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ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae).
Molecular Phylogenetics and Evolution ( IF 4.1 ) Pub Date : 2020-02-04 , DOI: 10.1016/j.ympev.2020.106758
Jing-Xia Liu 1 , Meng-Yuan Zhou 2 , Guo-Qian Yang 3 , Yu-Xiao Zhang 4 , Peng-Fei Ma 2 , Cen Guo 2 , Maria S Vorontsova 5 , De-Zhu Li 1
Affiliation  

The Bambusa-Dendrocalamus-Gigantochloa complex (BDG complex) is the most diversified and phylogenetically recalcitrant group of the paleotropical woody bamboos. Species of this complex occur in tropical and subtropical Asia and most of them are of great economic, cultural and ecological value. The lack of resolution achieved through the analyses of previous molecular datasets has long confounded its phylogenetic estimation and generic delimitation. Here, we adopted a ddRAD-seq strategy to investigate phylogenetic relationships of the four main genera (Bambusa, Dendrocalamus, Gigantochloa, and Melocalamus) in the BDG complex. A total of 102 species were sampled, and SNP data were generated. Both MP and ML analyses of the ddRAD-seq data resulted in a well-resolved topology with Gigantochloa and Melocalamus confirmed as monophyletic, and Melocalamus resolved as sister to the rest of the complex. Bambusa and Dendrocalamus were both resolved as paraphyletic. The phylogenetic relationships were mostly supported by morphological evidence including characters of the branch complement, rachilla, lodicules, filaments and stigma. We also generated and assembled complete plastid genomes of 48 representative species. There were conflicts between the plastome and the ddRAD topologies. Our study demonstrated that RAD-seq can be used to reconstruct evolutionary history of lineages such as the bamboos where ancient hybridization and polyploidy play a significant role. The four genera of the BDG complex have a complex evolutionary history which is likely a product of ancient introgression events.

中文翻译:

ddRAD分析揭示了Bambusa-Dendrocalamus-Gigantochloa复合体(禾本科:Bambusoideae)的四个主要属的可靠的系统发育关系。

Bambusa-Dendrocalamus-Gigantochloa复合体(BDG复合体)是古热带木质竹类中最多样化,系统发育最顽强的群体。这种复杂的物种分布在热带和亚热带亚洲,其中大多数具有重大的经济,文化和生态价值。通过对先前分子数据集的分析获得的分辨率不足,长期以来一直困扰着其系统发育估计和通用定界。在这里,我们采用了ddRAD-seq策略来研究BDG复合体中四个主要属(Bambusa,Dendrocalamus,Gigantochloa和Melocalamus)的系统发生关系。总共采样了102种,并生成了SNP数据。对ddRAD-seq数据进行的MP和ML分析都得出了一个很好解析的拓扑,其中巨人鱼和Melocalamus被确认为单系统的,Melocalamus下定决心要与其余建筑群结为姐妹。Bambusa和Dendrocalamus都被认为是寄生虫。系统发育关系主要由形态学证据支持,包括分支补体,山chill,lo,细丝和柱头的特征。我们还生成并组装了48个代表性物种的完整质体基因组。质体组和ddRAD拓扑之间存在冲突。我们的研究表明,RAD-seq可用于重建谱系(如竹子)的进化历史,而古代杂交和多倍体在其中起着重要作用。BDG复合体的四个属具有复杂的进化历史,这很可能是古代渗入事件的产物。Bambusa和Dendrocalamus都被认为是寄生虫。系统发育关系主要由形态学证据支持,包括分支补体,山chill,lo,细丝和柱头的特征。我们还生成并组装了48个代表性物种的完整质体基因组。质体组和ddRAD拓扑之间存在冲突。我们的研究表明,RAD-seq可用于重建谱系(如竹子)的进化历史,而古代杂交和多倍体在其中起着重要作用。BDG复合体的四个属具有复杂的进化历史,这很可能是古代渗入事件的产物。Bambusa和Dendrocalamus都被认为是寄生虫。系统发育关系主要由形态学证据支持,包括分支补体,山chill,lo,细丝和柱头的特征。我们还生成并组装了48个代表性物种的完整质体基因组。质体组和ddRAD拓扑之间存在冲突。我们的研究表明,RAD-seq可用于重建谱系(如竹子)的进化历史,而古代杂交和多倍体在其中起着重要作用。BDG复合体的四个属具有复杂的进化历史,这很可能是古代渗入事件的产物。花丝和柱头。我们还生成并组装了48个代表性物种的完整质体基因组。质体组和ddRAD拓扑之间存在冲突。我们的研究表明,RAD-seq可用于重建谱系(如竹子)的进化历史,而古代杂交和多倍体在其中起着重要作用。BDG复合体的四个属具有复杂的进化历史,这很可能是古代渗入事件的产物。花丝和柱头。我们还生成并组装了48个代表性物种的完整质体基因组。质体组和ddRAD拓扑之间存在冲突。我们的研究表明,RAD-seq可用于重建谱系(如竹子)的进化历史,而古代杂交和多倍体在其中起着重要作用。BDG复合体的四个属具有复杂的进化历史,这很可能是古代渗入事件的产物。
更新日期:2020-02-04
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