ABSTRACT Medlin tested multiple outgroups with 18S rRNA dataset and found that haptophytes, ciliates, prasinophytes, and chlorophytes recovered monophyletic Coscinodiscophyceae, Mediophyceae, Bacillariophyceae (CMB) with strong BT (bootstrap) support. Theriot et al. added six plastid genes to the diatom dataset but with only one outgroup, Bolidomonas, and omitted most of the V4 region of that gene and bases beyond position 1200. They recovered a grade of clades from radial into polar centrics, into araphid pennates into the monophyletic raphid pennates. Their structural gradation hypothesis (SGH) contrasts with the CMB hypothesis of Medlin and Kaczmarska. We selected only those species with all seven genes from their dataset and added the entire 18S RNA gene to make a new dataset to which we sequentially added heterokont, haptophyte, and prasinophyte/chlorophyte outgroups. We analysed it using: (1) evolutionary models with parameters relaxed across genes and codon positions for coding sequences (codon partition analysis scheme = CP), and (2) no partitions or evolutionary models as applied to each gene, using only optimised models of evolution for the entire dataset (NCP). CP recovered a monophyletic mediophycean and bacillariophycean clade and three coscinodiscophycean clades. Sequentially adding more outgroups did not change clade topology but dramatically increased BT support. NCP recovered a monophyletic Coscinodiscophyceae and Bacillariophyceae and three Mediophyceae clades, each with strong BT support. Morphological data were added and analysed similarly. NCP recovered three monophyletic classes and CP recovered the Bacillariophyceae arising from within the Mediophyceae, making the subphylum monophyletic but the class paraphyletic. Each analysis was tested with a Shimodeira–Hasegawa (SH) test in PAUP and IQ-TREE. Plastid inheritance in the diatoms is not homogenous and thus their phylogenies may not be homologous. If so, then our application of gene models may be overparametrising the data. The application of models with no partitioning with morphological data supported the CMB hypothesis.

中文翻译：

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使用七基因数据集、多个外群和形态学数据对硅藻进行系统发育重建，以采用全证据方法

摘要 Medlin 用 18S rRNA 数据集测试了多个外群，发现触生植物、纤毛虫、草本植物和叶绿植物在强大的 BT (bootstrap) 支持下恢复了单系 Coscinodiscophyceae、Mediophyceae、Bacillariophyceae (CMB)。Theriot 等。在硅藻数据集中添加了六个质体基因，但只有一个外群，Bolidomonas，并省略了该基因的大部分 V4 区域和位置 1200 以外的碱基。 raphid Pennates。他们的结构分级假说 (SGH) 与 Medlin 和 Kaczmarska 的 CMB 假说形成对比。我们只从数据集中选择了那些具有全部 7 个基因的物种，并添加了整个 18S RNA 基因以制作一个新的数据集，我们依次向其中添加了heterokot、haptophyte 和草本植物/叶绿植物外群。我们使用以下方法对其进行了分析：（1）在基因和编码序列的密码子位置之间放宽参数的进化模型（密码子分区分析方案 = CP），以及（2）没有应用于每个基因的分区或进化模型，仅使用优化的模型整个数据集 (NCP) 的演变。CP 回收了一个单系中藻纲和 bacillariophycean 进化枝以及三个 coscinodiscophycean 进化枝。依次添加更多外群并没有改变进化枝拓扑，而是显着增加了 BT 支持。NCP 恢复了单系 Coscinodiscophyceae 和 Bacillariophyceae 以及三个 Mediophyceae 进化枝，每个进化枝都有强大的 BT 支持。添加形态学数据并进行类似分析。NCP 恢复了三个单系类，CP 恢复了来自中间藻纲的芽孢杆菌科，使亚门单系但类并系。每个分析都使用 PAUP 和 IQ-TREE 中的 Shimodeira-Hasegawa (SH) 测试进行测试。硅藻中的质体遗传不是同质的，因此它们的系统发育可能不是同源的。如果是这样，那么我们对基因模型的应用可能会过度参数化数据。没有形态学数据分区的模型的应用支持了 CMB 假设。