DOI: 10.5061/dryad.61d1m
title: Data from: Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

description: Altitudinal gradients in mountain regions are short-range clines of
 different environmental parameters such as temperature or radiation. We
 investigated genomic and phenotypic signatures of adaptation to such
 gradients in five Arabidopsis thaliana populations from the North Italian
 Alps that originated from 580 to 2350 m altitude by resequencing pools of
 19–29 individuals from each population. The sample includes two pairs of
 low- and high-altitude populations from two different valleys.
 High-altitude populations showed a lower nucleotide diversity and negative
 Tajima's D values and were more closely related to each other than to
 low-altitude populations from the same valley. Despite their close
 geographic proximity, demographic analysis revealed that low- and
 high-altitude populations split between 260 000 and 15 000 years before
 present. Single nucleotide polymorphisms whose allele frequencies were
 highly differentiated between low- and high-altitude populations
 identified genomic regions of up to 50 kb length where patterns of genetic
 diversity are consistent with signatures of local selective sweeps. These
 regions harbour multiple genes involved in stress response. Variation
 among populations in two putative adaptive phenotypic traits, frost
 tolerance and response to light/UV stress was not correlated with
 altitude. Taken together, the spatial distribution of genetic diversity
 reflects a potentially adaptive differentiation between low- and
 high-altitude populations, whereas the phenotypic differentiation in the
 two traits investigated does not. It may resemble an interaction between
 adaptation to the local microhabitat and demographic history influenced by
 historical glaciation cycles, recent seed dispersal and genetic drift in
 local populations.
description: 2k_tableTable with per 2kb window Tajima D and pi for each of the populationsArabidopsis_2k_tablePub1_parameter_meansCalculating chromosome means for the poopolation output of the Tajima's D, nucleotide diversity and Wattersons theta values of the five populations.Pub2_correlationsSpearman and Pearsons correlations of the all five populationsPub3_arabidopsis_tableMaking the 2k table from PoPoolation output.Pub4_preliminary_parameter_plotsPreliminary plotting of D, pi, theta across chromosomes for all populations.Pub5_final_parameter_plotsFinal set of Tajima D and pi plots for the publication.Pub6_populations_mapPublication populations map. Making the Italy part of the map.Pub7_ABC_analysisThis presents the code to do the ABC analysis of the msABC output files.Pub8_treemix_fourpopTreemix input file generator.treemix_input_30_4Treemix input file.phenotypic_data_analysisThis folder contains an R-script with the complete data analysis for the phenotypic traints analized in this paper. Besides the folder contains all phenotpic data and the data logger data from the frost test experiment.temp_logger_high_altitudeTemperature logger data from the two high altitude sites. These data were used to produce fig. S9.