Abstract
The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially in aquatic environments. Environmental DNA metabarcoding is an approach that overcomes low detection probabilities and should consequently enhance estimates of biodiversity and its proxy, species richness. Here, we synthesize 37 studies in natural aquatic systems to compare species richness estimates for bony fish between eDNA metabarcoding and conventional methods, such as nets, visual census, and electrofishing. In freshwater systems with fewer than 100 species, we found eDNA metabarcoding detected more species than conventional methods. Using multiple genetic markers further increased species richness estimates with eDNA metabarcoding. For more diverse freshwater systems and across marine systems, eDNA metabarcoding reported similar values of species richness to conventional methods; however, more studies are needed in these environments to better evaluate relative performance. In systems with greater biodiversity, eDNA metabarcoding will require more populated reference databases, increased sampling effort, and multi-marker assays to ensure robust species richness estimates to further validate the approach. eDNA metabarcoding is reliable and provides a path for broader biodiversity assessments that can outperform conventional methods for estimating species richness.
Highlights
High-throughput sequencing (HTS) of macro-organismal DNA from environmental samples is an innovative conservation approach to detect and measure ecological communities (Thomsen and Willerslev, 2015; Deiner et al, 2017)
We identified 121 independent sites where authors compared fish species richness between environmental DNA (eDNA) metabarcoding and conventional surveys
In marine and more diverse systems, the relative performance of eDNA is unclear given few observations from these sites. It is possible there are proportionally many undetected taxa by eDNA metabarcoding in high-diversity systems due in part to false negatives stemming from single-marker assays, incomplete reference libraries, PCR inhibition, and insufficient sampling effort or sequencing depth
Summary
High-throughput sequencing (HTS) of macro-organismal DNA from environmental samples is an innovative conservation approach to detect and measure ecological communities (Thomsen and Willerslev, 2015; Deiner et al, 2017). EDNA metabarcoding for macro-organism detection works in various substrates, including freshwater (Olds et al, 2016), seawater (Thomsen et al, 2012), soil (Epp et al, 2012), sediment (Guardiola et al, 2015), and even air and snow (Kraaijeveld et al, 2015; Kinoshita et al, 2019) These methods have been used to characterize taxa from across the eukaryotic tree of life – including mammals (Foote et al, 2012; Ushio et al, 2017), amphibians (Lopes et al, 2017; Bálint et al, 2018), bony fishes (Yamamoto et al, 2017), elasmobranchs (Bakker et al, 2017; Boussarie et al, 2018), plants (Yoccoz et al, 2012), and macro-invertebrates (McGee and Eaton, 2015; Lacoursière-Roussel et al, 2018). On land and in the oceans, ecological communities are undergoing rapid compositional and geographic shifts (Pecl et al, 2017; Blowes et al, 2019) and are confronted with numerous threats (Tilman et al, 2017; Halpern et al, 2019; Reid et al, 2019), so it is critical that we better understand if eDNA metabarcoding could facilitate broad biodiversity assessment
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