Genetic basis and history of adaptive differentiation in Mytilus

Les bases génétiques et l'histoire de la différenciation adaptative ont été étudiées chez les moules du complexe d'espèces Mytilus edulis qui représente un modèle d'étude intéressant pour mieux comprendre comment se propage et se distribue la différenciation adaptative en population structurée. Grâce à la technique AFLP, une approche de génomique des populations (« scan génomique ») a été utilisée pour mesurer la différenciation entre des populations isolées sur des échelles de temps et d'espaces contrastées. Notre objectif était de vérifier si la différenciation génétique n'avait pas une origine plus complexe qu'habituellement proposé. Trois parties s'articulent autour de cette question centrale. La première s'intéresse à la différenciation entre l'Atlantique et la Méditerranée chez l'espèce M. galloprovincialis et a montré que la structure génétique était la conséquence d'un différentiel d'introgression avec l'espèce sœur M. edulis. Dans la deuxième partie de ce travail nous avons mis en évidence qu'une sélection directe, soit balancée soit intermittente, sur un polymorphisme pré-existant expliquait le niveau de différenciation anormalement élevé d'un gène de l'immunité entre populations de la côte européenne chez M. edulis. Enfin, la troisième partie s'est intéressée à revisiter un exemple classique de la littérature de la génétique des populations: le cas des M. edulis du détroit de Long Island et a permis de suggérer que la structure observée à très petite échelle spatiale correspondait probablement à un contact secondaire entre des moules européennes introduites et les moules américaines. D'une manière générale nos résultats démontrent que, quelque soit l'échelle à laquelle nous nous plaçons, la différentiation génétique tire son origine d'une histoire souvent plus complexe qu'attendu.The genetic basis and history of adaptive differentiation were studied in the species complex M. edulis which is an interesting model system to understand how adaptive differentiation spreads and structure itself in subdivided populations. Using the AFLP technique, a genome scan approach was undertaken to measure differentiation between populations on contrasted spacial and temporal scales. Our objective was to verify wether the origin of genetic differentiation could be more complex than anticipated. This question was addressed in three chapters. The first one focuses on the differentiation between populations of the Atlantic Ocean and Mediterranean Sea in M. galloprovincialis. Our results show that the genetic structure was the result of differential introgression with the sister hybridizing species M. edulis. In the second chapter of this work we demonstrated that direct selection on a pre-existing polymorphism explained the unusually high level of differentiation at a defensin locus between populations of the European coast in M. edulis. Finally, in the third chapter we revisited a classic example of the population genetics literature: the aminopeptidase cline in M. edulis populations of the Long Island Sound. We obtained evidence that the genetic differentiation observed at a very fine spatial scale in the sound was the consequence of a secondary contact between introduced mussels from Europe and indigenous American mussels. Whatever the spatio-temporal scale at which we analyzed genetic differentiation, its origin proved to originate from an unsuspectedly long and complex history

MEC-13-0218_MGD2_SeqDegapped

DNA sequence alignmen

Data from: Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis

Genome scans of population differentiation identify candidate loci for adaptation but provide little information on how selection has influenced the genetic structure of these loci. Following a genome scan, we investigated the nature of the selection responsible for the outlying differentiation observed between populations of the marine mussel Mytilus edulis at a leucine/arginine polymorphism (L31R) in the antimicrobial peptide MGD2. We analysed DNA sequence polymorphisms, allele frequencies and population differentiation of polymorphisms closely linked to L31R, and pairwise and third-order linkage disequilibria. An outlying level of population differentiation was observed at L31R only, while no departure from panmixia was observed at linked loci surrounding L31R, as in most of the genome. Selection therefore seems to affect L31R directly. Three hypotheses can explain the lack of differentiation in the chromosomal region close to L31R: (i) hitchhiking has occurred but migration and recombination subsequently erased the signal, (ii) selection was weak enough and recombination strong enough to limit the hitchhiking effect to a very small chromosomal region or (iii) selection acted on a pre-existing polymorphism (i.e. standing variation) at linkage equilibrium with its background. Linkage equilibrium was observed between L31R and linked polymorphisms in every population analysed, as expected under the three hypotheses. However, linkage disequilibrium was observed in some populations between pairs of loci located upstream and downstream to L31R, generating a complex pattern of third-order linkage disequilibria which is best explained by the hypothesis of selection on a pre-existing polymorphism. We hypothesise that selection could be either balanced, maintaining alleles at different frequencies depending on the pathogen community encountered locally by mussels, or intermittent, resulting in sporadic fluctuations in allele frequency

Self-incompatibility in Brassicaceae: identification and characterization of SRK-like sequences linked to the S-locus in the tribe Biscutelleae.

International audienceSelf-incompatibility (SI) is a genetic system that prevents self-fertilization in many Angiosperms. Although plants from the Brassicaceae family present an apparently unique SI system that is ancestral to the family, investigations at the S-locus responsible for SI have been mostly limited to two distinct lineages (Brassica and Arabidopsis-Capsella, respectively). Here, we investigated SI in a third deep-branching lineage of Brassicaceae: the tribe Biscutelleae. By coupling sequencing of the SI gene responsible for pollen recognition (SRK) with phenotypic analyses based on controlled pollinations, we identified 20 SRK-like sequences functionally linked to 13 S-haplotypes in 21 individuals of Biscutella neustriaca and 220 seedlings. We found two genetic and phylogenetic features of SI in Biscutelleae that depart from patterns observed in the reference Arabidopsis clade: (1) SRK-like sequences cluster into two main phylogenetic lineages interspersed within the many SRK lineages of Arabidopsis; and (2) some SRK-like sequences are transmitted by linked pairs, suggesting local duplication within the S-locus. Strikingly, these features also were observed in the Brassica clade but probably evolved independently, as the two main SRK clusters in Biscutella are distinct from those in Brassica. In the light of our results and of what has been previously observed in other Brassicaceae, we discuss the ecological and evolutionary implications on SI plant populations of the high diversity and the complex dominance relationships we found at the S-locus in Biscutelleae

MEC-13-0218_AFLP_Data

MEC-13-0218_AFLP_Dat

MGD2_poly

codominant nuclear marker datase