Feeding Ecology of Sidewinder Rattlesnakes, Crotalus cerastes (Viperidae)

Where the "ruber" Meets the Road: Using the Genome of the Red Diamond Rattlesnake to Unravel the Evolutionary Processes Driving Venom Evolution

Understanding the proximate and ultimate causes of phenotypic variation is fundamental in evolutionary research, as such variation provides the substrate for selection to act upon. Although trait variation can arise due to selection, the importance of neutral processes is sometimes understudied. We presented the first reference-quality genome of the Red Diamond Rattlesnake (Crotalus ruber) and used range-wide 'omic data to estimate the degree to which neutral and adaptive evolutionary processes shaped venom evolution. We characterized population structure and found substantial genetic differentiation across two populations, each with distinct demographic histories. We identified significant differentiation in venom expression across age classes with substantially reduced but discernible differentiation across populations. We then used conditional redundancy analysis to test whether venom expression variation was best predicted by neutral divergence patterns or geographically variable (a)biotic factors. Snake size was the most significant predictor of venom variation, with environment, prey availability, and neutral sequence variation also identified as significant factors, though to a lesser degree. By directly including neutrality in the model, our results confidently highlight the predominant, yet not singular, role of life history in shaping venom evolution.

A Review of Rattlesnake Venoms

Venom components are invaluable in biomedical research owing to their specificity and potency. Many of these components exist in two genera of rattlesnakes, Crotalus and Sistrurus, with high toxicity and proteolytic activity variation. This review focuses on venom components within rattlesnakes, and offers a comparison and itemized list of factors dictating venom composition, as well as presenting their known characteristics, activities, and significant applications in biosciences. There are 64 families and subfamilies of proteins present in Crotalus and Sistrurus venom. Snake venom serine proteases (SVSP), snake venom metalloproteases (SVMP), and phospholipases A2 (PLA2) are the standard components in Crotalus and Sistrurus venom. Through this review, we highlight gaps in the knowledge of rattlesnake venom; there needs to be more information on the venom composition of three Crotalus species and one Sistrurus subspecies. We discuss the activity and importance of both major and minor components in biomedical research and drug development.

Quantifying Southern Pacific Rattlesnake (Crotalus oreganus helleri) Hunting Behavior through Community Science

It is increasingly important to study animal behaviors as these are the first responses organisms mount against environmental changes. Rattlesnakes, in particular, are threatened by habitat loss and human activity, and require costly tracking by researchers to quantify the behaviors of wild individuals. Here, we show how photo-vouchered observations submitted by community members can be used to study cryptic predators like rattlesnakes. We utilized two platforms, iNaturalist and HerpMapper, to study the hunting behaviors of wild Southern Pacific Rattlesnakes. From 220 observation photos, we quantified the direction of the hunting coil (i.e., “handedness”), microhabitat use, timing of observations, and age of the snake. With these data, we looked at whether snakes exhibited an ontogenetic shift in behaviors. We found no age differences in coil direction. However, there was a difference in the microhabitats used by juveniles and adults while hunting. We also found that juveniles were most commonly observed during the spring, while adults were more consistently observed throughout the year. Overall, our study shows the potential of using community science to study the behaviors of cryptic predators.

Phylogenetically diverse diets favor more complex venoms in North American pitvipers

The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.

Intercontinental test of constraint-breaking adaptations: Testing behavioural plasticity in the face of a predator with novel hunting strategies

Constraint-breaking adaptations are evolutionary tools that provide a mechanism for incumbent-replacement between species filling similar ecological roles. In common-garden experiments, we exposed populations of two desert rodents to two different viper species, testing their ability to adjust to novel predators that use different hunting strategies. We aimed to understand whether both predators and prey with constraint-breaking adaptations actually manifest comparative advantage over their counterparts. We used convergent species from desert dunes in the Mojave Desert in North America, Merriam's kangaroo rat Dipodomys merriami and the sidewinder rattlesnake Crotalus cerastes, and from the Negev Desert in the Middle East, the greater Egyptian gerbil Gerbillus pyramidum and the Saharan horned viper Cerastes cerastes. Both Mojave species hold constraint-breaking adaptations in relation to their counterparts from the Negev. The rattlesnakes have heat sensing organs (pits) and the kangaroo rats have fur-lined cheek pouches that allow for greater foraging efficiency and food preservation. Using patch-use theory, we evaluated the rodents' risk-assessment from each snake-separately, together and in combination with barn owls. Initially each rodent species foraged less in the presence of its familiar snake, but within a month both foraged less in the presence of the pit-viper (sidewinder). Our findings indicate a level of learning, and behavioural plasticity, in both rodents and ability to assess the risk from novel predators. The kangaroo rats were capable of harvesting far greater amounts of resources under the same conditions of elevated risk. However, the reason for their advantage may lie in bi-pedal agility and not only their ability collect food more efficiently.

Intraspecific sequence and gene expression variation contribute little to venom diversity in sidewinder rattlesnakes ( Crotalus cerastes)

Traits can evolve rapidly through changes in gene expression or protein-coding sequences. However, these forms of genetic variation can be correlated and changes to one can influence the other. As a result, we might expect traits lacking differential expression to preferentially evolve through changes in protein sequences or morphological adaptation. Given the lack of differential expression across the distribution of sidewinder rattlesnakes ( Crotalus cerastes), we tested this hypothesis by comparing the coding regions of genes expressed in the venom gland transcriptomes and fang morphology. We calculated Tajima's D and F_ST across four populations comparing toxin and nontoxin loci. Overall, we found little evidence of directional selection or differentiation between populations, suggesting that changes to protein sequences do not underlie the evolution of sidewinder venom or that toxins are under extremely variant selection pressures. Although low-expression toxins do not have higher sequence divergence between populations, they do have more standing variation on which selection can act. Additionally, we found significant differences in fang length among populations. The lack of differential expression and sequence divergence suggests sidewinders-given their generalist diet, moderate gene flow and environmental variation-are under stabilizing selection which functions to maintain a generalist phenotype. Overall, we demonstrate the importance of examining the relationship between gene expression and protein-coding changes to understand the evolution of complex traits.

Infrared-sensing snakes select ambush orientation based on thermal backgrounds

Sensory information drives the ecology and behaviour of animals, and some animals are able to detect environmental cues unavailable to us. For example, rattlesnakes use infrared (IR) radiation to detect warm prey at night when visual cues are reduced. Until recently these sensory worlds have been inaccessible to human observers; now technology can allow us to "eavesdrop" on these species and understand how sensory perception drives ecology and behaviour. We used thermography and computer simulations to examine how prey-background temperature contrast and areas of temperature transitions influence the angular orientation of free-ranging rattlesnakes once they have selected an ambush site. We tracked free-ranging sidewinder rattlesnakes Crotalus cerastes to their selected ambush sites and recorded 360° near-ground thermographic panoramas from the centre of the ambush site. A computer simulation then moved a simulated prey item across the panorama and computed a contrast index for all directions. Rattlesnakes did not face ambush directions that offered stronger contrast than average, but they demonstrated a striking tendency to face directions with strong thermal transitions. Background transitions likely create a readily detected, rapidly changing stimulus when a prey animal passes. Quantifications of sensory environments like this one can boost our comprehension of how sensory function impacts the ecology, behaviour, and evolution of animals.

Ontogenetic Change in the Venom of Mexican Black-Tailed Rattlesnakes (Crotalus molossus nigrescens)

Ontogenetic changes in venom composition have important ecological implications due the relevance of venom in prey acquisition and defense. Additionally, intraspecific venom variation has direct medical consequences for the treatment of snakebite. However, ontogenetic changes are not well documented in most species. The Mexican Black-tailed Rattlesnake (Crotalus molossus nigrescens) is large-bodied and broadly distributed in Mexico. To document venom variation and test for ontogenetic changes in venom composition, we obtained venom samples from twenty-seven C. m. nigrescens with different total body lengths (TBL) from eight states in Mexico. The primary components in the venom were detected by reverse-phase HPLC, western blot, and mass spectrometry. In addition, we evaluated the biochemical (proteolytic, coagulant and fibrinogenolytic activities) and biological (LD₅₀ and hemorrhagic activity) activities of the venoms. Finally, we tested for recognition and neutralization of Mexican antivenoms against venoms of juvenile and adult snakes. We detected clear ontogenetic venom variation in C. m. nigrescens. Venoms from younger snakes contained more crotamine-like myotoxins and snake venom serine proteinases than venoms from older snakes; however, an increase of snake venom metalloproteinases was detected in venoms of larger snakes. Venoms from juvenile snakes were, in general, more toxic and procoagulant than venoms from adults; however, adult venoms were more proteolytic. Most of the venoms analyzed were hemorrhagic. Importantly, Mexican antivenoms had difficulties recognizing low molecular mass proteins (<12 kDa) of venoms from both juvenile and adult snakes. The antivenoms did not neutralize the crotamine effect caused by the venom of juveniles. Thus, we suggest that Mexican antivenoms would have difficulty neutralizing some human envenomations and, therefore, it may be necessary improve the immunization mixture in Mexican antivenoms to account for low molecular mass proteins, like myotoxins.

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation

Changes in gene expression can rapidly influence adaptive traits in the early stages of lineage diversification. Venom is an adaptive trait comprised of numerous toxins used for prey capture and defense. Snake venoms can vary widely between conspecific populations, but the influence of lineage diversification on such compositional differences are unknown. To explore venom differentiation in the early stages of lineage diversification, we used RNA-seq and mass spectrometry to characterize Sidewinder Rattlesnake (Crotalus cerastes) venom. We generated the first venom-gland transcriptomes and complementary venom proteomes for eight individuals collected across the United States and tested for expression differences across life history traits and between subspecific, mitochondrial, and phylotranscriptomic hypotheses. Sidewinder venom was comprised primarily of hemorrhagic toxins, with few cases of differential expression attributable to life history or lineage hypotheses. However, phylotranscriptomic lineage comparisons more than doubled instances of significant expression differences compared to all other factors. Nevertheless, only 6.4% of toxins were differentially expressed overall, suggesting that shallow divergence has not led to major changes in Sidewinder venom composition. Our results demonstrate the need for consensus venom-gland transcriptomes based on multiple individuals and highlight the potential for discrepancies in differential expression between different phylogenetic hypotheses.

Divergent behavior amid convergent evolution: A case of four desert rodents learning to respond to known and novel vipers

Desert communities world-wide are used as natural laboratories for the study of convergent evolution, yet inferences drawn from such studies are necessarily indirect. Here, we brought desert organisms together (rodents and vipers) from two deserts (Mojave and Negev). Both predators and prey in the Mojave have adaptations that give them competitive advantage compared to their middle-eastern counterparts. Heteromyid rodents of the Mojave, kangaroo rats and pocket mice, have fur-lined cheek pouches that allow them to carry larger loads of seeds under predation risk compared to gerbilline rodents of the Negev Deserts. Sidewinder rattlesnakes have heat-sensing pits, allowing them to hunt better on moonless nights when their Negev sidewinding counterpart, the Saharan horned vipers, are visually impaired. In behavioral-assays, we used giving-up density (GUD) to gauge how each species of rodent perceived risk posed by known and novel snakes. We repeated this for the same set of rodents at first encounter and again two months later following intensive "natural" exposure to both snake species. Pre-exposure, all rodents identified their evolutionarily familiar snake as a greater risk than the novel one. However, post-exposure all identified the heat-sensing sidewinder rattlesnake as a greater risk. The heteromyids were more likely to avoid encounters with, and discern the behavioral difference among, snakes than their gerbilline counterparts.

Seed ingestion and germination in rattlesnakes: overlooked agents of rescue and secondary dispersal

Seed dispersal is a key evolutionary process and a central theme in the population ecology of terrestrial plants. The primary producers of most land-based ecosystems are propagated by and maintained through various mechanisms of seed dispersal that involve both abiotic and biotic modes of transportation. By far the most common biotic seed transport mechanism is zoochory, whereby seeds, or fruits containing them, are dispersed through the activities of animals. Rodents are one group of mammals that commonly prey on seeds (granivores) and play a critical, often destructive, role in primary dispersal and the dynamics of plant communities. In North America, geomyid, heteromyid and some sciurid rodents have specialized cheek pouches for transporting seeds from plant source to larder, where they are often eliminated from the pool of plant propagules by consumption. These seed-laden rodents are commonly consumed by snakes as they forage, but unlike raptors, coyotes, bobcats, and other endothermic predators which eat rodents and are known or implicated to be secondary seed dispersers, the role of snakes in seed dispersal remains unexplored. Here, using museum-preserved specimens, we show that in nature three desert-dwelling rattlesnake species consumed heteromyids with seeds in their cheek pouches. By examining the entire gut we discovered, furthermore, that secondarily ingested seeds can germinate in rattlesnake colons. In terms of secondary dispersal, rattlesnakes are best described as diplochorous. Because seed rescue and secondary dispersal in snakes has yet to be investigated, and because numerous other snake species consume granivorous and frugivorous birds and mammals, our observations offer direction for further empirical studies of this unusual but potentially important channel for seed dispersal.

Do free-ranging rattlesnakes use thermal cues to evaluate prey?

Rattlesnakes use infrared radiation to detect prey animals such as small mammals and lizards. Because ectotherm locomotor performance depends on temperature, rattlesnakes could use prey temperature to evaluate the potential of lizards to evade attacks. Here, we tested whether hunting rattlesnakes use infrared information to (1) detect and (2) evaluate prey before attack. We expected thermal contrast between prey and background to be the best predictor of predatory behaviour under the prey detection hypothesis, and absolute prey temperature under the prey evaluation hypothesis. We presented lizard carcasses of varying temperatures to free-ranging sidewinder rattlesnakes (Crotalus cerastes) and scored behavioural responses as a function of thermal contrast, absolute lizard temperature, and light level. Thermal contrast and light level were the most salient predictors of snake behaviour. Snakes were more likely to respond to lizards and/or respond at greater distances at night and when thermal contrast was high, supporting the known prey detection function of infrared sensing. Absolute lizard temperature was not an important predictor of snake behaviour; thus, we found no evidence for temperature-based prey evaluation. Infrared sensing is still poorly understood in ecologically relevant contexts; future research will test whether rattlesnakes learn to evaluate prey based on temperature with experience.

Phylogenetic analysis of standard metabolic rate of snakes: a new proposal for the understanding of interspecific variation in feeding behavior

The current proposal about the variation of standard metabolic rates (SMR) in snakes predicts that SMR is influenced by the feeding frequency (frequent or infrequent feeders). However, feeding frequency in snakes is poorly studied and hard to quantify under natural conditions. Alternatively, foraging strategy was studied for a large number of species and is usually related to the feeding frequency. In this work, we performed a meta-analysis on the SMR of compiled data from 74 species of snakes obtained from the literature and five more different species of lanceheads (genus Bothrops), after categorization according to the foraging mode (ambush or active foraging) and regarding their phylogenetic history. We tested the hypothesis that foraging mode (FM) is a determinant factor on the interspecific variation of SMR despite the phylogenetic relationship among species. We demonstrated that FM predicted SMR, but there is also a partial phylogenetic structuration of SMR in snakes. We also detected that evolution rates of SMR in active foragers seem to be higher than ambush-hunting snakes. We suggested that foraging mode has a major effect over the evolution of SMR in snakes, which could represent an ecophysiological co-adaptation, since ambush hunters (with low feeding rates) present a lower maintenance energetic cost (SMR) when compared to active foragers. The higher SMR evolution rates for active foraging snakes could be related to a higher heterogeny in the degree of activity during hunting by active foragers when compared to ambush-hunting snakes.