The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among closely related clades, and the phylogenetic placement of recalcitrant species or lineages. Here, we investigated the deep phylogenetic relationships within Polypodiaceae by sampling all major lineages and using 81 plastid genomes (plastomes), of which 70 plastomes were newly sequenced with high-throughput sequencing technology. Based on parsimony, maximum-likelihood, Bayesian and multispecies coalescent analyses of genome skimming data, we achieved a better resolution of the backbone phylogeny of Polypodiaceae. Using simulated data matrices, we detected that potential phylogenetic artefacts, such as long-branch attraction and insufficient taxonomic sampling, may have a confounding impact on the incongruence of phylogenetic inferences. Furthermore, our phylogenetic analyses offer greater resolution than previous multilocus studies, providing a robust framework for future phylogenetic implications on the subfamilial taxonomy of Polypodiaceae. Our phylogenomic study not only demonstrates the advantage of a character-rich plastome dataset for resolving the recalcitrant lineages that have undergone rapid radiation, but also sheds new light on integrative explorations understanding the evolutionary history of large fern groups in the genomic era.

中文翻译：

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质体系统基因组学为Polypodiaceae的家族内关系提供了新的见解

polygrammoids (Polypodiaceae) 是物种最丰富和多样化的附生蕨类植物，对于了解植物生命树中的深层分化事件和快速适应不断变化的环境具有重要作用。尽管在以前的多位点系统发育研究中这组蕨类植物的系统发育取得了进展，但不确定性仍然存在，尤其是密切相关的进化枝之间的骨干关系以及顽固物种或谱系的系统发育位置。在这里，我们通过对所有主要谱系进行采样并使用 81 个质体基因组（质体）研究了水螅科内部的深层系统发育关系，其中 70 个质体是用高通量测序技术新测序的。基于基因组略读数据的简约、最大似然、贝叶斯和多物种合并分析，我们更好地解析了Polypodiaceae的骨干系统发育。使用模拟数据矩阵，我们检测到潜在的系统发育假象，例如长分支吸引和分类学采样不足，可能对系统发育推断的不一致产生混淆影响。此外，我们的系统发育分析提供了比以前的多位点研究更高的分辨率，为未来对 Polypodiaceae 亚科分类的系统发育影响提供了一个强大的框架。我们的系统基因组学研究不仅展示了特征丰富的质体数据集在解决快速辐射的顽固谱系方面的优势，而且为了解基因组时代大型蕨类群的进化历史的综合探索提供了新的思路。