Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar 16;13(1):4346.
doi: 10.1038/s41598-023-31410-4.

A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian

Lucia Zanovello  1   2   3 , Matteo Girardi  1 , Alexis Marchesini  4 , Giulio Galla  1 , Stefano Casari  1 , Diego Micheletti  5 , Sonia Endrizzi  2 , Chiara Fedrigotti  2 , Paolo Pedrini  2 , Giorgio Bertorelle  3 , Heidi Christine Hauffe  6   7
Affiliations

A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian

Lucia Zanovello et al. Sci Rep. .

Abstract

In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Map of the study region (Province of Trento, Italy) showing the 10 selected wetland sample sites, labeled according to Table 1. Site locations, abbreviations, coordinates, elevation and description are listed in Supplementary Information, Table S1. The map was generated using QGIS version 3.20 (http://www.qgis.org); Digital Terrain Model (DTM) for the study area was extracted from the 20 m-resolution DTM of Italy, publicly available at the National Geoportal of Italy (http://www.pcn.minambiente.it/mattm/servizio-di-scaricamento-wcs/).
Figure 2
Figure 2
Scatterplot of the correlation between the nucleotide diversity index values for Rana temporaria in the Province of Trento Italy, for two datasets: x-axis: standard tissue-based genetic survey ; y-axis: current study (eDNA metabarcoding).
Figure 3
Figure 3
Scatterplot of the correlation between the haplotype diversity index values for Rana temporaria in the Province of Trento Italy, for two datasets: x-axis: standard tissue-based genetic survey ; y-axis: current study (eDNA metabarcoding).
Figure 4
Figure 4
Non-metric multidimensional scaling (NMDS) plot, based on two Bray- Curtis dissimilarity matrices for Rana temporaria in the Province of Trento Italy, for two datasets: sites represented by a triangle and labeled with ‘*’ refer to the standard genetic survey dataset ; sites represented with a circle and without ‘*’ refer to the eDNA metabarcoding dataset.
See this image and copyright information in PMC

References

    1. Hoffmann M, et al. The impact of conservation on the status of the world’s vertebrates. Science. 2010;330:1503–1509. doi: 10.1126/science.1194442. - DOI - PubMed
    1. Mazerolle MJ, et al. Making great leaps forward: Accounting for detectability in herpetological field studies. J. Herpetol. 2007;41:672–689. doi: 10.1670/07-061.1. - DOI
    1. Ficetola GF, Manenti R, Taberlet P. Environmental DNA and metabarcoding for the study of amphibians and reptiles: species distribution, the microbiome, and much more. Amphibia-Reptilia. 2019;40(2):129–148. doi: 10.1163/15685381-20191194. - DOI
    1. Hoban SM, et al. Bringing genetic diversity to the forefront of conservation policy and management. Conserv. Genet. Resour. 2013;5:593–598. doi: 10.1007/s12686-013-9859-y. - DOI
    1. Pärli R, et al. Developing a monitoring program of genetic diversity: What do stakeholders say? Conserv. Gen. 2021;22(5):673–684. doi: 10.1007/s10592-021-01379-6. - DOI

Publication types