimes. Sphenacomorpha contains two lineages: Edaphosauridae (some of the most abundant terrestrial herbivores in the late Carboniferous and early Permian), and Sphenacodontia (the largest and most abundant carnivores of that time). Phylogenetic comparative analyses are used to compare trait evolution in sphenacomorphs, including a Bayesian method for identifying branches along which phenotypic selection occurred. Two branches show rapid increases in body size in the late Carboniferous. The first occurred in Edaphosauridae, along the branch leading to the herbivorous members. The later shift towards larger size occurred in Sphenacodontia, producing a clade of large carnivores. It is possible that the rapid appearance of large herbivorous synapsids in the Carboniferous provided the selective pressure for carnivores to increase their size. Following these two shifts, rates of evolution in edaphosaurids slowed significantly, but the carnivorous sphenacodontians showed further increases.

Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes

Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.

Massive increase in visual range preceded the origin of terrestrial vertebrates

The evolution of terrestrial vertebrates, starting around 385 million years ago, is an iconic moment in evolution that brings to mind images of fish transforming into four-legged animals. Here, we show that this radical change in body shape was preceded by an equally dramatic change in sensory abilities akin to transitioning from seeing over short distances in a dense fog to seeing over long distances on a clear day. Measurements of eye sockets and simulations of their evolution show that eyes nearly tripled in size just before vertebrates began living on land. Computational simulations of these animal's visual ecology show that for viewing objects through water, the increase in eye size provided a negligible increase in performance. However, when viewing objects through air, the increase in eye size provided a large increase in performance. The jump in eye size was, therefore, unlikely to have arisen for seeing through water and instead points to an unexpected hybrid of seeing through air while still primarily inhabiting water. Our results and several anatomical innovations arising at the same time suggest lifestyle similarity to crocodiles. The consequent combination of the increase in eye size and vision through air would have conferred a 1 million-fold increase in the amount of space within which objects could be seen. The "buena vista" hypothesis that our data suggest is that seeing opportunities from afar played a role in the subsequent evolution of fully terrestrial limbs as well as the emergence of elaborated action sequences through planning circuits in the nervous system.

Cranial Bosses of Choerosaurus dejageri (Therapsida, Therocephalia): Earliest Evidence of Cranial Display Structures in Eutheriodonts

Choerosaurus dejageri, a non-mammalian eutheriodont therapsid from the South African late Permian (~259 Ma), has conspicuous hemispheric cranial bosses on the maxilla and the mandible. These bosses, the earliest of this nature in a eutheriodont, potentially make C. dejageri a key species for understanding the evolutionary origins of sexually selective behaviours (intraspecific competition, ritualized sexual and intimidation displays) associated with cranial outgrowths at the root of the clade that eventually led to extant mammals. Comparison with the tapinocephalid dinocephalian Moschops capensis, a therapsid in which head butting is strongly supported, shows that the delicate structure of the cranial bosses and the gracile structure of the skull of Choerosaurus would be more suitable for display and low energy combat than vigorous head butting. Thus, despite the fact that Choerosaurus is represented by only one skull (which makes it impossible to address the question of sexual dimorphism), its cranial bosses are better interpreted as structures involved in intraspecific selection, i.e. low-energy fighting or display. Display structures, such as enlarged canines and cranial bosses, are widespread among basal therapsid clades and are also present in the putative basal therapsid Tetraceratops insignis. This suggests that sexual selection may have played a more important role in the distant origin and evolution of mammals earlier than previously thought. Sexual selection may explain the subsequent independent evolution of cranial outgrowths and pachyostosis in different therapsid lineages (Biarmosuchia, Dinocephalia, Gorgonopsia and Dicynodontia).

The sclerotic ring of squamates: an evo-devo-eco perspective

The sclerotic ring consists of several bones that form in the sclera of many reptiles. This element has not been well studied in squamates, a diverse order of reptiles with a rich fossil record but debated phylogeny. Squamates inhabit many environments, display a range of behaviours, and have evolved several different body plans. Most importantly, many species have secondarily lost their sclerotic rings. This research investigates the presence of sclerotic rings in squamates and traces the lineage of these bones across evolutionary time. We compiled a database on the presence/absence of the sclerotic ring in extinct and extant squamates and investigated the evolutionary history of the sclerotic ring and how its presence/absence and morphology is correlated with environment and behaviour within this clade. Of the 400 extant species examined (59 families, 214 genera), 69% have a sclerotic ring. Those species that do not are within Serpentes, Amphisbaenia, and Dibamidae. We find that three independent losses of the sclerotic ring in squamates are supported when considering both evolutionary and developmental evidence. We also show that squamate species that lack, or have a reduced, sclerotic ring, are fossorial and headfirst burrowers. Our dataset is the largest squamate dataset with measurements of sclerotic rings, and supports previous findings that size of the ring is related to both environment occupied and behaviour. Specifically, scotopic species tend to have both larger inner and outer sclerotic ring apertures, resulting in a narrower ring of bone than those found in photopic species. Non-fossorial species also have a larger sclerotic ring than fossorial species. This research expands our knowledge of these fascinating bones; with further phylogenetic analyses scleral ossicles could become an extremely useful character trait for inferring the behaviour of fossil squamates.

Palaeoneurological clues to the evolution of defining mammalian soft tissue traits

A rich fossil record chronicles the distant origins of mammals, but the evolution of defining soft tissue characters of extant mammals, such as mammary glands and hairs is difficult to interpret because soft tissue does not readily fossilize. As many soft tissue features are derived from dermic structures, their evolution is linked to that of the nervous syutem, and palaeoneurology offers opportunities to find bony correlates of these soft tissue features. Here, a CT scan study of 29 fossil skulls shows that non-mammaliaform Prozostrodontia display a retracted, fully ossified, and non-ramified infraorbital canal for the infraorbital nerve, unlike more basal therapsids. The presence of a true infraorbital canal in Prozostrodontia suggests that a motile rhinarium and maxillary vibrissae were present. Also the complete ossification of the parietal fontanelle (resulting in the loss of the parietal foramen) and the development of the cerebellum in Probainognathia may be pleiotropically linked to the appearance of mammary glands and having body hair coverage since these traits are all controlled by the same homeogene, Msx2, in mice. These suggest that defining soft tissue characters of mammals were already present in their forerunners some 240 to 246 mya.

Systematics of the Rubidgeinae (Therapsida: Gorgonopsia)

The subfamily Rubidgeinae, containing the largest known African gorgonopsians, is thoroughly revised. Rubidgeinae is diagnosed by the absence of a blade-like parasphenoid rostrum and reduction or absence of the preparietal. Seven rubidgeine species from the Karoo Basin of South Africa are recognized as valid: Aelurognathus tigriceps, Clelandina rubidgei, Dinogorgon rubidgei, Leontosaurus vanderhorsti, Rubidgea atrox, Smilesaurus ferox, and Sycosaurus laticeps. Rubidgeines are also present in other African basins: A. tigriceps and S. laticeps occur in the Upper Madumabisa Mudstone Formation of Zambia, and D. rubidgei, R. atrox, and the endemic species Ruhuhucerberus haughtoni comb. nov. and Sycosaurus nowaki comb. nov. occur in the Usili Formation of Tanzania. Aelurognathus nyasaensis from the Chiweta Beds of Malawi also represents a rubidgeine, but of uncertain generic referral pending further preparation. No rubidgeine material is known outside of Africa: the purported Russian rubidgeine Leogorgon klimovensis is not clearly referable to this group and may not be diagnosable. Phylogenetic analysis of rubidgeines reveals strong support for a clade (Rubidgeini) of advanced rubidgeines including Clelandina, Dinogorgon, Leontosaurus, and Rubidgea. Support for Smilesaurus as a rubidgeine is weak; it may, as previous authors have suggested, represent an independent evolution of large body size from an Arctops-like ancestor. Temporally, rubidgeines are restricted to the Late Permian, first appearing in the Tropidostoma Assemblage Zone and reaching highest diversity in the Cistecephalus and Daptocephalus assemblage zones of the Beaufort Group.

Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs

Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1) covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes), and 2) open nests, in which eggs are exposed in the nest and brooded (as in most birds). Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity) of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1) covered nests are likely the primitive condition for dinosaurs (and probably archosaurs), and 2) open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids) were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment. Open nests with fully exposed eggs only became widespread among Euornithes. A potential co-evolution of open nests and brooding behavior among maniraptorans may have freed theropods from the ground-based restrictions inherent to covered nests and allowed the exploitation of alternate nesting locations. These changes in nesting styles and behaviors thus may have played a role in the evolutionary success of maniraptorans (including birds).

The molecular origin and evolution of dim-light vision in mammals

The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels.

Olfaction, navigation, and the origin of isocortex

There are remarkable similarities between the brains of mammals and birds in terms of microcircuit architecture, despite obvious differences in gross morphology and development. While in reptiles and birds the most expanding component (the dorsal ventricular ridge) displays an overall nuclear shape and derives from the lateral and ventral pallium, in mammals a dorsal pallial, six-layered isocortex shows the most remarkable elaboration. Regardless of discussions about possible homologies between mammalian and avian brains, a main question remains in explaining the emergence of the mammalian isocortex, because it represents a unique phenotype across amniotes. In this article, we propose that the origin of the isocortex was driven by behavioral adaptations involving olfactory driven goal-directed and navigating behaviors. These adaptations were linked with increasing sensory development, which provided selective pressure for the expansion of the dorsal pallium. The latter appeared as an interface in olfactory-hippocampal networks, contributing somatosensory information for navigating behavior. Sensory input from other modalities like vision and audition were subsequently recruited into this expanding region, contributing to multimodal associative networks.