Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation

Abstract

Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.

Towards evidence‐based conservation of subterranean ecosystems

“…( Trends in subterranean conservation Pellegrini et al, 2016;Korbel et al, 2017;Mouser et al, 2021;Trevelin et al, 2021). Given that monitoring is applied to test the effectiveness of most other conservation interventions (Table 3), we need to ensure that the performance of monitoring technologies and the reliability of monitoring protocols are comprehensively tested.…”

“…Despite their perceived importance, only 11% of the proposed monitoring plans and methods were tested. Examples include comparing the effectiveness of different sampling methods in cave systems (Wynne et al ., 2018, 2019) or assessing the detection probability of a given method across diverse environmental conditions (Dole‐Olivier et al ., 2009; Pellegrini et al ., 2016; Korbel et al ., 2017; Mouser et al ., 2021; Trevelin et al ., 2021). Given that monitoring is applied to test the effectiveness of most other conservation interventions (Table 3), we need to ensure that the performance of monitoring technologies and the reliability of monitoring protocols are comprehensively tested.…”

Bat dynamics modelling as a tool for conservation management in subterranean environments

“…The focal bat species used open spaces within their roosts to hibernate or to raise their young, allowing for a standardised occurrence sampling strategy. Data collection within a controlled modelling environment, such as a cave or a mine, ensures a consistent sampling effort, but only when dealing with open space dwellers [ 84 ]. Most troglobiontes, which make use of an extensive network of cracks and superficial habitats, would be more difficult to sample using this approach [ 46 ].…”

“…but only when dealing with open space dwellers [84]. Most troglobiontes, which make use of an extensive network of cracks and superficial habitats, would be more difficult to sample using this approach [46].…”

Figure 1 from: Dooley KE, Niemiller KDK, Sturm N, Niemiller ML (2022) Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA. Subterranean Biology 43: 11-31. https://doi.org/10.3897/subtbiol.43.79993

“…The use of environmental DNA (eDNA) for detecting and monitoring groundwater organisms has become increasingly popular in recent years. This approach, which leverages DNA shed by organisms into their surrounding environment, has been employed with success in caves, springs, and wells for a diversity of groundwater organisms, including salamanders (Goricki et al 2016(Goricki et al , 2017Voros et al 2017;Lyons 2019), cavefishes (Lyons 2019;Mouser 2019;White et al 2020;Mouser et al 2021), amphipods (Niemiller et al 2018), and crayfishes (Boyd 2019;Mouser 2019;Boyd et al 2020;DiStefano et al 2020;Dooley 2021;Mouser et al 2021). With the first genetic data and tissues now available for O. sheltae, we recommend that a species-specific eDNA assay be developed and an eDNA survey study employed to potentially locate additional sites for this imperiled stygobiotic crayfish.…”