Molecular evolution of the large subunit of the RuBisCO enzyme is understudied in early diverging land plants. These groups show morphological and eco-physiological adaptations to the uneven and intermittent distribution of water in the terrestrial environment. This might have prompted a continuous fine-tuning of RuBisCO under a selective pressure modifying the species-specific optima for photosynthesis in contrasting microdistributions and environmental niches. To gain a better insight into the molecular evolution of RuBisCO large subunits, the aim of this study was to assess the pattern of evolutionary change in the amino acid residues in a monophyletic group of Bryophyta (Orthotrichaceae). Tests for positive, neutral, or purifying selection at the amino acid level were assessed by comparing rates (ω) of non-synonymous (d_N) and synonymous (d_S) nucleotide substitutions along a Maximum Likelihood phylogenetic tree. Molecular adaptation tests using likelihood ratio tests, reconstruction of ancestral amino acid sites, and intra-protein coevolution analyses were performed. Variable amino acid sites (39) were unevenly distributed across the LSU. The residues are located on rbcL sites that are highly variable in higher plants and close to key regions implying dimer–dimer (L₂L₂), RuBisCO-activase interactions, and conformational functions during catalysis. Ten rbcL sites (32, 33, 91, 230, 247, 251, 255, 424, 449 and 475) have been identified by the Bayesian Empirical Bayes inference to be under positive selection and under adaptive evolution under the M8 model. The pattern of amino acid variation suggests that it is not lineage specific, but rather representative of a case of convergent evolution, suggesting recurrent changes that potentially favor the same amino acid substitutions that are likely optimized the RuBisCO activity.

RuBisCO 酶的大亚基的分子进化在早期分化的陆生植物中研究不足。这些群体表现出对陆地环境中水的不均匀和间歇分布的形态和生态生理适应。这可能促使在选择压力下对 RuBisCO 进行持续微调，从而在对比微分布和环境生态位中修改特定物种的光合作用最佳值。为了更好地了解 RuBisCO 大亚基的分子进化，本研究的目的是评估苔藓植物（Orthotrichaceae）单系群中氨基酸残基的进化变化模式。通过比较比率（ω)沿最大似然系统发育树的非同义 ( d _N ) 和同义 ( d _S ) 核苷酸替换。使用似然比测试、祖先氨基酸位点重建和蛋白质内协同进化分析进行分子适应测试。可变氨基酸位点 (39) 在 LSU 中分布不均。残基位于高等植物中高度可变的rbc L 位点，靠近关键区域，暗示二聚体-二聚体 (L ₂ L ₂ )、RuBisCO-激活酶相互作用和催化过程中的构象功能。十个红细胞L 位点（32、33、91、230、247、251、255、424、449 和 475）已通过贝叶斯经验贝叶斯推理确定为正选择和 M8 模型下的适应性进化。氨基酸变异的模式表明它不是谱系特异性的，而是趋同进化的代表，表明可能有利于相同氨基酸替代的反复变化，这些氨基酸替代可能优化了 RuBisCO 活性。