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

Type Article
Date 2020-07
Language English
Author(s) Juhel Jean-Baptiste1, Utama Rizkie S.2, Marques Virginie1, Vimono Indra B.2, Sugeha Hagi Yulia2, Kadarusman 3, Pouyaud Laurent4, Dejean Tony5, Mouillot David1, 6, Hocdé Régis1
Affiliation(s) 1 : MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
2 : Research Center for Oceanography, Indonesian Institute of Sciences, Jl. Pasir Putih 1, Ancol Timur, Jakarta Utara, Indonesia
3 : Politeknik Kelautan dan Perikanan Sorong, KKD BP Sumberdaya Genetik, Konservasi dan Domestikasi, Papua Barat 98411, Indonesia
4 : Institut des Sciences de l'Evolution de Montpellier, Montpellier, France
5 : SPYGEN, 73370 Le Bourget-du-Lac, France
6 : ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
Source Proceedings Of The Royal Society B-biological Sciences (0962-8452) (The Royal Society), 2020-07 , Vol. 287 , N. 1930 , P. 20200248 (10p.)
DOI 10.1098/rspb.2020.0248
WOS© Times Cited 8
Keyword(s) eDNA metabarcoding, sequence clustering, Operational Taxonomic Unit, diversity assessment, detectability
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 (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.

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Juhel Jean-Baptiste, Utama Rizkie S., Marques Virginie, Vimono Indra B., Sugeha Hagi Yulia, Kadarusman, Pouyaud Laurent, Dejean Tony, Mouillot David, Hocdé Régis (2020). Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle. Proceedings Of The Royal Society B-biological Sciences, 287(1930), 20200248 (10p.). Publisher's official version : https://doi.org/10.1098/rspb.2020.0248 , Open Access version : https://archimer.ifremer.fr/doc/00640/75232/