Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

Environmental DNA (eDNA) has the potential to provide more
comprehensive biodiversity assessments particularly for vertebrates in
species-rich regions. Yet, this method requires the completeness of a
reference database, i.e. a list of DNA sequences attached to each
species, which is never met. As an alternative, a diversity 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 1,531 fish OTUs while 1,611 fish species are
recorded in the region. Besides, we also accurately predict (R² =
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.
Methods

Environmental DNA (eDNA) was extracted from 2L seawater samples as described in the file Methods section of the paper. Retrieved eDNA was then amplified using a teleost-specific 12S mitochondrial rDNA primer (teleo), sequenced and processed using two bioinformatics pipelines. The files obitools_lengguru.csv and swarm_lengguru.csv are the outputs of the OBITools and SWARM pipeline, respectively. It represents the raw data merged with metadata and linking the occurence tables with taxonomical assignments, prior to quality filtering.