Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Marques, Virginie; Castagné, Paul; Polanco, Andréa; Borrero-Pérez, Giomar Helena; Hocdé, Régis; Guérin, Pierre‐Édouard; Juhel, Jean‐Baptiste; Velez, Laure; Loiseau, Nicolas; Letessier, Tom B.; Bessudo, Sandra; Valentini, Alice; Déjean, Tony; Mouillot, David; Pellissier, Loïc; Villéger, Sébastien

doi:10.1111/cobi.13802

Cited by 32 publications

(26 citation statements)

References 86 publications

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“…This result can be considered as conservative since the spatial extent of the eDNA sampling is smaller than that of UVC so we could expect even more fish diversity detected with a more widespread eDNA sampling. This result is also consistent with many studies comparing sampling methods (Polanco Fernández et al 2021, Marques et al 2021). However, the incompleteness of reference databases limits the taxonomic assignment of eDNA sequences (Marques et al 2020a, Polanco Fernández et al 2021.…”

Section: Discussionsupporting

confidence: 92%

Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions

et al. 2022

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Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the 'Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies.

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Section: Discussionsupporting

confidence: 92%

Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions

et al. 2022

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“…Functional and phylogenetic characteristics are expected to offer higher dimensions of information to describe and manage ecosystems (Strecker et al, 2011). Coupling ecological indices with eDNA can provide more complete ecosystem information for coral reefs (Aglieri et al, 2021; Marques et al, 2021). As demonstrated previously with UVC (D'Agata et al, 2014), we found that functional and phylogenetic indices better discriminate between the two inventoried coastal areas than taxonomic information alone.…”

Section: Discussionmentioning

confidence: 99%

“…The massive amount of DNA sequence data from eDNA metabarcoding could be compounded into ecological indices, where the cumulated species‐specific responses translate into measures of environmental quality (Cordier, 2020). Furthermore, by combining with functional traits (e.g., including body size and trophic level) or phylogenetic information (Keck et al, 2018; Marques et al, 2021), eDNA could generate proxies of ecosystem structure and functioning more informative than those from taxonomic lists alone (D'Alessandro & Mariani, 2021). The use of functional or phylogenetic indices should be first evaluated along contemporary gradients of anthropogenic pressures before future application in monitoring of assemblages (Carvalho et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Studies of eDNA on coral reefs have shown a strong ability for biodiversity detection showing capacity to match inventories from traditional surveys (Polanco Fernández et al, 2021;Sigsgaard et al, 2020;West et al, 2021). Beyond inventories, eDNA could allow rapid quantification of biodiversity and ecosystem quality indices which, in combination with functional or phylogenetic information, may help monitor shifts in ecosystem processes and states (Holman et al, 2019;Marques et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Ecological indices from environmental DNA to contrast coastal reefs under different anthropogenic pressures

Waldock

Keggin

et al. 2022

Ecology and Evolution

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“…BRUVS offer an opportunity in this regard, as the video systems can be rapidly deployed at the exact location where eDNA is being sampled, while the bait may attract individuals in the vicinity that were also captured in the eDNA signal. Comparisons between eDNA and BRUVS have so far focused on biodiversity and community assessments (Boussarie et al, 2018; Jeunen, Lamare, et al, 2020; Marques et al, 2021; Mercaldo‐Allen et al, 2021; Stat et al, 2019), yet potential correlations between species‐specific qPCR detection and abundances recorded from BRUVS remain, to the best of our knowledge, untested.…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA reveals fine‐scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft‐ and hard‐bottom habitats

et al. 2022

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Accurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species–habitat associations in a patchy coastal area of the Baltic Sea. We directly compare species‐specific qPCR analysis of eDNA with baited remote underwater video systems (BRUVS), two non‐invasive methods widely used to monitor marine habitats. Four focal species (cod Gadus morhua, flounder Platichthys flesus, plaice Pleuronectes platessa, and goldsinny wrasse Ctenolabrus rupestris) were selected based on contrasting habitat associations (reef‐ vs. sand‐associated species), as well as differential levels of mobility and residency, to investigate whether these factors affected the detection of species–habitat associations from eDNA. To this end, a species‐specific qPCR assay for goldsinny wrasse is developed and made available herein. In addition, potential correlations between eDNA signals and abundance counts (MaxN) from videos were assessed. Results from Bayesian multilevel models revealed strong evidence for a sand association for sedentary flounder (98% posterior probability) and a reef association for highly resident wrasse (99% posterior probability) using eDNA, in agreement with BRUVS. However, contrary to BRUVS, eDNA sampling did not detect habitat associations for cod or plaice. We found a positive correlation between eDNA detection and MaxN for wrasse (posterior probability 95%), but not for the remaining species and explanatory power of all relationships was generally limited. Our results indicate that eDNA sampling can detect species–habitat associations on a fine spatial scale, yet this ability likely depends on the mobility and residency of the target organism, with associations for sedentary or resident species most likely to be detected. Combined sampling with conventional non‐invasive methods is advised to improve detection of habitat associations for mobile and transient species, or for species with low eDNA concentrations.

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Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Abstract: Article impact statement: Environmental DNA can be used effectively to survey taxonomic, functional, and phylogenetic diversity of tropical reef fishes.

Cited by 32 publications

References 86 publications

Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions

Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions

Ecological indices from environmental DNA to contrast coastal reefs under different anthropogenic pressures

Environmental DNA reveals fine‐scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft‐ and hard‐bottom habitats

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