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Auteur McLean, M.J.; Mouillot, D.; Goascoz, N.; Schlaich, I.; Auber, A. doi  openurl
  Titre Functional reorganization of marine fish nurseries under climate warming Type Article scientifique
  Année 2019 Publication Revue Abrégée Glob. Change Biol.  
  Volume 25 Numéro 2 Pages 660-674  
  Mots-Clés English Channel; community; ecosystem; fisheries; recruitment; functional traits; in-situ; connectivity; estuarine; climate change; life-history strategies; ecosystem function; life history; english-channel; Atlantic Multidecadal Oscillation; atlantic multidecadal oscillation; fuzzy-logic; r-selection  
  Résumé While climate change is rapidly impacting marine species and ecosystems worldwide, the effects of climate warming on coastal fish nurseries have received little attention despite nurseries' fundamental roles in recruitment and population replenishment. Here, we used a 26-year time series (1987-2012) of fish monitoring in the Bay of Somme, a nursery in the Eastern English Channel (EEC), to examine the impacts of environmental and human drivers on the spatial and temporal dynamics of fish functional structure during a warming phase of the Atlantic Multidecadal Oscillation (AMO). We found that the nursery was initially dominated by fishes with r-selected life-history traits such as low trophic level, low age and size at maturity, and small offspring, which are highly sensitive to warming. The AMO, likely superimposed on climate change, induced rapid warming in the late 1990s (over 1 degrees C from 1998 to 2003), leading to functional reorganization of fish communities, with a roughly 80% decline in overall fish abundance and increased dominance by K-selected fishes. Additionally, historical overfishing likely rendered the bay more vulnerable to climatic changes due to increased dominance by fishing-tolerant, yet climatically sensitive species. The drop in fish abundance not only altered fish functional structure within the Bay of Somme, but the EEC was likely impacted, as the EEC has been unable to recover from a regime shift in the late 1990s potentially, in part, due to failed replenishment from the bay. Given the collapse of r-selected fishes, we discuss how the combination of climate cycles and global warming could threaten marine fish nurseries worldwide, as nurseries are often dominated by r-selected species.  
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  ISSN 1354-1013 ISBN Médium  
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Auteur Rey, C.; Darnaude, A.; Ferraton, F.; Guinand, B.; Bonhomme, F.; Bierne, N.; Gagnaire, P.-A. url  doi
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  Titre Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream Type Article scientifique
  Année 2020 Publication Revue Abrégée Genes  
  Volume 11 Numéro 4 Pages 398  
  Mots-Clés antagonistic pleiotropy; fitness trade-off; habitat association; juvenile growth; polygenic scores; RAD-sequencing; spatially varying selection  
  Résumé Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance. Phenotypic differences among juveniles foraging in different habitats rapidly appear after larval settlement, but the relative role of local selection and plasticity in phenotypic variation remains unclear. Here, we combine phenotypic and genetic data to address this question. We first report correlations of opposite signs between growth and condition depending on juvenile habitat type. Then, we use single nucleotide polymorphism (SNP) data obtained by Restriction Associated DNA (RAD) sequencing to search for allele frequency changes caused by a single generation of spatially varying selection between habitats. We found evidence for moderate selection operating at multiple loci showing subtle allele frequency shifts between groups of marine and brackish juveniles. We identified subsets of candidate outlier SNPs that, in interaction with habitat type, additively explain up to 3.8% of the variance in juvenile growth and 8.7% in juvenile condition; these SNPs also explained significant fraction of growth rate in an independent larval sample. Our results indicate that selective mortality across environments during early-life stages involves complex trade-offs between alternative growth strategies.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2784  
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Auteur Vandeputte, M.; Bugeon, J.; Bestin, A.; Desgranges, A.; Allamellou, J.-M.; Tyran, A.-S.; Allal, F.; Dupont-Nivet, M.; Haffray, P. doi  openurl
  Titre First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements Type Article scientifique
  Année 2019 Publication Revue Abrégée Front. Genet.  
  Volume 10 Numéro Pages 1225  
  Mots-Clés aquaculture; body shape; carcass; carp cyprinus-carpio; fillet yield; fish; genetic-parameters; heritability; production efficiency; production traits; quality traits; ratio; selection response; selective breeding; tilapia oreochromis-niloticus  
  Résumé Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW-) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23-) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW- and E8/E23- (Both-), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both- (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates' own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2715  
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Auteur Vandeputte, M.; Fraslin, C.; Haffray, P.; Bestin, A.; Allal, F.; Kocour, M.; Prchal, M.; Dupont-Nivet, M. url  doi
openurl 
  Titre How to genetically increase fillet yield in fish: Relevant genetic parameters and methods to predict genetic gain Type Article scientifique
  Année 2020 Publication Revue Abrégée Aquaculture  
  Volume 519 Numéro Pages 734877  
  Mots-Clés Aquaculture; Genetics; Heritability; Linear index; Processing yields; Residual fillet weight; Selection; Selection response; Simulation  
  Résumé Fillet yield (i.e. the proportion of edible muscle in a fish) is a key economic trait for species sold as fillets. Its genetic improvement is complicated by several of its characteristics 1) it is a ratio trait, 2) its numerator (fillet weight) and denominator (body weight) are strongly correlated (correlations in the range 0.89–0.99), 3) it offers little phenotypic variation and 4) it cannot be measured on alive breeding candidates. In a former study, we showed that it could be improved by selection, especially with three selection indices, fillet yield, residual fillet weight and a ratio-specific linear index. However, it is well known that the heritability of ratio traits does not permit a reliable prediction of genetic gains. As predictability of genetic gains is a key requirement to define breeding programs, we investigated how genetic gains in fillet yield could be predicted by the genetic parameters of fillet yield, of residual fillet weight and of the component traits of the linear index. To this end, we compared simulated genetic gains with those estimated by classical prediction methods. This was done using real sets of genetic parameters obtained in nine populations of rainbow trout, European sea bass, gilthead sea bream and common carp. We show that the genetic parameters of fillet yield cannot be used to reliably predict genetic gains in fillet yield. Conversely, selection index theory using a linear index, combining either fillet weight and body weight or fillet weight and waste weight, provides almost perfect prediction of gains. Still, it is highly sensitive to the precision of the genetic and phenotypic correlations estimates, which should not be rounded to less than three decimals for fillet weight and body weight, while two decimals are appropriate for fillet weight and waste weight. A simple, reasonably precise alternative to the linear index is the use of residual fillet weight (the residual of the regression of fillet weight on body weight) as a surrogate for fillet yield.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2722  
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Auteur Vandeputte, M.; Puledda, A.; Tyran, A.S.; Bestin, A.; Coulombet, C.; Bajek, A.; Baldit, G.; Vergnet, A.; Allal, F.; Bugeon, J.; Haffray, P. url  doi
openurl 
  Titre Investigation of morphological predictors of fillet and carcass yield in European sea bass (Dicentrarchus labrax) for application in selective breeding Type Article scientifique
  Année 2017 Publication Revue Abrégée Aquaculture  
  Volume 470 Numéro Pages 40-49  
  Mots-Clés Genetics; Heritability; Indirect selection; Processing yields; Ultrasound tomography  
  Résumé Genetic parameters for carcass and fillet percentage were estimated in 760 European sea bass reared under commercial conditions and slaughtered at 573 days post fertilization (395 g mean body weight). Phenotyped fish were the offspring of 45 sires and 20 dams crossed in a factorial mating design. Pedigrees were re-constructed with 90.7% success using 12 microsatellites. The heritability of fillet yield was moderately low (0.21), while it was high for carcass yield (0.57). Both traits were poorly correlated (− 0.01 to 0.28) making space for their combined improvement. We investigated different predictors derived from measurement of surfaces on digital pictures and ultrasound measurements at several points of the body. The accuracy of the phenotypic prediction was rather low for fillet yield (r2 = 0.02–0.18), but higher for carcass yield (r2 = 0.27–0.41). However, genetic correlations of predictors with the traits to predict were reasonably high (up to 0.67 for fillet yield and 0.95 for carcass yield), thus allowing to consider them for performing indirect individual selection instead of sib selection. However, it was difficult to design a predictor that would simultaneously increase fillet yield and carcass yield because of contradicting effects of relative head size, an important component of the predictors which was positively correlated to carcass yield but not to fillet yield.

Statement of relevance

We estimated phenotypic predictors for processing yields in the European sea bass and estimated their genetic variation and correlations with the traits to predict. This is important to be able to apply indirect selection for processing yields in this species. This showed that although the traits of interest were hardly correlated, it was not possible to find external predictors having a significant positive impacts on both traits (carcass and fillet yield) simultaneously. This highlights the need to study specifically these issues in different species and conditions, as the picture here is very different to the well studied case of rainbow trout for example.
 
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  ISSN 0044-8486 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1719  
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