Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles

Evolutionary bursts drive morphological novelty in the world's largest skinks

Animal phenotypes evolve and diverge as a result of differing selective pressures and drift. These processes leave unique signatures in patterns of trait evolution, impacting the tempo and mode of morphological macroevolution. While there is a broad understanding of the history of some organismal traits (e.g., body size), there is little consensus about the evolutionary mode of most others. This includes the relative contribution of prolonged (Darwinian gradualist) and episodic (Simpsonian jump) changes toward the evolution of novel morphologies. Here, we use new exon-capture and linear morphological datasets to investigate the tempo and mode of morphological evolution in Australo-Melanesian Tiliquini skinks. We generate a well-supported time-calibrated phylogenomic tree from ∼400 nuclear markers for more than 100 specimens, including undescribed diversity, and provide unprecedented resolution of the rapid Miocene diversification of these lizards. By collecting a morphological dataset that encompasses the lizard body plan (19 traits across the head, body, limb, and tail), we are able to identify that most traits evolve conservatively, but infrequent evolutionary bursts result in morphological novelty. These phenotypic discontinuities occur via rapid rate increases along individual branches, inconsistent with both gradualistic and punctuated equilibrial evolutionary modes. Instead, this "punctuated gradualism" has resulted in the rapid evolution of blue-tongued giants and armored dwarves in the ∼20 million years since colonizing Australia. These results outline the evolutionary pathway toward new morphologies and highlight the heterogeneity of evolutionary tempo and mode, even within individual traits.

Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.

Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.

The postcranial skeleton of Teyujagua paradoxa (Reptilia: Archosauromorpha) from the early Triassic of South America

Teyujagua paradoxa is a remarkable early archosauromorph from the Lower Triassic Sanga do Cabral Formation, Brazil. The species was originally described from an almost complete skull and a few associated cervical vertebrae, and no further postcranial elements were known at that time. Additional fieldwork in the Sanga do Cabral Formation, however, was successful in recovering a fairly complete postcranial skeleton attributable to the holotype. Here, we describe this new postcranial material, which is composed of cervical, dorsal, sacral and caudal vertebrae, limbs, pectoral and pelvic girdles, ribs, and gastralia. The description of its postcranial skeleton makes T. paradoxa one of the best-known early-diverging archosauromorphs. The cladistic analysis performed after the scoring of postcranial data recovered T. paradoxa in the same position initially described, close to the node that defines the Archosauriformes. Teyujagua paradoxa shares morphological features with representatives of early-diverging archosauromorphs and archosauriforms, with certain traits demonstrating a mosaic of plesiomorphic and apomorphic character states. We also performed partitioned morphospace and disparity analysis to elucidate the morphological disparity and evolutionary patterns among archosauromorphs. Teyujagua paradoxa occupies a notable position, suggesting an intermediate morphology between early archosauromorphs and proterosuchids. Disparity estimates highlighted Pseudosuchia and Avemetatarsalia as having the highest median disparity, reflecting their diverse cranial and postcranial morphologies, respectively. These findings offer valuable insights into archosauromorph macroevolution and adaptation.

A new sphenodontian (Diapsida: Lepidosauria) from the Upper Triassic (Norian) of Germany and its implications for the mode of sphenodontian evolution

The Arnstadt Formation of Saxony-Anhalt, Germany has yielded some of Germany's most substantial finds of Late Triassic tetrapods, including the sauropodomorph Plateosaurus and the stem-turtle Proganochelys quenstedti. Here, we describe an almost complete skull of a new sphenodontian taxon from this formation (Norian, 227-208 Ma), making it the oldest known articulated sphenodontian skull from Europe and one of the oldest in the world. The material is represented by the dermal skull roof and by the complete maxilla and temporal region, as well as parts of the palate, braincase, and lower jaw. A phylogenetic assessment recovers it as a basal sphenodontian closely related to Planocephalosaurus robinsonae and to Eusphenodontia, making it the earliest-diverging sphenodontian known with an articulated skull. Its cranial anatomy is generally similar to the well-known Diphydontosaurus avonis from the Rhaetian of England, showing that this successful phenotype was already established in the clade around 10 myr earlier than assumed. An analysis of evolutionary change rates recovers high rates of evolution in basal sphenodontians, with decreasing rates throughout the evolution of the group. However, contrary to previous studies, reversals in this trend were identified, indicating additional peaks of evolutionary change. These results improve our understanding of the early sphenodontian diversity in Europe, providing critical information on evolutionary trends throughout the history of the clade and sparking renewed interest in its evolution.

Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration

The arrangement and morphology of the vertebrate skull reflect functional and ecological demands, making it a highly adaptable structure. However, the fundamental developmental and macroevolutionary mechanisms leading to different vertebrate skull phenotypes remain unclear. Here we exploit the morphological diversity of squamate reptiles to assess the developmental and evolutionary patterns of skull variation and covariation in the whole head. Our geometric morphometric analysis of a complex squamate ontogenetic dataset (209 specimens, 169 embryos, 44 species), covering stages from craniofacial primordia to fully ossified bones, reveals that morphological differences between snake and lizard skulls arose gradually through changes in spatial relationships (heterotopy) followed by alterations in developmental timing or rate (heterochrony). Along with dynamic spatiotemporal changes in the integration pattern of skull bone shape and topology with surrounding brain tissues and sensory organs, we identify a relatively higher phenotypic integration of the developing snake head compared with lizards. The eye, nasal cavity and Jacobson's organ are pivotal in skull morphogenesis, highlighting the importance of sensory rearrangements in snake evolution. Furthermore, our findings demonstrate the importance of early embryonic, ontogenetic and tissue interactions in shaping craniofacial evolution and ecological diversification in squamates, with implications for the nature of cranio-cerebral relations across vertebrates.

The macroevolutionary singularity of snakes

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

A century of exercise physiology: concepts that ignited the study of human thermoregulation. Part 4: evolution, thermal adaptation and unsupported theories of thermoregulation

This review is the final contribution to a four-part, historical series on human exercise physiology in thermally stressful conditions. The series opened with reminders of the principles governing heat exchange and an overview of our contemporary understanding of thermoregulation (Part 1). We then reviewed the development of physiological measurements (Part 2) used to reveal the autonomic processes at work during heat and cold stresses. Next, we re-examined thermal-stress tolerance and intolerance, and critiqued the indices of thermal stress and strain (Part 3). Herein, we describe the evolutionary steps that endowed humans with a unique potential to tolerate endurance activity in the heat, and we examine how those attributes can be enhanced during thermal adaptation. The first of our ancestors to qualify as an athlete was Homo erectus, who were hairless, sweating specialists with eccrine sweat glands covering almost their entire body surface. Homo sapiens were skilful behavioural thermoregulators, which preserved their resource-wasteful, autonomic thermoeffectors (shivering and sweating) for more stressful encounters. Following emigration, they regularly experienced heat and cold stress, to which they acclimatised and developed less powerful (habituated) effector responses when those stresses were re-encountered. We critique hypotheses that linked thermoregulatory differences to ancestry. By exploring short-term heat and cold acclimation, we reveal sweat hypersecretion and powerful shivering to be protective, transitional stages en route to more complete thermal adaptation (habituation). To conclude this historical series, we examine some of the concepts and hypotheses of thermoregulation during exercise that did not withstand the tests of time.

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

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

A century of exercise physiology: concepts that ignited the study of human thermoregulation. Part 1: Foundational principles and theories of regulation

This contribution is the first of a four-part, historical series encompassing foundational principles, mechanistic hypotheses and supported facts concerning human thermoregulation during athletic and occupational pursuits, as understood 100 years ago and now. Herein, the emphasis is upon the physical and physiological principles underlying thermoregulation, the goal of which is thermal homeostasis (homeothermy). As one of many homeostatic processes affected by exercise, thermoregulation shares, and competes for, physiological resources. The impact of that sharing is revealed through the physiological measurements that we take (Part 2), in the physiological responses to the thermal stresses to which we are exposed (Part 3) and in the adaptations that increase our tolerance to those stresses (Part 4). Exercising muscles impose our most-powerful heat stress, and the physiological avenues for redistributing heat, and for balancing heat exchange with the environment, must adhere to the laws of physics. The first principles of internal and external heat exchange were established before 1900, yet their full significance is not always recognised. Those physiological processes are governed by a thermoregulatory centre, which employs feedback and feedforward control, and which functions as far more than a thermostat with a set-point, as once was thought. The hypothalamus, today established firmly as the neural seat of thermoregulation, does not regulate deep-body temperature alone, but an integrated temperature to which thermoreceptors from all over the body contribute, including the skin and probably the muscles. No work factor needs to be invoked to explain how body temperature is stabilised during exercise.

The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order

Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.

Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].

Syngnathoid Evolutionary History and the Conundrum of Fossil Misplacement

Seahorses, pipefishes, trumpetfishes, shrimpfishes, and allies are a speciose, globally distributed clade of fishes that have evolved a large number of unusual body plans. The clade that includes all these forms, Syngnathoidei, has become a model for the study of life history evolution, population biology, and biogeography. Yet, the timeline of syngnathoid evolution has remained highly contentious. This debate is largely attributable to the nature of the syngnathoid fossil record, which is both poorly described and patchy for several major lineages. Although fossil syngnathoids have been used to calibrate molecular phylogenies, the interrelationships of extinct species and their affinities to major living syngnathoid clades have scarcely been quantitatively tested. Here, I use an expanded morphological dataset to reconstruct the evolutionary relationships and clade ages of fossil and extant syngnathoids. Phylogenies generated using different analytical methodologies are largely congruent with molecular phylogenetic trees of Syngnathoidei but consistently find novel placements for several key taxa used as fossil calibrators in phylogenomic studies. Tip-dating of the syngnathoid phylogeny finds a timeline for their evolution that differs slightly from the one inferred using molecular trees but is generally congruent with a post-Cretaceous diversification event. These results emphasize the importance of quantitatively testing the relationships of fossil species, particularly when they are critical to assessing divergence times.

The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases

Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.

Complex macroevolution of pterosaurs

Pterosaurs, the earliest flying tetrapods, are the subject of some recent quantitative macroevolutionary analyses from different perspectives.^1-2 Here, we use an integrative approach involving newly assembled phylogenetic and body size datasets, net diversification rates, morphological rates, and morphological disparity to gain a holistic understanding of the pterosaur macroevolution. The first two parameters are important in quantitative analyses of macroevolution, but they have been rarely used in previous pterosaur studies.^{1,3,4,2,5,6,7,8,9,10,11,12} Our study reveals an ∼115-Ma period-from Early Triassic to Early Cretaceous-of multi-wave increasing net diversification rates and disparity, as well as high morphological rates, followed by an ∼65-Ma period-from Early Cretaceous to the end of the Cretaceous-of mostly negative net diversification rates, decreasing disparity, and relatively low morphological rates in pterosaur evolution. Our study demonstrates the following: (1) body size plays an important role in pterosaur lineage diversification during nearly their whole evolutionary history, and the evolution of locomotion, trophic, and ornamental structures also plays a role in different periods; (2) birds, the other major flying tetrapod group at the time, might have affected pterosaur macroevolution for ∼100 Ma; and (3) different mass extinction events might have affected pterosaur evolution differently. Particularly, the revealed decline in pterosaur biodiversity during the Middle and Late Cretaceous periods provides further support for the possible presence of a biodiversity decline of large-sized terrestrial amniotes starting in the mid-Cretaceous,^13,14 which may have been caused by multiple factors including a global land area decrease during these periods.

Immunity in Sea Turtles: Review of a Host-Pathogen Arms Race Millions of Years in the Running

The immune system of sea turtles is not completely understood. Sea turtles (as reptiles) bridge a unique evolutionary gap, being ectothermic vertebrates like fish and amphibians and amniotes like birds and mammals. Turtles are ectotherms; thus, their immune system is influenced by environmental conditions like temperature and season. We aim to review the turtle immune system and note what studies have investigated sea turtles and the effect of the environment on the immune response. Turtles rely heavily on the nonspecific innate response rather than the specific adaptive response. Turtles' innate immune effectors include antimicrobial peptides, complement, and nonspecific leukocytes. The antiviral defense is understudied in terms of the diversity of pathogen receptors and interferon function. Turtles also mount adaptive responses to pathogens. Lymphoid structures responsible for lymphocyte activation and maturation are either missing in reptiles or function is affected by season. Turtles are a marker of health for their marine environment, and their immune system is commonly dysregulated because of disease or contaminants. Fibropapillomatosis (FP) is a tumorous disease that afflicts sea turtles and is thought to be caused by a virus and an environmental factor. We aim, by exploring the current understanding of the immune system in turtles, to aid the investigation of environmental factors that contribute to the pathogenesis of this disease and provide options for immunotherapy.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

A Late Devonian actinopterygian suggests high lineage survivorship across the end-Devonian mass extinction

Many accounts of the early history of actinopterygians (ray-finned fishes) posit that the end-Devonian mass extinction had a major influence on their evolution. Existing phylogenies suggest this episode could have acted as a bottleneck, paring the early diversity of the group to a handful of survivors. This picture, coupled with increases in taxonomic and morphological diversity in the Carboniferous, contributes to a model of explosive post-extinction radiation. However, most actinopterygians from within a roughly 20-million year (Myr) window surrounding the extinction are poorly known, contributing to uncertainty about the meaning of these patterns. Here, we report an exceptionally preserved fossil from 7 Myr before the extinction that reveals unexpected anatomical features. Palaeoneiros clackorum gen. et sp. nov. nests within a clade of post-Devonian species and, in an expanded phylogenetic analysis, draws multiple lineages of Carboniferous actinopterygians into the Devonian. This suggests cryptic but extensive lineage diversification in the latest Devonian, followed by more conspicuous feeding and locomotor structure diversification in the Carboniferous. Our revised model matches more complex patterns of divergence, survival and diversification around the Devonian/Carboniferous boundary in other vertebrate clades. It also fundamentally recalibrates the onset of diversification early in the history of this major radiation.

Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous

It has long been debated why groups such as non-avian dinosaurs became extinct whereas mammals and other lineages survived the Cretaceous/Paleogene mass extinction 66 million years ago. We used Markov networks, ecological niche partitioning, and Earth System models to reconstruct North American food webs and simulate ecospace occupancy before and after the extinction event. We find a shift in latest Cretaceous dinosaur faunas, as medium-sized species counterbalanced a loss of megaherbivores, but dinosaur niches were otherwise stable and static, potentially contributing to their demise. Smaller vertebrates, including mammals, followed a consistent trajectory of increasing trophic impact and relaxation of niche limits beginning in the latest Cretaceous and continuing after the mass extinction. Mammals did not simply proliferate after the extinction event; rather, their earlier ecological diversification might have helped them survive.

Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents

Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.

Evolutionary origins of the prolonged extant squamate radiation

Squamata is the most diverse clade of terrestrial vertebrates. Although the origin of pan-squamates lies in the Triassic, the oldest undisputed members of extant clades known from nearly complete, uncrushed material come from the Cretaceous. Here, we describe three-dimensionally preserved partial skulls of two new crown lizards from the Late Jurassic of North America. Both species are placed at the base of the skink, girdled, and night lizard clade Pan-Scincoidea, which consistently occupies a position deep inside the squamate crown in both morphological and molecular phylogenies. The new lizards show that several features uniting pan-scincoids with another major lizard clade, the pan-lacertoids, in trees using morphology were convergently acquired as predicted by molecular analyses. Further, the palate of one new lizard bears a handful of ancestral saurian characteristics lost in nearly all extant squamates, revealing an underappreciated degree of complex morphological evolution in the early squamate crown. We find strong evidence for close relationships between the two new species and Cretaceous taxa from Eurasia. Together, these results suggest that early crown squamates had a wide geographic distribution and experienced complicated morphological evolution even while the Rhynchocephalia, now solely represented by the tuatara, was the dominant clade of lepidosaurs.

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

Climate change-induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.

Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.

Evolvability and Macroevolution: Overview and Synthesis

Evolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.

Zebrafish heart regeneration after coronary dysfunction-induced cardiac damage

Over the past 20 years, various zebrafish injury models demonstrated efficient heart regeneration after cardiac tissue loss. However, no established coronary vessel injury methods exist in the zebrafish model, despite coronary endothelial dysfunction occurring in most patients with acute coronary syndrome. This is due to difficulties performing surgery on small coronary vessels and a lack of genetic tools to precisely manipulate coronary cells in zebrafish. We determined that the Notch ligand gene deltaC regulatory sequences drive gene expression in zebrafish coronary endothelial cells, enabling us to overcome these obstacles. We created a deltaC fluorescent reporter line and visualized robust coronary growth during heart development and regeneration. Importantly, this reporter facilitated the visualization of coronary growth without an endocardial background. Moreover, we visualized robust coronary growth on the surface of juvenile hearts and regrowth in the wounded area of adult hearts ex vivo. With this approach, we observed growth inhibition by reported vascular growth antagonists of the VEGF, EGF and Notch signaling pathways. Furthermore, we established a coronary genetic ablation system and observed that severe coronary endothelial cell loss resulted in fish death, whereas fish survived mild coronary cell loss. Coronary cell depletion triggered regenerative responses, which resulted in the restoration of damaged cardiac tissues within several weeks. Overall, our work demonstrated the efficacy of using deltaC regulatory elements for high-resolution visualization of the coronary endothelium; screening small molecules for coronary growth effects; and revealed complete recovery in adult zebrafish after coronary-induced heart damage.

Fast Likelihood Calculations for Automatic Identification of Macroevolutionary Rate Heterogeneity in Continuous and Discrete Traits

Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to datasets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large scale biodiversity dynamics.

The Jurassic rise of squamates as supported by lepidosaur disparity and evolutionary rates

The squamates (lizards, snakes, and relatives) today comprise more than 10,000 species, and yet their sister group, the Rhynchocephalia, is represented by a single species today, the tuatara. The explosion in squamate diversity has been tracked back to the Cretaceous Terrestrial Revolution, 100 million years ago (Ma), the time when flowering plants began their takeover of terrestrial ecosystems, associated with diversification of coevolving insects and insect-eating predators such as lizards, birds, and mammals. Squamates arose much earlier, but their long pre-Cretaceous history of some 150 million years (Myr) is documented by sparse fossils. Here, we provide evidence for an initial radiation of squamate morphology in the Middle and Late Jurassic (174-145 Ma), and show that they established their key ecological roles much earlier than had been assumed, and they have not changed them much since.

An exceptionally preserved Sphenodon-like sphenodontian reveals deep time conservation of the tuatara skeleton and ontogeny

Sphenodontian reptiles are an extremely old evolutionary lineage forming the closest relatives to squamates (lizards and snakes) and were globally distributed and more diverse than squamates during the first half of their evolutionary history. However, the majority of their fossils are highly fragmentary, especially within sphenodontines-the group including its single surviving species, Sphenodon punctatus (the tuatara of New Zealand)-thus severely hampering our understanding on the origins of the tuatara. Here, we present a new sphenodontian species from the Early Jurassic of North America (Arizona, USA) represented by a nearly complete articulated skeleton and dozens of upper and lower jaws forming the most complete ontogenetic series in the sphenodontian fossil record. CT-scanning provides plentitude of data that unambiguously place this new taxon as one of the earliest evolving and oldest known sphenodontines. Comparisons with Sphenodon reveal that fundamental patterns of mandibular ontogeny and skeletal architecture in Sphenodon may have originated at least ~190Mya. In combination with recent findings, our results suggest strong morphological stability and an ancient origin of the modern tuatara morphotype.

The causes and ecological context of rapid morphological evolution in birds

Episodic pulses in morphological diversification are a prominent feature of evolutionary history, driven by factors that remain widely disputed. Resolving this question has proved challenging because comprehensive species-level data are generally unavailable at sufficient scale. Combining global phylogenetic and morphological data for birds, we show that pulses of diversification in lineages and traits tend to occur independently and in different contexts. Speciation pulses are preceded by greater differentiation in overall morphology and habitat niche, then followed by increased rates of beak evolution. Contrary to standard hypotheses, pulses of morphological diversification tend to be associated with habitat niche stability rather than adaptation to different diets and habitat types. These patterns suggest that the timing of diversification varies across traits according to their ecological function, and that pulses of morphological evolution may occur when successful lineages subdivide niche space within particular habitat types. Our results highlight the growing potential of functional trait data sets to refine macroevolutionary models.

Reappraisal and new material of the holotype of Draconyx loureiroi (Ornithischia: Iguanodontia) provide insights on the tempo and modo of evolution of thumb-spiked dinosaurs

The Upper Jurassic Lourinhã Formation is well known for its rich assemblage of fossil vertebrates. In this formation, ornithopod dinosaurs are represented by two iguanodontian species, Eousdryosaurus nanohallucis and Draconyx loureiroi. We recently became aware of unreported material belonging to the holotype of Draconyx loureiroi, consisting of partially articulated manual elements. We here re-describe the holotype specimen ML 357, including the newly discovered material. The specimen was subjected to CT-scanning and its surface data used to assess anatomical characters. Linear measurements of metatarsal III were used to estimate the body length of the specimen. The Draconyx loureiroi holotype was included in two datasets and analysed with maximum parsimony and Bayesian inference approaches to estimate evolutionary rates among Iguanodontia. We present evidence that Draconyx loureiroi is a valid taxon nested in Styracosterna and is clearly diagnosable by a unique combination of characters. Both maximum parsimony and Bayesian inference indicate high evolutionary rates across the Jurassic/Cretaceous transition for the base of Iguanodontia. Length estimation suggests that Draconyx loureiroi was a relatively small, bipedal and possibly cursorial animal. Given its basal phyletic position, we interpret this bauplan was the ancestral condition for Styracosterna, that only later in the Cretaceous evolved into giant quadrupedal forms.

Early evolution of beetles regulated by the end-Permian deforestation

The end-Permian mass extinction (EPME) led to a severe terrestrial ecosystem collapse. However, the ecological response of insects—the most diverse group of organisms on Earth—to the EPME remains poorly understood. Here, we analyse beetle evolutionary history based on taxonomic diversity, morphological disparity, phylogeny, and ecological shifts from the Early Permian to Middle Triassic, using a comprehensive new dataset. Permian beetles were dominated by xylophagous stem groups with high diversity and disparity, which probably played an underappreciated role in the Permian carbon cycle. Our suite of analyses shows that Permian xylophagous beetles suffered a severe extinction during the EPME largely due to the collapse of forest ecosystems, resulting in an Early Triassic gap of xylophagous beetles. New xylophagous beetles appeared widely in the early Middle Triassic, which is consistent with the restoration of forest ecosystems. Our results highlight the ecological significance of insects in deep-time terrestrial ecosystems.

When adaptive radiations collide: Different evolutionary trajectories between and within island and mainland lizard clades

Oceanic islands are known as test tubes of evolution. Isolated and colonized by relatively few species, islands are home to many of nature's most renowned radiations from the finches of the Galápagos to the silverswords of the Hawaiian Islands. Despite the evolutionary exuberance of insular life, island occupation has long been thought to be irreversible. In particular, the presumed much tougher competitive and predatory milieu in continental settings prevents colonization, much less evolutionary diversification, from islands back to mainlands. To test these predictions, we examined the ecological and morphological diversity of neotropical Anolis lizards, which originated in South America, colonized and radiated on various islands in the Caribbean, and then returned and diversified on the mainland. We focus in particular on what happens when mainland and island evolutionary radiations collide. We show that extensive continental radiations can result from island ancestors and that the incumbent and invading mainland clades achieve their ecological and morphological disparity in very different ways. Moreover, we show that when a mainland radiation derived from island ancestors comes into contact with an incumbent mainland radiation the ensuing interactions favor the island-derived clade.

Multiple evolutionary origins and losses of tooth complexity in squamates

Teeth act as tools for acquiring and processing food, thus holding a prominent role in vertebrate evolution. In mammals, dental-dietary adaptations rely on tooth complexity variations controlled by cusp number and pattern. Complexity increase through cusp addition has dominated the diversification of mammals. However, studies of Mammalia alone cannot reveal patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, multiple-cusped teeth evolved over 20 times independently from a single-cusped common ancestor. Squamates frequently lost cusps and evolved varied multiple-cusped morphologies at heterogeneous rates. Tooth complexity evolved in correlation with changes in plant consumption, resulting in several major increases in speciation. Complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental-dietary evolution.

Multiple paths to morphological diversification during the origin of amniotes

Early terrestrial vertebrates (amniotes) provide a classic example of diversification following adaptive zone invasion. The initial terrestrialization of vertebrates was closely followed by dietary diversification, as evidenced by a proliferation of craniomandibular and dental adaptations. However, morphological evolution of early amniotes has received limited study, in analyses with restricted taxonomic scope, leaving substantial questions about the dynamics of this important terrestrial radiation. We use novel analyses of discrete characters to quantify variation in evolutionary rates and constraints during diversification of the amniote feeding apparatus. We find evidence for an early burst, comprising high rates of anatomical change that decelerated through time, giving way to a background of saturated morphological evolution. Subsequent expansions of phenotypic diversity were not associated with increased evolutionary rates. Instead, variation in the mode of evolution became important, with groups representing independent origins of herbivory evolving distinctive, group-specific morphologies and thereby exploring novel character-state spaces. Our findings indicate the importance of plant-animal interactions in structuring the earliest radiation of amniotes and demonstrate the importance of variation in modes of phenotypic divergence during a major evolutionary radiation.

A Triassic stem lepidosaur illuminates the origin of lizard-like reptiles

The early evolution of diapsid reptiles is marked by a deep contrast between our knowledge of the origin and early evolution of archosauromorphs (crocodiles, avian and non-avian dinosaurs) to that of lepidosauromorphs (squamates (lizards, snakes) and sphenodontians (tuataras)). Whereas the former include hundreds of fossil species across various lineages during the Triassic period¹, the latter are represented by an extremely patchy early fossil record comprising only a handful of fragmentary fossils, most of which have uncertain phylogenetic affinities and are confined to Europe^1-3. Here we report the discovery of a three-dimensionally preserved reptile skull, assigned as Taytalura alcoberi gen. et sp. nov., from the Late Triassic epoch of Argentina that is robustly inferred phylogenetically as the earliest evolving lepidosauromorph, using various data types and optimality criteria. Micro-computed tomography scans of this skull reveal details about the origin of the lepidosaurian skull from early diapsids, suggesting that several traits traditionally associated with sphenodontians in fact originated much earlier in lepidosauromorph evolution. Taytalura suggests that the strongly evolutionarily conserved skull architecture of sphenodontians represents the plesiomorphic condition for all lepidosaurs, that stem and crown lepidosaurs were contemporaries for at least ten million years during the Triassic, and that early lepidosauromorphs had a much broader geographical distribution than has previously been thought.

Sustained high rates of morphological evolution during the rise of tetrapods

The fish-to-tetrapod transition is one of the most iconic events in vertebrate evolution, yet fundamental questions regarding the dynamics of this transition remain unresolved. Here, we use advances in Bayesian morphological clock modelling to reveal the evolutionary dynamics of early tetrapodomorphs (tetrapods and their closest fish relatives). We show that combining osteological and ichnological calibration data results in major shifts on the time of origin of all major groups of tetrapodomorphs (up to 25 million years) and that low rates of net diversification, not fossilization, explain long ghost lineages in the early tetrapodomorph fossil record. Further, our findings reveal extremely low rates of morphological change for most early tetrapodomorphs, indicating widespread stabilizing selection upon their 'fish' morphotype. This pattern was broken only by elpistostegalians (including early tetrapods), which underwent sustained high rates of morphological evolution for ~30 Myr during the deployment of the tetrapod body plan.

Finding Solutions for Fibrosis: Understanding the Innate Mechanisms Used by Super-Regenerator Vertebrates to Combat Scarring

Soft tissue fibrosis and cutaneous scarring represent massive clinical burdens to millions of patients per year and the therapeutic options available are currently quite limited. Despite what is known about the process of fibrosis in mammals, novel approaches for combating fibrosis and scarring are necessary. It is hypothesized that scarring has evolved as a solution to maximize healing speed to reduce fluid loss and infection. This hypothesis, however, is complicated by regenerative animals, which have arguably the most remarkable healing abilities and are capable of scar-free healing. This review explores the differences observed between adult mammalian healing that typically results in fibrosis versus healing in regenerative animals that heal scarlessly. Each stage of wound healing is surveyed in depth from the perspective of many regenerative and fibrotic healers so as to identify the most important molecular and physiological variances along the way to disparate injury repair outcomes. Understanding how these powerful model systems accomplish the feat of scar-free healing may provide critical therapeutic approaches to the treatment or prevention of fibrosis.

Bayesian Morphological Clock versus Parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia)

Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein, we present a morphological dataset for a group of cricetid rodents to which we apply an array of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated and non-calibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.

Brain Allometry Across Macroevolutionary Scales in Squamates Suggests a Conserved Pattern in Snakes

Despite historical interest in brain size evolution in vertebrates, few studies have assessed variation in brain size in squamate reptiles such as snakes and lizards. Here, we analyzed the pattern of brain allometry at macroevolutionary scale in snakes and lizards, using body mass and snout vent length as measures of body size. We also assessed potential energetic trade-offs associated with relative brain size changes in Crotalinae vipers. Body mass showed a conserved pattern of brain allometry across taxa of snakes, but not in lizards. Body length favored changes of brain allometry in both snakes and lizards, but less variability was observed in snakes. Moreover, we did not find evidence for trade-offs between brain size and the size of other organs in Crotalinae. Thus, despite the contribution of body elongation to changes in relative brain size in squamate reptiles, snakes present low variation in brain allometry across taxa. Although the mechanisms driving this conserved pattern are unknown, we hypothesize that the snake body plan plays an important role in balancing the energetic demands of brain and body size increase at macroevolutionary scales. We encourage future research on the evolution of brain and body size in snakes to test this hypothesis.

Ecological opportunity and the rise and fall of crocodylomorph evolutionary innovation

Understanding the origin, expansion and loss of biodiversity is fundamental to evolutionary biology. The approximately 26 living species of crocodylomorphs (crocodiles, caimans, alligators and gharials) represent just a snapshot of the group's rich 230-million-year history, whereas the fossil record reveals a hidden past of great diversity and innovation, including ocean and land-dwelling forms, herbivores, omnivores and apex predators. In this macroevolutionary study of skull and jaw shape disparity, we show that crocodylomorph ecomorphological variation peaked in the Cretaceous, before declining in the Cenozoic, and the rise and fall of disparity was associated with great heterogeneity in evolutionary rates. Taxonomically diverse and ecologically divergent Mesozoic crocodylomorphs, like marine thalattosuchians and terrestrial notosuchians, rapidly evolved novel skull and jaw morphologies to fill specialized adaptive zones. Disparity in semi-aquatic predatory crocodylians, the only living crocodylomorph representatives, accumulated steadily, and they evolved more slowly for most of the last 80 million years, but despite their conservatism there is no evidence for long-term evolutionary stagnation. These complex evolutionary dynamics reflect ecological opportunities, that were readily exploited by some Mesozoic crocodylomorphs but more limited in Cenozoic crocodylians.

Ecomorphological diversification of squamates in the Cretaceous

Squamates (lizards and snakes) are highly successful modern vertebrates, with over 10 000 species. Squamates have a long history, dating back to at least 240 million years ago (Ma), and showing increasing species richness in the Late Cretaceous (84 Ma) and Early Palaeogene (66-55 Ma). We confirm that the major expansion of dietary functional morphology happened before these diversifications, in the mid-Cretaceous, 110-90 Ma. Until that time, squamates had relatively uniform tooth types, which then diversified substantially and ecomorphospace expanded to modern levels. This coincides with the Cretaceous Terrestrial Revolution, when angiosperms began to take over terrestrial ecosystems, providing new roles for plant-eating and pollinating insects, which were, in turn, new sources of food for herbivorous and insectivorous squamates. There was also an early Late Cretaceous (95-90 Ma) rise in jaw size disparity, driven by the diversification of marine squamates, particularly early mosasaurs. These events established modern levels of squamate feeding ecomorphology before the major steps in species diversification, confirming decoupling of diversity and disparity. In fact, squamate feeding ecomorphospace had been partially explored in the Late Jurassic and Early Cretaceous, and jaw innovation in Late Cretaceous squamates involved expansions at the extremes of morphospace.

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

BACKGROUND

The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored.

RESULTS

Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group.

CONCLUSIONS

We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.