Human pressure, habitat heterogeneity and species traits jointly determine the level of dark diversity in coastal fish communities
Abstract
Understanding how anthropogenic pressures and environmental gradients shape coastal fish communities is a central question in biogeography and marine conservation. Yet, the set of species expected to occur at a site given ecological conditions but being absent -the so-called dark diversity -has received far less attention than observed species, even if they hold key information about local extirpations and conservation effectiveness. Quantifying dark diversity in the sea is particularly challenging because many species are rare, cryptobenthic or mobile, while sampling effort is rarely standardized. Here we combined 930 environmental DNA (eDNA) samples collected at 401 sites along 2,000 km of the French Mediterranean coast with fine-scale mapping of habitats, anthropogenic pressures and protection levels. Using a Bayesian model of dark diversity affinity (DDA) that explicitly controls for sampling effort, we decomposed the correlates of species absences into site characteristics and species traits, separating dispersal-related from sensitivity-related signals. At the site level, fishing effort, marine traffic, and artificial habitats were associated with greater DDA, so a deficit of species, whereas protected areas and diverse natural habitats were associated with lower DDA, increasing the likelihood of observing more complete fish communities. At the species level, demersal and predator species, together with those bearing their eggs (e.g., many elasmobranchs) compared to species with demersal or pelagic eggs, exhibited the highest DDA, suggesting local extirpations linked to a combination of limited dispersal and higher sensitivity to cumulative pressures. Beyond the creation of marine protected areas, preserving habitat heterogeneity and mitigating coastal pressures therefore emerge as essential levers to limit the local erosion of fish biodiversity. More broadly, coupling eDNA with a sampling-effortcorrected DDA framework offers a transferable benchmark to evaluate where, and for which species, conservation efforts are most needed.
Related
- Acoustic indices can be driven by habitat characteristics rather than bird diversity
- Habitat Contractions to Drive Future Planktonic Foraminifera Distribution and Diversity Change
- Environmental heterogeneity shapes divergent assembly processes and network stability of plankton communities along a tropical island coast: Evidence from Hainan Island
- Diversity persists while function shifts: post-heatwave reorganization of reef fish communities in Baja California
- Habitat selection for trap building in antlion larvae: Influence of patch area and travelling distance
BibTeX
@article{sanchez2026human,
title = {{Human pressure, habitat heterogeneity and species traits jointly determine the level of dark diversity in coastal fish communities}},
author = {Loïc Sanchez and Jeanne Rolland and Adèle Barroil and Célia Bertrand and Agathe Blandin and Pierre Boissery and Thomas Bockel and Eric Charbonnel and Julie Deter and Régis Hocdé and Florian Holon and Jean‐baptiste Juhel and Nicolas Loiseau and Bastien Macé and Anthony Maire and Stéphanie Manel and Marie Orblin and Franck Pichot and Jean‐jacques Riutort and Lola Romant and Rémy Simide and Alice Valentini and Laure Velez and David Mouillot},
journal = {Ecography},
year = {2026},
month = sep,
doi = {10.1002/ecog.08522},
url = {https://hal.science/hal-05762295v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Human pressure, habitat heterogeneity and species traits jointly determine the level of dark diversity in coastal fish communities
AU - Loïc Sanchez
AU - Jeanne Rolland
AU - Adèle Barroil
AU - Célia Bertrand
AU - Agathe Blandin
AU - Pierre Boissery
AU - Thomas Bockel
AU - Eric Charbonnel
AU - Julie Deter
AU - Régis Hocdé
AU - Florian Holon
AU - Jean‐baptiste Juhel
AU - Nicolas Loiseau
AU - Bastien Macé
AU - Anthony Maire
AU - Stéphanie Manel
AU - Marie Orblin
AU - Franck Pichot
AU - Jean‐jacques Riutort
AU - Lola Romant
AU - Rémy Simide
AU - Alice Valentini
AU - Laure Velez
AU - David Mouillot
PY - 2026
DA - 2026/09/23
JO - Ecography
DO - 10.1002/ecog.08522
UR - https://hal.science/hal-05762295v1
AB - Understanding how anthropogenic pressures and environmental gradients shape coastal fish communities is a central question in biogeography and marine conservation. Yet, the set of species expected to occur at a site given ecological conditions but being absent -the so-called dark diversity -has received far less attention than observed species, even if they hold key information about local extirpations and conservation effectiveness. Quantifying dark diversity in the sea is particularly challenging because many species are rare, cryptobenthic or mobile, while sampling effort is rarely standardized. Here we combined 930 environmental DNA (eDNA) samples collected at 401 sites along 2,000 km of the French Mediterranean coast with fine-scale mapping of habitats, anthropogenic pressures and protection levels. Using a Bayesian model of dark diversity affinity (DDA) that explicitly controls for sampling effort, we decomposed the correlates of species absences into site characteristics and species traits, separating dispersal-related from sensitivity-related signals. At the site level, fishing effort, marine traffic, and artificial habitats were associated with greater DDA, so a deficit of species, whereas protected areas and diverse natural habitats were associated with lower DDA, increasing the likelihood of observing more complete fish communities. At the species level, demersal and predator species, together with those bearing their eggs (e.g., many elasmobranchs) compared to species with demersal or pelagic eggs, exhibited the highest DDA, suggesting local extirpations linked to a combination of limited dispersal and higher sensitivity to cumulative pressures. Beyond the creation of marine protected areas, preserving habitat heterogeneity and mitigating coastal pressures therefore emerge as essential levers to limit the local erosion of fish biodiversity. More broadly, coupling eDNA with a sampling-effortcorrected DDA framework offers a transferable benchmark to evaluate where, and for which species, conservation efforts are most needed.
SN - 1600-0587
ER -