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| Marandel, Florianne; Charrier, Gregory; Lamy, Jean-baptiste; Le Cam, Sabrina; Lorance, Pascal; Trenkel, Verena. |
| Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing... |
| Tipo: Text |
Palavras-chave: Effective population size; Linkage disequilibrium; NeEstimator; RADseq; Skates and rays. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00607/71934/70628.pdf |
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| Marandel, Florianne; Biais, Gerard; Bidault, Adeline; Charrier, Grégory; Cornette, Florence; Lapegue, Sylvie; Laroche, Jean; Le Cam, Sabrina; Stephan, Eric; Trenkel, Verena; Lorance, Pascal. |
| At the ecosystem level, sustainable exploitation of fisheries resources depends not only on the status of target species but also on that of bycatch species, some of which are even more sensitive to exploitation. This is the case for a number of elasmobranchs (skates, rays and sharks) species whose abundance declined during the 20th century. Further, the biology of elamobranchs is still poorly known and traditional fisheries stock assessment methods using fisheries catches and scientific survey data for estimating abundance are expensive or even inapplicable due to the small numbers observed. The GenoPopTaille project attempts to apply to the case of the thornback ray (Raja clavata) recent genetic-based methods for absolute population abundance estimation... |
| Tipo: Text |
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| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00343/45439/44960.pdf |
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| Marandel, Florianne; Lorance, Pascal; Andrello, Marco; Charrier, Gregory; Le Cam, Sabrina; Lehuta, Sigrid; Trenkel, Verena. |
| Studying demographic and genetic connectivity can help assessing marine meta-population structure. Rays and skates have no larval phase hence population connectivity can only result from active movement of individuals. Using thornback ray (Raja clavata) in European waters as a case study, demographic and genetic connectivity were studied for 11 putative populations for unequal population abundances and two hypotheses of dispersal rates. Genetic simulation results highlighted three large meta-populations: in the Mediterranean, around the Azores and on the Northeast Atlantic shelf. Demographic results highlighted a finer population structure indicating that several pairs of putative populations might be demographically linked. Results were highly... |
| Tipo: Text |
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| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00404/51535/52125.pdf |
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| Couton, Marjorie; Comtet, Thierry; Le Cam, Sabrina; Corre, Erwan; Viard, Frédérique. |
| High-throughput sequencing (HTS) technologies offer new promise to support surveillance programs targeting marine non-indigenous species (NIS). Metabarcoding might surpass traditional monitoring methods, for example through its ability to detect rare species, a key feature in early detection of NIS. Another interest of this approach is the identification of organisms difficult to identify based on morphology only (e.g., early developmental stages), making it relevant in the context of management programs. Because many marine benthic NIS have a biphasic benthopelagic life cycle, targeting their pelagic larval stages in zooplankton may allow early detection and assessment of their establishment and potential spread. We illustrate this approach with an... |
| Tipo: Text |
Palavras-chave: Zooplankton; Time-series; Non-indigenous species; Estuary; High-throughput sequencing; Surveillance; Monitoring. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00599/71127/69442.pdf |
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