Dataset S5 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’.

一个合理的假说认为，针对同一环境挑战的平行适应事件，会产生效应相似或相同的遗传改变，这取决于其背后的适合度景观（fitness landscape）。然而，针对该假说的系统性验证仍较为匮乏。本研究以两种近缘植物物种——高山拟南芥（Arabidopsis halleri）与砂生拟南芥（Arabidopsis arenosa）——为研究对象，二者共同分布于两处含菱锌矿的重金属污染（metalliferous, M）生境，这些生境中锌与镉的重金属含量达到毒性水平。我们对来自重金属污染（M）与非重金属污染（non-metalliferous, NM）土壤的8个种群的64株植物进行全基因组重测序，并同步开展土壤元素分析，进而鉴定出选择与局部适应的基因组印迹（genomic footprints）。选择性清除（selective sweep）与环境关联分析结果显示，基因与功能网络仅存在中等程度的趋同，而介导该趋同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，我们在两处独立定植的重金属污染生境的数个高山拟南芥（Arabidopsis halleri）基因中，观察到相同单核苷酸多态性（single nucleotide polymorphisms, SNPs）受到重复选择。本研究数据表明，物种特异性的重金属处理机制与其他生物学特征，或可解释物种间趋同程度较低的现象。在含菱锌矿的重金属污染土壤上平行建立植物种群涉及趋同演化，若选取土壤组成尽可能相似的生境时，这种趋同演化可能会更为普遍。本文属于期刊专题“基因组时代的趋同演化：新视角与研究方向”的组成部分。