The Foraging Behavior of Free-ranging Rattlesnakes (Crotalus oreganus) in California Ground Squirrel (Otospermophilus beecheyi) Colonies

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

Safety in coils: predation rates of ambush hunting rattlesnakes are extremely low

Rattlesnakes are widespread mesopredators that are themselves killed and eaten by a host of other predators, including birds of prey and carnivorous mammals. Although anecdotal accounts of rattlesnake depredation are common, there are few quantitative data on encounter rates between rattlesnakes and their predators. Here we review a large database of encounters between rattlesnakes and their predators recorded from field videography of snakes in the sit-and-wait phase of their ambush hunting strategy. We found that, across 8300 hours of observation, adult rattlesnakes of six species and multiple populations exhibit low encounter rates with predators; furthermore, when predators were encountered, we never observed them to attack or kill coiled snakes. Thus, we propose that rattlesnakes are preyed upon while performing other, riskier behaviors associated with moving through the landscape. We also discuss why rattlesnakes are at low risk of predation while hunting on the surface.

Genetic characterization of potential venom resistance proteins in California ground squirrels ( Otospermophilus beecheyi ) using transcriptome analyses

Understanding the molecular basis of adaptations in coevolving species requires identifying the genes that underlie reciprocally selected phenotypes, such as those involved in venom in snakes and resistance to the venom in their prey. In this regard, California ground squirrels (CGS; Otospermophilus beecheyi) are eaten by northern Pacific rattlesnakes (Crotalus oreganus oreganus), but individual squirrels may still show substantial resistance to venom and survive bites. A recent study using proteomics identified venom interactive proteins (VIPs) in the blood serum of CGS. These VIPs represent possible resistance proteins, but the sequences of genes encoding them are unknown despite the value of such data to molecular studies of coevolution. To address this issue, we analyzed a de novo assembled transcriptome from CGS liver tissue-where many plasma proteins are synthesized-and other tissues from this species. We then examined VIP sequences in terms of three characteristics that identify them as possible resistance proteins: evidence for positive selection, high liver expression, and nonsynonymous variation across CGS populations. Based on these characteristics, we identified five VIPs (i.e., α-2-macroglobulin, α-1-antitrypsin-like protein GS55-LT, apolipoprotein A-II, hibernation-associated plasma protein HP-20, and hibernation-associated plasma protein HP-27) as the most likely candidates for resistance proteins among VIPs identified to date. Four of these proteins have been previously implicated in conferring resistance to the venom in mammals, validating our approach. When combined with the detailed information available for rattlesnake venom proteins, these results set the stage for future work focused on understanding coevolutionary interactions at the molecular level between these species.

Promoting co-existence between humans and venomous snakes through increasing the herpetological knowledge base

Snakebite incidence at least partly depends on the biology of the snakes involved. However, studies of snake biology have been largely neglected in favour of anthropic factors, with the exception of taxonomy, which has been recognised for some decades to affect the design of antivenoms. Despite this, within-species venom variation and the unpredictability of the correlation with antivenom cross-reactivity has continued to be problematic. Meanwhile, other aspects of snake biology, including behaviour, spatial ecology and activity patterns, distribution, and population demography, which can contribute to snakebite mitigation and prevention, remain underfunded and understudied. Here, we review the literature relevant to these aspects of snakebite and illustrate how demographic, spatial, and behavioural studies can improve our understanding of why snakebites occur and provide evidence for prevention strategies. We identify the large gaps that remain to be filled and urge that, in the future, data and relevant metadata be shared openly via public data repositories so that studies can be properly replicated and data used in future meta-analyses.

Phenotypic and functional variation in venom and venom resistance of two sympatric rattlesnakes and their prey

Predator-prey interactions often lead to the coevolution of adaptations associated with avoiding predation and, for predators, overcoming those defences. Antagonistic coevolutionary relationships are often not simple interactions between a single predator and prey but rather a complex web of interactions between multiple coexisting species. Coevolution between venomous rattlesnakes and small mammals has led to physiological venom resistance in several mammalian taxa. In general, viperid venoms contain large quantities of snake venom metalloproteinase toxins (SVMPs), which are inactivated by SVMP inhibitors expressed in resistant mammals. We explored variation in venom chemistry, SVMP expression, and SVMP resistance across four co-distributed species (California Ground Squirrels, Bryant's Woodrats, Southern Pacific Rattlesnakes, and Red Diamond Rattlesnakes) collected from four different populations in Southern California. Our aim was to understand phenotypic and functional variation in venom and venom resistance in order to compare coevolutionary dynamics of a system involving two sympatric predator-prey pairs to past studies that have focused on single pairs. Proteomic analysis of venoms indicated that these rattlesnakes express different phenotypes when in sympatry, with Red Diamonds expressing more typical viperid venom (with a diversity of SVMPs) and Southern Pacifics expressing a more atypical venom with a broader range of non-enzymatic toxins. We also found that although blood sera from both mammals were generally able to inhibit SVMPs from both rattlesnake species, inhibition depended strongly on the snake population, with snakes from one geographic site expressing SVMPs to which few mammals were resistant. Additionally, we found that Red Diamond venom, rather than woodrat resistance, was locally adapted. Our findings highlight the complexity of coevolutionary relationships between multiple predators and prey that exhibit similar offensive and defensive strategies in sympatry.

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.

The Effects of Temperature on the Kinematics of Rattlesnake Predatory Strikes in Both Captive and Field Environments

The outcomes of predator-prey interactions between endotherms and ectotherms can be heavily influenced by environmental temperature, owing to the difference in how body temperature affects locomotor performance. However, as elastic energy storage mechanisms can allow ectotherms to maintain high levels of performance at cooler body temperatures, detailed analyses of kinematics are necessary to fully understand how changes in temperature might alter endotherm-ectotherm predator-prey interactions. Viperid snakes are widely distributed ectothermic mesopredators that interact with endotherms both as predator and prey. Although there are numerous studies on the kinematics of viper strikes, surprisingly few have analyzed how this rapid movement is affected by temperature. Here we studied the effects of temperature on the predatory strike performance of rattlesnakes (Crotalus spp.), abundant new world vipers, using both field and captive experimental contexts. We found that the effects of temperature on predatory strike performance are limited, with warmer snakes achieving slightly higher maximum strike acceleration, but similar maximum velocity. Our results suggest that, unlike defensive strikes to predators, rattlesnakes may not attempt to maximize strike speed when attacking prey, and thus the outcomes of predatory strikes may not be heavily influenced by changes in temperature.

Physiological Stress Integrates Resistance to Rattlesnake Venom and the Onset of Risky Foraging in California Ground Squirrels

Using venom for predation often leads to the evolution of resistance in prey. Understanding individual variation in venom resistance is key to unlocking basic mechanisms by which antagonistic coevolution can sustain variation in traits under selection. For prey, the opposing challenges of predator avoidance and resource acquisition often lead to correlated levels of risk and reward, which in turn can favor suites of integrated morphological, physiological and behavioral traits. We investigate the relationship between risk-sensitive behaviors, physiological resistance to rattlesnake venom, and stress in a population of California ground squirrels. For the same individuals, we quantified foraging decisions in the presence of snake predators, fecal corticosterone metabolites (a measure of “stress”), and blood serum inhibition of venom enzymatic activity (a measure of venom resistance). Individual responses to snakes were repeatable for three measures of risk-sensitive behavior, indicating that some individuals were consistently risk-averse whereas others were risk tolerant. Venom resistance was lower in squirrels with higher glucocorticoid levels and poorer body condition. Whereas resistance failed to predict proximity to and interactions with snake predators, individuals with higher glucocorticoid levels and in lower body condition waited the longest to feed when near a snake. We compared alternative structural equation models to evaluate alternative hypotheses for the relationships among stress, venom resistance, and behavior. We found support for stress as a shared physiological correlate that independently lowers venom resistance and leads to squirrels that wait longer to feed in the presence of a snake, whereas we did not find evidence that resistance directly facilitates latency to forage. Our findings suggest that stress may help less-resistant squirrels avoid a deadly snakebite, but also reduces feeding opportunities. The combined lethal and non-lethal effects of stressors in predator–prey interactions simultaneously impact multiple key traits in this system, making environmental stress a potential contributor to geographic variation in trait expression of toxic predators and resistant prey.

Foraging mode, relative prey size and diet breadth: A phylogenetically explicit analysis of snake feeding ecology

Foraging modes (ambush vs. active foraging) are often correlated with a suite of morphological, physiological, behavioural and ecological traits known as the "adaptive syndrome" or "syndrome hypothesis." In snakes, an ecological correlate often reported in the literature is that ambush-hunting snakes have a higher relative meal size compared to actively foraging snakes which feed on smaller prey items. This "large meal versus small meal" feeding hypothesis between ambush and active foragers has become a widely accepted paradigm of snake feeding ecology, despite the fact that no rigorous meta-analysis has been conducted to support this generalization. We conducted a phylogenetically explicit meta-analysis, which included ca. 100 species, to test this paradigm of snake feeding ecology. We gathered data on prey size by inducing regurgitation by palpation in free-ranging snakes and by examining the stomach contents of preserved museum specimens. When we found prey, we recorded both snake and prey mass to estimate relative prey mass (prey mass/snake mass). We also reviewed published studies of snake feeding ecology to gather similar information for other species. Ambush and active foragers did not differ in minimum or average meal size but the maximum meal sizes consumed by ambush-foraging snakes were larger than the maximum meal sizes eaten by active foragers. This results in ambush-foraging snakes consuming a significantly wider range of meal sizes, rather than being large meal specialists compared to active foragers. We argue that ambush foragers evolved to be more opportunistic predators because they encounter prey less frequently compared to active foragers. This hypothesis is further supported by the fact that ambush foragers also exhibited marginally wider diet breadths, consuming a broader range of prey types in comparison with active foragers. Our study challenges aspects of the foraging syndrome as it is currently conceived, and our results have important implications for our understanding of how foraging mode has shaped the behaviour and physiology of ambush-foraging snakes.

To forage, mate, or thermoregulate: Influence of resource manipulation on male rattlesnake behavior

Male animals should preferentially allocate their time to performing activities that promote enhancing reproductive opportunity, but the need to acquire resources for growth and survival may compete with those behaviors in the short term. Thus, behaviors which require differing movement patterns such as ambushing prey and actively searching for mates can be mutually exclusive. Consequently, males that succeed at foraging could invest greater time and energy into mate searching. We radio-tracked sixteen male massasauga rattlesnakes (Sistrurus catenatus) and supplemented the diets of half the snakes with mice across an active season. We tested the predictions that reduced foraging needs would allow fed snakes to move (i.e., mate search) more, but that they would consequently be stationary to thermoregulate less, than unfed controls. Contrary to our first prediction, we found no evidence that fed snakes altered their mate searching behavior compared to controls. However, we found controls maintained higher body temperatures than fed snakes during the breeding season, perhaps because fed snakes spent less time in exposed ambush sites. Fed snakes had higher body condition scores than controls when the breeding season ended. Our results suggest the potential costs incurred by devoting time to stationary foraging may be outweighed by the drive to increase mating opportunities. Such instances may be especially valuable for massasaugas and other temperate reptiles that can remain inactive for upwards of half their lives or longer in some cases, and for female rattlesnakes that generally exhibit biennial or more protracted reproductive cycles.

Understanding Biological Roles of Venoms Among the Caenophidia: The Importance of Rear-Fanged Snakes

Snake venoms represent an adaptive trophic response to the challenges confronting a limbless predator for overcoming combative prey, and this chemical means of subduing prey shows several dominant phenotypes. Many front-fanged snakes, particularly vipers, feed on various vertebrate and invertebrate prey species, and some of their venom components (e.g., metalloproteinases, cobratoxin) appear to have been selected for "broad-brush" incapacitation of different prey taxa. Using proteomic and genomic techniques, the compositional diversity of front-fanged snakes is becoming well characterized; however, this is not the case for most rear-fanged colubroid snakes. Because these species consume a high diversity of prey, and because venoms are primarily a trophic adaptation, important clues for understanding specific selective pressures favoring venom component composition will be found among rear-fanged snake venoms. Rear-fanged snakes typically (but not always) produce venoms with lower complexity than front-fanged snakes, and there are even fewer dominant (and, arguably, biologically most relevant) venom protein families. We have demonstrated taxon-specific toxic effects, where lizards and birds show high susceptibility while mammals are largely unaffected, for both Old World and New World rear-fanged snakes, strongly indicating a causal link between toxin evolution and prey preference. New data are presented on myotoxin a, showing that the extremely rapid paralysis induced by this rattlesnake toxin is specific for rodents, and that myotoxin a is ineffectual against lizards. Relatively few rear-fanged snake venoms have been characterized, and basic natural history data are largely lacking, but directed sampling of specialized species indicates that novel compounds are likely among these specialists, particularly among those species feeding on invertebrate prey such as scorpions and centipedes. Because many of the more than 2200 species of colubroid snakes are rear-fanged, and many possess a Duvernoy's venom gland, understanding the nature of their venoms is foundational to understanding venom evolution in advanced snakes.