Using environmental DNA to assess population‐wide spatiotemporal reserve use

Abstract

Scientists increasingly rely on protected areas to assist in biodiversity conservation, yet the efficacy of these areas is rarely systematically assessed, often because of underfunding. Still, adaptive management strategies to maximize conservation success often rely on understanding the temporal and spatial dynamism of populations therein. Examination of environmental DNA (eDNA) is a time and cost-effective way to monitor species' distribution, and quantitative polymerase chain reaction (qPCR) provides information on organismal abundance. To date, however, such techniques remain underused for population assessments in protected areas. We determined eDNA concentration of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) to describe its occurrence, range, and use of the Tian e-Zhou National Nature Reserve in Hubei, China, across seasons and hydrological depths. Despite the observation that total eDNA concentrations were highest in surface waters in summer, finless porpoise eDNA concentrations were significantly higher in deeper waters than in surface waters in summer. During the breeding season (spring), eDNA signals were site specific and restricted to the core area of the reserve. However, postbreeding eDNA concentrations were widespread across the reserve, encompassing sites previously thought to be unfrequented by the species. Our results suggest spatiotemporal idiosyncrasies in site, depth, and seasonal use of the reserve and a propensity for postbreeding population dispersal. With eDNA and qPCR we were able to assess an entire population's use of a protected area. Illuminating nuances in habitat use via eDNA could be valuable to set pragmatic conservation goals for this, and other, species.

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

“…Much of the published eDNA literature highlights the use and applications of eDNA as an important conservation tool for the monitoring of animal populations and provides compelling evidence for eDNA analysis as a potential replacement for traditional genetic sampling methods, for example, physical handling, biopsying and tagging of individuals (Deiner et al, 2017;Harper et al, 2018;Minamoto et al, 2017;Stewart, Ma, Zheng, & Zhao, 2017;Thomsen & Willerslev, 2015). While there have been many reviews and studies on best practices for eDNA studies (Alberdi et al, 2018;Spens et al, 2017) and on the influence of abiotic and biotic factors on the persistence of eDNA in aquatic systems (Barnes et al, 2014;Coble et al, 2018), very little of the eDNA published literature contain studies with false-negative results for target DNA, and thus, there is a gap in the literature.…”

Environmental DNA (eDNA) From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification

“…Here the DNA that is shed or excreted from individuals during normal activity can be collected from the environment, concentrated, and amplified via the Polymerase Chain Reaction (PCR) using primers targeted for specific taxonomic groups. eDNA has been used widely to detect vertebrate species in freshwater systems (Ficetola et al, 2008;Jerde et al, 2011;Ma et al, 2016;Stewart et al, 2017), and is now finding a growing number of applications in the marine environment (Thomsen et al, 2012), including detection and identification of marine megafauna (Foote et al, 2012;Port et al, 2016;Sigsgaard et al, 2016;Andruszkiewicz et al, 2017;Bakker et al, 2017;Gargan et al, 2017). Whales, dolphins and porpoises represent good candidates for eDNA sampling given their known tendency to release cellular DNA in shed skin (Amos et al, 1992), fecal plumes (Parsons, 1999), and the "spout" or blow (Hunt et al, 2013).…”

Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal

“…To verify primer efficiency, we tested whether these primer pairs could amplify YFP eDNA from a location where we knew this species to be present. Thus for a positive control, we collected water from the Bnetted cage^(approximately a 15 m × 15 m enclosure) within Tian-e-Zhou Baiji National Nature Reserve (29°51′ 11 N, 112°35′ 15E), a natural protected area for the YFP which runs parallel, and is hydrologically linked to, the Yangtze River (similar in protocol to Foote et al 2012), and acts as a lake due to limited water flow (Stewart et al 2017). This reserve is hydrologically similar to other natural lake systems within which over half the YFP species populations are found in China (e.g., Dongting and Poyang lake).…”

“…The YFP is a farranging aquatic species distributed across the middle-to-lower Yangtze River, many lake systems, and an oxbow lake reserve hydrologically linked to the Yangtze River, totally approximately 1890 km in length (Li 2011). Although a conservation priority for China, YFP natural history make it difficult to survey: i) they remain behaviorally elusive, ii) are benthic feeders infrequently surfacing to breathe, and iii) their dark coloration and lack of dorsal fin to break the water surface makes visual detection difficult (Stewart et al 2017). Thus, current traditional population monitoring for this taxon is primarily restricted to presence/absence information via visual or acoustic surveying unless individuals are physically captured for demographic information (although the invasiveness of the capture method remains a concern).…”