Abstract
AbstractEnvironmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.
Highlights
Coral reefs represent the most diverse marine ecosystems on the planet (Fisher et al, 2015) and are the most threatened (Williams et al, 2019)
Besides logistical difficulties to organize underwater sampling in remote locations, underwater visual census (UVC) can suffer from several observer biases, such as overlooking cryptobenthic (Bozec et al, 2011) or wideranged species such as sharks (Juhel et al, 2018)
We found that a large proportion of ecological traits was covered by the two sampling methods, even if UVC detected a smaller number of genera than Environmental DNA (eDNA). eDNA was better at detecting large piscivore and pelagic species belonging to genera such as Istiophorus, Euthynnus, Decapterus, Acanthocybium, and Strongylura, and smaller planktivorous species of Sardinella, Cetengraulis, Lycengraulis, and Engraulis (Figure 3b). eDNA further detected more small and bottom-associated species represented by the genera Liopropoma, Hypsoblennius and Arcos
Summary
Coral reefs represent the most diverse marine ecosystems on the planet (Fisher et al, 2015) and are the most threatened (Williams et al, 2019). Monitoring fishes on coral reefs has been performed using underwater visual censuses (UVC) or video surveys (Stat et al, 2019), which offer a partial view of the dynamics of reef biodiversity, from their degradation under global changes to their recovery (Bozec et al, 2011; Cinner et al, 2016) These methods are limited in both spatial and temporal coverage and are biased toward certain categories of species (Boussarie et al, 2018). EDNA is a noninvasive method demonstrating higher detection capabilities and cost-effectiveness compared to traditional methods, especially when deployed in remote locations (Dejean et al, 2011; Kelly et al, 2014; Thomsen & Willerslev, 2015) Before it can effectively complement traditional sampling methods, the ability of eDNA to recover signals of diversity and composition of marine systems should be evaluated. We explored (d) the signal of β diversity across eDNA samples by analyzing the compositional species dissimilarity between geographic locations
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