Supplementary files and data Files for "Discordance between mitochondrial, nuclear, and symbiont genomes in aphid phylogenetics: who is telling the truth?" Zoological journal of the Linnean society, 2024, vol 1, issue 4. https://doi.org/10.1093/zoolinnean/zlae098

<p>This repository comprises</p> <ul> <li>a file with all supplementary Tables&nbsp; (<strong>Supplementary_Tables</strong>). Table S1: Collection details and voucher ID for aphid samples from the CBGP-Inrae collection, data origin is given for other specimens.&nbsp;Table S2: Amplification success of long range DNA fragments from mitochondrial genomes .&nbsp;Table S3: Primers used for fluidigm aplification of nuclear genes and sequencing success.&nbsp;Table S4. Genomic features of newly sequenced Buchnera aphidicola with aphid taxonomic affiliation.&nbsp;Table S5: Summary of models used for each ML analysis&nbsp; and corresponding log-likelihood score of the best tree.Table S6: Output of RERConverge analyses.</li> <li>two Supplementary&nbsp; figures: Figure S1: Workflow of phylogenetic analyses as implemented on each dataset. Figure S2: Plot depicting the genome-wide pattern of molecular evolution (dN/dS) between disymbiotic (n = 15) and monosymbiotic aphid (n = 45) branches across the ML phylogeny (horizontal bars indicate 95% CI of the means). <em>P</em> value was calculated by using Wilcoxon Rank test.</li> <li>a word file (Text S1) with : &nbsp;Details of protocol for obtaining mitochondrial genomes through long-range DNA amplifications and Illumina sequencing, and two-step PCR protocole.</li> <li>an archive (archive1) with the mitochondrial AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses ;&nbsp;</li> </ul> <ul> <li>an archive (archive2) with the nuclear AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses</li> <li>an archive (archive 3) with the twelve new <em>Buchnera</em> genome drafts.</li> <li>&nbsp;an archive (archive4) with the <em>Buchnera</em> AA matrices and alternative topologies&nbsp;</li> </ul> <p>&nbsp;</p>