Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)
Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)
复制标题
紫堇（罂粟科）ITS2 系统发育中补偿性基础变化的替代分析
DOI：
10.1093/aob/mcz062
复制
发表时间：
2019-07-24
期刊：
影响因子：
4.2
通讯作者：
Simmons, Mark P.
中科院分区：
文献类型：
--
作者：
Li, Meihui;Zhao, Hong;Simmons, Mark P.
背景与目的
核糖体内部转录间隔区2（ITS2）茎区发生的补偿性碱基改变（CBCs）可能具有重要的系统发育意义，因为它们不应在一个物种内发生，并且还会影响合适的DNA替代模型的选择。在研究古老谱系时，这些影响已得到证实。在此，我们通过使用DNA特异性和RNA特异性模型来检验这些影响，以量化它们在一个较新谱系中的重要性。
方法
我们通过对来自10个密切相关的紫堇属物种的ITS2进行全面采样，研究了CBC过程的系统发育意义。我们利用同源建模预测了ITS2的二级结构，然后将其用于基于结构的比对。通过使用RNA特异性替代模型和常规DNA模型，分别以及联合分析配对区域和非配对区域。我们将CBCs的所有碱基对状态绘制在系统发育树上，以推断它们的进化和相对时间。
关键结果
我们的结果表明，选择作用增加了二级结构的热力学稳定性。因此，非配对区域和配对区域并非在一个共同的替代模型下进化。在采样的谱系中仅出现了两个CBCs，并且在使用DNA特异性或RNA特异性替代模型构建的树之间，在拓扑结构或对共有分支的支持方面未发现显著差异。
结论
尽管RNA特异性替代模型的应用仍然优于更常规的DNA模型，但我们推断，在对密切相关的谱系（其中观察到的CBCs很少）进行ITS2的系统发育分析时，应用常规DNA模型不太可能有问题。两个CBCs中的每一个都在相同的谱系中被发现，但在一个给定的物种内未被观察到，这支持了CBC物种概念的应用。
Background and Aims Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models.Methods We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing.Key Results Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models.Conclusions Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.