Lamprey HOX cluster - can somebody explain?

Smith et al., Feb. 2013, Nature Genetics

Here is a picture taken from a recent paper (doi:10.1038/ng) on the Lamprey genome. The authors make some interesting assumptions on the initial timing of whole genome duplications in the vertebrate lineage. However looking at this picture I just don't get it. Assuming that co-linearity is not really important (let's call it my own believe for now), but how to construct an ancestral* state of a cluster in this scenario? Or is there a problem with the assembly (could be when looking at the mirs)? Is it weird? Well, could well be, that I don't understand right now.


* "ancestral" is always a very bad word when looking a species we see today, but in this case it is called for by the paper itself I think.