Benchmarking eleven biodiversity indicators based on environmental <scp>DNA</scp> surveys: More diverse functional traits and evolutionary lineages inside marine reserves

Dalongeville, Alicia; Boulanger, Emilie; Marques, Virginie; Chabrière, Éric; Hartmann, Virginie; Santoni, Marie Catherine; Déter, Julie; Valentini, Alice; Lenfant, Philippe; Boissery, Pierre; Déjean, Tony; Velez, Laure; Pichot, Franck; Sanchez, Loïc; Arnal, Véronique; Bockel, Thomas; Delaruelle, Gwenaelle; Holon, Florian; Milhau, Tristan; Romant, Lola; Manel, Stéphanie; Mouillot, David

doi:10.1111/1365-2664.14276

Cited by 13 publications

(12 citation statements)

References 67 publications

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“…Furthermore, in the case of the Western Mediterranean eDNA dataset, ENNBetaDist revealed a clustering of protected sites (pink cluster on the map, Figure 4a, c). This result of an effect of protection on β-diversity supports previous eDNA studies analyzing the same dataset (Boulanger et al, 2021;Dalongeville, Boulanger, et al, 2022;Dalongeville, Nielsen, et al, 2022) and non-eDNA studies in the Mediterranean (Giakoumi et al, 2017).…”

Section: Discussionsupporting

confidence: 89%

New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data

Lamperti,

Sanchez,

Si Moussi

et al. 2023

Molecular Ecology Resources

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Environmental DNA (eDNA) metabarcoding provides an efficient approach for documenting biodiversity patterns in marine and terrestrial ecosystems. The complexity of these data prevents current methods from extracting and analyzing all the relevant ecological information they contain, and new methods may provide better dimensionality reduction and clustering. Here we present two new deep learning‐based methods that combine different types of neural networks (NNs) to ordinate eDNA samples and visualize ecosystem properties in a two‐dimensional space: the first is based on variational autoencoders and the second on deep metric learning. The strength of our new methods lies in the combination of two inputs: the number of sequences found for each molecular operational taxonomic unit (MOTU) detected and their corresponding nucleotide sequence. Using three different datasets, we show that our methods accurately represent several biodiversity indicators in a two‐dimensional latent space: MOTU richness per sample, sequence α‐diversity per sample, Jaccard's and sequence β‐diversity between samples. We show that our nonlinear methods are better at extracting features from eDNA datasets while avoiding the major biases associated with eDNA. Our methods outperform traditional dimension reduction methods such as Principal Component Analysis, t‐distributed Stochastic Neighbour Embedding, Nonmetric Multidimensional Scaling and Uniform Manifold Approximation and Projection for dimension reduction. Our results suggest that NNs provide a more efficient way of extracting structure from eDNA metabarcoding data, thereby improving their ecological interpretation and thus biodiversity monitoring.

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Section: Discussionsupporting

confidence: 89%

New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data

Lamperti,

Sanchez,

Si Moussi

et al. 2023

Molecular Ecology Resources

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“…Using multiple markers could be an alternative to overcome the incompleteness of genetic reference databases and the lack of primer resolution (Ruppert et al, 2019), but this approach would be much more expensive. Improving the accuracy of taxonomic assignment and completing genetic reference databases are thus urgently needed to improve estimates of large‐scale biodiversity patterns (Marques, Milhau, et al, 2020) and local monitoring (Dalongeville et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

The distribution of coastal fish eDNA sequences in the Anthropocene

Mathon

Marques

Manel

et al. 2023

Global Ecol Biogeogr

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Aim Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio‐economic factors. Location Tropical, temperate and polar coastal areas. Time period Present day. Major taxa studied Marine fishes. Methods We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio‐economic factors on α‐ and β‐diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α‐ and β‐diversity measured from our barcodes, and phylogenetic but also functional diversity. Results We show that fish eDNA MOTU and sequence α‐ and β‐diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.

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“…1) Particular characteristics of pelagic systems result in size structure that is highly sensitive to human pressure and render size indicators a powerful guide for priority placements of spatial protection, monitoring, and ecosystem-based management. In benthic systems, size indicators are comparatively less sensitive, so decisions should be informed through other indicators such as biomass ( 7 ) or functional diversity ( 49 ).…”

Section: Policy Implicationsmentioning

confidence: 99%

Divergent responses of pelagic and benthic fish body-size structure to remoteness and protection from humans

Letessier,

Mouillot,

Mannocci

et al. 2024

Science

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Animal body-size variation influences multiple processes in marine ecosystems, but habitat heterogeneity has prevented a comprehensive assessment of size across pelagic (midwater) and benthic (seabed) systems along anthropic gradients. In this work, we derive fish size indicators from 17,411 stereo baited-video deployments to test for differences between pelagic and benthic responses to remoteness from human pressures and effectiveness of marine protected areas (MPAs). From records of 823,849 individual fish, we report divergent responses between systems, with pelagic size structure more profoundly eroded near human markets than benthic size structure, signifying greater vulnerability of pelagic systems to human pressure. Effective protection of benthic size structure can be achieved through MPAs placed near markets, thereby contributing to benthic habitat restoration and the recovery of associated fishes. By contrast, recovery of the world’s largest and most endangered fishes in pelagic systems requires the creation of highly protected areas in remote locations, including on the High Seas, where protection efforts lag.

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

Cited by 13 publications

References 67 publications

New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data

New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data

The distribution of coastal fish eDNA sequences in the Anthropocene

Divergent responses of pelagic and benthic fish body-size structure to remoteness and protection from humans

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