As one of the four main lineages diverging from the early diversification of land plants, the phylogeny of liverworts holds the information about nearly 500 Myr of independent adaptation to changing environments. Thus, resolving the phylogenetic history of liverworts will provide unique insights into the successful diversification of early land plants in terrestrial ecosystems. However, the deep diverging events of this group remain incompletely resolved, such as the definite position of Ptilidiales. Here, we aimed to reconstruct the backbone relationships of liverworts using 84 protein‐coding chloroplast genes, a dataset comprising 35 representatives from all major lineages of liverworts, and three phylogenetic analyses, namely maximum parsimony, maximum likelihood and Bayesian inference. To test the impact of composition biases, the phylogenetic analyses were carried out using three alignments representing the same dataset either as: (i) nucleotides, (ii) amino acids, or (iii) recoded nucleotides applying ambiguity base code. Chloroplast genome data consistently supported the monophyletic origin of three major lineages in liverworts, as well as the majority of backbone relationships. Ptilidiales were found to be sister to Jungermanniales. The rapid accumulation of G/C tracks as a consequence of increased GC content is an important cause for the long branches inferred in this group. Our study not only provides empirical evidence to support the significance of plastid genome sequencing to reconstruct the phylogeny of this important plant lineage, but also suggests that the GC content has played a critical role in the evolutionary dynamics of plastid genomes in land plants.

中文翻译：

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地草的叶绿体系统基因组学：重新评估地草的主干系统发育，重点是 Ptilidiales

作为与早期陆生植物多样化不同的四个主要谱系之一，地苔的系统发育包含有关近 500 Myr 独立适应不断变化的环境的信息。因此，解决地衣的系统发育历史将为陆地生态系统中早期陆生植物的成功多样化提供独特的见解。然而，这个群体的深层分歧事件仍未完全解决，例如 Ptilidiales 的确定位置。在这里，我们的目标是使用 84 个蛋白质编码叶绿体基因、一个包含来自所有地草所有主要谱系的 35 个代表的数据集以及三个系统发育分析，即最大简约、最大似然和贝叶斯推理来重建地菜的骨架关系。为了测试成分偏差的影响，系统发育分析是使用代表相同数据集的三个比对进行的：（i）核苷酸，（ii）氨基酸，或（iii）应用歧义碱基代码重新编码的核苷酸。叶绿体基因组数据一致支持苔类中三个主要谱系的单系起源，以及大多数骨架关系。Ptilidiales被发现是Jungermanniales的姐妹。由于 GC 含量增加，G/C 轨迹的​​快速积累是在该组中推断出长分支的重要原因。我们的研究不仅提供了经验证据来支持质体基因组测序在重建这一重要植物谱系的系统发育方面的重要性，而且还表明 GC 含量在陆地植物质体基因组的进化动力学中发挥了关键作用。