Abstract
Abstract In the last decade, eDNA and metabarcoding have opened new avenues to biodiversity studies; amphibians and reptiles are animals for which these new approaches have allowed great leaps forward. Here we review different approaches through which eDNA can be used to study amphibians, reptiles and many more organisms. eDNA is often used to evaluate the presence of target species in freshwaters; it has been particularly useful to detect invasive alien amphibians and secretive or rare species, but the metabarcoding approach is increasingly used as a cost-effective approach to assess entire communities. There is growing evidence that eDNA can be also useful to study terrestrial organisms, to evaluate the relative abundance of species, and to detect reptiles. Metabarcoding has also revolutionized studies on the microbiome associated to skin and gut, clarifying the complex relationships between pathogens, microbial diversity and environmental variation. We also identify additional aspects that have received limited attention so far, but can greatly benefit from innovative applications of eDNA, such as the study of past biodiversity, diet analysis and the reconstruction of trophic interactions. Despite impressive potential, eDNA and metabarcoding also bear substantial technical and analytical complexity; we identify laboratory and analytical strategies that can improve the robustness of results. Collaboration among field biologists, ecologist, molecular biologists, and bioinformaticians is allowing fast technical and conceptual advances; multidisciplinary studies involving eDNA analyses will greatly improve our understanding of the complex relationships between organisms, and our effectiveness in assessing and preventing the impact of human activities.
Highlights
Just one species or the whole community?The first environmental DNA (eDNA) applications to macro-organisms used specific primers, targeted at amplifying just one species during PCR (Ficetola et al, 2008; Jerde et al, 2011; Thomsen et al, 2012b)
Introduction that theDNA of target organisms can be ex-Distribution records are among the most basic and pivotal data for many studies on species ecology, conservation and evolutionary biology
Despite we have shown that environmental DNA (eDNA) analyses improve the detection of rare and secretive aquatic amphibians and reptiles, field ecologists could rebut that the cost of molecular analyses would offset the advantage of such approach
Summary
The first eDNA applications to macro-organisms used specific primers, targeted at amplifying just one species during PCR (Ficetola et al, 2008; Jerde et al, 2011; Thomsen et al, 2012b). Valentini et al (2016) provide a complete example of the challenges and of the advantages of community-wide eDNA studies They developed pDroimwnelorasdedffororm tBhrilel.coamm11p/0l2i/2fi0c21at0i5o:0n3:24PM via free access of amphibians (and of bony fish). When Valentini et al (2016) used the metabarcoding approach to assess amphibian biodiversity, they consistently found that eDNA is able to detect amphibians better than traditional surveys, and provided more complete estimates of amphibian communities at all the study ponds. When analysing study systems where hybridization between species is possible, metabarcoding is generally unable to ascertain whether the retrieved sequences originated from parentDaolwnslopaedcediefrso,m oBrrill.fcormo1m1/0t2h/2e02ir1 0h5:y03-:24PM brids. This approach can have limited usefulness in exploring biodiversity gradients across hybrid zones. Community-wide data provide much more complete information on ongoing ecological processes and can be useful for conservation
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