Tetrapod Clades Research Articles

Cancer Prevalence across Vertebrates.

Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.

The evolution of larvae in temnospondyls and the stepwise origin of amphibian metamorphosis.

The question of what the ancient life cycle of tetrapods was like forms a key component in understanding the origin of land vertebrates. The existence of distinct larval forms, as exemplified by many lissamphibians, and their transformation into adults is an important aspect in this field. The temnospondyls, the largest clade of Palaeozoic-Mesozoic non-amniote tetrapods, covered a wide ecomorphological range from fully aquatic to terrestrial taxa. In various species, rich ontogenetic data have accumulated over the past 130 years, permitting the study of early phases of temnospondyl development. In temnospondyls, eight ontogenetic phases have been identified in which the skeleton formed. In branchiosaurids and the eryopiform Sclerocephalus, large parts of the ossification sequence are now known. Most taxa in which small specimens are preserved had aquatic larvae with external gills that superficially resemble larval salamanders. In the edopoids, dvinosaurs, and eryopiforms, the larvae developed slowly, with incompletely ossified axial and appendicular skeletons, but possessed a fast-developing dermal skull with strong teeth. Irrespective of adult terrestriality or a fully aquatic life, there was no drastic transformation during later ontogeny, but a slow and steady acquisition of adult features. In dissorophoids, the limbs developed at a much faster pace, whereas skull formation was slowed down, especially in the amphibamiforms, and culminating in the neotenic Branchiosauridae. In the zatracheid Acanthostomatops, slow but profound transformation led to a fully terrestrial adult. The basal dissorophoid Stegops retained rapid development of dermal skull bones and established a fully dentigerous, strongly ossified palate early. In Micromelerpeton, formation of the last skull bones was slightly delayed and metamorphosis remained a long and steady phase of morphological transformations. In amphibamiforms, metamorphosis became more drastic, with an increasing number of events packed into a short phase of ontogeny. This is exemplified by Apateon, Platyrhinops, and Amphibamus in which this condensation was maximised. We distinguish three different types of metamorphosis (morphological, ecological and drastic) that evolved cumulatively in early tetrapods and within temnospondyls.

Recumbirostran ‘microsaurs’ are not amniotes

Amniota is a tetrapod clade that includes extant mammals and reptiles, including birds, as well as a wealth of extinct taxa extending over 318 million years of Earth’s history. For over three decades, Amniota has been treated as a crown group, but the content of stem amniotes has varied among large-scale analyses of Palaeozoic tetrapods. Nine recent phylogenetic studies on Palaeozoic tetrapods, all derived from each other, have potentially changed our perspectives on amniote origins and early evolution. The first of these analyses posited that two particular clades of Palaeozoic tetrapods, Recumbirostra and Lysorophia, both previously considered to be lepospondyl stem-amniotes, are actually amniotes. This raises the possibility that early amniotes included both small fossorial and terrestrial animals, some of which show strong evidence of limb reduction. Here we show that the strange position of these small, often fossorial and limb-reduced tetrapods in Amniota is the result of two fundamental flaws: (1) the phylogenetic analysis combines two separate data matrices that were each designed to test only patterns of relationships among early anamniote tetrapods; and (2) the absence of key amniote characters. Our reanalysis of Palaeozoic tetrapod interrelationships reinstates recumbirostrans and lysorophians outside Amniota. The results of our study impact other recent studies that have simply accepted the codings in the data matrix that resulted in the hypothesis that recumbirostrans are amniotes and raises important questions about the initial diversification of amniotes and the evolution of fossoriality and limb reduction among tetrapods.

Self-organized BMP signaling dynamics underlie the development and evolution of digit segmentation patterns in birds and mammals.

Repeating patterns of synovial joints are a highly conserved feature of articulated digits, with variations in joint number and location resulting in diverse digit morphologies and limb functions across the tetrapod clade. During the development of the amniote limb, joints form iteratively within the growing digit ray, as a population of distal progenitors alternately specifies joint and phalanx cell fates to segment the digit into distinct elements. While numerous molecular pathways have been implicated in this fate choice, it remains unclear how they give rise to a repeating pattern. Here, using single-cell RNA sequencing and spatial gene expression profiling, we investigate the transcriptional dynamics of interphalangeal joint specification in vivo. Combined with mathematical modeling, we predict that interactions within the BMP signaling pathway-between the ligand GDF5, the inhibitor NOGGIN, and the intracellular effector pSMAD-result in a self-organizing Turing system that forms periodic joint patterns. Our model is able to recapitulate the spatiotemporal gene expression dynamics observed in vivo, as well as phenocopy digit malformations caused by BMP pathway perturbations. By contrasting in silico simulations with in vivo morphometrics of two morphologically distinct digits, we show how changes in signaling parameters and growth dynamics can result in variations in the size and number of phalanges. Together, our results reveal a self-organizing mechanism that underpins amniote digit segmentation and its evolvability and, more broadly, illustrate how Turing systems based on a single molecular pathway may generate complex repetitive patterns in a wide variety of organisms.

A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus).

Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.

A Morrison stem gekkotan reveals gecko evolution and Jurassic biogeography.

Geckos are a speciose and globally distributed clade of Squamata (lizards, including snakes and amphisbaenians) that are characterized by a host of modifications for nocturnal, scansorial and insectivorous ecologies. They are among the oldest divergences in the lizard crown, so understanding the origin of geckoes (Gekkota) is essential to understanding the origin of Squamata, the most species-rich extant tetrapod clade. However, the poor fossil record of gekkotans has obscured the sequence and timing of the assembly of their distinctive morphology. Here, we describe the first North American stem gekkotan based on a three-dimensionally preserved skull from the Morrison Formation of western North America. Despite its Late Jurassic age, the new species already possesses several key characteristics of the gekkotan skull along with retained ancestral features. We show that this new stem gekkotan, and several previously named species of uncertain phylogenetic relationships, comprise a widespread clade of early crown lizards, substantiating faunal homogeneity in Laurasia during the Late Jurassic that extended across disparate ecological, body-size and physiological classes.

How to tuna fish: constraint, convergence and integration in the neurocranium of pelagiarian fishes.

Morphological evolution of the vertebrate skull has been explored across a wide range of tetrapod clades using geometric morphometrics, but the application of these methods to teleost fishes, accounting for roughly half of all vertebrate species, has been limited. Here we present the results of a study investigating three-dimensional morphological evolution of the neurocranium across 114 species of Pelagiaria, a diverse clade of open-ocean teleost fishes that includes tuna and mackerel. Despite showing high shape disparity overall, taxa from all families fall into three distinct morphological clusters. Convergence in shape within clusters is high, and phylogenetic signal in shape data is significant but low. Neurocranium shape is significantly correlated with body elongation and significantly but weakly correlated with size. Diet and habitat depth are weakly correlated with shape, and non-significant after accounting for phylogeny. Evolutionary integration in the neurocranium is high, suggesting that convergence in skull shape and the evolution of extreme morphologies are associated with the correlated evolution of neurocranial elements. These results suggest that shape evolution in the pelagiarian neurocranium reflects the extremes in elongation found in body shape but is constrained along relatively few axes of variation, resulting in repeated evolution towards a restricted range of morphologies.

Macroecological and biogeographical patterns of limb reduction in the world's skinks

AbstractAimLimb reduction is a dramatic evolutionary transition, yet whether it is achieved in similar trajectories across clades, and its environmental drivers, remain unclear. We investigate the macroevolutionary and biogeographical patterns of limb reduction in skinks, where limb reduction occurred more often than in any other tetrapod clade, and test their associations with substrate categories using a global database. We test for habitat associations of body shapes in a group of Australian skinks using quantitative habitat data.LocationGlobal (Scincidae), Australia (Sphenomorphinae).TaxonSkinks, Australian Sphenomorphinae.Materials and MethodsWe use morphological data to explore the patterns of limb reduction in the world's skinks, investigating how body proportions differ across skink clades and subfamilies. We examine the relationships between body shape and substrate (coarsely classified). Further, we investigate the relationships between body shape and high‐resolution soil and climate properties extracted from each species' distribution for Australian sphenomorphines.ResultsRelationships between limb lengths and trunk elongation show idiosyncratic patterns across skink clades. Presacral vertebrae numbers positively correlate with trunk elongation in all taxa, except Glaphyromorphus. Skinks from sandy habitats show greater disparity between forelimb and hindlimb lengths than all other substrate categories. In sphenomorphines, shorter limbs and elongated trunks correlate with colder, more humid microhabitats and richer soils; high limb disparity correlates with hot, arid microhabitats and sandy, poor substrates.Main ConclusionsThe evolutionary trajectories of limb reduction in skinks are clade‐specific and sometimes unique. Selection for specific limb proportions and body sizes in limb‐reduced forms changes across substrates. On poor, sandy substrates of arid environments, body shapes with longer hindlimbs may be more efficient for locomotion in a granular fluid (i.e. sand) and exploit the air–substrate interface than complete limblessness. On richer, more humid substrates, such morphology is rare, indicating that navigating cluttered substrates selects for more equal and shorter limb lengths.

Fossil bone histology reveals ancient origins for rapid juvenile growth in tetrapods

Patterns of growth throughout the lifetime of an animal reflect critical life history traits such as reproductive timing, physiology, and ecological interactions. The ancestral growth pattern for tetrapods has traditionally been described as slow-to-moderately paced, akin to modern amphibians, with fast growth and high metabolic rates considered a specialized physiological trait of amniotes. Here, we present bone histology from an ontogenetic series of the Early Carboniferous stem tetrapod Whatcheeria deltae, and document evidence of fibrolamellar bone—primary bone tissue associated with fast growth. Our data indicate that Whatcheeria juveniles grew rapidly and reached skeletal maturity quickly, allowing them to occupy a large-bodied predator niche in their paleoenvironment. This life history strategy contrasts with those described for other stem tetrapods and indicates that a diversity of growth patterns existed at the origins of tetrapod diversification. Importantly, Whatcheeria marks an unexpectedly early occurrence of fibrolamellar bone in Tetrapoda, both temporally and phylogenetically. These findings reveal that elevated juvenile growth is not limited to amniotes, but has a deep history in the tetrapod clade and may have played a previously unrecognized role in the tetrapod invasion of land.

On the estimation of body mass in temnospondyls: a case study using the large‐bodied Eryops and Paracyclotosaurus

AbstractTemnospondyli are a morphologically varied and ecologically diverse clade of tetrapods that survived for over 200 million years. The body mass of temnospondyls is a key variable in inferring their ecological, physiological and biomechanical attributes. However, estimating the body mass of these extinct creatures has proven difficult because the group has no extant descendants. Here we apply a wide range of body mass estimation techniques developed for tetrapods to the iconic temnospondyls Paracyclotosaurus davidi and Eryops megacephalus. These same methods are also applied to a collection of extant organisms that serve as ecological and morphological analogues. These include the giant salamanders Andrias japonicus and Andrias davidianus, the tiger salamander Ambystoma tigrinum, the California newt Taricha torosa and the saltwater crocodile, Crocodylus porosus. We find that several methods can provide accurate mass estimations across this range of living taxa, suggesting their suitability for estimating the body masses of temnospondyls. Based on this, we estimate the mass of Paracyclotosaurus to have been between 159 and 365 kg, and that of Eryops between 102 and 222 kg. These findings provide a basis for examining body size evolution in this clade across their entire temporal span.

Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes.

Functional diversification, a higher evolutionary rate, and intense positive selection help a limited number of immune genes interact with many pathogens. Repeats in protein-coding regions are a well-known source of functional diversification, adaptive variation, and evolutionary novelty in a short time. Repeats play a crucial role in biochemical functions like functional diversification of transcription regulation, protein kinases, cell adhesion, signaling pathways, morphogenesis, DNA repair, recombination, and RNA processing. Repeat length variation can change the associated protein's interaction, efficacy, and overall protein network. Repeats have an intrinsic unstable nature and can potentially evolve rapidly and expedite the acquisition of complex phenotypic traits and functions. Because of their ability to generate rapid, adaptive variations over short evolutionary distances, repeats are considered "tuning knobs." Repeat length variation in specific genes, like RUNX2 and ALX4, is associated with morphological and physiological changes across vertebrates. Here we study repeat length variation as a potent source of species-specific immune diversification across several clades of tetrapods. Moreover, we provide a clade-wise comprehensive list of immune genes with repeat types for future studies of morphological/evolutionary changes within species groups. We observe significant repeat length variation of FASLG and C1QC in Rodentia and Primates' contrasting species groups, respectively.

Trends of avian locomotion in water – an overview of swimming styles

Abstract Adaptation to an aquatic lifestyle occurred in the evolution of several primarily terrestrial clades of tetrapods. Among these lineages, aquatic birds’ adaptations differ in many ways from other secondarily aquatic vertebrates. As a consequence of the evolution of flight, birds with swimming and diving abilities represent unique locomotion skills and complex anatomical solutions. Here we attempt to overview some of the main aspects of avian locomotion in water and highlight the diversity of their aquatic habits and locomotion types, with the best-known extinct and extant examples. The main features that can distinguish the different groups among these swimmers and divers are their different techniques to overcome buoyancy, the transformation of wings or hind limbs into aquatic propulsive organs, and their swimming techniques besides the presence or absence of the flying and/or terrestrial abilities. Understanding how the musculoskeletal system of aquatic birds evolved to face the requirements of moving in various environments with different physical characteristics provides a good opportunity to get a better view of convergent and divergent evolution.

Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli).

The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for which there appear to be unstated working assumptions to scoring that are incompatible with the character definitions (e.g., scoring of taxa with incomplete skulls for characters based on skull length). Correction of these scores and other pervasive errors recovered a distinctly less resolved topology than previous studies, more in agreement with my own matrix. This suggests that previous analyses may have been compromised, and that the only real consensus of dissorophid phylogeny is the lack of one.

A New Late Permian Burnetiamorph From Zambia Confirms Exceptional Levels of Endemism in Burnetiamorpha (Therapsida: Biarmosuchia) and an Updated Paleoenvironmental Interpretation of the Upper Madumabisa Mudstone Formation

A new burnetiamorph therapsid, Isengops luangwensis, gen. et sp. nov., is described on the basis of a partial skull from the upper Madumabisa Mudstone Formation of the Luangwa Basin of northeastern Zambia. Isengops is diagnosed by reduced palatal dentition, a ridge-like palatine-pterygoid boss, a palatal exposure of the jugal that extends far anteriorly, a tall trigonal pyramid-shaped supraorbital boss, and a recess along the dorsal margin of the lateral temporal fenestra. The upper Madumabisa Mudstone Formation was deposited in a rift basin with lithofacies characterized by unchannelized flow, periods of subaerial desiccation and non-deposition, and pedogenesis, and can be biostratigraphically tied to the upper Cistecephalus Assemblage Zone of South Africa, suggesting a Wuchiapingian age. Isengops is the second burnetiamorph recognized from Zambia and is part of a tetrapod assemblage remarkably similar to others across southern Pangea during the Wuchiapingian. A revised cladistic analysis of Biarmosuchia yielded over 500 most parsimonious trees that generally reaffirm the results of previous analyses for burnetiamorphs: Lemurosaurus is basal, Lobalopex and Isengops are proximate burnetiid outgroups, and Bullacephalus, Burnetia, Mobaceras, Niuksenitia, and Pachydectes are burnetiines. Furthermore, Russian biarmosuchians are scattered throughout the tree and do not form sister taxon relationships with each other. Burnetiamorphs display a wide disparity of cranial adornments and are relatively speciose (13 species), especially when compared to the number of specimens discovered to date (∼16 specimens). As has been suggested in some other tetrapod clades (e.g., ceratopsian dinosaurs), the burnetiamorph fossil record supports an inferred macroevolutionary relationship between cranial adornment and increased speciation rate.

Identification of two interleukin 17 receptor C (IL-17RC) genes and their binding activities to three IL-17A/F ligands in the Japanese medaka, Oryzias latipes

In mammals, interleukin (IL)-17 receptor C (IL-17RC) and IL-17RA mediate IL-17A and IL-17F signaling to produce mucin, antimicrobial peptides, and maintain healthy intestinal flora. However, IL-17RC signaling in fish remains unclear. In this study, three il17rc transcripts (il17rca1, il17rca2, and il17rcb) from the Japanese medaka (Oryzias latipes) were cloned; il17rca1 and il17rca2 mRNAs were alternatively spliced from il17rca pre-mRNA as transcript variants. The il17rca and il17rcb genes were located on chromosomes 7 and 5, respectively. Teleost clades containing medaka il17rca and il17rcb clustered separately from the tetrapod clade. In adult tissues, il17rca1 expression was significantly higher than il17rca2 and il17rcb. Conversely, il17rcb expression was significantly higher in embryos and larvae. These expression patterns changed following infection with Edwardsiella piscicida and Aeromonas hydrophila. Furthermore, an immunoprecipitation assay using recombinant IL-17RCs and rIL-17A/Fs suggested that, in teleosts, three ligands could function in signaling through two IL-17RCs.

The Role of the Tail or Lack Thereof in the Evolution of Tetrapod Aquatic Propulsion.

Secondary aquatic vertebrates exhibit a diversity of swimming modes that use paired limbs and/or the tail. Various secondarily aquatic tetrapod clades, including amphibians, reptiles, and mammals use transverse undulations or oscillations of the tail for swimming. These movements have often been classified according to a kinematic gradient that was established for fishes but may not be appropriate to describe the swimming motions of tetrapods. To understand the evolution of movements and design of the tail in aquatic tetrapods, we categorize the types of tails used for swimming and examine swimming kinematics and hydrodynamics. From a foundation of a narrow, elongate ancestral tail, the tails used for swimming by aquatic tetrapods are classified as tapered, keeled, paddle, and lunate. Tail undulations are associated with tapered, keeled, and paddle tails for a diversity of taxa. Propulsive undulatory waves move down the tail with increasing amplitude toward the tail tip, while moving posteriorly at a velocity faster than the anterior motion of the body indicating that the tail is used for thrust generation. Aquatic propulsion is associated with the transfer of momentum to the water from the swimming movements of the tail, particularly at the trailing edge. The addition of transverse extensions and flattening of the tail increases the mass of water accelerated posteriorly and affects vorticity shed into the wake for more aquatically adapted animals. Digital Particle Image Velocimetry reveals that the differences were exhibited in the vortex wake between the morphological and kinematic extremes of the alligator with a tapering undulating tail and the dolphin with oscillating wing-like flukes that generate thrust. In addition to exploring the relationship between the shape of undulating tails and the swimming performance across aquatic tetrapods, the role of tail reduction or loss of a tail in aquatic-tetrapod swimming was also explored. For aquatic tetrapods, the reduction would have been due to factors including locomotor and defensive specializations and phylogenetic and physiological constraints. Possession of a thrust-generating tail for swimming, or lack thereof, guided various lineages of secondarily aquatic vertebrates into different evolutionary trajectories for effective aquatic propulsion (i.e., speed, efficiency, and acceleration).

Ecophysiological steps of marine adaptation in extant and extinct non-avian tetrapods.

Marine reptiles and mammals are phylogenetically so distant from each other that their marine adaptations are rarely compared directly. We reviewed ecophysiological features in extant non-avian marine tetrapods representing 31 marine colonizations to test whether there is a common pattern across higher taxonomic groups, such as mammals and reptiles. Marine adaptations in tetrapods can be roughly divided into aquatic and haline adaptations, each of which seems to follow a sequence of three steps. In combination, these six categories exhibit five steps of marine adaptation that apply across all clades except snakes: Step M1, incipient use of marine resources; Step M2, direct feeding in the saline sea; Step M3, water balance maintenance without terrestrial fresh water; Step M4, minimized terrestrial travel and loss of terrestrial feeding; and Step M5, loss of terrestrial thermoregulation and fur/plumage. Acquisition of viviparity is not included because there is no known case where viviparity evolved after a tetrapod lineage colonized the sea. A similar sequence is found in snakes but with the haline adaptation step (Step M3) lagging behind aquatic adaptation (haline adaptation is Step S5 in snakes), most likely because their unique method of water balance maintenance requires a supply of fresh water. The same constraint may limit the maximum body size of fully marine snakes. Steps M4 and M5 in all taxa except snakes are associated with skeletal adaptations that are mechanistically linked to relevant ecophysiological features, allowing assessment of marine adaptation steps in some fossil marine tetrapods. We identified four fossil clades containing members that reached Step M5 outside of stem whales, pinnipeds, sea cows and sea turtles, namely Eosauropterygia, Ichthyosauromorpha, Mosasauroidea, and Thalattosuchia, while five other clades reached Step M4: Saurosphargidae, Placodontia, Dinocephalosaurus, Desmostylia, and Odontochelys. Clades reaching Steps M4 and M5, both extant and extinct, appear to have higher species diversity than those only reaching Steps M1 to M3, while the total number of clades is higher for the earlier steps. This suggests that marine colonizers only diversified greatly after they minimized their use of terrestrial resources, with many lineages not reaching these advanced steps. Historical patterns suggest that a clade does not advance to Steps M4 and M5 unless these steps are reached early in the evolution of the clade. Intermediate forms before a clade reached Steps M4 and M5 tend to become extinct without leaving extant descendants or fossil evidence. This makes it difficult to reconstruct the evolutionary history of marine adaptation in many clades. Clades that reached Steps M4 and M5 tend to last longer than other marine tetrapod clades, sometimes for more than 100 million years.

Dispersal vs. vicariance: the origin of India’s extant tetrapod fauna

Given the Indian block’s ancient association with Gondwana and subsequent separation from Africa, then Madagascar, then the Seychelles, vicariance has often been invoked to explain the distribution of some of India’s extant biota that might have had Gondwanan origins. Here I review phylogenetic studies and fossil data of Indian tetrapods to ascertain the contribution of dispersal and vicariance in shaping the assemblage. Paleogene dispersal into India accounts for almost all of the tetrapod clades in India. Vicariance is invoked for three groups, all fossorial; the caecilians, the frog family Nasikabatrachidae and the blindsnake family Gerrhopilidae. This review concludes that practically all of India’s Late Cretaceous tetrapod fauna (of Gondwanan origin) was extirpated during the Cretaceous-Paleogene mass extinction, which may have been exacerbated by the coeval volcanism associated with the emplacement of the Deccan Trap large igneous province. Subsequently, the tetrapod fauna was built up by incoming elements as India advanced towards Asia, docking with the continent in the Paleogene.

Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

AbstractMammals are the only surviving group of Cynodontia, a synapsid clade that first appeared in the fossil record in the late Permian, ~260 million years ago. Using three metrics that capture skeletal completeness, we quantify the quality of the early cynodont fossil record in time and space to evaluate the impact of sampling and preservational biases on our understanding of the group's evolutionary history. There is no consistent global sampling signal for early cynodonts. Completeness of the cynodont fossil record increases across the Permian–Triassic boundary, peaking in the Early to early Late Triassic. This peak is dominated by specimens from southern Africa and South America, where a highly seasonal climate probably favoured preservation. Completeness is generally lower thereafter, correlating with a shift from a Gondwanan to a predominantly Laurasian fossil record. Phylogenetic and stratigraphic congruence in early cynodonts is high, although their fossil record exhibits less skeletal completeness overall than other tetrapod clades, including the contemporaneous anomodont synapsids. This discrepancy could be due to differences in the diagnosability of their fossils, especially for small‐bodied species. Establishing the timing and assembly of derived (‘mammalian’) anatomical features in Cynodontia is obscured by sampling. Two of the major nodes at which acquisition of mammalian features is concentrated (Cynodontia and Mammaliamorpha) suffer from lengthy intervals of poor sampling before becoming abundant parts of tetrapod faunas. Low completeness in these intervals limits our ability to determine when certain ‘key’ mammalian characteristics evolved, or to identify the selective pressures that might have driven their origins.

Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition.

Simple SummaryMudskippers are amphibious fish that spend most of their lives on mudflats. The morphological and physiological adaptations of mudskippers resemble water-to-land transition of ancient tetrapod, yet comparative studies on the genetic backgrounds underlying the adaptation are still limited. The aim of this study is to compare genome-wide signatures of positive selection and gene family evolution between mudskipper and tetrapods. Here, we performed comparative genomics analysis between terrestrial tetrapods, coelacanth, mudskipper, and aquatic fish species. As a result, we discovered genes with selective signature in tetrapod and mudskipper lineages associated with immune responses, mitochondrial oxidative phosphorylation, kidney development, and DNA repair processes. In both tetrapod and mudskipper linages, we found convergent contraction of the gene family encoding βγ-crystallins that are found in the lens of vertebrate eye and involved in the refraction of the light. Our results present similar genetic adaptations in mudskipper and tetrapod lineages, which independently adapted to land environment.Water-to-land transition has been independently evolved in multiple vertebrate lineages including the most recent common ancestor of tetrapod and multiple fish clades, and among them, mudskippers uniquely adapted to the mudflat. Even though physiological and morphological adaptation of mudskippers is thought to resemble that of the ancestral tetrapod, it is unclear if they share genome-wide evolutionary signatures. To detect potential signatures of positive selection in mudskipper and tetrapods, we analyzed 4118 singleton orthologues of terrestrial tetrapods, coelacanth, mudskipper, and fully aquatic fishes. Among positively selected genes identified in mudskipper and tetrapod lineages, genes involved in immune responses, mitochondrial oxidative phosphorylation, and kidney development were detected. On the other hand, tetrapod-specific and mudskipper-specific positively selected genes were functionally enriched for DNA repair processes, which could be associated with higher exposure to UV light. We also performed gene family analysis and discovered convergent contraction of eight gene families, including βγ-crystallin coding genes in both tetrapod and mudskipper lineages. Findings of this study suggest the similar genetic adaptation against environmental constraints between the ancient tetrapod and mudskippers for their land adaptation.