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

Citation

Juhel, Jean-Baptiste et al. (2020), Data from: Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle, Dryad, Dataset, https://doi.org/10.5061/dryad.t1g1jwt05

Abstract

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. 

 

Usage Notes

The bioinformatic pipelines scripts used to generate both datasets are available in Gitlab following the links below :

https://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools

https://gitlab.mbb.univ-montp2.fr/edna/bash_swarm