Data from: Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species

It has long been discussed to what extent related species develop similar
genetic mechanisms to adapt to similar environments. Most studies
documenting such convergence have either used different lineages within
species or surveyed only a limited portion of the genome. Here, we
investigated whether similar or different sets of orthologous genes were
involved in genetic adaptation of natural populations of three related
plant species to similar environmental gradients in the Alps. We used
whole-genome pooled population sequencing to study genome-wide SNP
variation in 18 natural populations of three Brassicaceae (Arabis alpina,
Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We
first de novo assembled draft reference genomes for all three species. We
then ran population and landscape genomic analyses with ~3 million SNPs
per species to look for shared genomic signatures of selection and
adaptation in response to similar environmental gradients acting on these
species. Genes with a signature of convergent adaptation were found at
significantly higher numbers than expected by chance. The most closely
related species pair showed the highest relative over-representation of
shared adaptation signatures. Moreover, the identified genes of convergent
adaptation were enriched for non-synonymous mutations, suggesting
functional relevance of these genes, even though many of the identified
candidate genes have hitherto unknown or poorly described functions based
on comparison with Arabidopsis thaliana. We conclude that
adaptation to heterogeneous Alpine environments in related species is
partly driven by convergent evolution, but that most of the genomic
signatures of adaptation remain species-specific.