Figure 1

Phylogenetic relationships among major Brachyuran clades and BraGO vs PanGO. The tree depicts the phylogenetic relationships among the major Brachyura lineages cited in the main text. The values in the green/red box refer to the full-length mtDNAs available for that lineage. The taxa names are coloured according to the current placement of taxa themselves within the major Brachyuran groups (e.g. all families belonging to fresh water crabs are in orange). The genomic transformation from PanGO to BraGO is provided below the tree. PanGO is linearized starting from cox1. The genes encoded on the α-strand (orientation from right to left in Fig. 1) are green-boxed, while those encoded on the β-strand (orientation from left to right in Fig. 1) are underlined and red-boxed. Nomenclature: atp6 and atp8: ATP synthase subunits 6 and 8; cob: apocytochrome b; cox1-3: cytochrome c oxidase subunits 1–3; nad1-6 and nad4 L: NADH dehydrogenase subunits 1–6 and 4 L; rrnS and rrnL: small and large subunit ribosomal RNA (rRNA) genes; X: transfer RNA (tRNA) genes, where X is the one-letter abbreviation of the corresponding amino acid, in particular L1 (CTN codon family) L2 (TTR codon family), S1 (AGN codon family) S2 (TCN codon family); CoRe: Control Region. T: transposition event. Tdrl: tandem duplication random loss mechanism producing the observed rearrangement. TrnH, that changed its position relative to PanGO, through a transposition event, is shown with a yellow background. Conversely, the passively-shifted genes are figured with their original background (see Methods section). The extra copy of every gene that is lost in the genomic rearrangement is figured with a light brown background. A blue circle marks an intergenic spacer present in a position associated to genomic rearrangement.