Supplementary files and data Files for "Discordance between mitochondrial, nuclear, and symbiont genomes in aphid phylogenetics: who is telling the truth?"

This repository comprises

a file with all supplementary Tables  (Supplementary_Tables). Table S1: Collection details and voucher ID for aphid samples from the CBGP-Inrae collection, data origin is given for other specimens. Table S2: Amplification success of long range DNA fragments from mitochondrial genomes . Table S3: Primers used for fluidigm aplification of nuclear genes and sequencing success. Table S4. Genomic features of newly sequenced Buchnera aphidicola with aphid taxonomic affiliation. Table S5: Summary of models used for each ML analysis  and corresponding log-likelihood score of the best tree.Table S6: Output of RERConverge analyses.

two Supplementary  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). P value was calculated by using Wilcoxon Rank test.

a word file (Text S1) with :  Details of protocol for obtaining mitochondrial genomes through long-range DNA amplifications and Illumina sequencing, and two-step PCR protocole.

an archive (archive1) with the mitochondrial AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses ; 

an archive (archive2) with the nuclear AA and DNA matrices and alternative phylogenetic trees under ML and Bayesian analyses

an archive (archive3) with the twelve new Buchnera genome drafts and reannotated mitogenomes.

 an archive (archive4) with the Buchnera AA matrices and alternative topologies