Character state analyses on the 188-taxon tree summarized at the family-level. Ancestral states for habitat type and six morphological traits were reconstructed and tested for correlation on each of 1000 bootstrap replicates of our 188-taxon dataset. Extant morphological state presence for the six characters examined is shown in tip boxes as follows: accessory nidamental gland (yellow); branchial canal (pink); corneas (violet); right oviduct (teal); autogenic photophore (green); and bacteriogenic photophore (orange). The taxa found in pelagic habitats are shaded in grey while demersal taxa are white in the tree at right. More detail on character states and coding can be found in Additional file 2. Internal branches are shaded with: trait color, when ASR tests significantly favored the presence of the trait; white, when ASR tests significantly favored an absent state; black, when neither state fit significantly better.