Data from: Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

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.

山地中的海拔梯度是温度、辐射等多种环境参数的短距离渐变群。本研究以源自意大利北部阿尔卑斯山区、海拔跨度为580至2350米的5个拟南芥（Arabidopsis thaliana）种群为研究对象，通过对每个种群的19至29个个体构建的混合测序池进行重测序，解析其适应此类海拔梯度的基因组与表型印记。该样本包含来自两个不同山谷的两对低海拔与高海拔种群。高海拔种群的核苷酸多样性更低，塔伊马D（Tajima's D）值为负值，且相较于同山谷的低海拔种群，彼此间的亲缘关系更为紧密。尽管地理毗邻，种群历史动态分析结果显示，高低海拔种群的分歧时间距今约26万至1.5万年。通过筛选高低海拔种群间等位基因频率分化显著的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，我们定位到了最长达50kb的基因组区域，该区域的遗传多样性模式符合局部选择性清除（selective sweep）的特征。这些区域包含多个参与胁迫响应的基因。两个推定的适应性表型性状——抗冻性与光/紫外（UV）胁迫响应——的种群间变异与海拔并无相关性。综上，遗传多样性的空间分布反映了高低海拔种群间潜在的适应性分化，而本研究所考察的两个性状的表型分化则未呈现此规律。该现象或体现了局部微生境适应与受历史冰期循环、近期种子扩散及局域种群遗传漂变影响的种群历史动态之间的相互作用。