Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle

Abstract

Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

“…The development of eDNA as a reliable method to monitor biodiversity and evaluate anthropogenic impacts is crucial because important changes in biodiversity might currently occur under our radar [39,57]. Depending on the organisms of interest, eDNA can be used to sample whole eukaryote assemblages [58] or more specific taxonomic groups ranging from sponges and corals [59] to larger taxa such as sharks [30].…”

“…As an alternative, the environmental DNA (eDNA) metabarcoding approach overcomes some shortcomings of classical surveys to characterize marine fish assemblages [35,36] including small, cryptic, and elusive species [33,37]. eDNA is made of small fragments of intra-and extracellular DNA generated by organisms in their proximate environment, and can be sampled to infer the presence of species, monitor coastal ecosystems, and unveil ecological processes [33,[38][39][40]. Yet, the gaps in public genetic databases can limit the breadth of species inventories based on eDNA metabarcoding [41].…”

Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot

“…Therefore, this step needs to be performed prospectively when developing a metabarcoding study. Additional options include the use of an alternative barcode targeting the same taxonomic group to increase the precision in the taxonomic assignment (Alberdi et al, 2017;Lecaudey et al, 2019), and the implementation of taxonomyfree studies (Callahan et al, 2017;Cordier et al, 2018;Juhel et al, 2020;Pawlowski et al, 2018).…”

“…For example, Cilleros et al, (2018) in their study on high-biodiversity freshwater environments using "teleo" primers, conducted 12 PCR replicates and 50 PCR cycles during PCR1. Recently, Juhel et al, (2020) also performed 12 PCR replicates with the same primers in a species-rich environment.…”

“…Thorough and accurate detection of species from DNA amplicons requires a taxonomically comprehensive coverage of known taxa in reference databases (Andersen et al, 2019;Weigand et al, 2019). However, such reference databases are often missing for local faunas (Juhel et al, 2020) and their completeness varies for different regions. Thus, the impact of the taxonomic gaps in the reference database on the final taxonomic assignment and on the ecological inferences derived from eDNA data (Chen et al, 2017), and the extent of improvement gained with the development and use of a local database, are relevant aspects needing evaluation in eDNA studies.…”