Fig. 3

Glossina whole-genome alignment, phylogenetic analysis of orthologous protein-coding nuclear genes, and phylogenetic analysis of mitochondrial sequences. a Analysis of whole-genome and protein-coding sequence alignment. The left graph reflects the percentage of total genomic sequence aligning to the G. m. morsitans reference. The right side of the graph represents the alignment of all predicted coding sequences from the genomes with coloration representing matches, mismatches, insertions, and uncovered exons. b Phylogenic tree from conserved protein-coding sequences. Black dots at nodes indicate full support from maximum likelihood (Raxml), Bayesian (Phylobayes), and coalescent-aware (Astral) analyses. Raxml and Phylobayes analyses are based on an amino acid dataset of 117,782 positions from 286 genes from 12 species. The Astral analyses are based on a 1125-nucleotide dataset of 478,617 positions from the 6 Glossina (full trees are in Additional file 2: Figure S2A-C). The values at nodes represent the bootstrap supports and posterior probabilities from the maximum likelihood and Bayesian analyses, respectively (Bootstrap/posterior probability). c Molecular phylogeny derived from whole mitochondrial genome sequences. The analysis was performed using the maximum likelihood method with MEGA 6.0