Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (\u3ci\u3eCrotalus cerastes\u3c/i\u3e) 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

Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes

The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow

Phylogenomics of Vipers and the Role of Competition on Venom Evolution

Competition is a critical selective force for diversification; however, empirical studies on its role promoting differentiation of adaptive phenotypes have largely been limited to small spatial and taxonomic scales. Here, we test the effect of competition on the evolution of pitviper venoms – a cross-continental radiation of venomous snakes each with tens to hundreds of individual toxins varying in expression, composition, and overall complexity among species. By inferring a novel phylogenomic tree and reconstructing the biogeography of the Viperidae, we demonstrate a rapid radiation occurred upon invasion of the New World. Using \u3e500 venom gland transcriptomes and phylogenetic comparative modeling, we reveal that venom phenotypes diverge when multiple species coexist in a given area through time via positive diversity dependence. Furthermore, we find that pitviper communities have evolved to maximize functional diversity despite comparatively low phylogenetic diversity, suggesting an evolutionary response of venom rather than communities accumulating phylogenetically diverse species. Together, these findings support competition as a likely selective pressure driving venom diversification in pitvipers

Stopped Dead In Their Tracks: The Impact Of Railways On Gopher Tortoise (Gopherus Polyphemus) Movement And Behavior

Habitat fragmentation is one of the leading causes of biodiversity decline and most commonly results from urbanization and construction of transportation infrastructure. Roads are known to negatively impact species, but railways can often cause similar effects. Certain taxa, such as turtles and tortoises, are more vulnerable to railways than others due to limitations in mobility. We studied the impact of rails on the movement and behavior of Gopher Tortoises (Gopherus polyphemus), a threatened, highly terrestrial species likely in frequent contact with railways. First, we used radio-telemetry to determine the frequency of railway crossings and compared this to correlated random walk (CRW) simulations to assess if tortoises were crossing the rails less frequently than is expected by unconstrained movement. Second, we placed tortoises into the railway and measured behavior for one hour to assess crossing ability. Lastly, we tested whether trenches dug underneath the rails could allow safe passage for tortoises. We found that railways impacted the movement of Gopher Tortoises. Gopher Tortoises crossed the railway less often than what would be expected by unhindered movement for five of our ten tortoises tracked. During behavioral trials, 0 of 24 tortoises placed within the railways were capable of escaping from the rails. Using game cameras, we detected tortoises using trenches dug underneath the rails and between the ties 68 times over the course of a single summer. For minimal financial cost, the trenches facilitated tortoise movement across the railway, maintained full rail functionality, and created an escape route for individuals that were trapped between the rails, and thus should be implemented as a mitigation strategy. Given the thousands of km of railways around the world, we recommend future studies focus on the new field of rail ecology

On The Road Again: Assessing The Use Of Roadsides As Wildlife Corridors For Gopher Tortoises (Gopherus Polyphemus)

Small populations resulting from the impacts of habitat fragmentation are prone to increased risks of extinction because of a lack of population connectivity. Roads increase habitat fragmentation, but properly managed roadsides may be able to function as wildlife corridors. Here we use radiotelemetry to observe movement patterns of Gopher Tortoises (Gopherus polyphemus) along potential roadside corridors at the John F. Kennedy Space Center (KSC) in Florida, USA, to determine if tortoises use roadsides as movement pathways between larger habitat patches or as residential habitat. Additionally, we translocated tortoises to study the feasibility of roadsides to function as movement corridors. We found that roadsides are not used as a movement pathway but rather as an apparent long-term residential habitat. Only one tortoise was observed exiting the roadside corridor, and minimum convex polygon (MCP) home range sizes and distances traveled remain similar to those exhibited by tortoises in larger habitat patches. Following translocation, we observed a failure to return home, either by direct paths or by corridor use, for all but one tortoise. Instead, most tortoises remained along roadsides after only a brief period of exploration. Overall, we find that roadsides act as independent, residential habitat instead of as a movement corridor. Future studies should focus on understanding the actual suitability of roadsides, as they may function as ecological traps given their attractiveness but high risk of mortality. While we urge caution, current management should treat roadsides as residential locations for Gopher Tortoises and focus on reducing road mortality

Set Ahdrift: Applying Game Cameras To Drift Fences For Surveying Herpetofauna And Small Mammals

The use of game cameras by wildlife biologists and managers to survey wildlife, particularly medium- and large-bodied mammals, has increased dramatically. Previous attempts to survey small mammals and ectotherms have had limited detection success or were focused solely on a single species. We describe the Adapted-Hunt Drift Fence Technique (AHDriFT), which combines commercially available game cameras and traditional drift fences to survey reptiles, amphibians, and small mammals. Across 4,502 trap-nights at the Merritt Island National Wildlife Refuge, Florida, USA (Jun 2014 to Jun 2015), we recorded images for 2,523 unique vertebrate detections (2% unidentifiable) averaging 0.56 unique triggers/night. Using AHDriFT enables long-duration surveys with high detectability while minimizing observer time. Guide-boards increased terrestrial vertebrate image capture at minimal cost. During 1 year of usage, no mortality was documented using this camera-trap system and field time was reduced by 95%, requiring only monthly visits of approximately 3 hr for 9 fence arrays to download images from the camera systems, compared with pitfall or funnel traps that require at least daily monitoring. © 2017 The Wildlife Society

Combining hierarchical distance sampling with occupancy modeling to measure population density from indirect signs

Text S1. An R Markdown script in ‘html’ format complete with step-by-step data analysis, model results, and simulations. The script also includes comments and guidelines for researchers to fit their own data. Data S1. All data for the analysis of Gopher Tortoise burrow surveys. Data includes transect observations, transect covariates, survey covariates, and burrow occupancy data. Additionally, the 50 m x 50 m grid covariates used to predict Gopher Tortoise density is included. Table S1. Covariates used in modelling and their predicted effects. Check marks for each location correspond to whether the habitat was present in that location. Table S2. Estimates of signal and animal density and abundance. LCL, Lower Confidence Limits; UCL, Upper Confidence Limit; SE, Standard Error; CV, Coefficient of Variatio

Adapting Coastal Management To Climate Change: Mitigating Our Shrinking Shorelines

Sea-level rise due to climate change is a major threat to coastal ecosystems worldwide. Current management to reduce beach erosion often focuses on protecting human structures and research on effects on wildlife is lacking. Using a combination of hierarchical models and generalized linear models, we evaluated how the gopher tortoise (Gopherus polyphemus) colonized constructed dunes along coastal scrub at the Merritt Island National Wildlife Refuge, central Florida, USA. Over 2 years, we surveyed tortoise populations along natural dunes and 2 constructed dunes (completed in 2012 and in 2014) and estimated tortoise density each summer and winter. Our models indicated that tortoise density along the 2014 dune was comparable to that of natural dunes ((Formula presented.) = 0–8 tortoises/ha), and density peaked at a mean of 21 tortoises/ha along the 2012 constructed dune. Gopher tortoises rapidly colonized constructed dunes, and dune construction may represent effective management against habitat loss for this species. © 2017 The Wildlife Society

Estimating The Response Of Wildlife Communities To Coastal Dune Construction

Coastal ecosystems worldwide are being impacted by sea-level rise caused by climate change. As mitigation efforts increase to protect these threatened ecosystems, a deeper understanding of how wildlife adapt to coastal management techniques is needed. We monitored three constructed sand dunes (built in 2010 and 2014) and two natural dunes in central Florida from June 2015 through June 2016 to assess the impact of dune construction as a management technique on terrestrial vertebrates. Specifically, we tested if constructed dunes accumulated and maintained similar community composition and species richness to natural dunes. We used AHDriFT, a game camera-based trapping technique, to monitor terrestrial wildlife communities in both the natural and human-modified landscapes. After 4502 camera nights, we documented 2537 unique photo-capture events, comprised of 33 different species. Species communities were compared by constructing species accumulation curves for each dune type, and by modeling community similarity through multivariate hierarchical clustering. Species accumulation curves overlapped among all dune types, and the cluster analysis showed no pattern separating natural and constructed dunes. However, PERMANOVA found a difference between constructed and natural dunes, which was verified by a NMDS ordination that separated out constructed and natural dunes. Differences between dunes was likely driven by rare species, as commonly observed species overlapped across all dunes, including one protected species. Given the similarity between overall species richness, and that differences in community composition may be due to microhabitat variation and species rarity, we conclude that constructing dunes to increase coastal resilience does not negatively impact endemic wildlife in coastal zones and may provide suitable habitat for many wildlife species