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RAD-Seq genome scan for locally adaptive polymorphisms maintained by spatially varying selection in the European sea bass, Dicentrarchus labrax – LABRAD-Seq

LABRAD-Seq

RAD-Seq genome scan for locally adaptive polymorphisms maintained by spatially varying selection in the European sea bass, Dicentrarchus labrax.

Genomic bases of local adaptation and adaptation load

In the marine environment, many species are characterized by a planktonic larval stage conferring high dispersal potential across the habitat. Since this habitat is usually spatially heterogeneous, variations in environmental parameters may affect individual survival with respect to allelic combinations at polymorphic loci involved in local adaptation. Therefore, variable environmental conditions across species’ ranges provide a basis for differential selection at polymorphic loci responsible for such local adaptations. When the global effect of local selective forces is balanced, polymorphism may be stably maintained at the species scale over generations. However, theoretical studies have showed that the conditions necessary to this equilibrium are relatively restrictive, especially when gene flow is high and habitat choice inexistent. When the spatial scales of dispersal and environmental variations are similar, this particular type of balancing selection is costly because maladapted genotypes recurrently occur in a habitat where their chance of survival is reduced. <br />However, marine species seem to compensate this maladaptation by high fecundity rates. Although there are good examples of loci involved in genetic-by-environment interactions in marine species, our understanding of the genetic basis of local adaptation remains very incomplete at the genome scale. Theory predicts that the number of locally adaptive polymorphisms should be limited in order to maintain the cost of local adaptation sustainable. On the other hand, we usually don’t have the necessary knowledge to perform a meticulous search of such polymorphisms across the genome. <br />

The LABRAD-Seq project proposes to investigate the genomic basis of local adaptation in a high gene flow marine species: the European sea bass, Dicentrarchus labrax. Previous studies have showed evidence for differential selection between marine and lagoon habitats in this species. In parallel, the recent release of the complete genome sequence of this economically important fish provides the opportunity to implement a new generation of high-density genome scan method (RAD-Seq), with an unpreceded genomic resolution for a non-model organism.
Several thousands of polymorphisms precisely located on the European sea bass genome will be genotyped in natural populations samples collected in marine and lagoon environments. Analysing the degree of genetic differentiation between habitats along the genome will allow identifying the genomic regions influenced by selection. These regions will then be investigated in detail, to identify the polymorphic sites directly undergoing spatially varying selection. Important parameters such as the direction and strength of local selective effects, and the age of adaptive mutations will be estimated by resequencing the genomic regions located in the neighborhood of the selected sites. In order to precisely estimate these parameters, a new extension of the seminal model by Levene will be developed to predict the chromosomal signature of spatially varying selection.

A new population genetic model has been developed to test whether a neutral mechanism based on habitat choice can explain the allele frequency patterns at loci exhibiting strong association with habitat.
RAD libraries are being constructed and the sequencing is scheduled for the end of summer.

The scientific objectives of the LABRAD-Seq project are clearly dealing with the most important questions in modern evolutionary genetics. In addition to these fundamental motivations, important applications are expected for the conservation of exploited marine species and the development of aquaculture.

Under review:
Microsatellite length variation in candidate genes is associated with habitat type in the gilthead sea bream Sparus aurata
Lamya Chaoui1, 2,*, Pierre-Alexandre Gagnaire1,*, Bruno Guinand1, Jean-Pierre Quignard3, Costas Tsigenopou

In the marine environment, many species are characterized by a planktonic larval stage conferring high dispersal potential across the usable habitat. Since this habitat is usually not homogeneous in space, variations in environmental parameters may affect individual survival with respect to allelic combinations at polymorphic loci involved in local adaptation. Therefore, variable environmental conditions across species’ ranges provide a basis for differential selection at polymorphic loci responsible for such local adaptations. When the global effect of local selective forces is balanced, polymorphism may be stably maintained at the species scale over generations. However, theoretical studies have showed that the conditions necessary to this equilibrium are relatively restrictive, especially when gene flow is high and habitat choice inexistent. When the spatial scales of dispersal and environmental variations are similar, this particular type of balancing selection is costly because maladapted genotypes recurrently occur within a habitat where the chance of survival is reduced. However, marine species seem to compensate this maladaptation by high fecundity rates.

Although there are good examples of loci involved in genetic-by-environment interactions in marine species, our understanding of the genetic basis of local adaptation remains very incomplete at the genome scale. Theory predicts that the number of locally adaptive polymorphisms should be limited to maintain a sustainable cost of local adaptation. On the other hand, we usually don’t have the necessary knowledge to perform a meticulous search of such polymorphisms across the genome.

The LABRAD-Seq project proposes to investigate the genomic basis of local adaptation in a high gene flow marine species: the European sea bass, Dicentrarchus labrax. Previous studies have showed evidence for differential selection between marine and lagoon habitats in this species. In parallel, the recent release of the complete genome sequence of this economically important fish provides the opportunity to implement a new generation of high-density genome scan method (RAD-Seq), with an unpreceded genomic resolution for a non-model organism.

Several thousands of polymorphisms precisely located on the European sea bass genome will be genotyped in natural populations samples collected in marine and lagoon environments. Analysing the degree of genetic differentiation between habitats along the genome will allow identifying the genomic regions influenced by selection. These regions will then be investigated in detail, to find the polymorphic sites directly undergoing spatially varying selection. Important parameters such as the direction and strength of local selective effects, and the age of adaptive mutations will by estimated by resequencing the genomic regions located in the neighborhood of the selected sites. In order to precisely estimate these parameters, a new extension of the seminal Levene model will be developed to predict the chromosomal signature of spatially varying selection.

The scientific objectives of the LABRAD-Seq project are clearly dealing with the most important questions in modern evolutionary genetics. In addition to these fundamental motivations, important applications are expected for the conservation of exploited marine species and the development of aquaculture.

Project coordinator

Monsieur Pierre-Alexandre GAGNAIRE (CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE LANGUEDOC-ROUSSILLON) – pagagnaire@gmail.com

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

ISEM CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE - DELEGATION REGIONALE LANGUEDOC-ROUSSILLON

Help of the ANR 209,900 euros
Beginning and duration of the scientific project: November 2011 - 30 Months

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