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.