Phenotypic and genomic differentiation of Arabidopsis thaliana

10 Altitudinal gradients represent short-range clines of environmental parameters like tem11 perature, radiation, seasonality and pathogen abundance, which allows to study the foot12 prints of natural selection in geographically close populations. We investigated phenotypic 13 variation for frost resistance and light response in five Arabidopsis thaliana populations rang14 ing from 580 to 2,350 meters altitude at two different valleys in the North Italian Alps. All 15 populations were resequenced as pools and we used a Bayesian method to detect correlations 16 between allele frequencies and altitude while accounting for sampling, pooled sequencing and 17 the expected amount of shared drift among populations. The among population variation 18 to frost resistance was not correlated with altitude. An anthocyanin deficiency causing a 19 high leaf mortality was present in the highest population, which may be non-adaptive and 20 potentially deleterious phenotypic variation. The genomic analysis revealed that the two 21 high-altitude populations are more closely related than the geographically close low-altitude 22 populations. A correlation of genetic variation with altitude revealed an enrichment of 23 highly differentiated SNPs located in genes that are associated with biological processes 24 like response to stress and light. We further identified regions with long blocks of presence 25 absence variation suggesting a sweep-like pattern across populations. Our analysis indicate 26 a complex interplay of local adaptation and a demographic history that was influenced by 27 glaciation cycles and/or rapid seed dispersal by animals or other forces. 28