while not necessarily due to "HOX genes or other controlling genes" there are many examples of saltationist speciation through polyploidy, most common in plants, but not unknown in animals. Polyploidy involves the sudden duplication of chromosomes that make interbreeding between parent and daughter population impossible, thus speciation has occurred.
You are correct. But I'm not a botany kind of guy. I endured my botany classes and it has affected my views of evolutionary biology. Of course polyploidy in plants can cause a new species in two generations. Sometimes it is genome duplication in a single species that produces a 3n offspring. While it is unlikely that such an offspring could breed with the parent, in self fertilizing plants, this isn't a problem. There is also the hybridization between two related species. While such crosses are generally sterile, sometimes such plants are actually inter-fertile. As I recall, wheat is the result of a cross between a 1n grass and a 2n grass, producing 3n wheat.
This has been observed in the field under controlled conditions, and in the lab.
In fact, I believe that it has been induced in the field and the lab.
However, what I had in mind was the experiment in which the genome of a shrimp was altered in a laboratory experiment. The result was that the the production of abdominal appendages (swimmerets) in offspring was suppressed. A similar mutation would be necessary in the transition from crustacean to insect and arachnid.
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