Regis Hocde
@ird.fr
Scopus Publications
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Scopus Publications
Anaïs Beauvieux, Bastien Mérigot, Jérémy Le Luyer, Jean-Marc Fromentin, Nathan Couffin, Adrien Brown, Olivier Bianchimani, Régis Hocdé, Didier Aurelle, Jean-Baptiste Ledoux,et al.
Springer Science and Business Media LLC
Laetitia Mathon, Virginie Marques, Stéphanie Manel, Camille Albouy, Marco Andrello, Emilie Boulanger, Julie Deter, Régis Hocdé, Fabien Leprieur, Tom B. Letessier,et al.
Wiley
Marion Muff, Mélissa Jaquier, Virginie Marques, Laurent Ballesta, Julie Deter, Thomas Bockel, Régis Hocdé, Jean‐Baptiste Juhel, Emilie Boulanger, Nacim Guellati,et al.
Wiley
Jean‐Baptiste Juhel, Virginie Marques, Rizkie Satriya Utama, Indra Bayu Vimono, Hagi Yulia Sugeha, Kadarusman Kadarusman, Christophe Cochet, Tony Dejean, Andrew Hoey, David Mouillot,et al.
Wiley
Annisa Annisa, Sharifuddin Bin Andy Omar, Fatmawati Marasabessy, Ernawati Ernawati, Rike Kagiling, Emmanuel Manangkalangi, Ralph August Nicodemus Tuhumury, Wero Febriadi Mandala, Henderite Loisa Ohee, Edy Hery Polikarpus Melmambessy,et al.
College of Graduate Studies, Walailak University
Abstract
 Ellochelon vaigiensis is a monotypic, catadromous, and widespread species throughout Indo-Pacific region. Taxonomy of the species is ancient and somewhat confused by morphological resemblance. Here, we present and compare the morphological characteristics of E. vaigiensis from 3 distinct areas, respectively from the type locality (Waigeo Island, Raja Ampat), from Cendrawasih Bay (Biak Island), and Kaimana (Venu and Aiduma Islands). All the samples belong to E. vaigiensis following the species diagnosis given by Harrison and Senou (1999). No significant differentiation is found for all meristic and morphological characters between specimens caught from the type locality and Biak Island. Nevertheless, specimens from Kaimana have a slender body width compared to specimens from Waigeo Island (type locality) and Biak Island. Specimens from Kaimana also display a longer head and a larger eye diameter than specimens from Biak Island. A canonical discriminant analysis made on all morphometric data confirms the morphological differentiation of Kaimana‘s specimens compared to the type locality and Biak Island. These results suggest the possibility of the presence of cryptic species in E. vaigiensis and emphasize the necessity to conduct molecular taxonomy to definitely solve the taxonomic status of Kaimana specimens.
 HIGHLIGHTS
 
 The present study provided a detailed morphological study of E. vaigiensis based on specimens collected at the type of locality of Waigeo and samples caught from localities in the western part of New Guinea
 No significant differentiation is found for all meristic and morphological characters between specimens caught from the type locality and Biak Island. Nevertheless, specimens from Kaimana have a slender body width at origin of first dorsal fin compared to specimens from type locality and Biak Island. Specimens from Kaimana also display a longer head and a larger eye diameter than specimens from Biak Island
 A canonical discriminant analysis confirms the morphological differentiation of Kaimana‘s specimens suggesting the possibility of the presence of cryptic species in E. vaigiensis and emphasize the necessity to conduct molecular taxonomy
 
 GRAPHICAL ABSTRACT
Bastien Macé, Régis Hocdé, Virginie Marques, Pierre‐Edouard Guerin, Alice Valentini, Véronique Arnal, Loïc Pellissier, and Stéphanie Manel
Wiley
Laetitia Mathon, Virginie Marques, David Mouillot, Camille Albouy, Marco Andrello, Florian Baletaud, Giomar H. Borrero-Pérez, Tony Dejean, Graham J. Edgar, Jonathan Grondin,et al.
The Royal Society
Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.
Madeline Steinberg, Jean-Baptiste Juhel, Virginie Marques, Clara Péron, Régis Hocdé, Andréa Polanco Fernández, Loïc Pellissier, Sébastien Villéger, David Mouillot, and Tom B. Letessier
Springer Science and Business Media LLC
Virginie Marques, Paul Castagné, Andréa Polanco, Giomar Helena Borrero‐Pérez, Régis Hocdé, Pierre‐Édouard Guérin, Jean‐Baptiste Juhel, Laure Velez, Nicolas Loiseau, Tom Bech Letessier,et al.
Wiley
Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long‐term remote video to assess species’ phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
Salomé Stauffer, Meret Jucker, Thomas Keggin, Virginie Marques, Marco Andrello, Sandra Bessudo, Marie‐Charlotte Cheutin, Giomar Helena Borrero‐Pérez, Eilísh Richards, Tony Dejean,et al.
Wiley
Quantifying the diversity of species in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, the reliability of biodiversity detection from eDNA samples can be low in marine environments because eDNA density is low and certainly patchy in this vast, heterogenous and dynamic environment. So, the number of sampling replicates and filtered volume necessary to obtain accurate estimates of biodiversity in rich tropical marine environments using eDNA metabarcoding is still unknown. Here, we used a paired sampling design of 30L per replicate on 68 reef transects from 8 sites in three tropical regions and identified fish Molecular Taxonomic Units (MOTUs) using a 12S marker. We quantified local biodiversity variation as MOTU richness, compositional turnover and compositional nestedness between replicated pairs of seawater samples. We report strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one-another. As a result, localised diversity accumulation curves showed that even 6 replicates (180L) in the same location underestimated local diversity (for an area <1km). However, sampling of regional diversity using ∼25 replicates in variable locations (often covering 10s of km) achieved saturation of biodiversity accumulation curves. Our results demonstrate high variability of diversity estimates perhaps arising from heterogeneous and local distribution of eDNA distribution in seawater or highly skewed frequencies of eDNA traces. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes of local assemblages. Future biomonitoring efforts could be strongly undermined by a high level of false-negative detections under low replication protocols. We reveal the need to increase replicates or increase sampled water volume to better inform management of marine biodiversity using eDNA.
Andrea Polanco F., Maria Mutis Martinezguerra, Virginie Marques, Francisco Villa‐Navarro, Giomar Helena Borrero Pérez, Marie‐Charlotte Cheutin, Tony Dejean, Régis Hocdé, Jean‐Baptiste Juhel, Eva Maire,et al.
Wiley
Estuaries are characterized by a tidal regime and are strongly influenced by hydrodynamics and host diverse and highly dynamic habitats, from fresh, brackish, or saltwater to terrestrial, whose biodiversity is especially difficult to monitor. Here, we investigated the potential of environmental DNA (eDNA) metabarcoding, with three primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the estuary of the Don Diego River in Colombia. With eDNA, we detected not only aquatic organisms, including fishes, amphibians, and reptiles, but also a large diversity of terrestrial, arboreal, and flying vertebrates, including mammals and birds, living in the estuary surroundings. Further, the eDNA signal remained relatively localized along the watercourse. A transect from the deep outer section of the estuary, across the river mouth toward the inner section of the river, showed marked taxonomic turnover from typical marine to freshwater fishes, while eDNA of terrestrial and arboreal species was mainly found in the inner section of the estuary. Our results indicate that eDNA enables the detection of a large diversity of vertebrates and could become an important tool for biodiversity monitoring in estuaries, where water integrates information across the ecosystem.
Evy Arida, Hidayat Ashari, Hadi Dahruddin, Yuli Sulistya Fitriana, Amir Hamidy, Mohammad Irham, Kadarusman, Awal Riyanto, Sigit Wiantoro, Moch Syamsul Arifin Zein,et al.
Wiley
Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA‐based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species‐delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.
Jean‐Baptiste Juhel, Virginie Marques, Andrea Polanco Fernández, Giomar H. Borrero‐Pérez, Maria Mutis Martinezguerra, Alice Valentini, Tony Dejean, Stéphanie Manel, Nicolas Loiseau, Laure Velez,et al.
Wiley
Abstract Monitoring large marine mammals is challenging due to their low abundances in general, an ability to move over large distances and wide geographical range sizes. The distribution of the pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales is informed by relatively rare sightings, which does not permit accurate estimates of their distribution ranges. Hence, their conservation status has long remained Data Deficient (DD) in the Red list of the International Union for Conservation of Nature (IUCN), which prevent appropriate conservation measures. Environmental DNA (eDNA) metabarcoding uses DNA traces left by organisms in their environments to detect the presence of targeted taxon, and is here proved to be useful to increase our knowledge on the distribution of rare but emblematic megafauna. Retrieving eDNA from filtered surface water provides the first detection of the Dwarf sperm whale (Kogia sima) around the remote Malpelo island (Colombia). Environmental DNA collected during oceanic missions can generate better knowledge on rare but emblematic animals even in regions that are generally well sampled for other taxa.
Andrea Polanco Fernández, Virginie Marques, Fabian Fopp, Jean‐Baptiste Juhel, Giomar Helena Borrero‐Pérez, Marie‐Charlotte Cheutin, Tony Dejean, Juan David González Corredor, Andrés Acosta‐Chaparro, Régis Hocdé,et al.
Wiley
Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species-rich ecosystems such as coral reefs is a prerequisite for their application in long-term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and
Kadarusman, Hagi Yulia Sugeha, Laurent Pouyaud, Régis Hocdé, Intanurfemi B. Hismayasari, Endang Gunaisah, Santoso B. Widiarto, Gulam Arafat, Ferliana Widyasari, David Mouillot,et al.
Springer Science and Business Media LLC
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Kadarusman, Hagi Yulia Sugeha, Laurent Pouyaud, Régis Hocdé, Intanurfemi B. Hismayasari, Endang Gunaisah, Santoso B. Widiarto, Gulam Arafat, Ferliana Widyasari, David Mouillot,et al.
Springer Science and Business Media LLC
AbstractCoelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these ‘living fossils’ using new molecular data, including the possibility of ‘cryptic’ species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.
Jean-Baptiste Juhel, Rizkie S. Utama, Virginie Marques, Indra B. Vimono, Hagi Yulia Sugeha, Kadarusman, Laurent Pouyaud, Tony Dejean, David Mouillot, and Régis Hocdé
The Royal Society
Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
Erwan Delrieu‐Trottin, Jean‐Dominique Durand, Gino Limmon, Tedjo Sukmono, Kadarusman, Hagi Yulia Sugeha, Wei‐Jen Chen, Frédéric Busson, Philippe Borsa, Hadi Dahruddin,et al.
Wiley
DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA‐based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo‐Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA‐based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA‐based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo‐Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.
Lucie Cocquempot, Christophe Delacourt, Jérôme Paillet, Philippe Riou, Jérôme Aucan, Bruno Castelle, Guillaume Charria, Joachim Claudet, Pascal Conan, Laurent Coppola,et al.
Frontiers Media SA
To understand and predict the physical, chemical, and biological processes at play in coastal and nearshore marine areas requires an integrated, interdisciplinary approach. The case study of the French structuration of coastal ocean and nearshore observing systems provides an original overview on a federative research infrastructure named ILICO. It is a notable example of national structuration and pan-institution efforts to investigate the forefront of knowledge on the processes at work within the critical coastal zone. ILICO comprises, in a pluridisciplinary approach, eight distributed network-systems of observation and data analysis that are accredited and financially supported by French research institutions and the French Ministry for Higher Education, Research, and Innovation. ILICO observation points are implemented along metropolitan and overseas French coasts, where coastline dynamics, sea level evolution, physical and biogeochemical water properties, coastal water dynamics, phytoplankton composition, and health of coral reefs are monitored in order to address a wide range of scientific questions. To give an overview of the diversity and potential of the observations carried out, this paper offers a detailed presentation of three constituting networks: Service Observation en Milieu LITtoral (SOMLIT), with homogeneous sampling strategies, DYNALIT, with heterogeneous sampling strategies adapted to different environments, and Mediterranean Ocean Observing System for the Environment (MOOSE), an integrated, pluri-disciplinary coastal/offshore regional observatory in the northwestern Mediterranean Sea. ILICO was conceived using a European framework. It addresses the great challenges of the next decade in terms of sustainability, cost-efficiency, interoperability, and innovation. This paper emphasizes the added-value of federating these systems, and highlights some recommendations for the future.