Wei Ran, Yan Yue-Hong, Harris A J, Kang Jong-Soo, Shen Hui, Xiang Qiao-Ping, Zhang Xian-Chun
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China.
Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China.
Genome Biol Evol. 2017 Jun 1;9(6):1646-1657. doi: 10.1093/gbe/evx107.
The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae-Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.
真水龙骨类II蕨类植物是进化辐射的经典案例，同时，其替换率也表现出高度的异质性。在多位点系统发育研究中，这些因素被认为是导致该蕨类植物类群内各分支间存在争议性系统发育关系的原因。我们通过对所有主要科进行采样，并使用40个质体基因组（或叶绿体基因组），对真水龙骨类II蕨类植物的深层系统发育关系进行了研究，其中33个是利用新一代测序技术新测序得到的。我们进行了基于模型的分析，以评估这些蕨类植物分子进化速率的多样性。我们的叶绿体基因组数据包含超过26,000个信息性特征，为真水龙骨类II内部的深层关系提供了良好的分辨率，并明确了乌毛蕨科的位置以及蹄盖蕨科的单系性。速率异质性分析结果显示，真水龙骨类II蕨类植物中大约有33个显著的速率变化，其中速率变化最大（包括加速和减速）的情况出现在两个系统发育关系复杂的分支中，即乌毛蕨科-铁角蕨科和蹄盖蕨科分支。这些观察结果支持了这样一种假设，即速率异质性先前限制了真水龙骨类II蕨类植物的深层系统发育分辨率。根据叶绿体基因组数据，我们提出14个叶绿体标记对于真水龙骨类II蕨类植物在科级和属级水平上的系统发育尤其具有信息价值。我们的研究证明了富含特征的叶绿体基因组数据集和高通量测序在解析经历了快速进化辐射和替换率剧烈变化的顽固分支方面的强大作用。
