Periodic Reporting for period 1 - INVERT2ADAPT (Chromosomal inversions in Atlantic herring and adaptation to changing sea water temperature)
Reporting period: 2022-07-01 to 2024-06-30
Large chromosomal inversions have been increasingly linked to local adaptation in natural populations. Despite their importance, there is current debate about what evolutionary forces maintain inversion polymorphisms in natural populations, particularly regarding the interplay between balancing and divergent selection. Furthermore, limitations of sequencing technologies often result in poor characterization of inversion breakpoints obscuring our understanding of their functional impact. This project focuses on Atlantic herring (Clupea harengus) as a model system to study the contribution of chromosomal inversions to local adaptation using multiple genomics tools.The project is divided in three work packages with the following aims: 1) Characterize the chromosomal inversions and date their origin relatively to the evolutionary history of Atlantic herring using comparative genomics and phylogenomics; 2) Study the selection regimes that maintain the inversions across a gradient of sea water temperate using population genomics; 3) Pinpoint the genes and regulatory elements within the inversions that are involved in adaptation to sea water temperature using gene expression and functional genomics.
We used comparative genomics and state-of-the-art long read sequencing to study in great detail the genomic location of the inversions and determine the content of the area around the breakpoints. This revealed that the inversions did not disrupt any important genes, but likely impact the regulation of genes. It also showed that there are repeated sequences around the inversions that would have been in their origin.We used population genomics to study the evolutionary history of the inversions and show that they are old genetic variants in Atlantic herring. We estimated the age and ancestrality of the inversions by comparing data to a closely related species, the European sprat. We also showed that the inversions are maintained in natural populations of Atlantic herring by divergent selection associated with adaptation to sea water temperature, as opposed to balancing selection.
The results of this fellowship can inform stock management of Atlantic herring, by including the genetic markers studied here in a set of markers used to determine the origin of fished stocks. Further research based on the results of the fellowship can be conducted to better understand the function of inversions using functional genomic tools.