Scopus Publications
- Drone photogrammetry reveals contrasting body conditions of dugongs across the Indo-Pacific
Camille Goudalier, David Mouillot, Léa Bernagou, Taha Boksmati, Caulvyn Bristol, et al.
Remote Sensing in Ecology and Conservation, 2025
The monitoring of body condition, reflecting the state of individuals' energetic reserves, can provide early warning signals of population decline, facilitating prompt conservation actions. However, environmental and anthropogenic drivers of body condition are poorly known for rare and elusive marine mammal species over their entire ranges. We assessed the global patterns and drivers of body condition for the endangered dugong (Dugong dugon) across its Indo‐Pacific range. To do so, we applied the body condition index (BCI) developed for the related manatee based on the ratio of umbilical girth (approximated as maximum width times π), to straight body length measured in drone images. To cover the entire dugong's range, we took advantage of drone footage published on social media. Combined with footage from scientific surveys, social media footage provided body condition estimates for 272 individual dugongs across 18 countries. Despite small sample sizes relative to local population sizes, we found that dugong BCI was better, that is, individuals were ‘plumper’, in New Caledonia, the United Arab Emirates, Australia and Qatar where populations are the largest globally. Dugong BCI was comparatively poorer in countries hosting very small dugong populations such as Mozambique, suggesting a link between body condition and population size. Using statistical models, we then investigated potential environmental and anthropogenic drivers of dugong BCI, while controlling for seasonal and individual effects. The BCI decreased with human gravity, a variable integrating human pressures on tropical reefs, but increased with GDP per capita, indicating that economic wealth positively affects dugong energetic state. The BCI also showed a dome‐shaped relationship with marine protected area coverage, suggesting that extensive spatial protection is not sufficient to maintain dugongs in good state. Our study provides the first assessment of dugong body condition through drone photogrammetry, underlining the value of this non‐invasive, fast and low‐cost approach for monitoring elusive marine mammals. - eDNA surveys substantially expand known geographic and ecological niche boundaries of marine fishes
Loïc Sanchez, Nicolas Loiseau, Camille Albouy, Morgane Bruno, Adèle Barroil, et al.
Plos Biology, 2025
Assessing species geographic distributions is critical to approximate their ecological niches, understand how global change may reshape their occurrence patterns, and predict their extinction risks. Yet, species records are over-aggregated across taxonomic, geographic, environmental, and anthropogenic dimensions. The under-sampling of remote locations biases the quantification of species geographic distributions and ecological niche for most species. Here, we used nearly one thousand environmental DNA (eDNA) samples across the world’s oceans, including polar regions and tropical remote islands, to determine the extent to which the geographic and ecological niche ranges of marine fishes are underestimated through the lens of global occurrence records based on conventional surveys. Our eDNA surveys revealed that the known geographic ranges for 93% of species and the ecological niche ranges for 7% of species were underestimated, and contributed to filling them. We show that the probability to detect a range filling for a given species is primarily shaped by the GBIF/OBIS sampling effort in a cell, but also by the number of occurrences available for the species. Most gap fillings were achieved by addressing a methodological sampling bias, notably when eDNA facilitated the detection of small fishes in previously sampled locations using conventional methods. Using a machine learning model, we found that a local effort of 10 eDNA samples would detect 24 additional fish species on average and a maximum of 98 species in previously unsampled tropical areas. Yet, a null model revealed that only half of ecological niche range fillings would be due to eDNA surveys, beyond a random allocation of classical sampling effort. Altogether, our results suggest that sampling in remote areas and performing eDNA surveys in over-sampled areas may both increase fish ecological niche ranges toward unexpected values with consequences in biodiversity modeling, management, and conservation. - ReefTEMPS: the Pacific Islands coastal temperature network
Romain Le Gendre, David Varillon, Sylvie Fiat, Régis Hocdé, Antoine de Ramon N'Yeurt, et al.
Earth System Science Data, 2025
While the rise in global ocean temperature continues its course, reaching 1.45±0.12 °C above pre-industrial level according to the World Meteorological Organization in 2023, marine heatwave frequencies and intensities increase. Consequently, coral reef ecosystems, which are among the most vulnerable environments, are strongly impacted by dystrophic events and corals experiencing increasing frequencies of bleaching events. That has devastating consequences for the Pacific Island countries and territories (PICTs) that strongly rely on these ecosystems. In situ observation remains the best alternative for providing accurate characterization of long-term trends and extremes in these shallow environments. This paper presents the coastal temperature dataset of the ReefTEMPS monitoring network (Varillon et al., 2025, https://doi.org/10.17882/55128; Liao et al., 2025, https://doi.org/10.17882/82291) in which moored stations are implemented over a number of PICTs over a wide region in the western and central South Pacific from New Caledonia to French Polynesia. These in situ temperature time series are unique in several ways: in the length of some historical stations dating back to 1958 for the oldest, thus providing more than 65 years of daily data; in the number of countries sampled (16 PICTs); and in the variety of coral ecosystems monitored (from atolls to high islands and from barrier reefs' external slopes to shallow and narrow lagoons). Measurement devices have evolved over the years to provide increasingly precise and frequent observations, so the ReefTEMPS network was endorsed as a French National Observation Service in 2020, a label ensuring quality-controlled and open-access data of long-term observations. All stations are publicly available in ASCII or formatted NetCDF files either in the ReefTEMPS dedicated information system, which also allows for a quick visualization of time series, or on the SEANOE marine data platform. All links and accesses to these temperature time series are provided herein. The longevity of these temperature time series allows for diagnosing long-term trends, highlighting the influence of multiple processes on temperature dynamics (e.g. internal waves, cyclones, seasonal, and climate modes) and documenting the time evolution of extreme events. All files are made publicly available on dedicated SEANOE repositories. - Improving the Monitoring of the Invasive Blue Crab (Callinectes sapidus): Combining Environmental DNA and Citizen Observations
Erwan Delrieu‐Trottin, Mathieu Bianic, Claude Miaud, Manon Garcia, Véronique Arnal, et al.
Aquatic Conservation Marine and Freshwater Ecosystems, 2025
Early detection is a crucial tool for identifying the spread of invasive species. In this study, we validated a probe‐based quantitative polymerase chain reaction (qPCR) assay for the detection of the invasive Blue Crab, Callinectes sapidus, in the Mediterranean Sea, using 22 initial eDNA environmental samples (eDNA) collected from three coastal lagoons. A subsequent large‐scale eDNA sampling campaign (61 samples in 31 sites), conducted in collaboration with local stakeholders, was carried out to map the distribution of C. sapidus along the Occitanie coastline (Western Mediterranean, France). Using eDNA probe‐based qPCR, C. sapidus was detected in 32 out of the 61 samples (52%), confirming its presence in 24 out of 31 sites surveyed, including the 13 lagoons where its occurrence had already been reported, as well as two additional lagoons and at sea where no prior records existed. Our results demonstrate the utility of eDNA probe‐based qPCR for effective monitoring of the invasive Blue Crab. The integration of eDNA analysis with citizen science observations enhances the monitoring framework, facilitating early detection and contributing to improved management strategies at the very beginning of species colonization when practical actions could be implemented. - Diversity of long-spined sea urchins (Diadema spp.) in the Indo-Malay archipelago
I. B. Vimono, P. Borsa, R. Hocdé, U. Y. Arbi, H. Kadarusman, et al.
Arxius De Miscellania Zoologica, 2025
Long-spined sea urchin species (genus Diadema) are important to the ecology of coral-reef ecosystems. The objective of this paper is to inventory Diadema species occurring in the so far under-sampled Indo-Malay archipelago at the core of the tropical Indo-West Pacific ensemble and to produce point maps. Records of Diadema spp. were compiled from the literature and from the GBIF database. New records were obtained by visual censuses at 52 coastal locations across the Indo-Malay archipelago. Specimens were collected and their nucleotide sequences at the mitochondrial COI gene locus were produced. Photographs were taken, voucher specimens were deposited in scientific collections. Nucleotide sequences revealed three mitochondrial lineages in the Indo-Malay archipelago, which clustered with the D. paucispinum, D. savignyi and D. setosum-a lineages. The distinction between D. paucispinum and D. savignyi was possible only through COI barcoding. D. paucispinum was thus recorded for the first time in the Andaman Sea, in Makassar Strait and in the Banda Sea. D. savignyi was recorded for the first time in the Andaman Sea, in the Bali Sea, in the Flores Sea and on the Pacific shores of West Papua. We failed to sample D. clarki despite extensive reef surveys in Makassar Strait and in the Banda Sea, the two regions where this species had been reported previously. The present study provides the first comprehensive COI-based inventory of long-spined sea urchin species inhabiting the coral reef ecosystems of the Indo-Malay archipelago. This information is important to our understanding of the biogeography of Diadema sea urchin communities and it can be useful to their fisheries and conservation management in this region. Dataset published through GBIF (DOI: 10.15470/weeuk1) - Seasonal dynamics of Mediterranean fish communities revealed by eDNA: Contrasting compositions across depths and Marine Fully Protected Area boundaries
Romane Rozanski, Laure Velez, Régis Hocdé, Agnès Duhamet, Conor Waldock, et al.
Ecological Indicators, 2024 - Mesophotic zone as refuge: acclimation and in-depth proteomic response of yellow gorgonians in the Mediterranean sea
Anaïs Beauvieux, Bastien Mérigot, Jérémy Le Luyer, Jean-Marc Fromentin, Nathan Couffin, et al.
Coral Reefs, 2024 - Updating the Cetacean Species List of Raja Ampat, Indonesia, with Additional Sightings of the Rarely Documented Omura’s Whale (Balaenoptera omurai)
Achmad Sahri, Régis Hocdé, Muhammad R. Nandika, Fahmi, Lay Tjarles, et al.
Aquatic Mammals, 2024 - The distribution of coastal fish eDNA sequences in the Anthropocene
Laetitia Mathon, Virginie Marques, Stéphanie Manel, Camille Albouy, Marco Andrello, et al.
Global Ecology and Biogeography, 2023 - Phylogeography of Long-spined Sea Urchin Diadema setosum Across the Indo-Malay Archipelago
Zoological Studies, 2023 - Environmental DNA highlights fish biodiversity in mesophotic ecosystems
Marion Muff, Mélissa Jaquier, Virginie Marques, Laurent Ballesta, Julie Deter, et al.
Environmental DNA, 2023 - Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions
Jean‐Baptiste Juhel, Virginie Marques, Rizkie Satriya Utama, Indra Bayu Vimono, Hagi Yulia Sugeha, et al.
Ecography, 2022 - Taxonomic Note on Ellochelon vaigiensis (Quoy & Gaimard, 1825) (Mugilidae: Mugiliformes) from West New Guinea, Indonesia
Annisa Annisa, Sharifuddin Bin Andy Omar, Fatmawati Marasabessy, Ernawati Ernawati, Rike Kagiling, et al.
Trends in Sciences, 2022 - Evaluating bioinformatics pipelines for population-level inference using environmental DNA
Bastien Macé, Régis Hocdé, Virginie Marques, Pierre‐Edouard Guerin, Alice Valentini, et al.
Environmental DNA, 2022 - Similar trait structure and vulnerability in pelagic fish faunas on two remote island systems
Madeline Steinberg, Jean-Baptiste Juhel, Virginie Marques, Clara Péron, Régis Hocdé, et al.
Marine Biology, 2022 - Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding
Laetitia Mathon, Virginie Marques, David Mouillot, Camille Albouy, Marco Andrello, et al.
Proceedings of the Royal Society B Biological Sciences, 2022 - Use of environmental DNA in assessment of fish functional and phylogenetic diversity
Virginie Marques, Paul Castagné, Andréa Polanco, Giomar Helena Borrero‐Pérez, Régis Hocdé, et al.
Conservation Biology, 2021 - Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
Andrea Polanco F., Maria Mutis Martinezguerra, Virginie Marques, Francisco Villa‐Navarro, Giomar Helena Borrero Pérez, et al.
Biotropica, 2021 - How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?
Salomé Stauffer, Meret Jucker, Thomas Keggin, Virginie Marques, Marco Andrello, et al.
Ecology and Evolution, 2021 - Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes
Evy Arida, Hidayat Ashari, Hadi Dahruddin, Yuli Sulistya Fitriana, Amir Hamidy, et al.
Molecular Ecology Resources, 2021 - Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia)
Jean‐Baptiste Juhel, Virginie Marques, Andrea Polanco Fernández, Giomar H. Borrero‐Pérez, Maria Mutis Martinezguerra, et al.
Ecology and Evolution, 2021 - Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes
Andrea Polanco Fernández, Virginie Marques, Fabian Fopp, Jean‐Baptiste Juhel, Giomar Helena Borrero‐Pérez, et al.
Environmental DNA, 2021 - A thirteen-million-year divergence between two lineages of Indonesian coelacanths
Kadarusman, Hagi Yulia Sugeha, Laurent Pouyaud, Régis Hocdé, Intanurfemi B. Hismayasari, et al.
Scientific Reports, 2020 - Publisher Correction: A thirteen-million-year divergence between two lineages of Indonesian coelacanths (Scientific Reports, (2020), 10, 1, (192), 10.1038/s41598-019-57042-1)
Kadarusman, Hagi Yulia Sugeha, Laurent Pouyaud, Régis Hocdé, Intanurfemi B. Hismayasari, et al.
Scientific Reports, 2020 - Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle
Jean-Baptiste Juhel, Rizkie S. Utama, Virginie Marques, Indra B. Vimono, Hagi Yulia Sugeha, et al.
Proceedings of the Royal Society B Biological Sciences, 2020
RECENT SCHOLAR PUBLICATIONS
- Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions
JB Juhel, V Marques, RS Utama, IB Vimono, HY Sugeha, K Kadarusman, ...
Ecography 2022 (10), e06299 , 2022
2022
Citations: 23 - Environmental DNA highlights fish biodiversity in mesophotic ecosystems
M Muff, M Jaquier, V Marques, L Ballesta, J Deter, T Bockel, R Hocdé, ...
Environmental DNA , 2022
2022
Citations: 28 - Taxonomic Note on Ellochelon vaigiensis (Quoy & Gaimard, 1825)(Mugilidae: Mugiliformes) from West New Guinea, Indonesia
A Annisa, SBA Omar, F Marasabessy, E Ernawati, R Kagiling, ...
Trends in Sciences 19 (17), 5750-5750 , 2022
2022
Citations: 2 - Transmission de données océanographiques via le réseau IoT LoRaWAN sur une bouée instrumentée du Service National d'Observation ReefTEMPS
F Sylvie, R Hocdé
JRES 2022 , 2022
2022 - Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
B Macé, R Hocdé, V Marques, PE Guerin, A Valentini, V Arnal, L Pellissier, ...
Environmental DNA 4 (3), 674-686 , 2022
2022
Citations: 37 - Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding
L Mathon, V Marques, D Mouillot, C Albouy, M Andrello, F Baletaud, ...
Proceedings of the Royal Society B 289 (1973), 20220162 , 2022
2022
Citations: 85 - Similar trait structure and vulnerability in pelagic fish faunas on two remote island systems
M Steinberg, JB Juhel, V Marques, C Péron, R Hocdé, ...
Marine Biology 169, 1-9 , 2022
2022
Citations: 5 - Use of environmental DNA in assessment of fish functional and phylogenetic diversity
V Marques, P Castagné, A Polanco, GH Borrero‐Pérez, R Hocdé, ...
Conservation Biology 35 (6), 1944-1956 , 2021
2021
Citations: 68 - ReefTEMPS documents the local impact of climate change and the parameters that influence the resilience of reef ecosystems
R Hocdé, S Fiat, D Varillon, F Magron, M Allenbach, T Hoibian, ...
ILICO EVOLECO 2021: Long Term Evolution of Coastal Ecosystems , 2021
2021 - ReefTEMPS documente l'impact local du changement climatique et les paramètres qui influent sur la résilience des écosystèmes récifaux
R Hocdé, S Fiat, D Varillon, F Magron, M Allenbach, T Hoibian, ...
ILICO EVOLECO 2021: Long Term Evolution of Coastal Ecosystems , 2021
2021
Citations: 1 - Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
A Polanco F, M Mutis Martinezguerra, V Marques, F Villa‐Navarro, ...
Biotropica 53 (6), 1606-1619 , 2021
2021
Citations: 56 - How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?
S Stauffer, M Jucker, T Keggin, V Marques, M Andrello, S Bessudo, ...
Ecology and Evolution 11 (21), 14630-14643 , 2021
2021
Citations: 80 - Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes
E Arida, H Ashari, H Dahruddin, YS Fitriana, A Hamidy, M Irham, ...
Molecular Ecology Resources 21 (7), 2369-2387 , 2021
2021
Citations: 26 - CO-UNE INFRASTRUCTURE DE RECHERCHE FRANÇAISE POUR L'OBSERVATION DES OCÉANS ET DES LITTORAUX CÔTIERS
L Cocquempot, J Burden, C Delacourt, J Paillet, P Raimbault, G Charria, ...
2021 - Taxonomic Note on Ellochelon vaigiensis (Quoy & Gaimard, 1825)(Mugilidae: Mugiliformes) from West New Guinea, Indonesia
SBA Omar, F Marasabessy, R Kagiling, E Manangkalangi, ...
TRENDS IN SCIENCES 2022 19 (17), 1-11 , 2021
2021 - Similar Trait Structure and Vulnerability in Pelagic Fish Faunas on Two Remote Islands
M Steinberg, JB Juhel, V Marques, C Péron, R Hocdé, AF Polanco, ...
2021 - ReefTEMPS: the Pacific Insular coastal water observation network
R Hocdé, S Fiat, D Varillon, J Aucan
9th EuroGOOS International conference, 292-295 , 2021
2021 - ILICO-A FRENCH RESEARCH INFRASTRUCTURE FOR COASTAL OCEAN AND SEASHORE OBSERVATIONS
L Cocquempot, J Burden, C Delacourt, J Paillet, P Raimbault, G Charria, ...
9th EuroGOOS International conference , 2021
2021 - ReefTEMPS, FAIRs access to Reef ecosystem environmental measurements
F Sylvie, J Aucan, D Varillon, R Hocdé
IMDIS 2021 62, 307-308 , 2021
2021 - Circumglobal distribution of fish environmental DNA in coral reefs
L Mathon, V Marques, D Mouillot, C Albouy, M Andrello, F Baletaud, ...
ARPHA Conference Abstracts 4, e64792 , 2021
2021
Citations: 2
MOST CITED SCHOLAR PUBLICATIONS
- Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes
A Polanco Fernández, V Marques, F Fopp, JB Juhel, GH Borrero‐Pérez, ...
Environmental DNA 3 (1), 142-156 , 2021
2021
Citations: 143 - Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding
L Mathon, V Marques, D Mouillot, C Albouy, M Andrello, F Baletaud, ...
Proceedings of the Royal Society B 289 (1973), 20220162 , 2022
2022
Citations: 85 - How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?
S Stauffer, M Jucker, T Keggin, V Marques, M Andrello, S Bessudo, ...
Ecology and Evolution 11 (21), 14630-14643 , 2021
2021
Citations: 80 - Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle
JB Juhel, RS Utama, V Marques, IB Vimono, HY Sugeha, n Kadarusman, ...
Proceedings of the Royal Society B 287 (1930), 20200248 , 2020
2020
Citations: 74 - Use of environmental DNA in assessment of fish functional and phylogenetic diversity
V Marques, P Castagné, A Polanco, GH Borrero‐Pérez, R Hocdé, ...
Conservation Biology 35 (6), 1944-1956 , 2021
2021
Citations: 68 - Coastal ocean and nearshore observation: A French case study
L Cocquempot, C Delacourt, J Paillet, P Riou, J Aucan, B Castelle, ...
2019
Citations: 58 - Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA
A Polanco F, M Mutis Martinezguerra, V Marques, F Villa‐Navarro, ...
Biotropica 53 (6), 1606-1619 , 2021
2021
Citations: 56 - Detection of the elusive Dwarf sperm whale (Kogia sima) using environmental DNA at Malpelo island (Eastern Pacific, Colombia)
JB Juhel, V Marques, AP Fernández, GH Borrero‐Pérez, ...
Ecology and Evolution 11 (7), 2956 , 2021
2021
Citations: 47 - Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo‐Australian Archipelago through the iterative use of DNA‐based species delimitation and …
E Delrieu‐Trottin, JD Durand, G Limmon, T Sukmono, HY Sugeha, ...
Evolutionary applications 13 (6), 1451-1467 , 2020
2020
Citations: 41 - Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
B Macé, R Hocdé, V Marques, PE Guerin, A Valentini, V Arnal, L Pellissier, ...
Environmental DNA 4 (3), 674-686 , 2022
2022
Citations: 37 - Environmental DNA highlights fish biodiversity in mesophotic ecosystems
M Muff, M Jaquier, V Marques, L Ballesta, J Deter, T Bockel, R Hocdé, ...
Environmental DNA , 2022
2022
Citations: 28 - Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes
E Arida, H Ashari, H Dahruddin, YS Fitriana, A Hamidy, M Irham, ...
Molecular Ecology Resources 21 (7), 2369-2387 , 2021
2021
Citations: 26 - Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions
JB Juhel, V Marques, RS Utama, IB Vimono, HY Sugeha, K Kadarusman, ...
Ecography 2022 (10), e06299 , 2022
2022
Citations: 23 - Courants, vagues et marées(Les mouvements de l'eau)
P Le Hir, RS Jacinto, B Thouvenin, L Guézennec, P Bassoullet, P Cugier, ...
Programme scientifique Seine-aval , 2001
2001
Citations: 21 - A thirteen-million-year divergence between two lineages of Indonesian coelacanths
HY Sugeha, L Pouyaud, R Hocdé, IB Hismayasari, E Gunaisah, ...
Scientific reports 10 (1), 192 , 2020
2020
Citations: 14 - Patrimoine biologique et chaînes alimentaires
K Costil, JC Dauvin, S Duhamel, R Hocdé, P Mouny, G De Roton, ...
Fascicule Seine-Aval, 48 , 2002
2002
Citations: 11 - Démarche prospective à l’horizon 2025 sur l’estuaire de la Seine
AD Haute-Normandie
Annexes. France, 129 , 2004
2004
Citations: 10 - ReefTEMPS: The Pacific Island coastal ocean observation network
D Varillon, S Fiat, F Magron, M Allenbach, T Hoibian, ...
SEANOE , 2019
2019
Citations: 9 - Patrimoine biologique et chaînes alimentaires
JC Dauvin
Editions Quae , 2002
2002
Citations: 8 - Similar trait structure and vulnerability in pelagic fish faunas on two remote island systems
M Steinberg, JB Juhel, V Marques, C Péron, R Hocdé, ...
Marine Biology 169, 1-9 , 2022
2022
Citations: 5
