Dataset S6 from Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa 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’.

存在这样一项合理假说：针对同一环境挑战的平行适应事件，应会产生相似或等效的遗传变异，具体结果取决于背后的适合度景观（fitness landscape）。然而，针对该假说的系统性检验却十分匮乏。本研究以两个近缘拟南芥属物种——高山拟南芥（Arabidopsis halleri）与沙生拟南芥（Arabidopsis arenosa）为研究对象，二者共同栖息于两处菱锌矿型重金属污染（以下简称M）生境，该生境中锌与镉重金属含量达到毒性水平。我们对采自M土壤与非重金属污染（以下简称NM）土壤的8个种群共64株植物开展了个体基因组重测序（genome resequencing），并同步开展土壤元素分析（soil elemental analysis），同时鉴定了选择与本地适应的基因组印记。选择性清除（selective sweep）分析与环境关联分析结果显示，基因层面与功能网络层面仅存在中等程度的趋同演化，且介导该趋同的近端分子因子在不同生境配对与物种间大多存在差异。值得注意的是，我们在两处独立定植的M生境的多个高山拟南芥基因中，观察到相同单核苷酸多态性（single nucleotide polymorphism, SNP）位点受到重复选择的现象。我们的数据表明，物种特异性的重金属调控机制与其他生物学特征，或可解释物种间趋同程度较低的原因。菱锌矿型M生境中植物种群的平行定植过程涉及趋同演化；若选取土壤组成尽可能相似的生境开展研究，这类趋同演化的特征可能会更为显著。本文属于“基因组学时代的趋同演化：新见解与新方向”专题专辑的内容。