It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole‐genome pooled population sequencing to study genome‐wide SNP variation in 18 natural populations of three Brassicaceae (Arabis alpina, Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We first de novo assembled draft reference genomes for all three species. We then ran population and landscape genomic analyses with ~3 million SNPs per species to look for shared genomic signatures of selection and adaptation in response to similar environmental gradients acting on these species. Genes with a signature of convergent adaptation were found at significantly higher numbers than expected by chance. The most closely related species pair showed the highest relative over‐representation of shared adaptation signatures. Moreover, the identified genes of convergent adaptation were enriched for nonsynonymous mutations, suggesting functional relevance of these genes, even though many of the identified candidate genes have hitherto unknown or poorly described functions based on comparison with Arabidopsis thaliana. We conclude that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species‐specific.

中文翻译：

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三种十字花科植物对高山环境的适应适应性的基因组特征。

长期以来一直在讨论相关物种在多大程度上发展出相似的遗传机制以适应相似的环境。大多数证明这种趋同的研究要么在物种内部使用了不同的谱系，要么仅对基因组的一小部分进行了调查。在这里，我们调查了在阿尔卑斯山中，三种相关植物物种的自然种群对相似环境梯度的遗传适应是否涉及相似或不同组的直系同源基因。我们使用全基因组合并种群测序技术研究了三个十字花科的18个自然种群中的全基因组SNP变异（拟南芥，拟南芥和Cardamine resedifolia），来自瑞士阿尔卑斯山。我们首先从头开始组装这三个物种的参考基因组草案。然后，我们对每个物种进行大约300万个SNP的种群和景观基因组分析，以寻找对这些物种起作用的相似环境梯度做出响应的选择和适应的共享基因组特征。发现具有收敛适应特征的基因的数量大大高于偶然的预期。最密切相关的物种对显示出共享适应特征的相对过高代表。此外，所鉴定的收敛适应基因富含非同义突变，表明这些基因具有功能相关性，即使许多已鉴定的候选基因迄今为止具有未知的或描述较差的功能，基于与拟南芥。我们得出结论，在相关物种中对异质高山环境的适应部分是由趋同进化驱动的，但是适应的大多数基因组特征仍然是物种特异性的。