Discovery of an unrecorded population of Yamato salamander (Hynobius vandenburghi) by GIS and eDNA analysis

Abstract

Background Biodiversity loss is a serious environmental problem, and human activities might be primarily responsible for the marked decline in animal populations globally. Amphibians, in particular, have significantly decreased in number in recent decades. One example is the endangered Yamato salamander (Hynobius vandenburghi), which is distributed in Central Japan and has a very restricted distribution in Gifu Prefecture. Aims We aimed to discover new populations of H. vandenburghi using a combination of GIS and environmental DNA (eDNA) analysis. Materials & Methods Firstly, we designed two primer sets for amplifying Hynobius species targeting mitochondrial 12S rRNA and cytochrome b genes. Next, we performed aquarium experiments to detect H. vandenburghi DNA in aquarium water. We also conducted sequential eDNA detection surveys in five known habitats in Gifu City, Japan, 17 times from January to August 2016. Following these basic eDNA studies, we used GIS to characterize the vegetation and topography of known habitats of H. vandenburghi. We collected water samples in the potential habitats identified by GIS and analyzed eDNA for the presence of H. vandenburghi using the designed primers. Finally, we conducted physical collection surveys in these potential habitats. Results We successfully developed two Hynobius‐specific primer sets and detected H. vandenburghi eDNA in aquarium water. The eDNA of the target species was detected in almost all (94%–100%) samples from four habitats, whereas only 29% of samples were positive for one habitat. We identified five potential habitats by GIS analysis. The DNA of H. vandenburghi was detected in three of five potential habitats. Finally, we discovered a new population in one of the potential sites. Discussion Our approach combining GIS and eDNA enabled the detection of novel population of an endangered amphibian species. This study was conducted by high school students under the supervision of teachers with the help of university researchers, suggesting the applicability of eDNA studies as a tool of citizen science. Conclusion The combination of GIS and eDNA will allow to detect cryptic populations on which conservation efforts may be focused and to alert people to the need for conservation action.

Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan

“…We used two qPCR assays for Siberian salamander eDNA in this study. One, which was newly designed, targeted the Cytb region, and the other targeted the 12S rRNA region (Sakai et al, 2019).…”

“…For 12S, we used an existing primer set (Sakai et al, 2019). This primer set was originally designed for Hynobius species, but an in silico test with Primer-Blast, confirmed that there is no substitution with the sequence of the Siberian salamander.…”

“…To assess the specificity of the detection assay for 12S, we conducted real-time PCR with the 12S assay (primers Hynobius_12S_F1 and Hynobius_12S_R1 (Sakai et al, 2019), and probe Skey_12S_MGB_P). Concentration and volume of the primer set and the probe were the same as above.…”

A Standardized Procedure for Monitoring Harmful Algal Blooms in Chile by Metabarcoding Analysis

“…The molecular-based analysis on the local algal-bacterial relationship may contribute to a step forward clarification for such a subject. For example, the technique can search the algal and bacterial species that were not present in the target oceanic area before but have increased dramatically in recent years, which is somewhat similar to the study done by Sakai et al for the discovery of an unrecorded population of Yamato salamander (Hynobius vandenburghi) by GIS and eDNA analysis 34 . Therefore, beyond the HAB…”

Applications of eDNA Metabarcoding for Vertebrate Diversity Studies in Northern Colombian Water Bodies

“…Environmental DNA metagenomics analysis has helped in the study of entire communities (Handley et al, 2019;Nichols and Marko, 2019), specific taxonomic groups (Ostberg et al, 2019), rare/cryptic species (Sakai et al, 2019), vulnerable species (Hunter et al, 2018), and also invasive species (Hunter et al, 2015;Robinson et al, 2019) making it an ideal tool to work on distribution censuses of many taxa. Presence/absence measures are now possible but abundance measures are still not entirely achievable since correct estimations of abundance based on eDNA are not precise enough currently, due to primer sensitivity to target DNA, seasonal variation of eDNA and environmental factors that diminish the correlation between eDNA and abundance (Bylemans et al, 2019;Yates et al, 2019).…”