Nuclear loci developed from multiple transcriptomes yield high resolution in phylogeny of scaly tree ferns (Cyatheaceae) from China and Vietnam
Nuclear loci developed from multiple transcriptomes yield high resolution in phylogeny of scaly tree ferns (Cyatheaceae) from China and Vietnam
复制标题
从多个转录组开发的核位点在中国和越南的鳞状树蕨（桫椤科）的系统发育中产生高分辨率
DOI：
10.1016/j.ympev.2019.106567
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发表时间：
2019-10-01
影响因子：
4.1
通讯作者：
Kang, Ming
中科院分区：
文献类型：
--
作者：
Dong, Shiyong;Xiao, Yong;Kang, Ming
有鳞的树蕨，桫椤科，形成一个大的自然组约。640种。它们是研究植物地理学的理想模型，因为它们广泛分布于世界的热带和南温带地区。然而，追踪这个高度多样化的群体的地理历史一直受到主要分支之间未解决的进化关系的阻碍。在这里，我们产生的转录组序列的5个物种在三个属的桫椤科（Alsophila，Gymnosphaera，Sphaeropteris），并用它们来寻找单拷贝核基因座的系统发育重建。我们确定了818个候选单拷贝基因座在多个桫椤科物种。为了检验它们的系统发育效用，我们进一步获得了76个样本的12个位点的序列数据，这些样本代表了中国和越南所有13种已知的鳞叶树蕨。系统发育分析的基础上，多物种结合，或者，串联模型产生了一致的结果，高分辨率。此外，我们还利用这12个基因座来鉴定杂交的遗传信号。总体而言，我们的研究结果表明，多个单拷贝基因座是信息丰富和有效的工具，系统发育或进化研究的鳞叶树蕨。
The scaly tree ferns, Cyatheaceae, form a large natural group of ca. 640 species. They comprise an ideal model for studying the biogeography of plants due to their broad distribution across the tropical to south-temperate areas of the world. However, tracing the biogeographic history of this highly diversified group has been hampered by unresolved evolutionary relationships among the major clades. Here, we generated transcriptome sequences of five species in three genera of Cyatheaceae (Alsophila, Gymnosphaera, and Sphaeropteris) and used them to search for single-copy nuclear loci for phylogenetic reconstruction. We identified a total of 818 candidate single-copy loci across multiple Cyatheaceae species. To test their phylogenetic utility, we further obtained sequence data of 12 of these loci for 76 samples representing all 13 known species of scaly tree ferns in China and Vietnam. Phylogenetic analyses based on multispecies coalescent and, alternatively, concatenation models yielded congruent results with high resolution. Additionally, we used the 12 loci to identify genetic signals of hybridization. Overall, our results demonstrated that multiple, single-copy loci are informative and efficient tools for phylogenetic or evolutionary studies of scaly tree ferns.