Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding

As elasmobranchs are becoming increasingly threatened, efficient methods
for monitoring the distribution and diversity of elasmobranch populations
are required. Environmental DNA (eDNA) metabarcoding is an increasingly
applied technique that enables mass identification of entire communities
and is an effective method for the detection of rare and elusive species.
We performed an eDNA metabarcoding survey for fish communities around a
coral reef atoll in the Chagos Archipelago and assessed the diversity and
distribution of elasmobranch species detected within these communities.
Our eDNA survey detected 353 amplicon sequence variants (ASVs) attributed
to fishes, 12 of which were elasmobranchs. There were no differences in
fish communities based on the presence and absence of ASVs between sample
depth (surface and 40m) or sampling habitat, but communities based on read
abundance were significantly different between habitats. The dominant
elasmobranch species were grey reef (Carcharhinus amblyrhynchos) and
silvertip (C. albimarginatus) sharks, and elasmobranch communities were
significantly different between sampling depth and habitat. Overall, we
find that eDNA metabarcoding can be used to reveal the diversity of
elasmobranchs within broader taxonomic assays, but further research and
development of targeted metabarcoding primers may be required before it
can be integrated into a toolkit for monitoring these species.