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| Nikolic, Natacha; Devloo-delva, Floriaan; Bailleul, Diane; Noskova, Ekaterina; Rougeux, Clément; Liautard-haag, Cathy; Hassan, Mohamad; Marie, Amandine; Borsa, Philippe; Feutry, Pierre; Grewe, Peter; Davies, Campbell; Farley, Jessica; Fernando, Daniel; Biton Porsmoguer, Sébastien; Poisson, Francois; Parker, Denham; Aulich, Jorden; Lansdell, Matt; Marsac, Francis; Arnaud-haond, Sophie. |
| The blue shark Prionace glauca is a cosmopolitan species that inhabits all oceans worldwide except the poles. Several IUCN regional assessments have classified it as Near Threatened, mostly due to overfishing. Previous genetic studies that have used classical genetic markers failed to reject the hypothesis that the species is a single worldwide population (panmixia). As such, the blue shark was proposed to be an archetype of the ‘grey zone of population differentiation’, named to signify those cases common in the marine realm, where the split among population is too recent or too faint to be detected using classical genetic markers. Here, samples collected across the majority of the global range of blue shark were sequenced (using a specific genome scan... |
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| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00645/75701/76606.pdf |
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| Brandt, Miriam; Pradillon, Florence; Trouche, Blandine; Henry, Nicolas; Liautard-haag, Cathy; Cambon-bonavita, Marie-anne; Cueff-gauchard, Valerie; Wincker, Patrick; Belser, Caroline; Poulain, Julie; Arnaud-haond, Sophie; Zeppilli, Daniela. |
| Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively... |
| Tipo: Text |
Palavras-chave: Biodiversity; Ecological genetics; Microbial ecology; Molecular ecology. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00689/80094/83149.pdf |
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| Brandt, Miriam; Trouche, Blandine; Henry, Nicolas; Liautard-haag, Cathy; Maignien, Lois; De Vargas, Colomban; Wincker, Patrick; Poulain, Julie; Zeppilli, Daniela; Arnaud-haond, Sophie. |
| The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular... |
| Tipo: Text |
Palavras-chave: Environmental metabarcoding; RNA versus DNA; Extracellular DNA; Deep-sea biodiversity; Benthic ecology; Biomonitoring; Method testing. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00630/74165/73774.pdf |
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