Dataset S1 from Convergent evolution in <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i> on calamine metalliferous soils.

It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, <i>Arabidopsis halleri</i> and <i>Arabidopsis arenosa</i>, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide poly-morphisms in several <i>A. halleri</i> genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.已有合理假说指出：针对同一环境挑战的平行适应事件，其所引发的遗传变化效应应相似或完全一致，具体取决于其背后的适合度景观（fitness landscapes）。然而，针对该假说的系统性检验仍较为稀缺。本研究以两种近缘植物——高山拟南芥（Arabidopsis halleri）与沙生拟南芥（Arabidopsis arenosa）为研究对象，二者共同栖息于两处锌矿污染金属富集场地（下称M场地），这些场地中含有毒浓度的重金属锌与镉。我们对采自M场地与非金属污染（non-metalliferous, NM）土壤的8个种群的共64株植物，开展了单株基因组重测序与土壤元素分析，并鉴定出与选择及本地适应相关的基因组印迹。选择性清除（selective sweep）与环境关联分析结果显示，基因与功能网络的趋同程度较为有限，且介导该趋同过程的近端分子因子在不同场地组与物种间大多存在差异。值得注意的是，我们在两处独立定殖的M场地的数种高山拟南芥基因中，观察到针对相同单核苷酸多态性（single nucleotide polymorphisms, SNPs）的重复选择事件。本研究数据表明，物种特异性的金属处理机制与其他生物学特征，可解释物种间趋同程度较低的现象。在锌矿污染M土壤上实现植物种群的平行定殖，涉及趋同演化过程；若在为最大化土壤组成相似性而特意选取的场地中开展相关研究，该趋同演化现象可能会更为普遍。本文隶属于主题专栏“基因组学时代的趋同演化：新认知与研究方向”。