Postglacial ecotype formation under outcrossing and self-fertilization in Arabidopis lyrata

The process of ecotype formation has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and subsequently experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here we studied the genomic footprint of ecotype formation in Arabidopsis lyrata subsp. lyrata. The species colonized both rocky and sandy substrates during its postglacial range expansion, while it also shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole-genome re-sequence data of 20 populations, which suggested genes and gene ontology terms related to substrate adaptation. We validated results by comparing root growth between plants from the two substrates in a common environment and found that plants originating from sand – independent of mating system – grew roots faster and produced more side-roots, potentially as a response to water limitation in the wild. Furthermore, we found single nucleotide polymorphisms associated with substrate-related ecotypes to be more clustered among selfing populations, presumably due to higher genome-wide linkage disequilibrium. Overall we show that a shift to selfing could initially facilitate ecotype formation linked to substrate, likely because selfing reduces effective recombination.