Early origin of viviparity and multiple reversions to oviparity in squamate reptiles

Maternal investment evolves with larger body size and higher diversification rate in sharks and rays

Across vertebrates, live bearing evolved at least 150 times from ancestral egg laying into diverse forms and degrees of prepartum maternal investment.1,2 A key question is how reproductive diversity arose and whether reproductive diversification underlies species diversification.3,4,5,6,7,8,9,10,11 To test this, we evaluate the most basal jawed vertebrates: the sharks, rays, and chimaeras, which have one of the greatest ranges of reproductive and ecological diversity among vertebrates.2,12 We reconstruct the sequence of reproductive mode evolution across a phylogeny of 610 chondrichthyans.13 We reveal egg laying as ancestral, with live bearing evolving at least seven times. Matrotrophy evolved at least 15 times, with evidence of one reversal. In sharks, transitions to live bearing and matrotrophy are more prevalent in larger-bodied tropical species. Further, the evolution of live bearing is associated with a near doubling of the diversification rate, but there is only a small increase associated with the appearance of matrotrophy. Although pre-copulatory sexual selection is associated with increased rates of speciation in teleosts,3 sexual size dimorphism in chondrichthyans does not appear to be related to sexual selection,14,15 and instead we find increased rates of speciation associated with the colonization of novel habitats. This highlights a potential key difference between chondrichthyans and other fishes, specifically a slower rate of evolution of reproductive isolation following speciation, suggesting different rate-limiting mechanisms for diversification between these clades.16 The chondrichthyan diversification and radiation, particularly throughout shallow tropical shelf seas and oceanic pelagic habitats, appear to be associated with the evolution of live bearing and proliferation of a wide range of maternal investment in developing offspring.

Viviparity imparts a macroevolutionary signature of ecological opportunity in the body size of female Liolaemus lizards

Viviparity evolved ~115 times across squamate reptiles, facilitating the colonization of cold habitats, where oviparous species are scarce or absent. Whether the ecological opportunity furnished by such colonization reconfigures phenotypic diversity and accelerates evolution is unclear. We investigated the association between viviparity and patterns and rates of body size evolution in female Liolaemus lizards, the most species-rich tetrapod genus from temperate regions. Here, we discover that viviparous species evolve ~20% larger optimal body sizes than their oviparous relatives, but exhibit similar rates of body size evolution. Through a causal modeling approach, we find that viviparity indirectly influences body size evolution through shifts in thermal environment. Accordingly, the colonization of cold habitats favors larger body sizes in viviparous species, reconfiguring body size diversity in Liolaemus. The catalyzing influence of viviparity on phenotypic evolution arises because it unlocks access to otherwise inaccessible sources of ecological opportunity, an outcome potentially repeated across the tree of life.

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.

Agency in Reproduction

While niche construction theory and developmental approaches to evolution have brought to the front the active role of organisms as ecological and developmental agents, respectively, the role of agents in reproduction has been widely neglected by organismal perspectives of evolution. This paper addresses this problem by proposing an agential view of reproduction and shows that such a perspective has implications for the explanation of the origin of modes of reproduction, the evolvability of reproductive modes, and the coevolution between reproduction and social behavior. After introducing the two prevalent views of agency in evolutionary biology, namely those of organismal agency and selective agency, I contrast these two perspectives as applied to the evolution of animal reproduction. Taking eutherian pregnancy as a case study, I wonder whether organismal approaches to agency forged in the frame of niche construction and developmental plasticity theories can account for the goal-directed activities involved in reproductive processes. I conclude that the agential role of organisms in reproduction is irreducible to developmental and ecological agency, and that reproductive goals need to be included into our definitions of organismal agency. I then explore the evolutionary consequences of endorsing an agential approach to reproduction, showing how such an approach might illuminate our understanding of the evolutionary origination and developmental evolvability of reproductive modes. Finally, I analyze recent studies on the coevolution between viviparity and social behavior in vertebrates to suggest that an agential notion of reproduction can provide unforeseen links between developmental and ecological agency.

Evolution of reproductive modes in sharks and rays

The ecological and life history drivers of the diversification of reproductive modes in early vertebrates are not fully understood. Sharks, rays and chimaeras (group Chondrichthyes) have an unusually diverse variety of reproductive modes and are thus an ideal group to test the factors driving the evolution of reproductive complexity. Here, using 960 species representing all major Chondrichthyes taxa, we reconstruct the evolution of their reproduction modes and investigate the ecological and life history predictors of reproduction. We show that the ancestral Chondrichthyes state was egg-laying and find multiple independent transitions between egg-laying and live-bearing via an intermediate state of yolk-only live-bearing. Using phylogenetically informed analysis, we also show that live-bearing species have larger body size and larger offspring than egg-laying species. In addition, live-bearing species are distributed over shallow to intermediate depths, while egg-layers are typically found in deeper waters. This suggests that live-bearing is more closely associated with pelagic, rather than demersal habitats. Taken together, using a basal vertebrate group as a model, we demonstrat how reproductive mode co-evolves with environmental conditions and life-history traits.

The affinities of the Late Triassic Cryptovaranoides and the age of crown squamates

Most living reptile diversity is concentrated in Squamata (lizards, including snakes), which have poorly known origins in space and time. Recently, †Cryptovaranoides microlanius from the Late Triassic of the United Kingdom was described as the oldest crown squamate. If true, this result would push back the origin of all major lizard clades by 30-65 Myr and suggest that divergence times for reptile clades estimated using genomic and morphological data are grossly inaccurate. Here, we use computed tomography scans and expanded phylogenetic datasets to re-evaluate the phylogenetic affinities of †Cryptovaranoides and other putative early squamates. We robustly reject the crown squamate affinities of †Cryptovaranoides, and instead resolve †Cryptovaranoides as a potential member of the bird and crocodylian total clade, Archosauromorpha. Bayesian total evidence dating supports a Jurassic origin of crown squamates, not Triassic as recently suggested. We highlight how features traditionally linked to lepidosaurs are in fact widespread across Triassic reptiles. Our study reaffirms the importance of critically choosing and constructing morphological datasets and appropriate taxon sampling to test the phylogenetic affinities of problematic fossils and calibrate the Tree of Life.

The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota

The microbiome is an interactive and fluctuating community of microbes that colonize and develop across surfaces, including those associated with organismal hosts. A growing number of studies exploring how microbiomes vary in ecologically relevant contexts have recognized the importance of microbiomes in affecting organismal evolution. Thus, identifying the source and mechanism for microbial colonization in a host will provide insight into adaptation and other evolutionary processes. Vertical transmission of microbiota is hypothesized to be a source of variation in offspring phenotypes with important ecological and evolutionary implications. However, the life-history traits that govern vertical transmission are largely unexplored in the ecological literature. To increase research attention to this knowledge gap, we conducted a systematic review to address the following questions: (1) How often is vertical transmission assessed as a contributor to offspring microbiome colonization and development? (2) Do studies have the capacity to address how maternal transmission of microbes affects the offspring phenotype? (3) How do studies vary based on taxonomy and life history of the study organism, as well as the experimental, molecular, and statistical methods employed? Extensive literature searches reveal that many studies examining vertical transmission of microbiomes fail to collect whole microbiome samples from both maternal and offspring sources, particularly for oviparous vertebrates. Additionally, studies should sample functional diversity of microbes to provide a better understanding of mechanisms that influence host phenotypes rather than solely taxonomic variation. An ideal microbiome study incorporates host factors, microbe-microbe interactions, and environmental factors. As evolutionary biologists continue to merge microbiome science and ecology, examining vertical transmission of microbes across taxa can provide inferences on causal links between microbiome variation and phenotypic evolution.

Show Me Your Teeth And I Will Tell You What You Eat: Differences in Tooth Enamel in Snakes with Different Diets

Teeth are composed of the hardest tissues in the vertebrate body and have been studied extensively to infer diet in vertebrates. The morphology and structure of enamel is thought to reflect feeding ecology. Snakes have a diversified diet, some species feed on armored lizards, others on soft invertebrates. Yet, little is known about how tooth enamel, and specifically its thickness, is impacted by diet. In this study, we first describe the different patterns of enamel distribution and thickness in snakes. Then, we investigate the link between prey hardness and enamel thickness and morphology by comparing the dentary teeth of 63 species of snakes. We observed that the enamel is deposited asymmetrically at the antero-labial side of the tooth. Both enamel coverage and thickness vary a lot in snakes, from species with thin enamel, only at the tip of the tooth to a full facet covered with enamel. There variations are related with prey hardness: snakes feeding on hard prey have a thicker enamel and a lager enamel coverage while species. Snakes feeding on softer prey have a thin enamel layer confined to the tip of the tooth.

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.

Extended embryo retention and viviparity in the first amniotes

The amniotic egg with its complex fetal membranes was a key innovation in vertebrate evolution that enabled the great diversification of reptiles, birds and mammals. It is debated whether these fetal membranes evolved in eggs on land as an adaptation to the terrestrial environment or to control antagonistic fetal-maternal interaction in association with extended embryo retention (EER). Here we report an oviparous choristodere from the Lower Cretaceous period of northeast China. The ossification sequence of the embryo confirms that choristoderes are basal archosauromorphs. The discovery of oviparity in this assumed viviparous extinct clade, together with existing evidence, suggests that EER was the primitive reproductive mode in basal archosauromorphs. Phylogenetic comparative analyses on extant and extinct amniotes suggest that the first amniote displayed EER (including viviparity).

Reptile Evolution and Genetics: An Overview

The study of evolution has been indissolubly linked to the study of heredity since its inception [1]. [...].

Measuring the shape of mortality across animals and plants: Alternatives to H entropy metrics reveal hidden type IV survivorship curves and associations with parental care at macro-ecological scales

The shape of mortality, or how mortality is spread across an organism's life course, is fundamental to a range of biological processes, with attempts to quantify it rooted in ecology, evolution, and demography. One approach to quantify the distribution of mortality over an organism's life is the use of entropy metrics whose values are interpreted within the classical framework of survivorship curves ranging from type I distributions, with mortality concentrated in late life stages, to type III survivorship curves associated with high early stage mortality. However, entropy metrics were originally developed using restricted taxonomic groups and the behavior of entropy metrics over larger scales of variation may make them unsuitable for wider-ranging contemporary comparative studies. Here, we revisit the classic survivorship framework and, using a combination of simulations and comparative analysis of demography data spanning the animal and plant kingdoms, we show that commonly used entropy metrics cannot distinguish between the most extreme survivorship curves, which in turn can mask important macroecological patterns. We show how using H entropy masks a macroecological pattern of how parental care is associated with type I and type II species and for macroecological studies recommend the use of metrics, such as measures of area under the curve. Using frameworks and metrics that capture the full range of variation of survivorship curves will aid in our understanding of the links between the shape of mortality, population dynamics, and life history traits.

Armed to the teeth: The underestimated diversity in tooth shape in snakes and its relation to feeding behavior and diet

The structure, composition, and shape of teeth have been related to dietary specialization in many vertebrate species, but comparative studies on snakes' teeth are lacking. Yet, snakes have diverse dietary habits that may impact the shape of their teeth. We hypothesize that prey properties, such as hardness and shape, as well as feeding behavior, such as aquatic or arboreal predation, or holding vigorous prey, impose constraints on the evolution of tooth shape in snakes. We compared the morphology of the dentary teeth of 63 species that cover the phylogenetic and dietary diversity of snakes, using 3D geometric morphometrics and linear measurements. Our results show that prey hardness, foraging substrate, and the main feeding mechanical challenge are important drivers of tooth shape, size, and curvature. Overall, long, slender, curved teeth with a thin layer of hard tissue are observed in species that need to maintain a grip on their prey. Short, stout, less curved teeth are associated with species that undergo high or repeated loads. Our study demonstrates the diversity of tooth morphology in snakes and the need to investigate its underlying functional implications to better understand the evolution of teeth in vertebrates.

Vitellogenin uptake activity in the intestinal ducts of intraovarian embryos in a viviparous teleost Xenotoca eiseni

In the viviparous teleost species belonging to the family Goodeidae, intraovarian embryos absorb maternal supplements while they grow during the gestation period. They take up the components via trophotaeniae, a hindgut-derived placental structure. Our previous study using a goodeid species Xenotoca eiseni revealed that intraovarian embryos absorb the yolk protein vitellogenin (Vtg) via the trophotaenia. However, another group indicated yolk components accumulate in the intestinal lumen of X. eiseni embryos. Here, we investigated whether the intestinal duct is capable of protein uptake, as is the trophotaenia. Immunohistochemical studies indicated that endogenous vitellogenin is detected in the intestinal epithelial cells of the intraovarian embryo. Tracer analysis using FITC-Vtg also indicated that intestinal tissues can take up protein. The endocytosis-related genes expressed in trophotaenia were also detected in the intestinal tissues of the embryo. Lipid transporter genes which are not expressed in the trophotaenia were detected in the embryonic intestine. This evidence suggests that the intraovarian embryo of X. eiseni possesses two distinct sites for uptake of the maternal proteins. However, the presumed functions of the embryonic intestine and trophotaenia might be not identical. The study provides a new perspective on how mother-to-embryo matrotrophic interactions have changed in the evolution of viviparous teleosts.

Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.

Madagascar Leaf-Tail Geckos (Uroplatus spp.) Share Independently Evolved Differentiated ZZ/ZW Sex Chromosomes

Geckos are an excellent group to study the evolution of sex determination, as they possess a remarkable variability ranging from a complete absence of sex chromosomes to highly differentiated sex chromosomes. We explored sex determination in the Madagascar leaf-tail geckos of the genus Uroplatus. The cytogenetic analyses revealed highly heterochromatic W chromosomes in all three examined species (Uroplatus henkeli, U. alluaudi, U. sikorae). The comparative gene coverage analysis between sexes in U. henkeli uncovered an extensive Z-specific region, with a gene content shared with the chicken chromosomes 8, 20, 26 and 28. The genomic region homologous to chicken chromosome 28 has been independently co-opted for the role of sex chromosomes in several vertebrate lineages, including monitors, beaded lizards and monotremes, perhaps because it contains the amh gene, whose homologs were repeatedly recruited as a sex-determining locus. We demonstrate that all tested species of leaf-tail geckos share homologous sex chromosomes despite the differences in shape and size of their W chromosomes, which are not homologous to the sex chromosomes of other closely related genera. The rather old (at least 40 million years), highly differentiated sex chromosomes of Uroplatus geckos can serve as a great system to study the convergence of sex chromosomes evolved from the same genomic region.

A Triassic crown squamate

Mammals, birds, and squamates (lizards, snakes, and relatives) are key living vertebrates, and thus understanding their evolution underpins important questions in biodiversity science. Whereas the origins of mammals and birds are relatively well understood, the roots of squamates have been obscure. Here, we report a modern-type lizard from the Late Triassic of England [202 million years (Ma)], comprising a partial skeleton, skull, and mandibles. It displays at least 15 unique squamate traits and further shares unidentatan and anguimorph apomorphies. The new discovery fixes the origin of crown Squamata as much older than had been thought, and the revised dating shows substantial diversification of modern-type squamates following the Carnian Pluvial Episode, 232 Ma ago.

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.

How do ectotherms perform in cold environments? Physiological and life-history traits in an Andean viviparous lizard

Both the mean and the variation in environmental temperature are increasing globally. Indeed, the predicted increases in temperature range from 2 to 4°C in the next 50 years. Ectotherms control body temperature by means of behavior selecting microsites with different temperatures, which makes them more susceptible to changes in climate. Nevertheless, lizards living in high mountain environments have developed several mechanisms to inhabit and colonize variable environments with extreme temperatures. These mechanisms include a high metabolism to be active at lower temperatures and viviparity to improve embryonic development. Despite behavioral thermoregulation acting as a buffer to changes in environmental temperature, other traits such as life-history traits may be less flexible. Consequently, in an attempt to understand how lizards cope with harsh habitats, we evaluated some physiological traits and responses of females of Liolaemus bellii from two contrasting slope sites with differences in environmental temperature and humidity, but at the same altitude in the southern Andes range. We collected pregnant females from opposite slopes and maintained them until parturition in a common-garden experiment. Females from the south-facing slope (S-slope) had higher preferred body temperature (Tpref) values before and after parturition and exhibited higher daily energy expenditure before parturition. Nevertheless, no difference in Tpref was shown by their offspring, suggesting a developmental plastic response or adaptation to lower environmental temperature. For instance, the higher metabolism during pregnancy could be associated with a shorter activity period on the snowy S-slope. Additionally, females from the S-slope had larger kidneys and gave birth later than N-slope females, likely due to developmental plasticity or genetic differentiation. How fixed these traits are, in individuals from the contrasting slopes, will determine the response capacity of the L. bellii population to climate change.

Effects of incubation temperature on development, morphology, and thermal physiology of the emerging Neotropical lizard model organism Tropidurus torquatus

Incubation temperature is among the main phenotypic trait variation drivers studied since the developmental trajectory of oviparous animals is directly affected by environmental conditions. In the last decades, global warming predictions have aroused interest in understanding its impacts on biodiversity. It is predicted that the effects of direct warming will be exacerbated by other anthropogenic factors, such as microclimatic edge effects. Although the Brazilian Cerrado biome is one of the most affected by these issues, little is known about the aforementioned effects on its biodiversity. Therefore, the aim of our study is to investigate the influence of incubation temperature on developmental parameters, morphology and thermal physiology traits of the collared lizard (Tropidurus torquatus). Furthermore, we discuss our findings regarding lizard developmental biology and the climate change paradigm. Therefore, we incubated T. torquatus eggs under five temperature regimes ranging from artificial nest temperature (28.7 °C) to 35.0 °C. We found that elevated incubation temperatures affect several investigated traits: egg mass gain is positively affected, without any influence in newborn mass; incubation period is broadly reduced with temperature increase; survival rate is negatively affected by temperature, constant 35.0 °C regime is confirmed as a lethal incubation temperature, and the sex ratio is affected at 30.0 °C, with a prevailing outbreak of females. Increased incubation temperature also affects body and head size but has no effect on limb size. Newborn thermoregulation and the critical thermal maximum (CT_max) are not affected by incubation temperature. On the other hand, basal body temperature (T_bb) and the critical thermal minimum (CT_min) were positively affected. Thermal physiology was also affected by age, with newborns differing from adults for all analyzed thermal traits. Our findings indicate that future modifications in incubation temperature regimes at nesting sites caused by warming may affect several features of the development, morphology, and thermal physiology of newborns of this species. Laboratory experiments have pointed to possible drastic effects of warming on lizard survival rates, also affecting aspects of its natural history and population distribution. Moreover, in addition to being more vulnerable than adults in aspects such as predation and feeding, T. torquatus newborns are also more vulnerable regarding thermal physiological traits.

Evolution of the rostral scale and mimicry in the genus Xenodon Boie, 1826 (Serpentes: Dipsadidae: Xenodontinae)

Snakes are a stimulating life form from an evolutionary perspective. Despite the basic morphological body shape (limbless, with a tubular body), these vertebrates are extremely diverse. The Neotropical region is one of the most diverse regions for snakes in the world, with >650 known species. Within this great diversity, the genus Xenodon includes 12 species with interesting adaptations to terrestrial and semi-fossorial habitats. Members of this genus are mostly diurnal and terrestrial, feed mainly on anurans and exhibit Batesian mimicry of venomous snakes of the genera Bothrops or Micrurus. Here, through phylogenetic analysis and ancestral state estimation, we explore the evolution of the rostral scale and mimicry within the genus Xenodon. Our results suggest that the ancestral lineage of Xenodon had a rounded rostral scale and exhibited Bothrops mimicry. The evolution of the rostral scale in Xenodon might be related to abiotic factors, as an adaptation for open and forested habitats, and mimicry is likely to be related to biotic factors, as a defensive strategy resembling those of venomous snakes.

The diverse terminology of reptile eggshell microstructure and its effect on phylogenetic comparative analyses

Reptile eggshell ensures water and gas exchange during incubation and plays a key role in reproductive success. The diversity of reptilian incubation and life history strategies has led to many clade-specific structural adaptations of their eggshell, which have been studied in extant taxa (i.e. birds, crocodilians, turtles, and lepidosaurs). Most studies on non-avian eggshells were performed over 30 years ago and categorized reptile eggshells into two main types: "hard" and "soft" - sometimes with a third intermediate category, "semi-rigid." In recent years, however, debate over the evolution of eggshell structure of major reptile clades has revealed how definitions of hard and soft eggshells influence inferred deep-time evolutionary patterns. Here, we review the diversity of extant and fossil eggshell with a focus on major reptile clades, and the criteria that have been used to define hard, soft, and semi-rigid eggshells. We show that all scoring approaches that retain these categories discretize continuous quantitative traits (e.g. eggshell thickness) and do not consider independent variation of other functionally important microstructural traits (e.g. degree of calcification, shell unit inner structure). We demonstrate the effect of three published approaches to discretizing eggshell type into hard, semi-rigid, and soft on ancestral state reconstructions using 200+ species representing all major extant and extinct reptile clades. These approaches result in different ancestral states for all major clades including Archosauria and Dinosauria, despite a difference in scoring for only 1-4% of the sample. Proposed scenarios of reptile eggshell evolution are highly conditioned by sampling, tree calibration, and lack of congruence between definitions of eggshell type. We conclude that the traditional "soft/hard/semi-rigid" classification of reptilian eggshells should be abandoned and provide guidelines for future descriptions focusing on specific functionally relevant characteristics (e.g. inner structures of shell units, pores, and membrane elements), analyses of these traits in a phylogenetic context, and sampling of previously undescribed taxa, including fossil eggs.

Endocytosis-mediated vitellogenin absorption and lipid metabolism in the hindgut-derived placenta of the viviparous teleost Xenotoca eiseni

Certain viviparous animals possess mechanisms for mother-to-embryo nutrient transport during gestation. Xenotoca eiseni is one such viviparous teleost species in which the mother supplies proteins and other components to the offspring developing in the ovary. The embryo possesses trophotaenia, hindgut-derived placental structure, to receive the maternal supplement. However, research on the molecular mechanisms underlying viviparous species is scarce in non-mammalian vertebrates, including teleosts. Thus, we conducted this study to investigate the mechanism for nutrient absorption and degradation in trophotaeniae of X. eiseni. A tracer assay indicated that a lipid transfer protein, vitellogenin (Vtg), was absorbed into the epithelial layer cells of the trophotaeniae. Vtg uptake was significantly suppressed by Pitstop-2, an inhibitor of clathrin-mediated endocytosis. Gene expression analysis indicated that the genes involved in endocytosis-mediated lipolysis and lysosomal cholesterol transport were expressed in the trophotaeniae. In contrast, plasma membrane transporters expressed in the intestinal tract were not functional in the trophotaeniae. Our results suggested that endocytosis-mediated lysosomal lipolysis is one of the mechanisms underlying maternal component metabolism. Thus, our study demonstrated how viviparous teleost species have acquired a unique developmental system that is based on the hindgut-derived placenta.

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.

Ecological and life-history correlates of erythrocyte size and shape in Lepidosauria

Blood oxygen‐carrying capacity is shaped both by the ambient oxygen availability as well as species‐specific oxygen demand. Erythrocytes are a critical part of oxygen transport and both their size and shape can change in relation to species‐specific life‐history, behavioural or ecological conditions. Here, we test whether components of the environment (altitude), life history (reproductive mode, body temperature) and behaviour (diving, foraging mode) drive erythrocyte size variation in the Lepidosauria (lizards, snakes and rhynchocephalians). We collected data on erythrocyte size (area) and shape (L/W: elongation ratio) from Lepidosauria across the globe (N = 235 species). Our analyses show the importance of oxygen requirements as a driver of erythrocyte size. Smaller erythrocytes were associated with the need for faster delivery (active foragers, high‐altitude species, warmer body temperatures), whereas species with greater oxygen demands (diving species, viviparous species) had larger erythrocytes. Erythrocyte size shows considerable cross‐species variation, with a range of factors linked to the oxygen delivery requirements being major drivers of these differences. A key future aspect for study would include within‐individual plasticity and how changing states, for example, pregnancy, perhaps alter the size and shape of erythrocytes in Lepidosaurs.

Premeiotic endoreplication is essential for obligate parthenogenesis in geckos

Obligate parthenogenesis evolved in reptiles convergently several times, mainly through interspecific hybridization. The obligate parthenogenetic complexes typically include both diploid and triploid lineages. Offspring of parthenogenetic hybrids are genetic copies of their mother; however, the cellular mechanism enabling the production of unreduced cells is largely unknown. Here, we show that oocytes go through meiosis in three widespread, or even strongly invasive, obligate parthenogenetic complexes of geckos, namely in diploid and triploid Lepidodactylus lugubris, and triploid Hemiphyllodactylus typus and Heteronotia binoei. In all four lineages, the majority of oocytes enter the pachytene at the original ploidy level, but their chromosomes cannot pair properly and instead form univalents, bivalents and multivalents. Unreduced eggs with clonally inherited genomes are formed from germ cells that had undergone premeiotic endoreplication, in which appropriate segregation is ensured by the formation of bivalents made from copies of identical chromosomes. We conclude that the induction of premeiotic endoreplication in reptiles was independently co-opted at least four times as an essential component of parthenogenetic reproduction and that this mechanism enables the emergence of fertile polyploid lineages within parthenogenetic complexes.

The Evolution of Viviparity in Vertebrates

In the vertebrate tree of life, viviparity or live birth has independently evolved many times, resulting in a rich diversity of reproductive strategies. Viviparity is believed to be a mode of reproduction that evolved from the ancestral condition of oviparity or egg laying, where most of the fetal development occurs outside the body. Today, there is not a simple model of parity transition to explain this species-specific divergence in modes of reproduction. Most evidence points to a gradual series of evolutionary adaptations that account for this phenomenon of reproduction, elegantly displayed by various viviparous squamates that exhibit placentae formed by the appositions of maternal and embryonic tissues, which share significant homology with the tissues that form the placenta in therian mammals. In an era where the genomes of many vertebrate species are becoming available, studies are now exploring the molecular basis of this transition from oviparity to viviparity, and in some rare instances its possible reversibility, such as the Australian three-toed skink (Saiphos equalis). In contrast to the parity diversity in squamates, mammals are viviparous with the notable exception of the egg-laying monotremes. Advancing computational tools coupled with increasing genome availability across species that utilize different reproductive strategies promise to reveal the molecular underpinnings of the ancestral transition of oviparity to viviparity. As a result, the dramatic changes in reproductive physiology and anatomy that accompany these parity changes can be reinterpreted. This chapter will briefly explore the vertebrate modes of reproduction using a phylogenetic framework and where possible highlight the role of potential candidate genes that may help explain the polygenic origins of live birth.

Understanding the evolution of viviparity using intraspecific variation in reproductive mode and transitional forms of pregnancy

How innovations such as vision, flight and pregnancy evolve is a central question in evolutionary biology. Examination of transitional (intermediate) forms of these traits can help address this question, but these intermediate phenotypes are very rare in extant species. Here we explore the biology and evolution of transitional forms of pregnancy that are midway between the ancestral state of oviparity (egg‐laying) and the derived state, viviparity (live birth). Transitional forms of pregnancy occur in only three vertebrates, all of which are lizard species that also display intraspecific variation in reproductive phenotype. In these lizards (Lerista bougainvillii, Saiphos equalis, and Zootoca vivipara), geographic variation of three reproductive forms occurs within a single species: oviparity, viviparity, and a transitional form of pregnancy. This phenomenon offers the valuable prospect of watching ‘evolution in action’. In these species, it is possible to conduct comparative research using different reproductive forms that are not confounded by speciation, and are of relatively recent origin. We identify major proximate and ultimate questions that can be addressed in these species, and the genetic and genomic tools that can help us understand how transitional forms of pregnancy are produced, despite predicted fitness costs. We argue that these taxa represent an excellent prospect for understanding the major evolutionary shift between egg‐laying and live birth, which is a fundamental innovation in the history of animals.

Effects of moisture during incubation on green sea turtle (Chelonia mydas) development, morphology and performance

While the effect of temperature on embryonic development in sea turtles has been well studied over recent years, our understanding of the effect of substrate moisture, another important environmental variable, is limited. High sand moisture decreases nest temperature through evaporative and direct cooling during rainfall, but its direct effect on hatchling development, morphology and performance is unclear. To address this knowledge gap, we incubated 40 green sea turtle Chelonia mydas clutches in a beach hatchery under either high (~8% v/v) or low (~5% v/v) sand moisture concentrations for the duration of embryonic development. In half of the clutches, temperature sensors were deployed to measure any effect of sand moisture on nest temperature. As hatchlings emerged, we measured body size and locomotory performance during the first 24 h, an important period of frenzied activity for sea turtles. We excavated clutches post-emergence to determine hatching success, emergence success and to determine the stage of embryonic death for unsuccessful eggs. High moisture concentrations increased incubation duration, decreased nest temperature and had marginal effects on hatchling morphology, but no effect on hatching success, stage of embryonic death, crawling speed or initial swimming performance. However, after 24 h of swimming, hatchlings from high-moisture clutches produced less mean swim thrust and spent less time powerstroking than hatchlings from low-moisture clutches, suggesting reduced swimming endurance and potentially impacting the ability of hatchlings to successfully disperse. The effect of moisture on nest temperature and hatchling endurance highlights the importance of considering rainfall patterns when predicting future impacts of climate change on sea turtle populations.

Multilocus phylogeny, natural history traits and classification of natricine snakes (Serpentes: Natricinae)

Natricine snakes are geographically widespread, species rich (with ~250 extant species) and both morphologically and ecologically diverse. We present a multilocus DNA sequence phylogeny for 249 natricine specimens representing 189 named species, including 69 specimens and 21 species not previously sampled. Our inferred Bayesian and maximum likelihood trees form the basis for evaluations of genus-level classification, historical biogeography, lineage diversification, and dietary, habit and reproductive-mode diversity and evolution, although several, mostly deeper, relationships remain poorly resolved. The optimal trees support natricine origins in Asia, with dispersals to Australo-Melanesia, sub-Saharan Africa (including Seychelles Archipelago, excluding Aldabra), Europe and North Africa and into North and Central America. Viviparity appears to have evolved independently three times in Natricinae but was not significantly associated with an aquatic habit. We found limited associations between habit and diet categories. We propose generic reallocations for four natricine species and highlight other points of uncertainty in natricine classification.

A staging table of embryonic development for a viviparous (live-bearing) lizard Eremias multiocellata (Squamata: Lacertidae)

As the only viviparous reptile in China that has both temperature-dependent sex determination (TSD) and genetic-dependent sex determination (GSD) mechanisms, Eremias multiocellata is considered as an ideal species for studying the sex determination mechanism in viviparous lizards. However, studies on embryonic stage of viviparous lizards and morphological characteristics of each stage are limited. In the present study, the embryonic development process of E. multiocellata is divided into 15 stages (stages 28-42) according to the morphology of embryos. Embryos sizes are measured and continuous dynamic variation of some key features, including limbs, genitals, eyes, pigments, and brain scales are color imaged by a stereoscopic microscope. Furthermore, based on these morphological characteristics, we compare the similarities and differences in the embryonic development of E. multiocellata with other squamate species. Our results not only identified the staging table of E. multiocellata with continuous changes of external morphological characteristics but also developed a staging scheme for an important model species that provides a necessary foundation for study of sex determination in a viviparous lizard.

Ecological Filtering and Exaptation in the Evolution of Marine Snakes

AbstractConvergent evolution is often attributed to adaptation of form to function, but it can also result from ecological filtering, exaptation, or nonaptation. Testing among these possibilities is critical to understanding how and why morphological similarities emerge independently in multiple lineages. To address this challenge, we combined multiple preexisting phylogenetic methods to jointly estimate the habitats and morphologies of lineages within a phylogeny. We applied this approach to the invasions of snakes into the marine realm. We utilized a data set for 1,243 extant snake species consisting of newly compiled biome occupancy information and preexisting data on reproductive strategy, body mass, and environmental temperature and elevation. We find evidence for marine clades arising from a variety of aquatic and terrestrial habitats. Furthermore, there is strong evidence of ecological filtering for nonmarine ancestors that were already viviparous, had slightly larger-than-average body sizes, and lived in environments with higher-than-average temperatures and lower-than-average elevations. In aggregate, similarities among independent lineages of marine snakes result from a combination of exaptation and strong ecological filtering. Strong barriers to entry of new habitats appear to be more important than common adaptations following invasions for producing similarities among independent lineages invading a shared, novel habitat.

Inside the head of snakes: influence of size, phylogeny, and sensory ecology on endocranium morphology

Environmental properties, and the behavioral habits of species impact sensory cues available for foraging, predator avoidance and inter/intraspecific communication. Consequently, relationships have been discovered between the sensory ecology and brain morphology in many groups of vertebrates. However, these types of studies have remained scare on snake. Here, we investigate the link between endocranial shape and the sensory-related ecology of snakes by comparing 36 species of snakes for which we gathered six sensory-ecology characteristics. We use µCT scanning and 3D geometric morphometrics to compare their endocranium in a phylogenetically informed context. Our results demonstrate that size is a major driver of endocranial shape, with smaller species tending to maximize endocranial volume using a more bulbous shape, while larger species share an elongate endocranial morphology. Phylogeny plays a secondary role with more derived snakes diverging the most in endocranial shape, compared to other species. The activity period influences the shape of the olfactory and optic tract, while the foraging habitat impacts the shape of the cerebellum and cranial nerve regions: structures involved in orientation, equilibrium, and sensory information. However, we found that endocranial morphology alone is not sufficient to predict the activity period of a species without prior knowledge of its phylogenetic relationship. Our results thus demonstrate the value of utilizing endocranial shape as complementary information to size and volume in neurobiological studies.

Viviparous Reptile Regarded to Have Temperature-Dependent Sex Determination Has Old XY Chromosomes

The water skinks Eulamprus tympanum and Eulamprus heatwolei show thermally induced sex determination where elevated temperatures give rise to male offspring. Paradoxically, Eulamprus species reproduce in temperatures of 12–15 °C making them outliers when compared with reptiles that use temperature as a cue for sex determination. Moreover, these two species are among the very few viviparous reptiles reported to have thermally induced sex determination. Thus, we tested whether these skinks possess undetected sex chromosomes with thermal override. We produced transcriptome and genome data for E. heatwolei. We found that E. heatwolei presents XY chromosomes that include 14 gametologs with regulatory functions. The Y chromosomal region is 79–116 Myr old and shared between water and spotted skinks. Our work provides clear evidence that climate could be useful to predict the type of sex determination systems in reptiles and it also indicates that viviparity is strictly associated with sex chromosomes.

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity

Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species' abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth's Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth's biodiversity.

Climatic niche differences among Zootoca vivipara clades with different parity modes: implications for the evolution and maintenance of viviparity

Parity mode (oviparity/viviparity) importantly affects the ecology, morphology, physiology, biogeography and evolution of organisms. The main hypotheses explaining the evolution and maintenance of viviparity are based on bioclimatic predictions and also state that the benefits of viviparity arise during the reproductive period. We identify the main climatic variables discriminating between viviparous and oviparous Eurasian common lizard (Zootoca vivipara) occurrence records during the reproductive period and over the entire year.

Analyses based on the climates during the reproductive period show that viviparous clades inhabit sites with less variable temperature and precipitation. On the contrary, analyses based on the annual climates show that viviparous clades inhabit sites with more variable temperatures.

Results from models using climates during reproduction are in line with the “selfish-mother hypothesis”, which can explain the success of viviparity, the maintenance of the two reproductive modes, and why viviparous individuals cannot colonize sites inhabited by oviparous ones (and vice versa). They suggest that during the reproductive period viviparity has an adaptive advantage over oviparity in less risky habitats thanks to the selfish behaviour of the mothers. Moreover, the results from both analyses stress that hypotheses about the evolution and maintenance of viviparity need to be tested during the reproductive period.

Evolutionary origins of viviparity consistent with palaeoclimate and lineage diversification

It is of fundamental importance for the field of evolutionary biology to understand when and why major evolutionary transitions occur. Live-bearing young (viviparity) is a major evolutionary change and has evolved from egg-laying (oviparity) independently in many vertebrate lineages and most abundantly in lizards and snakes. Although contemporary viviparous squamate species generally occupy cold climatic regions across the globe, it is not known whether viviparity evolved as a response to cold climate in the first place. Here, we used available published time-calibrated squamate phylogenies and parity data on 3,498 taxa. We compared the accumulation of transitions from oviparity to viviparity relative to background diversification and a simulated binary trait. Extracting the date of each transition in the phylogenies and informed by 65 my of global palaeoclimatic data, we tested the nonexclusive hypotheses that viviparity evolved under the following: (a) cold, (b) long-term stable climatic conditions and (c) with background diversification rate. We show that stable and long-lasting cold climatic conditions are correlated with transitions to viviparity across squamates. This correlation of parity mode and palaeoclimate is mirrored by background diversification in squamates, and simulations of a binary trait also showed a similar association with palaeoclimate, meaning that trait evolution cannot be separated from squamate lineage diversification. We suggest that parity mode transitions depend on environmental and intrinsic effects and that background diversification rate may be a factor in trait diversification more generally.

Exploring diversification drivers in golden orbweavers

Heterogeneity in species diversity is driven by the dynamics of speciation and extinction, potentially influenced by organismal and environmental factors. Here, we explore macroevolutionary trends on a phylogeny of golden orbweavers (spider family Nephilidae). Our initial inference detects heterogeneity in speciation and extinction, with accelerated extinction rates in the extremely sexually size dimorphic Nephila and accelerated speciation in Herennia, a lineage defined by highly derived, arboricolous webs, and pronounced island endemism. We evaluate potential drivers of this heterogeneity that relate to organisms and their environment. Primarily, we test two continuous organismal factors for correlation with diversification in nephilids: phenotypic extremeness (female and male body length, and sexual size dimorphism as their ratio) and dispersal propensity (through range sizes as a proxy). We predict a bell-shaped relationship between factor values and speciation, with intermediate phenotypes exhibiting highest diversification rates. Analyses using SSE-class models fail to support our two predictions, suggesting that phenotypic extremeness and dispersal propensity cannot explain patterns of nephilid diversification. Furthermore, two environmental factors (tropical versus subtropical and island versus continental species distribution) indicate only marginal support for higher speciation in the tropics. Although our results may be affected by methodological limitations imposed by a relatively small phylogeny, it seems that the tested organismal and environmental factors play little to no role in nephilid diversification. In the phylogeny of golden orbweavers, the recent hypothesis of universal diversification dynamics may be the simplest explanation of macroevolutionary patterns.

Local superimpositions facilitate morphometric analysis of complex articulating structures

Articulating structures, such as the vertebrate skeleton or the segmented arthropod exoskeleton, comprise a majority of the morphological diversity across the eukaryotic tree of life. Quantifying the form of articulating structures is therefore imperative for a fuller understanding of the factors influencing biological form. A wealth of freely available 3D data capturing this morphological diversity is stored in online repositories such as Morphosource, but the geometric morphometric analysis of an articulating structure is impeded by arbitrary differences in the resting positions of its individual articulating elements. In complex articulating structures, where the angles between articulating elements cannot be standardized, landmarks on articulating elements must be Procrustes superimposed independently (locally) and then recombined to quantify variation in the entire articulating structure simultaneously. Here, we discuss recent advances in local superimposition techniques, namely the “matched local superimpositions” approach, which incorporates anatomically accurate relative sizes, positions, and orientations of locally-superimposed landmarks, enabling clearer biological interpretation. We also use simulations to evaluate the consequences of choice of superimposition approach. Our results show that local superimpositions will isolate shape variation within locally-superimposed landmark subsets by sacrificing size and positional variation. They may also create morphometric “modules” when there are none by increasing integration within the locally-superimposed subsets; however, this effect is no greater than the spurious between-module integration created when superimposing landmark subsets (i.e., articulating elements) together. Taken together, our results show that local superimposition techniques differ from conventional Procrustes superimpositions in predictable ways. Finally, we use empirical datasets of the skulls of wrasses and colubriform snakes to highlight the promise of local superimpositions and their utility. Complex articulating structures must be studied, and the only current solution to do so is local superimpositions.

Venomous Snakes Reveal Ecological and Phylogenetic Factors Influencing Variation in Gut and Oral Microbiomes

The gastrointestinal tract (GIT) of vertebrates contains a series of organs beginning with the mouth and ending with the anus or cloacal opening. Each organ represents a unique environment for resident microorganisms. Due to their simple digestive anatomy, snakes are good models for studying microbiome variation along the GIT. Cloacal sampling captures the majority of the microbial diversity found in the GIT of snakes—yet little is known about the oral microbiota of snakes. Most research on the snake mouth and gut microbiota are limited to studies of a single species or captive-bred individuals. It therefore remains unclear how a host’s life history, diet, or evolutionary history correlate with differences in the microbial composition within the mouths and guts of wild snakes. We sampled the mouth and gut microbial communities from three species of Asian venomous snakes and utilized 16S rRNA microbial inventories to test if host phylogenetic and ecological differences correlate with distinct microbial compositions within the two body sites. These species occupy three disparate habitat types: marine, semi-arboreal, and arboreal, our results suggest that the diversity of snake mouth and gut microbial communities correlate with differences in both host ecology and phylogeny.

Convergence and divergence in anti-predator displays: a novel approach to quantitative behavioural comparison in snakes

Animals in nature use many strategies to evade or deter their predators. Within venomous snake mimicry, stereotyped anti-predator behaviours are hypothesized to be effective warning signals under strong selection for independent convergence across species. However, no studies have systematically quantified snake anti-predator displays across taxonomically broad clades to examine how these behaviours evolve within a comparative methods framework. Here we describe a new high-throughput approach for collecting and quantifying anti-predator displays in snakes that demonstrates both low observer bias and infinite extension. Then, we show this method’s utility by comparing 20 species spanning six taxonomic families from Peru. We found that a simple experimental set-up varying simulated predator cues was successful in eliciting displays across species and that high-speed videography captured a great diversity of anti-predator responses. Although display components show complicated patterns of covariance, we found support for behavioural convergence in anti-predator displays among elapid coral snakes and their distantly related mimics. Our approach provides new analytical opportunities for both behaviour and kinematics, especially macroevolutionary analyses across clades with similar difficulty in observing or comparing trait diversity.