Abstract
Given the rapid rise of environmental DNA (eDNA) surveys in ecology and environmental science, it is important to be able to compare the results of these surveys to traditional methods of measuring biodiversity. Here we compare samples from a traditional method (a manual tow-net) to companion eDNA samples sequenced at three different genetic loci. We find only partial taxonomic overlap among the resulting datasets, with each reflecting a portion of the larger suite of taxa present in the sampled nearshore marine environment. In the larger context of eDNA sequencing surveys, our results suggest that primer amplification bias drives much of the taxonomic bias in eDNA detection, and that the baseline probability of detecting any given taxon with a broad-spectrum primer set is likely to be low. Whether catching fish with different nets or using different PCR primer sets, multiple data types can provide complementary views of a common ecosystem. However, it remains difficult to cross-validate eDNA sequencing techniques in the field, either for presence/absence or for abundance, particularly for primer sets that target very wide taxonomic ranges. Finally, our results highlight the breadth of diversity in a single habitat, and although eDNA does capture a richer sample of the community than traditional methods of sampling, a large number of eDNA primer sets focusing on different subsets of the biota would be necessary to survey any ecological community in a reasonably comprehensive way.
Highlights
Environmental DNA—genetic traces of organisms taken from a sample of water, soil, or other medium—is increasingly useful for ecological surveys, where traditional sampling is difficult or expensive (Foote et al, 2012; Kelly et al, 2014b)
Our tow-net surveys recovered 45 distinct animal taxa, of which 32 could be identified to Family level. Environmental DNA (eDNA) surveys with PCR primers targeting three gene regions—16S, COI, and 18S— resulted in sequences detecting a total of 1.8 × 104 unique operational taxonomic units (OTUs), of which a total of 1.3 × 104 could be classified by matching known sequences in GenBank (Table 1)
In order to confidently interpret eDNA results in the context of existing ecological study, it is necessary to compare the results of this emerging technique with those of more established methods of ecological sampling
Summary
Environmental DNA (eDNA)—genetic traces of organisms taken from a sample of water, soil, or other medium—is increasingly useful for ecological surveys, where traditional sampling is difficult or expensive (Foote et al, 2012; Kelly et al, 2014b). A seemingly straightforward way of assessing the performance of the DNA surveys is to compare sequencing results to a known community (Kelly et al, 2014a; Evans et al, 2016) or to compare eDNA results to those from a traditional sampling technique (Lacoursière-Roussel et al, 2015; de Vargas et al, 2015; Port et al, 2016) These studies have tended to show a correlation between results obtained through traditional sampling methods and those using environmental DNA (but see Adams et al, 2013), the relationship between traditionally collected results (e.g., manual counts or biomass) and relative eDNA sequence abundance clearly varies by taxon and with environmental context
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