Additional file 2 of New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves

Additional file 2: Table S1. Characteristics of primers and PCR reactions for amplification of CR1/CR2 fragments. Sequences of primers, their internal laboratory numbering and naming as well as positions according to reference mitogenomes are included. Reactions that failed are marked with an asterisk. Reactions whose products were finally sequenced are marked in grey shading. Table S2. Characteristics of control regions in Palaeognathae species based on mitochondrial fragments obtained in this study and previously published mitogenomes. Table S3. Characteristics of alignments between ND6 copies for various avian taxa. Table S4. Substitution models, partitions and their relative rate in MrBayes analysis. Table S5. Results of tests comparing various palaeognath tree topologies. The topology t1 corresponds to the best tree found for the full alignment. The topologies are shown in Fig. 5. The table includes: p-value from an approximately unbiased test (AU), the bootstrap probability calculated from the multiscale bootstrap (NP), the bootstrap probability calculated in the usual manner (BP), Bayesian posterior probability calculated by the BIC approximation (PP), p-value of the Shimodaira-Hasegawa (SH) and the weighted Shimodaira-Hasegawa tests (WSH), Bayes factor (BF) expressed in natural logarithm units as differences between marginal likelihoods of the given and the topology (t1). Table S6. Number of known mitogenomic sequences and species in terms of duplication for individual avian orders. Table S7. Avian species in which GO-FD gene order was identified in their mitogenomes. Previous annotations assuming single, i.e. without duplication, version were also included. Incomplete mitogenomes are marked with an asterisk. Table S8. Substitution models and partitions used in IQ-TREE analysis. Table S9. Characteristics of primers and PCR reactions for amplification of mitochondrial fragments from Neoaves and Galloanserae representatives. Sequences of primers, their internal laboratory numbering and naming as well as positions according to reference mitogenomes are included. Reactions that failed are marked with an asterisk. Reactions whose products were finally sequenced are marked in grey shading. Table S10. Substitution models and partitions used in IQ-TREE analysis for RY-recoded sequences.附加文件2：表S1 用于扩增CR1/CR2片段的引物及聚合酶链式反应（PCR）特征。包含引物序列、其内部实验室编号与命名，以及参照参考线粒体基因组（mitogenome）的位置。扩增失败的反应以星号标注，最终产物完成测序的反应以灰色底纹标注。 表S2 基于本研究获得的线粒体片段及已发表线粒体基因组的古颚总目（Palaeognathae）物种控制区特征。 表S3 不同鸟类类群ND6基因拷贝序列比对的特征。 表S4 MrBayes分析中使用的替换模型、分区方案及其相对速率。 表S5 不同古颚类树拓扑结构的比较检验结果。其中拓扑结构t1对应全序列比对得到的最优树，各拓扑结构详见图5。该表包含：近似无偏检验（AU）的p值、基于多尺度自助法（NP）计算的自助概率、常规方式计算的自助概率（BP）、通过贝叶斯信息准则（BIC）近似得到的贝叶斯后验概率（PP）、Shimodaira-Hasegawa（SH）检验及加权Shimodaira-Hasegawa检验（WSH）的p值、以自然对数为单位表示的贝叶斯因子（BF），即给定拓扑结构与t1的边际似然之差。 表S6 各鸟类目级类群已知线粒体基因组序列及发生基因重复的物种数量。 表S7 线粒体基因组中鉴定出GO-FD基因序列的鸟类物种，同时纳入了此前假设单拷贝（无基因重复）版本的注释结果。不完整的线粒体基因组以星号标注。 表S8 IQ-TREE分析中使用的替换模型与分区方案。 表S9 用于扩增新鸟下纲（Neoaves）与鸡雁小纲（Galloanserae）类群线粒体片段的引物及聚合酶链式反应特征，包含引物序列、其内部实验室编号与命名，以及参照参考线粒体基因组的位置。扩增失败的反应以星号标注，最终产物完成测序的反应以灰色底纹标注。 表S10 针对RY编码序列进行IQ-TREE分析时使用的替换模型与分区方案。