The LCA of protostomes likely retained 24 ALGs (PALGs) that show one-to-one correspondence with the 24 bilaterian ALGs. During protostome evolution, different chromosomal rearrangement events occurred in the spiralian and ecdysozoan lineages. All examined spiralian species, including 3 bivalves and 2 annelids, share 4 fusion events (L⊗J2, O2⊗K, Q⊗H, and O1⊗R), indicating that their LCA (presumably the LCA of spiralians) already possessed the 4 fused ALGs, so the overall number of SpALGs is 20. The LCA of the 3 bivalve species is deduced to have the same complement of ALGs (BiALGs) as the SpALGs, and lineage-specific fusion events are found in the 3 bivalves (see S13 Fig). On the other hand, it can be inferred that the 2 annelids share an additional fusion event (SpALGs C2 and L⊗J2), which brings the number of the annelid ALGs (AnALGs) to 19. Notably, the 4 common fusion events in spiralians were not detected in the ecdysozoan species we examined (red crosses over the fused chromosomes) (see S14 Fig). Weak syntenic conservation between chromosomes of ecdysozoans and other bilaterians suggests that ecdysozoans underwent more complex chromosomal rearrangements. Box sizes do not reflect the actual sizes of chromosomes.
