Station d'Ecologie Théorique et Expérimentale de Moulis, UMR CNRS 5321, Moulis, France.
InBioS-PhytoSYSTEMS, Unité de Phylogénomique des Eucaryotes, Université de Liège, Liège, Belgium.
Mol Biol Evol. 2022 Jan 7;39(1). doi: 10.1093/molbev/msab300.
It is commonly assumed that increasing the number of characters has the potential to resolve evolutionary radiations. Here, we studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous origin mitochondrion, plastid, and nucleus. Surprisingly while statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion (6,762 sites) and plastid (21,692 sites) trees, it decreases in the nuclear (209,105 sites) tree. Statistical support is not simply related to the data set size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that this ability for current phylogenetic methods is limited, because conflicting results were obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid data set provided higher statistical support for the ochrophyte radiation than the larger nucleus data set. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear data set. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of data sets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.
人们通常认为增加字符数量有可能解决进化辐射问题。在这里，我们使用异质起源的线粒体、质体和细胞核的比对研究了光合丝状体（Ochrophyta）。令人惊讶的是，虽然比较线粒体（6762 个位点）和质体（21692 个位点）树时，六大 Ochrophyta 谱系之间的关系的统计支持增加了，但在核（209105 个位点）树中却减少了。统计支持不仅仅与数据集大小有关，还与每个位置的系统发育信号的数量以及我们提取它的能力有关。在这里，我们表明，当前的系统发育方法的这种能力是有限的，因为在改变分类群采样时会得到相互矛盾的结果。尽管使用更好的拟合模型提高了信号提取并减少了观察到的冲突，但质体数据集为 Ochrophyta 辐射提供的统计支持高于更大的核数据集。我们提出，在质体树中观察到的更高支持是由于一个短的深内部分支的进化率加速，这意味着在质体数据集中，每个位置的系统发育信号更多，有助于解析 Ochrophyta 辐射，而不是核数据集。因此，我们的工作表明，为了解决辐射问题，除了明显使用具有更多位置的数据集之外，我们还需要继续开发更好地提取系统发育信号的序列进化模型，并设计方法来搜索包含更多信号的基因/特征，特别是针对短的内部分支。
