A landscape genetic analysis of swamp rabbits (Sylvilagus aquaticus) suggests forest canopy cover enhances gene flow in an agricultural matrix

Habitat loss and fragmentation pose a continued and immediate threat to wildlife and create a persistent need for ecological information at the landscape scale to guide conservation efforts. Landscape features influence population connectivity for many species and genetic analyses can be employed to determine which of these features are most important. Because population connectivity through dispersal is important to the persistence of swamp rabbits (Sylvilagus aquaticus Bachman, 1837) at the northern edge of their range, we used a landscape genetic approach to relate gene flow to landscape features that may impact dispersal success. We tested resistance values for attributes of land cover, watercourse corridors, canopy cover, and roads, and used causal modeling and redundancy analysis to relate these representations of landscapes to genetic distance for swamp rabbits in southern Illinois, USA. Models that included canopy cover had the strongest correlations to genetic distance and were supported by our methods whereas other models were not. We concluded high tree canopy cover enhances gene flow and landscape connectivity for swamp rabbits in southern Illinois. Our study provides important empirical evidence that landscape variables may impact the habitat connectivity of swamp rabbits. Preserving dispersal routes for swamp rabbits should focus on improving canopy cover, both in bottomland and upland, to connect suitable habitat.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

A Comparison of eDNA and Visual Survey Methods for Detection of Longnose Darter <i>Percina nasuta</i> in Missouri

The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species’ range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA further upstream in the mainstem St. Francis River than previously reported and in a tributary for the first time. Our multi-scale occupancy approach compared models where detection was constant against a model that allowed detection to vary by survey method. The constant model received the most support indicating survey method was not a strong predictor and detection was estimated at 0.70 (0.45–0.86; 95% CI) across both methods. Our study produced effective longnose darter eDNA primers and demonstrated the application of eDNA for sampling small-bodied, cryptic fish. We detected longnose darter eDNA 27 km upstream of their known range and determined that snorkel surveys are the most efficient sampling method if water clarity allows. We recommend target sample sizes to achieve various detection goals for both sample methods and our results inform future design of distributional and monitoring efforts

Putting eDNA to the Test: A Field Comparison of eDNA Metabarcoding to Established Protocols for Assessing Biodiversity in Missouri’s Ozark Highland Streams

Aquatic biodiversity monitoring to inform conservation and management efforts in stream systems has increasingly begun to incorporate eDNA-based sampling methods. We conducted a comparison of eDNA metabarcoding to a traditional protocol of combined seining and electrofishing methods to assess fish biodiversity of wadeable stream sites in six separate drainages in the Ozark Highlands of Missouri. The study further focused on the headwaters of the Meramec River, which included eleven sites and seasonal sampling (summer and winter). We compared estimates of diversity across sampling methods, assessed hypothesized relationships of habitat (depth and velocity) and season (summer vs winter) to eDNA detection, and tested the effects of sampling method and site locality on fish assemblage structural dynamics. eDNA sampling detected approximately double the number of species detected compared to traditional methods, providing higher diversity estimates while maintaining the relative ranking of sites. eDNA detection probabilities were positively associated with stream depth and velocity and were generally higher in summer than in winter but not for all species. Assemblage differences between tributary and mainstem sites were attributable to a small number of species that were found predominantly in one stream size category or the other, indicating that eDNA was sensitive to within-drainage assemblage structure relationships. Improved species detection and a more comprehensive understanding of assemblage structural dynamics are important benefits encouraging the use of eDNA metabarcoding as a primary collection method in future stream biodiversity assessment and monitoring programs

Putting eDNA to the test: A field comparison of eDNA metabarcoding to established protocols for assessing biodiversity in Missouri's Ozark Highland streams

AbstractAquatic biodiversity monitoring to inform conservation and management efforts in‐stream systems has increasingly begun to incorporate environmental DNA (eDNA)‐based sampling methods. We conducted a comparison of eDNA metabarcoding to a traditional protocol of combined seining and electrofishing methods to assess fish biodiversity of wadeable stream sites in six separate drainages in the Ozark Highlands of Missouri (USA). The study further focused on the headwaters of the Meramec River, which included 11 sites and seasonal sampling (summer and winter). We compared estimates of diversity across sampling methods, assessed the influences of water flow (depth, velocity, and discharge) and season, and tested the effects of sampling method and site locality on fish assemblage composition. eDNA sampling detected approximately double the number of species compared to traditional methods, providing higher diversity estimates while maintaining the relative ranking of sites. eDNA detection probabilities were positively associated with stream depth and velocity and were generally higher in summer than in winter but not for all species. Estimated species richness was positively associated with discharge for both methods but the relationship was stronger with eDNA sampling. Assemblage differences between tributary and mainstem sites were attributable to a small number of species that were found predominantly in one stream size category or the other, indicating that eDNA was sensitive to within‐drainage assemblage structure relationships. We highlight improved species detection, a more comprehensive understanding of assemblage structural dynamics, and the potential ability to integrate data across sampling methods as important benefits that encourage the use of eDNA metabarcoding as a primary collection method in future stream biodiversity assessment and monitoring programs