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Abstract All species evolve under selective pressures that emerge from their interactions, often antagonistic, with other species. Phenotypes mediating species interactions manifest as the combined products of the genomes of interacting species; understanding the evolutionary processes acting in one lineage therefore cannot be attained without bridging the genomes of interacting species. Venoms have arisen independently more than 100 times in animals and serve diverse roles in species interactions, including predation and defense. Each venom is evolutionarily entwined with reciprocal phenotypes, such as venom resistance, in often diverse recipient species. Despite extensive work on venoms, the full genetic basis for resistance to whole venoms is largely unknown. Using the venom of the Florida blue centipede (Scolopendra viridis) comprised of 35 toxins and Drosophila melanogaster as model prey, we investigated the genetics of venom resistance for a naive prey through experimental evolution and genetic-mapping approaches. We identified 12 consensus genes across techniques associated with venom resistance, yet individual experiments suggested a genome-wide basis for resistance involving hundreds to thousands of genes, despite the relative simplicity of the venom of S. viridis. We found no evidence for fitness trade-offs associated with the evolution of resistance and revealed a stark contrast in the nature of venom resistance between prey sexes. The disparity in resistance genetics between prey sexes as well as the relative genetic complexity of venom versus resistance may ultimately give venomous predators a coevolutionary advantage over their prey. 

Our current understanding of snake venom is highly biased towards species known to be medically significant in human envenomations. This vastly under-represents the true evolutionary and ecological breadth of snake venom, with gaps spanning entire clades and unique lifestyles. As a result, many genera of rear-fanged snakes lack well-understood venom profiles despite these taxa composing around 65% of known extant snake species. Methodological challenges associated with venom extraction have long been a key reason responsible for the lack of venom research on this group. Modern advancements in venomics technologies have allowed researchers to overcome many of these challenges and investigate the venom components of understudied genera. The genus Coniophanes (black-striped snakes) presents an ideal system for investigating venom and the venom delivery system in a rear-fanged venomous species with well-documented accounts of human envenomations. We sequenced and annotated de novo transcriptomes of the Duvernoy’s gland (DVG) for seven individuals across four species of Coniophanes (Dipsadidae) and confirmed toxin expression in representative venom proteomes. We assessed interspecific venom variation within this genus and further examined intraspecific venom variation within C. imperialis. We found that toxins account for 38.8% to 66% of the total DVG transcriptomes and that 18 toxin families are represented in this genus, with prominent expression of cystine-rich secretory proteins (CRiSPs) in three species and snake venom metalloproteinases (SVMPs) in all four species. In addition, we used diffusible iodine-based contrast-enhanced computed tomography (diceCT) to better understand the venom delivery system for C. fissidens, a widespread species within this genus, showcasing enlarged, grooved, rear fangs in close proximity to a prominent DVG. We provide the first ever characterization of the venom profiles of Coniophanes, highlight venom variation between and within species, and outline the venom delivery system of this understudied genus. 

Abstract Background The explosive radiation and diversification of the advanced snakes (superfamily Colubroidea) was associated with changes in all aspects of the shared venom system. Morphological changes included the partitioning of the mixed ancestral glands into two discrete glands devoted for production of venom or mucous respectively, as well as changes in the location, size and structural elements of the venom-delivering teeth. Evidence also exists for homology among venom gland toxins expressed across the advanced snakes. However, despite the evolutionary novelty of snake venoms, in-depth toxin molecular evolutionary history reconstructions have been mostly limited to those types present in only two front-fanged snake families, Elapidae and Viperidae. To have a broader understanding of toxins shared among extant snakes, here we first sequenced the transcriptomes of eight taxonomically diverse rear-fanged species and four key viperid species and analysed major toxin types shared across the advanced snakes. Results Transcriptomes were constructed for the following families and species: Colubridae - Helicops leopardinus , Heterodon nasicus , Rhabdophis subminiatus ; Homalopsidae – Homalopsis buccata ; Lamprophiidae - Malpolon monspessulanus , Psammophis schokari , Psammophis subtaeniatus , Rhamphiophis oxyrhynchus ; and Viperidae – Bitis atropos , Pseudocerastes urarachnoides , Tropidolaeumus subannulatus , Vipera transcaucasiana . These sequences were combined with those from available databases of other species in order to facilitate a robust reconstruction of the molecular evolutionary history of the key toxin classes present in the venom of the last common ancestor of the advanced snakes, and thus present across the full diversity of colubroid snake venoms. In addition to differential rates of evolution in toxin classes between the snake lineages, these analyses revealed multiple instances of previously unknown instances of structural and functional convergences. Structural convergences included: the evolution of new cysteines to form heteromeric complexes, such as within kunitz peptides (the beta-bungarotoxin trait evolving on at least two occasions) and within SVMP enzymes (the P-IIId trait evolving on at least three occasions); and the C-terminal tail evolving on two separate occasions within the C-type natriuretic peptides, to create structural and functional analogues of the ANP/BNP tailed condition. Also shown was that the de novo evolution of new post-translationally liberated toxin families within the natriuretic peptide gene propeptide region occurred on at least five occasions, with novel functions ranging from induction of hypotension to post-synaptic neurotoxicity. Functional convergences included the following: multiple occasions of SVMP neofunctionalised in procoagulant venoms into activators of the clotting factors prothrombin and Factor X; multiple instances in procoagulant venoms where kunitz peptides were neofunctionalised into inhibitors of the clot destroying enzyme plasmin, thereby prolonging the half-life of the clots formed by the clotting activating enzymatic toxins; and multiple occasions of kunitz peptides neofunctionalised into neurotoxins acting on presynaptic targets, including twice just within Bungarus venoms. Conclusions We found novel convergences in both structural and functional evolution of snake toxins. These results provide a detailed roadmap for future work to elucidate predator–prey evolutionary arms races, ascertain differential clinical pathologies, as well as documenting rich biodiscovery resources for lead compounds in the drug design and discovery pipeline. 

Developmental phenotypic changes can evolve under selection imposed by age- and size-related ecological differences. Many of these changes occur through programmed alterations to gene expression patterns, but the molecular mechanisms and gene-regulatory networks underlying these adaptive changes remain poorly understood. Many venomous snakes, including the eastern diamondback rattlesnake (Crotalus adamanteus), undergo correlated changes in diet and venom expression as snakes grow larger with age, providing models for identifying mechanisms of timed expression changes that underlie adaptive life history traits. By combining a highly contiguous, chromosome-level genome assembly with measures of expression, chromatin accessibility, and histone modifications, we identified cis-regulatory elements and trans-regulatory factors controlling venom ontogeny in the venom glands ofC. adamanteus. Ontogenetic expression changes were significantly correlated with epigenomic changes within genes, immediately adjacent to genes (e.g., promoters), and more distant from genes (e.g., enhancers). We identified 37 candidate transcription factors (TFs), with the vast majority being up-regulated in adults. The ontogenetic change is largely driven by an increase in the expression of TFs associated with growth signaling, transcriptional activation, and circadian rhythm/biological timing systems in adults with corresponding epigenomic changes near the differentially expressed venom genes. However, both expression activation and repression contributed to the composition of both adult and juvenile venoms, demonstrating the complexity and potential evolvability of gene regulation for this trait. Overall, given that age-based trait variation is common across the tree of life, we provide a framework for understanding gene-regulatory-network-driven life-history evolution more broadly. 

Abstract Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey. 

The genus Calliophis is the most basal branch of the family Elapidae and several species in it have developed highly elongated venom glands. Recent research has shown that C. bivirgatus has evolved a seemingly unique toxin (calliotoxin) that produces spastic paralysis in their prey by acting on the voltage-gated sodium (NaV) channels. We assembled a transcriptome from C. bivirgatus to investigate the molecular characteristics of these toxins and the venom as a whole. We find strong confirmation that this genus produces the classic elapid eight-cysteine three-finger toxins, that δδ-elapitoxins (toxins that resemble calliotoxin) are responsible for a substantial portion of the venom composition, and that these toxins form a distinct clade within a larger, more diverse clade of C. bivirgatus three-finger toxins. This broader clade of C. bivirgatus toxins also contains the previously named maticotoxins and is somewhat closely related to cytotoxins from other elapids. However, the toxins from this clade that have been characterized are not themselves cytotoxic. No other toxins show clear relationships to toxins of known function from other species.