Felipe Gobbi Grazziotin

High-quality genomic resources are important for accurate assessments of adaptive evolution in rapidly evolving island endemic species. The golden lancehead (Bothrops insularis) is a critically endangered venomous species endemic to the Queimada Grande island located on the southeast coast of Brazil, with no reference genome available. Here, we present a high-quality near chromosome-level and well-annotated genome for the golden lancehead. A macrosyntenic analysis using genomes from other viper species revealed that microchromosomes present higher rearrangements consisting of fission and fusion events. Using our genome and genomic data from eight individuals, we conducted a survey of the genetic variation of toxin genes, which included the nucleotide diversity and copy-number variation (CNV). We also inferred a demographic history for the species in the last 100,000 years. The genetic variation analysis revealed that major components of B. insularis venom appear to be evolving largely under natural selection processes rather than genetic drift as expected for an insular species. PLA2s and CTLs are under balancing selection, whereas SVMPs and SVSPs are under positive selection. The CNV suggests recent duplication events in SVMPs and CTLs and deletion events in SVSPs and PLA2s. The demographic history indicates a stable population size over the last 10,000 years, suggesting that B. insularis is both genetically and demographically healthy. Altogether, we provide a genomic resource to better understand the differentiation of an iconic snake and evidence that selection has driven the evolution of diverse venom genes over short evolutionary timescales in an insular species.

Feeding specialization in organisms with indeterminate growth often leads to size-structured populations characterized by ontogenetic shifts in prey preferences (OSPPs). These shifts drive phenotypic changes that enhance feeding performance for specific prey. In snakes, OSPP is widely common, with juveniles typically consuming small ectotherms and transitioning to larger and potentially more dangerous endothermic prey as they grow. These transitions impose selective pressures on skull structure that are likely to influence cranial development in gape-limited predators, such as snakes. We examined skull ontogeny in pitvipers of the genus Bothrops, comparing species born as endotherm specialists [early-stage endotherm specialists (ESEnS)] with those that become endotherm specialists later through OSPPs [late-stage endotherm specialists (LSEnS)]. Using linear and geometric morphometric data, we analysed skull shape relative to body size through ontogenetic allometric trajectories (OATs). We hypothesized that ESEnS undergo slower, more gradual, and stable morphological changes throughout ontogeny, without abrupt shifts in OAT slopes, whereas LSEnS exhibit faster morphological changes, with shifts in OAT slopes coinciding with the onset of endothermic prey consumption. Our findings supported these predictions, revealing slower cranial morphological changes in ESEnS and rapid alterations in gnathic bones (key determinants of gape size) in LSEnS. These accelerations coincided with their dietary transition, supporting the hypothesis that divergent feeding strategies drive differential cranial development in Bothrops.

Although biologists have described biofluorescence in a diversity of taxa, there have been few systematic efforts to document the extent of biofluorescence within a taxonomic group or investigate its general significance. Through a field survey across South America, we discover and document patterns of biofluorescence in tropical amphibians. We more than triple the number of anuran species that have been tested for this trait. We find evidence for ecological tuning (i.e., the specific adaptation of a signal to the environment in which it is received) of the biofluorescent signals. For 56.58% of species tested, the fluorescence excitation peak matches the wavelengths most abundant at twilight, the light environment in which most frogs are active. Additionally, biofluorescence emission spans both wavelengths of low availability in twilight and the peak sensitivity of green-sensitive rods in the anuran eye, likely increasing contrast of this signal for a conspecific receiver. We propose an expanded key for testing the ecological significance of biofluorescence in future studies, providing potential explanations for the other half of fluorescent signals not originally meeting formerly proposed criteria. With evidence of tuning to the ecology and sensory systems of frogs, our results suggest frog biofluorescence is likely functioning in anuran communication.

Snake venoms have evolved in several families of Caenophidae, and their toxins have been assumed to be biochemical weapons with a role as a trophic adaptation. However, it remains unclear how venom contributes to the success of venomous species for adaptation to different environments. Here we compared the venoms from Bothrocophias hyoprora, Bothrops taeniatus, Bothrops bilineatus smaragdinus, Bothrops brazili, and Bothrops atrox collected in the Amazon Rainforest, aiming to understand the ecological and toxinological consequences of venom composition. Transcriptomic and proteomic analyses indicated that the venoms presented the same toxin groups characteristic from bothropoids, but with distinct isoforms with variable qualitative and quantitative abundances, contributing to distinct enzymatic and toxic effects. Despite the particularities of each venom, commercial Bothrops antivenom recognized the venom components and neutralized the lethality of all species. No clear features could be observed between venoms from arboreal and terrestrial habitats, nor in the dispersion of the species throughout the Amazon habitats, supporting the notion that venom composition may not shape the ecological or toxinological characteristics of these snake species and that other factors influence their foraging or dispersal in different ecological niches.

Aim: The widespread megadiverse Neotropical snake family Dipsadidae occurs in a large range of diverse habitats. Therefore, it represents an excellent model to study the diversification of Neotropical biota. Herein, by generating a time‐calibrated species‐level phylogeny, we investigate the origin and historical biogeography of Dipsadidae and test if its two main Neotropical subfamilies, Xenodontinae and Dipsadinae, have different geographical origins.Location: Neotropical region.Taxon: Dipsadidae (Serpentes).Methods: We generated a new Bayesian time‐calibrated phylogeny based on published sequences from six genes for 344 species, including 287 species of Dipsadidae. We subsequently estimated ancestral areas of distribution by comparing models in BioGeoBEARS: DEC (subset sympatry, narrow vicariance), DIVALIKE (narrow and wide vicariance), BAYAREALIKE (no vicariance and widespread sympatry), also testing jump dispersal. We also estimated shifts in the diversification of this group using BAMM, exploring possible relationships with its historical biogeography.Results: The best models show that Dipsadidae likely originated approximately 50 million years ago (mya) in Asia. Dispersal was a fundamental process in its historical biogeography. The DEC model with jump dispersal indicated that this family underwent a range extension from Asia and posterior vicariance of North and Central America ancestors. Both Xenodontinae and Dipsadinae originated in Central America and dispersed to South America during Middle Eocene, but did so to different regions (cis and trans‐Andean South America, respectively). Xenodontinae entered cis‐Andean South America around 39 mya and jump dispersed to the West Indies around 33 mya, while Dipsadinae entered trans‐Andean South America multiple times 20–38 mya. The diversification rate decreased through time, except for a clade within Dipsadinae composed of the Dipsadini tribe and the Atractus and Geophis genera.Main Conclusions: Our results show that Dipsadidae has an Asian origin and that the two main Neotropical subfamilies originated in Central America, later dispersing to South America in different time periods. This difference is also reflected in the higher diversification rate for the ‘goo‐eaters’ in the Dipsadinae subfamily. The current biogeographical patterns of the family Dipsadidae, the most species‐rich snake family in the world, have likely been shaped by complex evolutionary and geological processes such as Eocene land bridges, Andean uplift and the formation of the Panama isthmus.

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.

Snakes of the Philodryadini tribe are included in the Dipsadidae family, which is a diverse group of rear-fanged snakes widespread in different ecological conditions, including habitats and diet. However, little is known about the composition and effects of their venoms despite their relevance for understanding the evolution of these snakes or even their impact on the occasional cases of human envenoming. In this study, we integrated venom gland transcriptomics, venom proteomics and functional assays to characterize the venoms from eight species of the Philodryadini tribe, which includes the genus Philodryas, Chlorosoma and Xenoxybelis. The most abundant components identified in the venoms were snake venom metalloproteinases (SVMPs), cysteine-rich secretory proteins (CRISPs), C-type lectins (CTLs), snake endogenous matrix metalloproteinases type 9 (seMMP-9) and snake venom serinoproteinases (SVSPs). These protein families showed a variable expression profile in each genus. SVMPs were the most abundant components in Philodryas, while seMMP-9 and CRISPs were the most expressed in Chlorosoma and Xenoxybelis, respectively. Lineage-specific differences in venom composition were also observed among Philodryas species, whereas P. olfersii presented the highest amount of SVSPs and P. agassizii was the only species to express significant amounts of 3FTx. The variability observed in venom composition was confirmed by the venom functional assays. Philodryas species presented the highest SVMP activity, whereas Chlorosoma species showed higher levels of gelatin activity, which may correlate to the seMMP-9 enzymes. The variability observed in the composition of these venoms may be related to the tribe phylogeny and influenced by their diets. In the presented study, we expanded the set of venomics studies of the Philodryadini tribe, which paves new roads for further studies on the evolution and ecology of Dipsadidae snakes.