Figure 4. A, B in A phylogenomic look into the systematics of oceanic squids (order Oegopsida)

Figure 4. A, B, maximum parsimony (A) and maximum likelihood (B) ancient state reconstruction of the mitogenome gene order of oceanic squids implemented in MESQUITE v.3.61. C, hypothetical mitochondrion including the plesiomorphic positions for trnM and trnI. D, hypothetical mitochondrial gene order of Lampadioteuthis megaleia. E, hypothetical mitochondrial gene order of Histioteuthidae. F, hypothetical mitochondrial gene order of Cranchiidae, Ommastrephidae and Thysanoteuthidae. G, hypothetical mitochondrial gene order of Neoteuthidae. H, mitochondrial gene order of Lepidoteuthidae and Octopoteuthidae. I, mitochondrial gene order of Joubiniteuthidae. J, mitochondrial gene order of Architeuthidae based on Winkelmann et al. (2013) and the GenBank sequence FJ429092 (Elliger CA, Lebaric ZN, Gilly WF & Robison BH, unpublished). In all mitogenomes, the plus (+) strand is represented in the direction 5′ → 3′. Arrowheads indicate the points where one or more genes were lost; arrows signal the position of gene transposition (highlighted) and the position of that gene in the plesiomorphic gene order; diamonds signal the position of non-functional copies of genes. The non-coding regions are indicated in black; genes from the minus (−) strand of the mitogenome are coloured in light grey. Squares are not proportional to the size of the genes. See the Material and Methods section for gene abbreviations. Where multiple duplicate genes prevented NOVOPLASTY from returning a single circular contig, we curated the contigs obtained to match the gene order in Figure 2E (see the Material and Methods section). Almost all published oegopsid genomes follow the order depicted in Figure 2E, whereas those reported for Architeuthis dux (Winkelmann et al., 2013) and the bathyteuthid Bathyteuthis abyssicola Hoyle, 1885 (Kawashima et al., 2013) follow Figure 2F, and our assumption regarding the arrangement of blocks (but not the order of genes within them) could be wrong for some species.