Dataset S5 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, Arabidopsis halleri and Arabidopsis arenosa, 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 A. halleri 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’.针对同一环境挑战的平行适应性演化事件，其产生的遗传变异效应应相似甚至完全相同——这一合理假说取决于潜在的适应度景观。但目前针对该假说的系统性检验仍较为匮乏。本研究以两个近缘植物物种——高山拟南芥（Arabidopsis halleri）与沙生拟南芥（Arabidopsis arenosa）为研究对象，二者共同栖息于两个含菱锌矿的金属污染（M）生境中，该生境的锌与镉重金属含量达到毒性水平。我们对采自8个分别生于M型与非金属污染（NM）土壤的种群的64株植株开展全基因组重测序，并同步开展土壤元素组成分析，以此鉴定受选择与局部适应性相关的基因组印迹。选择性清除分析与环境关联分析结果显示，基因与功能网络层面存在一定程度的趋同演化，但介导该趋同演化的近端分子因子在不同生境对与物种间大多存在差异。值得注意的是，在两个独立定殖的M生境中，我们观察到多个高山拟南芥基因受到相同单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的重复选择。本研究数据表明，物种特异性的金属耐受机制与其他生物学特征，或可解释物种间趋同演化程度较低的现象。在菱锌矿污染M生境中植物种群的平行定殖涉及趋同演化，若选取土壤组成尽可能相似的生境开展研究，该趋同演化特征可能会更为普遍。本文隶属于主题专栏“基因组学时代的趋同演化：新视角与研究方向（Convergent evolution in the genomics era: new insights and directions）”。