Data from: Genome-wide analysis of colonization history and concomitant selection in Arabidopsis lyrata

The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modelling we found strong reduction in the effective population size of the species in general within the past 100 000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modelling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into post-glacial Scandinavian colonization history and its genome-wide effects.

过去十万年间的剧烈气候波动，已对诸多物种的种群动态与适应进程造成显著影响，尤其波及正经历冰期循环的寒带与温带区域。此类气候波动同时亦塑造了全基因组核苷酸变异（genome-wide nucleotide variation）的分布模式，但其相关影响的具体细节迄今仍未得到充分阐明。本研究以多年生草本植物岩生拟南芥（Arabidopsis lyrata）为研究对象，选取其分布范围内不同环境条件下的本地适应种群（涵盖德国、英国、挪威、瑞典及美国），通过解析全基因组变异模式推断该物种的定殖历史与选择作用模式。借助基于位点频率谱（site frequency spectra）的种群历史建模分析，本研究发现该物种在过去十万年间的有效种群大小（effective population size）整体出现显著缩减，而定殖种群的缩减幅度更为显著。进一步研究显示，西北欧的岩生拟南芥种群（英国与斯堪的纳维亚种群）彼此间的亲缘关系较中欧种群更为紧密；基于溯祖理论（coalescent theory）的种群分化建模结果表明，西欧与斯堪的纳维亚种群在冰期退却后相对近期才发生隔离。本研究同时鉴定出与斯堪的纳维亚定殖过程相关的、携带本地选择信号的基因位点。本次研究结果为冰期后斯堪的纳维亚的物种定殖历史及其全基因组层面的影响提供了全新的认知视角。