Altitudinal gradients represent short-range clines of environmental parameters like temperature, radiation, seasonality and pathogen abundance, which allows to study the footprints of natural selection in geographically close populations. We investigated phenotypic variation for frost resistance and light response in five Arabidopsis thaliana populations ranging from 580 to 2,350 meters altitude at two different valleys in the North Italian Alps. All populations were resequenced as pools and we used a Bayesian method to detect correlations between allele frequencies and altitude while accounting for sampling, pooled sequencing and the expected amount of shared drift among populations. The among population variation to frost resistance was not correlated with altitude. An anthocyanin deficiency causing a high leaf mortality was present in the highest population, which may be non-adaptive and potentially deleterious phenotypic variation. The genomic analysis revealed that the two high-altitude populations are more closely related than the geographically close low-altitude populations. A correlation of genetic variation with altitude revealed an enrichment of highly differentiated SNPs located in genes that are associated with biological processes like response to stress and light. We further identified regions with long blocks of presence absence variation suggesting a sweep-like pattern across populations. Our analysis indicate a complex interplay of local adaptation and a demographic history that was influenced by glaciation cycles and/or rapid seed dispersal by animals or other forces.

Phenotypic and genomic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian alps