The accurate analyses of massive amounts of data obtained through next‐generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate “supergene” approach. The effects of molecular evolutionary models and character partition strategies on plastome‐based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well‐supported conflicting topologies). We compared different datasets (e.g., non‐coding regions, exons, and codon‐aligned and translated amino acids) using concatenated approaches under site‐heterogeneous and site‐homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

中文翻译：

---

在低分类水平上评估质体系统基因组学中的特征划分和分子模型：使用 Amphilophium（Bignoniaeae，Bignoniaceae）的案例研究

对通过下一代测序获得的大量数据的准确分析取决于选择合适的进化模型。许多质体系统发育研究通常使用串联“超基因”方法将质体数据分析为单个分区或按区域划分。分子进化模型和特征划分策略对基于塑性体的系统发育的影响通常在绿色植物的更高分类学水平上进行评估。使用来自新热带藤本植物属的 32 种 Amphilophium 的质体数据，我们探索了不同质体基因组数据集和方法的拓扑不一致的潜在来源。具体来说，我们评估了组成异质性、密码子使用偏倚、正选择、和不完整的谱系排序作为系统错误的来源（即恢复良好支持的冲突拓扑）。我们在位点异质和位点同质模型下使用串联方法以及多物种聚结 (MSC) 方法比较了不同的数据集（例如，非编码区、外显子和密码子对齐和翻译的氨基酸）。我们在恢复的系统发育关系中发现了不一致，主要位于短节间。MSC 和级联方法恢复了类似的拓扑结构。GC 含量和密码子使用偏差的分析表明，第三个密码子位置的替代率更高，AT 过量，我们发现了 3% 的氨基酸位点正选择的证据。在场地生化特征方面，物种之间没有显着差异。