So, skyfauna is a bit dangerous to ships, consisting of giant fliers and all. So, in order for long-distance travels to be safe, you need to keep them away from the shipping lines. This is done by the Guild, who thereby pretty much control trade in its entirety, and use this control to make a tidy profit as well as influencing every siginificant area of politics and commerce. Don't ask me how they do it, though. At first I was thinking of airborne pathogens, but those would disperse fairly quickly in the winds. Oooh, there's an idea, use streams to carry the ships, big, large currents of air. That would take care of the dispersion problem, a bit. Inject the whale-ex into the beginning of the stream, and have it carried through there. Or, even better, attach a dispersal device to every travelling ship.
Anyway, the problem is that, slowly, the skyfauna is developing a resistance to the pathogen, and that the shipping lines are becoming more and more dangerous. The guild has to use stronger / different pathogens, but they know it's a losing battle. As a result, trade goods are becoming more and more expensive. God, my writing's horrible today. It's not that the pathogen actually harms the skyfauna, it's more that they don't like the smell, so they avoid the area. Because, y'know, there's lots of sky left. Unfortunately, some smaller bird-thingies and insects don't really mind, and fly through the canals as usual, ingesting and picking up the pathogen. This serves as a second avenue for spreading the pathogen beyond the canal, and also makes it wander up the foodchain. As a result, the larger skyfauna is slowly becoming desensitized to the pathogen, and starts reclaiming the canals, which, in their absence, have become more nutrient-rich.
The guild started out like CST, a bunch of clever / lucky people finding a out that the skyfauna doesn't like and then capitalizing on it. They rode the wave of the shipping boom, and made a massive fortune in the process, which left them firmly in control of the shipping lines. Eventually, their product was being duplicated by people who wanted to escape the grasp of their rather expensive shipping rates. The Guild responded by greatly lowering the prices for the product, introducing shipping permits, and decreeing that any ship found without a permit would be forfeit.
Open question: how did the colonies come to be established?
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