Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction

Characterization of genome-wide phylogenetic conflict uncovers evolutionary modes of carnivorous fungi

Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps (Drechslerella spp.), three-dimensional (3D) adhesive traps (Arthrobotrys spp.), and two-dimensional (2D) adhesive traps (Dactylellina spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that Drechslerella emerged earlier than Arthrobotrys and Dactylellina. Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.

The rise of dietary diversity in coral reef fishes

Diet has been identified as a major driver of reef fish lineage diversification, producing one of the most speciose vertebrate assemblages today. Yet, there is minimal understanding of how, when and why diet itself has evolved. To address this, we used a comprehensive gut content dataset, alongside a recently developed phylogenetic comparative method to assess multivariate prey use across a diverse animal assemblage, coral reef fishes. Specifically, we investigated the diversification, transitions and phylogenetic conservatism of fish diets through evolutionary time. We found two major pulses of diet diversification: one at the end-Cretaceous and one during the Eocene, suggesting that the Cretaceous-Palaeogene mass extinction probably provided the initial ecological landscape for fish diets to diversify. The birth of modern families during the Eocene then provided the foundation for a second wave of dietary expansion. Together, our findings showcase the role of extinction rebound events in shaping the dietary diversity of fishes on present-day coral reefs.

Ecological drivers of ultraviolet colour evolution in snakes

Ultraviolet (UV) colour patterns invisible to humans are widespread in nature. However, research bias favouring species with conspicuous colours under sexual selection can limit our assessment of other ecological drivers of UV colour, like interactions between predators and prey. Here we demonstrate widespread UV colouration across Western Hemisphere snakes and find stronger support for a predator defence function than for reproduction. We find that UV colouration has evolved repeatedly in species with ecologies most sensitive to bird predation, with no sexual dichromatism at any life stage. By modelling visual systems of potential predators, we find that snake conspicuousness correlates with UV colouration and predator cone number, providing a plausible mechanism for selection. Our results suggest that UV reflectance should not be assumed absent in "cryptically coloured" animals, as signalling beyond human visual capacities may be a key outcome of species interactions in many taxa for which UV colour is likely underreported.

Paedomorphosis and retention of juvenile diet lead speciation in a group of Neotropical snakes (Colubroides-Philodryadini)

Dipsadidae is one of the largest clades of extant reptiles, showing an impressive morphological and ecological diversity. Despite this fact, the developmental processes behind its diversity are still largely unknown. In this study, we used 3D reconstructions based on micro-CT data and geometric morphometrics to evaluate the skull morphology of Philodryas agassizii, a small, surface-dwelling dipsadid that consume spiders. Adult individuals of P. agassizii exhibit a cranial morphology frequently observed in juveniles of other surface-dwelling colubroideans, represented in our analysis by its close relative Philodryas patagoniensis. Large orbits, gibbous neurocranial roof and a relatively short jaw complex are features present in juveniles of the latter species. Furthermore, we performed an extensive survey about diet of P. patagoniensis in which we detected an ontogenetic dietary shift, indicating that arthropods are more frequently consumed by juveniles of this dietary generalist. Thus, we infer that P. agassizzii retained not only the ancestral juvenile skull morphology but also dietary preferences. This study reveals that morphological changes driven by heterochronic changes, specifically paedomorphosis, influenced the retention of ancestral life history traits in P. agassizii, and therefore promoted cladogenesis. In this way, we obtained first evidence that heterochronic processes lead speciation in the snake megadiverse clade Dipsadidae.

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.

Reconstructing the origin and early evolution of the snake brain

Snakes represent one-eighth of terrestrial vertebrate diversity, encompassing various lifestyles, ecologies, and morphologies. However, the ecological origins and early evolution of snakes are controversial topics in biology. To address the paucity of well-preserved fossils and the caveats of osteological traits for reconstructing snake evolution, we applied a different ecomorphological hypothesis based on high-definition brain reconstructions of extant Squamata. Our predictive models revealed a burrowing lifestyle with opportunistic behavior at the origin of crown snakes, reflecting a complex ancestral mosaic brain pattern. These findings emphasize the importance of quantitatively tracking the phenotypic diversification of soft tissues-including the accurate definition of intact brain morphological traits such as the cerebellum-in understanding snake evolution and vertebrate paleobiology. Furthermore, our study highlights the power of combining extant and extinct species, soft tissue reconstructions, and osteological traits in tracing the deep evolution of not only snakes but also other groups where fossil data are scarce.

Ecological correlates of cranial evolution in the megaradiation of dipsadine snakes

BACKGROUND

Dipsadine snakes represent one of the most spectacular vertebrate radiations that have occurred in any continental setting, with over 800 species in South and Central America. Their species richness is paralleled by stunning ecological diversity, ranging from arboreal snail-eating and aquatic eel-eating specialists to terrestrial generalists. Despite the ecological importance of this clade, little is known about the extent to which ecological specialization shapes broader patterns of phenotypic diversity within the group. Here, we test how habitat use and diet have influenced morphological diversification in skull shape across 160 dipsadine species using micro-CT and 3-D geometric morphometrics, and we use a phylogenetic comparative approach to test the contributions of habitat use and diet composition to variation in skull shape among species.

RESULTS

We demonstrate that while both habitat use and diet are significant predictors of shape in many regions of the skull, habitat use significantly predicts shape in a greater number of skull regions when compared to diet. We also find that across ecological groupings, fossorial and aquatic behaviors result in the strongest deviations in morphospace for several skull regions. We use simulations to address the robustness of our results and describe statistical anomalies that can arise from the application of phylogenetic generalized least squares to complex shape data.

CONCLUSIONS

Both habitat and dietary ecology are significantly correlated with skull shape in dipsadines; the strongest relationships involved skull shape in snakes with aquatic and fossorial lifestyles. This association between skull morphology and multiple ecological axes is consistent with a classic model of adaptive radiation and suggests that ecological factors were an important component in driving morphological diversification in the dipsadine megaradiation.

Dietary niche partitioning of three Sky Island Sceloporus lizards as revealed through DNA metabarcoding

Lizard diets are highly diverse and have contributed to the diversification, biogeographical distributions, and evolution of novel traits across this global radiation. Many parts of a lizard's ecology-including habitat preferences, foraging modes, predation risks, interspecific competition, and thermal constraints, among others-interact to shape diets, and dietary niche partitioning simultaneously contributes to co-occurrence within communities. We used DNA metabarcoding of fecal samples to identify prey items in the diets of three sympatric Sceloporus lizards in the Madrean Sky Islands of Arizona, USA. We found evidence for dietary niche partitioning between interacting species concomitant with their respective ecologies. We also compared diet composition between populations to understand how conserved or plastic species' diets are between different environments. Our findings suggest that habitat generalists are also diet generalists in this system, while the same may be true for specialists. The identification of prey items to much lower taxonomic levels than previously documented further reveals hidden diversity in the diets of these species and underscores the utility of metabarcoding for understanding the full complexity of lizard diets.

Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

Patterns of morphological variation and ecological correlates in the skull of vipers (Serpentes: Viperidae)

The skull of vipers is a highly kinetic anatomical structure involved in envenomating and consuming of prey. Morphological knowledge about the viperid skull is based on studies on some groups of species, but information on its variation within the whole family and its functional morphology is still scarce. In this study, we aimed to explore variation in skull morphology among species of the three subfamilies of Viperidae, and test whether that variation correlates with macrohabitat and diet. We performed quantitative analyses of the viperid skull based on broad taxonomic sampling and two methodological approaches: linear and geometric morphometrics. The results of both approaches showed that much of the variation lies in differences of shape and relative size of the premaxilla, the nasals, the frontals, and the parietals. The results indicated that phylogeny and size influence the shape of the skull, but we also found evidence of morphological differentiation between arboreal and terrestrial species and in species with mammal specialist diet. Our findings imply that, besides evolutionary allometry and phylogenetic signal, demands of particular diets coupled with use of certain habitats have in part shaped morphological evolution of the viperid skull.

The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini)

North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.

Using natricine snakes to test how prey type and size affect predatory behaviors and performance

Introduction

Predation is a complex process for which behavior, morphology, and size of both predator and prey can affect the success and effectiveness of the predator. For predators such as snakes that swallow prey whole, gape ultimately limits prey size, but the behaviors used to select, capture, and consume prey and attributes of the prey can also affect maximal prey size. For example, swallowing live, struggling prey is difficult, but using coiling or envenomation to restrain or kill prey has evolved repeatedly in snakes.

Methods

To test the potential benefits of these behaviors, we manipulated the type and size of prey, and determined how stereotyped predatory behavior was in a snake species (Liodytes rigida) that uses both coiling and envenomation to restrain and immobilize its formidable prey of crayfish. We also studied a close relative (Liodytes pygaea) that eats fish and salamanders to gain insights into the evolution of these traits.

Results

For L. rigida, envenomation of hard-shell crayfish via their soft underside was very stereotyped (100% of feedings). Envenomation of soft-shell crayfish was less frequent (59% of feedings) but became more likely both with increased relative prey size and increased time after molt (hardness). L. rigida coiled more for hard-shell than soft-shell crayfish (77% vs. 30%). The probability of coiling was unaffected by prey size, but it increased with increased time after molt for the soft-shell crayfish. Liodytes rigida waited to swallow crayfish until they were completely immobile in 75% and 37% of the feedings with hard- and soft-shelled crayfish, respectively. Even with large prey L. pygaea never used coiling or envenomation, whereas previous studies of L. alleni, the sister species of L. rigida, observed non-lethal coiling without envenomation when eating hard-shell crayfish.

Discussion

Our findings for the Liodytes clade of three species suggest that coiling evolved ancestral to the crayfish specialists (L. alleni; L. rigida), and envenomation by L. rigida subsequently evolved as an additional means of subduing formidable prey. The proximate benefits observed for coiling and envenomation in L. rigida support the evolutionary scenario that both traits evolved to enhance the feeding performance for more formidable prey.

Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family

The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.

Snake life history traits and their association with urban habitat use in a tropical city

Urbanisation changes landscapes, often simplifying and homogenising natural ecosystems while introducing novel environments. Although this transformation often adversely impacts native wildlife, generalist species that exhibit broad dietary and habitat requirements can persist and take advantage of urban environments. To understand which life history traits most influence the occurrence of a diverse snake assemblage in an urban environment, we leveraged a dataset of 5102 detection records for 12 snake species in the tropical city of Darwin, Australia. By building ecological niche models, calculating urban niche hypervolume, and compiling life history data, we analysed the diversity of environments occupied by each species and determined which landscape components were most associated with occurrence data. In keeping with our hypothesis that generalist species would be more successful, we found that species with broader habitat and dietary preferences, as well as a penchant for arboreality, were associated with larger urban niche hypervolumes and more frequent human–snake interactions. Additionally, we found that colubrid snakes had significantly larger urban niche hypervolumes than elapid species. These findings contribute to understanding how life history traits aid wildlife persistence in, and adaptation to, urban ecosystems, and have implications for landscape design and conservation management.

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.

Scaling Relationships of Maximal Gape in Two Species of Large Invasive Snakes, Brown Treesnakes and Burmese Pythons, and Implications for Maximal Prey Size

Snakes are a phylogenetically diverse (> 3500 species) clade of gape-limited predators that consume diverse prey and have considerable ontogenetic and interspecific variation in size, but empirical data on maximal gape are very limited. To test how overall size predicts gape, we quantified the scaling relationships between maximal gape, overall size, and several cranial dimensions for a wide range of sizes (mass 8-64,100 g) for two large, invasive snake species: Burmese pythons (Python molorus bivittatus) and brown treesnakes (Boiga irregularis). Although skull size scaled with negative allometry relative to overall size, isometry and positive allometry commonly occurred for other measurements. For similar snout-vent lengths (SVL), the maximal gape areas of Burmese pythons were approximately 4-6 times greater than those of brown treesnakes, mainly as a result of having a significantly larger relative contribution to gape by the intermandibular soft tissues (43% vs. 17%). In both snake species and for all types of prey, the scaling relationships predicted that relative prey mass (RPM) at maximal gape decreased precipitously with increased overall snake size. For a given SVL or mass, the predicted maximal values of RPM of the Burmese pythons exceeded those of brown treesnakes for all prey types, and predicted values of RPM were usually least for chickens, greatest for limbed reptiles and intermediate for mammals. The pythons we studied are noteworthy for having large overall size and gape that is large even after correcting for overall size, both of which could facilitate some large individuals (SVL = 5 m) exploiting very large vertebrate prey (e.g., deer > 50 kg). Although brown treesnakes had longer quadrate bones, Burmese pythons had larger absolute and larger relative gape as a combined result of larger overall size, larger relative head size, and most importantly, greater stretch of the soft tissues.

Giant gar from directly above the Cretaceous-Palaeogene boundary suggests healthy freshwater ecosystems existed within thousands of years of the asteroid impact

The Cretaceous-Palaeogene (K-Pg) mass extinction was responsible for the destruction of global ecosystems and loss of approximately three-quarters of species diversity 66 million years ago. Large-bodied land vertebrates suffered high extinction rates, whereas small-bodied vertebrates living in freshwater ecosystems were buffered from the worst effects. Here, we report a new species of large-bodied (1.4-1.5 m) gar based on a complete skeleton from the Williston Basin of North America. The new species was recovered 18 cm above the K-Pg boundary, making it one of the oldest articulated vertebrate fossils from the Cenozoic. The presence of this freshwater macropredator approximately 1.5-2.5 thousand years after the asteroid impact suggests the rapid recovery and reassembly of North American freshwater food webs and ecosystems after the mass extinction.

Differences in PLA2 Constitution Distinguish the Venom of Two Endemic Brazilian Mountain Lanceheads, Bothrops cotiara and Bothrops fonsecai

Interspecific differences in snake venom compositions can result from distinct regulatory mechanisms acting in each species. However, comparative analyses focusing on identifying regulatory elements and patterns that led to distinct venom composition are still scarce. Among venomous snakes, Bothrops cotiara and Bothrops fonsecai represent ideal models to complement our understanding of the regulatory mechanisms of venom production. These recently diverged species share a similar specialized diet, habitat, and natural history, but each presents a distinct venom phenotype. Here, we integrated data from the venom gland transcriptome and miRNome and the venom proteome of B. fonsecai and B. cotiara to better understand the regulatory mechanisms that may be acting to produce differing venom compositions. We detected not only the presence of similar toxin isoforms in both species but also distinct expression profiles of phospholipases A2 (PLA2) and some snake venom metalloproteinases (SVMPs) and snake venom serine proteinases (SVSPs) isoforms. We found evidence of modular expression regulation of several toxin isoforms implicated in venom divergence and observed correlated expression of several transcription factors. We did not find strong evidence for miRNAs shaping interspecific divergence of the venom phenotypes, but we identified a subset of toxin isoforms whose final expression may be fine-tuned by specific miRNAs. Sequence analysis on orthologous toxins showed a high rate of substitutions between PLA2s, which indicates that these toxins may be under strong positive selection or represent paralogous toxins in these species. Our results support other recent studies in suggesting that gene regulation is a principal mode of venom evolution across recent timescales, especially among species with conserved ecotypes.