|
|
|
|
|
| Juhel, Jean-baptiste; Utama, Rizkie S.; Marques, Virginie; Vimono, Indra B.; Sugeha, Hagi Yulia; Kadarusman,; Pouyaud, Laurent; Dejean, Tony; Mouillot, David; Hocdé, Régis. |
| 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... |
| Tipo: Text |
Palavras-chave: EDNA metabarcoding; Sequence clustering; Operational Taxonomic Unit; Diversity assessment; Detectability. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00640/75232/79601.pdf |
| |
|
|
| Marques, Virginie; Guérin, Pierre-édouard; Rocle, Mathieu; Valentini, Alice; Manel, Stéphanie; Mouillot, David; Dejean, Tony. |
| Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non‐invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species of the regional pool, which is rarely met. As an alternative, molecular operational taxonomic units (MOTUs) can be extracted as clusters of sequences. However, the extent to which the diversity of MOTUs can predict the diversity of species across spatial scales is unknown. Here, we used 196 samples along the Rhone river (France) for which the reference... |
| Tipo: Text |
Palavras-chave: 12S primer; Alpha-beta-delta-diversity; Clustering; Metabarcoding; MOTUs; Reference database. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00643/75506/76373.pdf |
| |
|
|
| Polanco Fernández, Andrea; Marques, Virginie; Fopp, Fabian; Juhel, Jean‐baptiste; Borrero‐pérez, Giomar Helena; Cheutin, Marie‐charlotte; Dejean, Tony; González Corredor, Juan David; Acosta‐chaparro, Andrés; Hocdé, Régis; Eme, David; Maire, Eva; Spescha, Manuel; Valentini, Alice; Manel, Stéphanie; Mouillot, David; Albouy, Camille; Pellissier, Loïc. |
| 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... |
| Tipo: Text |
Palavras-chave: Biodiversity; Biomonitoring; Caribbean Sea; Environmental DNA; Reef fishes; Underwater visual census. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00653/76543/77643.pdf |
| |
|
|
| Juhel, Jean‐baptiste; Marques, Virginie; Polanco Fernández, Andrea; Borrero‐pérez, Giomar H.; Mutis Martinezguerra, Maria; Valentini, Alice; Dejean, Tony; Manel, Stéphanie; Loiseau, Nicolas; Velez, Laure; Hocdé, Régis; Letessier, Tom B.; Richards, Eilísh; Hadjadj, Florine; Bessudo, Sandra; Ladino, Felipe; Albouy, Camille; Mouillot, David; Pellissier, Loïc. |
| 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... |
| Tipo: Text |
Palavras-chave: EDNA; Megafauna; Mobile species; Pelagic. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00683/79484/82076.pdf |
| |
|
|
| Boulanger, Emilie; Loiseau, Nicolas; Valentini, Alice; Arnal, Véronique; Boissery, Pierre; Dejean, Tony; Deter, Julie; Guellati, Nacim; Holon, Florian; Juhel, Jean-baptiste; Lenfant, Philippe; Manel, Stéphanie; Mouillot, David. |
| Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual... |
| Tipo: Text |
Palavras-chave: Environmental DNA metabarcoding; Marine reserves; Alpha and beta diversity. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00692/80374/83491.pdf |
| |
|
|
| Marques, Virginie; Milhau, Tristan; Albouy, Camille; Dejean, Tony; Manel, Stéphanie; Mouillot, David; Juhel, Jean‐baptiste; Dutta, Trishna. |
| Aim Environmental DNA metabarcoding has recently emerged as a non‐invasive tool for aquatic biodiversity inventories, frequently surpassing traditional methods for detecting a wide range of taxa in most habitats. The major limitation currently impairing the large‐scale application of eDNA‐based inventories is the lack of species sequences available in public genetic databases. Unfortunately, these gaps are still unknown spatially and taxonomically, hindering targeted future sequencing efforts. Innovation We propose GAPeDNA, a user‐friendly web interface that provides a global overview of genetic database completeness for a given taxon across space and conservation status. As an application, we synthetized data from regional checklists for marine and... |
| Tipo: Text |
Palavras-chave: Environmental DNA; Genetic markers; IUCN; Marine and freshwater fish; Non‐indigenous species; Reference database; Shiny; Threatened species. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00688/79976/82921.pdf |
| |
|
|
| Mariani, Gaël; Cheung, William W. L.; Lyet, Arnaud; Sala, Enric; Mayorga, Juan; Velez, Laure; Gaines, Steven D.; Dejean, Tony; Troussellier, Marc; Mouillot, David. |
| Contrary to most terrestrial organisms, which release their carbon into the atmosphere after death, carcasses of large marine fish sink and sequester carbon in the deep ocean. Yet, fisheries have extracted a massive amount of this “blue carbon,” contributing to additional atmospheric CO2 emissions. Here, we used historical catches and fuel consumption to show that ocean fisheries have released a minimum of 0.73 billion metric tons of CO2 (GtCO2) in the atmosphere since 1950. Globally, 43.5% of the blue carbon extracted by fisheries in the high seas comes from areas that would be economically unprofitable without subsidies. Limiting blue carbon extraction by fisheries, particularly on unprofitable areas, would reduce CO2 emissions by burning less fuel and... |
| Tipo: Text |
|
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00658/77008/78264.pdf |
| |
|
|
|
