The genomic basis of adaptation to calcareous and siliceous soils in Arabidopsis lyrata

Abstract

Edaphic conditions are important determinants of plant fitness. While much has been learnt in recent years about plant adaptation to heavy metal contaminated soils, the genomic basis underlying adaptation to calcareous and siliceous substrates remains largely unknown. We performed a reciprocal germination experiment and whole‐genome resequencing in natural calcareous and siliceous populations of diploid Arabidopsis lyrata to test for edaphic adaptation and detect signatures of selection at loci associated with soil‐mediated divergence. In parallel, genome scans on respective diploid ecotypes from the Arabidopsis arenosa species complex were undertaken, to search for shared patterns of adaptive genetic divergence. Soil ecotypes of A. lyrata display significant genotype‐by‐treatment responses for seed germination. Sequence (SNPs) and copy‐number variants (CNVs) point towards loci involved in ion transport as the main targets of adaptive genetic divergence. Two genes exhibiting high differentiation among soil types in A. lyrata further share trans‐specific single nucleotide polymorphisms with A. arenosa. This work applies experimental and genomic approaches to study edaphic adaptation in A. lyrata and suggests that physiological response to elemental toxicity and deficiency underlies the evolution of calcareous and siliceous ecotypes. The discovery of shared adaptive variation between sister species indicates that ancient polymorphisms contribute to adaptive evolution.

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

“…10) and the absolute number of de-novo originated variants was low across all divergence levels. This corresponds to predictions about a substantial amount of shared variation between related species with high genetic diversity 33 and frequent adaptive trans-specific polymorphism in Arabidopsis 11,[45][46][47] . Absence of interspecific parallelism from gene flow was in line with the lack of genome-wide signal of recent migration between A. arenosa and A. halleri inferred by coalescent simulations ( Supplementary Fig.…”

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

“…Studies screening the whole genome or exome of different species, however, are still largely restricted to model species (e.g., Zhao & Begun, 2017), with some exceptions (e.g. Guggisberg et al., 2018; Yeaman et al., 2016). Here, we used two types of genome scans ( F ST outlier tests and EAA) in three Brassicaceae species to test whether the same genomic regions were involved in adaptation to heterogeneous environmental conditions in the Alps.…”

Parallel adaptation in autopolyploidArabidopsis arenosais dominated by repeated recruitment of shared alleles

“…Then, we checked whether the candidate alleles, inferred as serpentine specific in our dataset, are also absent in a published broad non-serpentine sampling among outcrossing Arabidopsis species 8,33,[94][95][96][97][98][99] . We downloaded all the available short-read genomic sequences published with the referred studies, called variants using the same approach as described above and checked the genotypes at the candidate site (630 residue in A. arenosa and 633 in A. lyrata and A. halleri).…”