GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding

Abstract

Aim Environmental DNA metabarcoding has recently emerged as a non‐invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. The major limitation currently impairing the large‐scale application of eDNA‐based inventories is the lack of species sequences available in public genetic databases. Unfortunately, these gaps are still unknown spatially and taxonomically, hindering targeted future sequencing efforts. Innovation We propose GAPeDNA, a user‐friendly web interface that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an application, we synthetized data from regional checklists for marine and freshwater fishes along with their IUCN conservation status to provide global maps of species coverage using the European Nucleotide Archive public reference database for 19 metabarcoding primers. This tool automatizes the scanning of gaps in these databases to guide future sequencing efforts and support the deployment of eDNA inventories at larger scale. This tool is flexible and can be expanded to other taxa and primers upon data availability. Main conclusions Using our global fish case study, we show that gaps increase towards the tropics where species diversity and the number of threatened species are the highest. It highlights priority areas for fish sequencing like the Congo, the Mekong and the Mississippi freshwater basins which host more than 60 non‐sequenced threatened fish species. For marine fishes, the Caribbean and East Africa host up to 42 non‐sequenced threatened species. By presenting the global genetic database completeness for several primers on any taxa and building an open‐access, updatable and flexible tool, GAPeDNA appears as a valuable contribution to support any kind of eDNA metabarcoding study.

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

“…In our case, we potentially missed some native and common species in the Mediterranean Sea since the teleo marker cannot distinguish the wrasses Symphodus rostratus, S. cinnereus, S. mediterraneus, and S. roissali from each other, or Labrus merula from L. viridis, as well as the rarer pipefishes Syngnathus abaster and S. sp cfr taenionotus. Most regional and global reference databases for the teleo metabarcode also still need to be completed to avoid limited species assignments [41]. In our case, we enriched the online genetic database (European Nucleotide Archive) which covered only 31% of all Mediterranean fish species by sampling and sequencing additional 115 species to reach 75% coverage of the regional species pool (see Methods).…”

“…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]. In this study, we take advantage of eDNA detectability potential, using a regionally augmented genetic reference database, to uncover a previously hidden conservation paradox in coastal fish assemblages: marine reserves host less species than nearby fished areas after controlling for environmental conditions.…”

How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

“…eDNA-based methods rely on the detection of DNA fragments from various sources including faeces, shed skin cells, organelles, or extruded waste of animals, which become suspended in the water (Dejean et al ., 2012; Collins et al ., 2018; Harrison, Sunday and Rogers, 2019). Using filtered water and molecular analyses, eDNA metabarcoding can estimate biodiversity across kingdoms at different taxonomic levels without isolating any target organisms (Valentini et al ., 2016; Holman et al ., 2021), and even without exhaustive genetic reference databases (Flynn et al ., 2015; Juhel et al ., 2020; Marques et al ., 2020, 2021). Overall, eDNA metabarcoding has the potential to overcome some limitations of common sampling methods by targeting complete species assemblages, detecting rare (Rees et al ., 2014), elusive (Boussarie et al ., 2018) or non-indigenous species (Ficetola et al ., 2008; Holman et al ., 2019) and is harmless to organisms and less time-consuming (Bohmann et al ., 2014; Smart et al ., 2016).…”

Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia)

“…Given its greater sensitivity and the fact that samples can be obtained from a wide variety of platforms (Harrison et al, 2019), eDNA has the potential to rapidly fill data gaps for cetaceans. Studies using this census method are usually limited by the completeness of genetic databases to taxonomically assign the retrieved sequences (Marques et al, 2020). However, strandings of cetaceans along the shores provide a valuable source of genetic material that can be sequenced on eDNA genetic markers to complete reference databases and investigate within species genetic diversity.…”