Benchmarking eleven biodiversity indicators based on environmental DNA surveys: more diverse functional traits and evolutionary lineages inside marine reserves

Type Article
Date 2022-11
Language English
Author(s) Dalongeville AliciaORCID1, Boulanger Emilie2, Marques VirginieORCID3, Charbonnel Eric4, Hartmann Virginie5, Santoni Marie Catherine6, Deter Julie1, 7, Valentini Alice8, Lenfant Philippe9, Boissery Pierre10, Dejean Tony8, Velez Laure1, Pichot Franck1, Sanchez Loic1, 3, Arnal Veronique3, Bockel Thomas7, Delaruelle Gwenaelle7, Holon Florian7, Milhau TristanORCID8, Romant Lola1, Manel StéphanieORCID3, Mouillot David1, 11
Affiliation(s) 1 : MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier, France
2 : Aix‐Marseille Université Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110 Marseille ,France
3 : CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier ,France
4 : Parc Marin de la Côte Bleue, Observatoire, plage du Rouet. 31 Av. J. Bart. BP 42. 13820 Carry‐le‐Rouet ,France
5 : Reserve Naturelle Marine de Cerbère‐Banyuls, Département des Pyrénées‐Orientales, 5 rue Roger David 66650 Banyuls‐sur‐mer ,France
6 : Office de l’Environnement de la Corse, 14 Avenue Jean Nicoli, 20250 Corte, France
7 : Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio, France
8 : SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac ,France
9 : Université Perpignan Via Domitia Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110, 58 Avenue Paul Alduy Perpignan ,France
10 : Agence de l’Eau Rhône‐Méditerranée‐Corse, Délégation de Marseille, 2 rue Barbusse, CS 90464, 13207 Marseille Cedex ,France
11 : Institut Universitaire de France Paris, France
Source Journal Of Applied Ecology (0021-8901) (Wiley), 2022-11 , Vol. 59 , N. 11 , P. 2803-2813
DOI 10.1111/1365-2664.14276
WOS© Times Cited 5
Keyword(s) bioindicator, crypto-benthic fish, elasmobranch, environmental DNA metabarcoding, marine protected areas, Mediterranean Sea, monitoring

To mitigate the ongoing threats to coastal ecosystems, and the biodiversity erosion they are causing, Marine Protected Areas (MPAs) have emerged as powerful and widespread conservation tools. Strictly no-take MPAs, also called marine reserves, undeniably promote fish biomass and density, but it remains unclear how biodiversity responds to protection. Identifying which facets of biodiversity respond to protection is critical for the management of MPAs and the development of relevant conservation strategies towards the achievement of biodiversity targets.

We collected 99 environmental DNA (eDNA) samples inside and outside nine marine reserves in the Mediterranean Sea to assess the effect of protection on 11 biodiversity indicators based on fish traits, phylogeny and vulnerability to fishing. We controlled for the effect of environmental heterogeneity (habitat, bathymetry, productivity, temperature, and accessibility) using a Principal Component Analysis, and for spatial autocorrelation due to potential unmeasured factors.

We found a positive and significant effect of protection on only 3 out of 11 indicators: functional and phylogenic diversity but also the ratio between demerso-pelagic and benthic species richness. Rather, total fish richness responded significantly and negatively to protection. We did not detect any significant effect of protection on threatened and elasmobranch species richness, probably due to their large home range compared to the size of Mediterranean marine reserves.

Synthesis and applications: Our findings highlight the importance of looking beyond the mere number of species to fully depict and understand the effect of marine reserves on biodiversity and evaluate the effectiveness of conservation measures. Rather, we propose a dashboard of three eDNA-based indicators that can provide an early signal of ecosystem deterioration or recovery. eDNA metabarcoding offers a powerful tool to supply site-specific and standardized taxonomic-, phylogenetic- and trait-based biodiversity assessments, in complement to other classical technics, such as visual censuses or video surveys, able to estimate species abundance but also individual life-stage and size.

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AppendixS 1 29 KB Open access
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TableS 4 35 KB Open access
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Dalongeville Alicia, Boulanger Emilie, Marques Virginie, Charbonnel Eric, Hartmann Virginie, Santoni Marie Catherine, Deter Julie, Valentini Alice, Lenfant Philippe, Boissery Pierre, Dejean Tony, Velez Laure, Pichot Franck, Sanchez Loic, Arnal Veronique, Bockel Thomas, Delaruelle Gwenaelle, Holon Florian, Milhau Tristan, Romant Lola, Manel Stéphanie, Mouillot David (2022). Benchmarking eleven biodiversity indicators based on environmental DNA surveys: more diverse functional traits and evolutionary lineages inside marine reserves. Journal Of Applied Ecology, 59(11), 2803-2813. Publisher's official version : , Open Access version :