Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae)
Target‐enrichment sequencing reveals for the first time a well‐resolved phylogeny of the core Bromelioideae (family Bromeliaceae)
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DOI：
10.1002/tax.12831
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发表时间：
2022-11
期刊：
影响因子：
3.4
通讯作者：
Fabian Bratzel;Juraj Paule;J. Leebens-Mack;E. Leme;R. Forzza;M. Koch;Sascha Heller;G. Zizka
中科院分区：
文献类型：
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作者：
Fabian Bratzel;Juraj Paule;J. Leebens-Mack;E. Leme;R. Forzza;M. Koch;Sascha Heller;G. Zizka
通过对凤梨亚科(Bromeliaceae，简称：菠萝科)的系统发育分析，推断了该亚科的种间关系，为进一步的分类研究、属概念的稳定以及该亚科的进化和生物地理学分析奠定了基础。选择了靶浓缩方法，使用被子植物353 v.4试剂盒RNA诱饵，包括代表先前已确定的主要进化谱系的86个菠萝亚科物种。系统发育分析基于125个目标核基因座、组装的非靶标质体以及有丝分裂组读数。根据核(194 kBP)、质体组(109 kBP)和有丝分裂组(34 kBP)的数据，提供了一个脊椎科的系统发育图。对于核标记，进行了基于合并的单基因座基因树分析以及串联基因比对的超矩阵分析。核和质体组数据集提供了解析良好的树，这些树只显示了轻微的拓扑不一致。有丝分裂组树没有得到充分的分辨。总共确定了26个得到良好支持的分支。Aechmea属、Canstrum属、Hohenbergia属、Neoregelia属和Quesnelia属均为多系。在菠萝亚科的核心，棘穗与其余部分为姐妹种。在26个已识别的支系中，有12个与目前采用的分类概念相对应。因此，所提出的系统发育框架将作为未来分类学修订的重要基础，以及更好地理解这个令人兴奋的亚家族的进化驱动因素和过程。
A phylogenomic analysis of the so far phylogenetically unresolved subfamily Bromelioideae (Bromeliaceae) was performed to infer species relationships as the basis for future taxonomic treatment, stabilization of generic concept, and further analyses of evolution and biogeography of the subfamily. A target‐enrichment approach was chosen, using the Angiosperms353 v.4 kit RNA‐baits and including 86 Bromelioideae species representing previously identified major evolutionary lineages. Phylogenetic analyses were based on 125 target nuclear loci, assembled off‐target plastome as well as mitogenome reads. A Bromelioideae phylogeny with a mostly well‐resolved backbone is provided based on nuclear (194 kbp), plastome (109 kbp), and mitogenome data (34 kbp). For the nuclear markers, a coalescent‐based analysis of single‐locus gene trees was performed as well as a supermatrix analysis of concatenated gene alignments. Nuclear and plastome datasets provide well‐resolved trees, which showed only minor topological incongruences. The mitogenome tree is not sufficiently resolved. A total of 26 well‐supported clades were identified. The generaAechmea,Canistrum,Hohenbergia,Neoregelia, andQuesneliawere revealed polyphyletic. In core Bromelioideae,Acanthostachysis sister to the remainder. Among the 26 recognized clades, 12 correspond with currently employed taxonomic concepts. Hence, the presented phylogenetic framework will serve as an important basis for future taxonomic revisions as well as to better understand the evolutionary drivers and processes in this exciting subfamily.