同义密码子使用偏倚超越系统发育以反映快速辐射的蕨类家族Thelypteridaceae的趋同羽片架构
Synonymous Codon Usage Bias Overrides Phylogeny to Reflect Convergent Frond Architecture in a Rapidly Radiating Fern Family Thelypteridaceae
AI总结：
研究通过整合叶绿素基因组学与密码子使用分析，发现Thelypteridaceae家族的密码子使用偏倚与系统发育不一致，且与趋同的羽片基部架构相关，揭示了适应性历史的分子趋同。
摘要：
趋同进化提供了自然选择的有力证据，但其分子基础通常在蛋白质编码氨基酸替代中寻找。是否适应性压力能驱动同义密码子使用偏倚（CUB）的趋同进化以超越系统发育历史仍是一个基本问题。本文在快速辐射的蕨类家族Thelypteridaceae中进行研究，建立了整合叶绿素基因组学与密码子使用降维、形态数据和分化时间估计的比较框架。结果表明，叶绿素CUB模式与该家族的系统发育不一致，反而将物种分成不同的簇，强烈相关于趋同进化的形态特征，即叶片基部架构，这是我们追溯到早新第三纪的关键适应。这种趋同的分子信号由特定的光合作用相关基因（ndhJ、psaA和psbD）驱动，这些基因表现出高密度的特定类型第三位密码子替换。这些发现表明，CUB可以作为强大的、可量化的适应历史指示器，揭示了与蛋白质合成调控相关的隐秘分子趋同层。我们的工作提供了一个新的框架，用于揭示被复杂进化过程掩盖的适应性历史。
英文摘要：
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon usage bias (CUB) to override phylogenetic history remains a fundamental question. Here, we investigate this within the rapidly radiating fern family Thelypteridaceae by establishing a comparative framework that integrates chloroplast phylogenomics with dimensionality reduction of codon usage, morphological data, and divergence time estimation. Our results reveal that chloroplast CUB patterns are strikingly incongruent with the phylogeny of this family. Instead, they partition species into distinct clusters that strongly correlate with a convergently evolved morphological trait, lamina base architecture, a key adaptation whose radiation we date to the early Neogene. This convergent molecular signal is driven by a specific subset of photosynthesis-related genes (ndhJ, psaA, and psbD), which exhibit a high density of type-specific, third-position codon substitutions. These findings demonstrate that CUB can serve as a powerful, quantifiable indicator of adaptive history, revealing a cryptic layer of molecular convergence linked to the regulation of protein synthesis. Our work providing a new framework for uncovering adaptive histories obscured by complex evolutionary processes.
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