Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada.
Mol Phylogenet Evol. 2024 Sep;198:108120. doi: 10.1016/j.ympev.2024.108120. Epub 2024 Jun 7.
Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.
藻褐菌是光合生物谱系，位于不等鞭毛类（Stramenopiles）的系统发育树的顶端，不等鞭毛类是主要真核超类群之一。由于它们作为主要初级生产者的生态影响，与不等鞭毛类的其余部分相比，藻褐菌类相对得到了较好的研究，但它们的进化关系仍知之甚少。这在一定程度上是由于在大规模多基因分析中存在一些缺失的谱系，以及在树中藻褐菌类亚群之间出现的快速辐射导致许多短的内节点。这些短的内节点也存在于具有有限系统发育信号的不等鞭毛类的深分支谱系中，导致许多关系总体上存在争议。我们最近已经解决了这个问题，现在研究是否可以通过在藻褐菌类的更新系统基因组数据集，以及探索各种基因过滤标准来鉴定最具系统发育信息量的基因中填补缺失的谱系，来解决藻褐菌类内部有争议的关系。我们从各种培养物收集物和环境样本的单细胞分离物中生成了十个新的转录组，并将这些添加到现有的藻褐菌类系统基因组数据集中，并研究了选择具有高系统发育信号或低系统发育噪声的基因的影响。对于一些以前有争议的关系，我们发现各种分析和基因过滤标准一致地将以前不稳定的分组与强烈的统计支持结合在一起。例如，我们恢复了 Eustigmatophyceae 与 Raphidophyceae-Phaeophyceae-Xanthophyceae 的紧密分组，而 Olisthodiscophyceae 形成了 Pinguiophyceae 的姊妹谱系。选择具有高系统发育信号或数据质量的基因恢复了更稳定的拓扑结构。总体而言，我们发现添加不同谱系中代表性不足的群体仍然是解决系统发育关系的关键，离散的基因特性对不等鞭毛类的谱系有不同的影响。这是可以进一步探索的，以增进我们对不等鞭毛类分子进化的理解。
