An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis

This Zenodo archive contains the dataset analysed in the paper "An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis" published in Evolutionary Application in 2022:

FAB_LG3_maf1_SNP_Hexcess_depth10.vcf : vcf for LG3 unpruned for LD containing 295 individuals genotyped at 58,246 filtered SNPs

FAB_LG3_maf1_SNP_Hexcess_depth10_thin.vcf : vcf for LG3 pruned for LD containing 295 individuals genotyped at 9,905 filtered SNPs

FAB_AK_maf1_SNP_Hexcess_depth10.vcf : vcf for contig265 containing the arginine kinase gene: 295 individuals genotyped at 70 filtered SNPs

The archive also include some of the R script used to performed the analyses of the manuscrit:

Population_genetic_Ark_analyses.R : Script to perform PCA +phenotypic cline + FST  + Hobs + FIS

Suspension_bridge_fit.R : Script to perform the suspension bridge fit used to found evidence of gene flux inside the inversion.

Cline_function.R : function used to fit  the allelic frequency variation (cline) along the transect

The raw sequences are available in NCBI.

Abstract of the study: Understanding the genetic targets of natural selection is one of the most challenging goalsof population genetics. Some of the earliest candidate genes were identified from associations between allozyme allele frequencies and environmental variation. One such example is the clinal polymorphism in the arginine kinase (Ak) gene in the marine snail Littorina fabalis. While other enzyme loci do not show differences in allozyme frequencies among populations, the Ak alleles are near differential fixation across repeated wave exposure gradients in Europe. Here, we use this case to illustrate how a new sequencing toolbox can be employed to characterize the genomic architecture associated with historical candidate genes. We found that the Ak alleles differ by 9 non-synonymous substitutions, which perfectly explain the different migration patterns of the allozymes during electrophoresis. Moreover, by exploring the genomic context of the Ak gene, we found that the three main Ak alleles are located on different arrangements of a putative chromosomal inversion that reaches near fixation at the opposing ends of two transects covering a wave exposure gradient. This shows Ak is part of a large (3/4 of the chromosome) genomic block of differentiation, in which Ak is unlikely to be the only target of divergent selection. Nevertheless, the non-synonymous substitutions among Ak alleles and the complete association of one allele with one inversion arrangement suggest that the Ak gene is a strong candidate to contribute to the adaptive significance of the inversion.