The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon-sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony-informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.

中文翻译：

---

来自 18 种被子植物的线粒体基因填补了开花植物早期多样化系统发育推断的采样空白

被子植物的早期多样化被认为是一个快速的过程，这可能会使早期被子植物关系的系统发育分析复杂化。质体和核系统基因组学研究提出了几个关于整体被子植物系统发育的相互矛盾的假设，但线粒体基因组作为相关信息来源在很大程度上被忽略了。在这里，我们对 18 种被子植物的线粒体基因组进行了测序，以填补 Austrobaileyales、木兰、Chloranthales、Ceratophyllales 以及真双子叶植物和单子叶植物主要谱系的分类群采样空白。我们组装了来自 107 个分类群的 38 个线粒体基因的数据矩阵，以评估线粒体基因组数据如何解决当前被子植物关系中的不确定性。尽管我们根据不同的数据集和分析方法恢复了相互冲突的系统发育，我们还观察到几个主要被子植物谱系的深层关系的一致性：Chloranthales 总是被推断为 Ceratophyllales、Austrobaileyales 和 Mesangiosperms 的姐妹群，而未放置的 Diilleniales 一直被认为是超级小行星的姐妹。替代饱和、GC 组成异质性和密码子使用偏差是可能影响系统发育重建的噪声/冲突的可能原因；和被子植物线粒体基因可能基本上不受这些因素的影响。线粒体基因的第三个密码子位置似乎比第一个和第二个密码子位置包含更多的简约信息位点，因此产生了更好解析的系统发育关系，通常有强有力的支持。这些主要谱系之间的关系仍未完全解决，这可能是由于早期辐射的快速性。然而，来自线粒体基因组的数据为探索被子植物的早期进化和多样化提供了额外的证据和替代假设。