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| Juhel, Jean-baptiste; Maire, Eva; Sucré, Elliott; Cheutin, Marie-charlotte; Marques, Virginie; Benkwitt, Cassandra; Gunn, Rachel L.; Richards, Eilísh; Albouy, Camille. |
| The observation of trophic interactions such as predation provide valuable information to model food webs and better understand ecosystem functioning. Such information is crucial for rare and endangered species in order to adapt management measures and ensure their conservation. However, trophic interactions are rarely observed in the marine realm, even for well-known or widespread species. During a scientific cruise in the Scattered Islands (Southwestern Indian Ocean), we observed endangered green turtle hatchlings (Chelonia mydas) in the gut content of two subadults two-spots red snappers (Lutjanus bohar). This trophic link involving emblematic species has not been previously described. The two-spots red snapper is a widespread coral reef fish in the... |
| Tipo: Text |
Palavras-chave: Trophic interaction; Marine turtle; Red bass; Snapper; Lutjanids. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00589/70160/68162.pdf |
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| 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 |
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| 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 |
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| 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 |
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| Brosset, Pablo; Lloret, Josep; Munoz, Marta; Fauvel, Christian; Van Beveren, Elisabeth; Marques, Virginie; Fromentin, Jean-marc; Menard, Frederic; Saraux, Claire. |
| Limited resources in the environment prevent individuals from simultaneously maximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) were examined based on morphometric historical data from the 1970s and from 2003 to 2015. Additionally, potential maternal effects on egg quantity and quality were examined in 2014/2015. After 2008, the gonadosomatic index increased for... |
| Tipo: Text |
Palavras-chave: Maternal effect; Northwest Mediterranean; Anchovy; Sardine. |
| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00353/46458/46233.pdf |
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| Brosset, Pablo; Fromentin, Jean-marc; Van Beveren, Elisabeth; Lloret, Josep; Marques, Virginie; Basilone, Gualtiero; Bonanno, Angelo; Carpi, Piera; Donato, Fortunata; Kec, Vanja Cikes; De Felice, Andrea; Ferreri, Rosalia; Gasparevic, Denis; Giraldez, Ana; Gucu, Ali; Iglesias, Magdalena; Leonori, Iole; Palomera, Isabel; Somarakis, Stylianos; Ticina, Vjekoslav; Torres, Pedro; Ventero, Ana; Zorica, Barbara; Menard, Frederic; Saraux, Claire. |
| Small pelagic fish are among the most ecologically and economically important marine fish species and are characterized by large fluctuations all over the world. In the Mediterranean Sea, low catches and biomass of anchovies and sardines have been described in some areas during the last decade, resulting in important fisheries crises. Therefore, we studied anchovy and sardine body condition variability, a key index of population health and its response to environmental and anthropogenic changes. Wide temporal and spatial patterns were investigated by analyzing separately data from scientific surveys and fisheries in eight Mediterranean areas between 1975 and 2015. Results showed that anchovy and sardine body condition as well as maximum size in some areas... |
| Tipo: Text |
Palavras-chave: Anchovy; Sardine; Fish health; Marine monitoring. |
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00363/47400/47936.pdf |
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| 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 |
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| 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 |
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