BACKGROUND The genus Ilex (Aquifoliaceae) has a near-cosmopolitan distribution in mesic habitats from tropical to temperate lowlands and in alpine forests. It has a high rate of hybridization and plastid capture, and comprises four geographically structured plastid groups. A previous study showed that the plastid rbcL gene, coding for the large subunit of Rubisco, has a particularly high rate of non-synonymous substitutions in Ilex, when compared with other plant lineages. This suggests a strong positive selection on rbcL, involved in yet unknown adaptations. We therefore investigated positive selection on rbcL in 240 Ilex sequences from across the global range. RESULTS The rbcL gene shows a much higher rate of positive selection in Ilex than in any other plant lineage studied so far (> 3000 species) by tests in both PAML and SLR. Most positively selected residues are on the surface of the folded large subunit, suggesting interaction with other subunits and associated chaperones, and coevolution between positively selected residues is prevalent, indicating compensatory mutations to recover molecular stability. Coevolution between positively selected sites to restore global stability is common. CONCLUSIONS This study has confirmed the predicted high incidence of positively selected residues in rbcL in Ilex, and shown that this is higher than in any other plant lineage studied so far. The causes and consequences of this high incidence are unclear, but it is probably associated with the similarly high incidence of hybridization and introgression in Ilex, even between distantly related lineages, resulting in large cytonuclear discordance in the phylogenies.

中文翻译：

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Ilex（Aquifoliaceae）属中rbcL基因的阳性选择率极高。

背景技术冬青属（Aquifoliaceae）在从热带到温带低地的高寒生境以及高山森林中具有近世界性的分布。它具有很高的杂交率和质体捕获率，并包含四个地理结构化的质体组。先前的研究表明，与其他植物谱系相比，编码Rubisco大亚基的质体rbcL基因在Ilex中具有特别高的非同义取代率。这表明对rbcL有很强的积极选择，涉及未知的适应。因此，我们研究了全球范围内240个Ilex序列中rbcL的阳性选择。结果到目前为止，通过PAML和SLR测试，rbxL基因在Ilex中的阳性选择率比迄今为止研究的任何其他植物谱系（> 3000种）要高得多。大多数阳性选择的残基在折叠的大亚基的表面上，表明与其他亚基和相关的伴侣分子相互作用，并且阳性选择的残基之间的共进化是普遍的，表明补偿性突变可恢复分子稳定性。在积极选择的地点之间恢复整体稳定的共同进化是很普遍的。结论这项研究证实了Ilex中rbcL阳性选择残基的预测高发生率，并且表明这比迄今为止研究的任何其他植物谱系都高。这种高发生率的原因和后果尚不清楚，但可能与Ilex中同样高的杂交和渗入发生率有关，即使在远缘谱系之间也是如此，从而导致系统发育中的大细胞核不一致。