Living quarters of a living fossil—Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

Abstract

One of the greatest challenges of effective conservation measures is the correct identification of sites where rare and elusive organisms reside. The recently rediscovered Hula painted frog (Latonia nigriventer) has not been seen for many decades and was therefore categorized extinct. Since its rediscovery in 2011, individuals from the critically endangered species have been found, with great effort, only in four restricted sites. We applied the environmental DNA (eDNA) approach to search for new populations of the Hula painted frog in suitable aquatic habitats. We further used the eDNA data to classify the landscape factors associated with the species distribution and to predict its suitable habitats. We sampled 52 aquatic sites in the Hula Valley during the spring of 2015 and 2016 and amplified the samples with a species-specific qPCR assay. DNA of the Hula painted frog was detected in 22 of the sites, all of which clustered within three main areas. A boosting classification model showed that soil type, vegetation cover and the current and former habitats are all key predictors of the frog's current distribution. Intriguingly, the habitat suitability models reveal a high affinity of the species to its long-lost habitat of the historical wetlands. Our findings encourage a series of informed searches for new populations of this threatened frog and provide guidance for future conservation management programmes. In the era of global conservation crisis of amphibians, developing the eDNA approach, a reliable detection method for many critically endangered and elusive amphibians, is of particular importance.

Pitfalls during in silico prediction of primer specificity for eDNA surveillance

“…eDNA techniques are theoretically capable of detecting even a single copy of target DNA (Jerde et al 2011), so the potential applications of eDNA techniques are substantial (Goldberg et al 2016). Such methods have been used to detect rare and endangered freshwater species whose presence cannot be confirmed easily by more conventional means (Laramie et al 2015, Sigsgaard et al 2015, Eva et al 2016, Renan et al 2017), and to monitor the colonization of new habitat by invasive species (Jerde et al 2013, Nathan et al 2014, Rees et al 2014). The high sensitivity of eDNA, relative to more traditional survey methods (Goldberg et al 2013, Takahara et al 2013), has contributed to its increasing prevalence as a research tool (Goldberg et al 2016).…”

Environmental DNA analysis confirms extant populations of the cryptic Irwin’s turtle within its historical range

“…While direct observations of E. irwini are needed to gather data on population size, age classes and female-male ratios (required for listing the species and developing management actions to protect the species), eDNA analysis provides valuable information on population distribution and potential changes over time. Environmental DNA has been suggested as the only efficient tool for rare and cryptic species detection [ 49 ]. In the case of E. irwini in the Burdekin River, we propose eDNA sampling as the most pragmatic detection method due to high water turbidity, the presence of crocodiles and the inability to reliably attract these turtles to traps.…”

Development and validation of rapid environmental DNA (eDNA) detection methods for bog turtle (Glyptemys muhlenbergii)

“…Suspended cells or other eDNA-containing particles are often concentrated on polycarbonate or glass fiber filters[14,33,34], which offer practical advantages over eDNA extraction from sediment. However, direct filtration at all sites was unfeasible in this study due to surface waters either being non-existent or extremely rich in organics which clogged filters almost immediately.…”

“…DNA is known to rapidly diffuse from the source in aquatic systems and, where flux is relatively high in streams or rivulets, DNA is transported out of the system relatively quickly[34]. Furthermore, most eDNA-containing particles including skin cells settle out of slow-moving water into the sediment[33] where eDNA has been shown to persist longer than in surface water[35]. Our findings suggest that these dynamics may also be controlling the fate, transport, and storage of eDNA in bogs where eDNA is stored mostly in sediment in or near hibernacula and a targeted sampling approach incorporating prior knowledge of the site as well as animal behavior may lead to higher detection rates.…”