Hoxness -- confusing, yet simple.
Perhaps because the original paper is behind a paywall, the stories describing it have wandered off the proper path into the quicksand.
The underlying question is, can we propose a plausible way (evolutionarily and genomically) to go from your extremities being fins to your extremities being rather more physically substantial (the stump-like "autopods"). This paper suggests that the answer is "yes."
The authors of the paper hypothesize that all you have to do is to crank up the amount of the product of the genes near the 5' end of the hoxd gene complex (a set of hoxd genes lined up in a row on the chromosomal DNA) and Bob's no longer a flounder, but rather your stumpy uncle. Essentially, hox genes are expressed at different levels in different regions of the developing embryo, and act as part of a code that directs each such region what type of structure to form. The authors think that boosting amounts of one of the 5'hoxd genes, hoxd13, throughout the developing extremity will make each subpart "think" it is closer to the fish's body, and to thus form a more robust structure than it would normally do. In particular, the cells in the very thin "finfold" region at the end of the fin instead will form a more thick and robust structure like that normally found further up the center of the fin. Thus, a fin becomes an "autopod" merely by boosting the level of a single gene product!
To test this, the authors try boosting hoxd13 levels by injecting a mouse version of the gene into the fish embryos; they see that those embryos with the gene do in fact form autopods instead of fins. (We assume that they did proper controls to show that hoxd13 levels increased compared to normal embryos, and that increased gene product levels caused the change, and not just the fact of using a mouse version of the gene rather than a zebrafish version) OK, so boosting a 5'hoxd gene DOES cause changes that look like extremities becoming autopods instead of fins.
Now, how might one boost 5'hoxd gene levels in a straightforward evolutionarily-plausible way (mouse-gene-injecting biologists having been rather thin on the ground hundreds of millions of years ago when autopods came into being)? The authors propose that genetic elements (DNA sequences) called "enhancers" might be the answer.
As their name suggests, enhancers boost the expression of nearby genes, and conveniently, tend to be much shorter than and much more robust to changes in their DNA sequence and location than are actual protein coding genes. Thus, it is plausible that a "new" enhancer might have been created by mutations near the 5' end of the ancestral tetrapod hoxd gene complex, or perhaps more likely, that a copy of an enhancer sequence from elsewhere in the genome (with some minor DNA changes to allow it to be controlled separately from its original) might have been spliced into the DNA 5' of the hoxd gene complex.
To test the plausibility of this enhancer hypothesis, it seems that the authors inserted an enhancer DNA sequence called "CsC", normally found 5' of the hoxd gene complex in tetrapods (but not fish), into zebrafish embryos. They found that it promotes nearby gene expression similarly in the zebrafish embryo fin regions and in its "normal" mouse limb environment.
Thus, the authors propose that fish fins evolved into stumpy autopods (later to become the slender limbs of fashion week runway models around the world) simply by the addition of novel enhancer DNA sequences in the region 5' of the Hoxd gene complex.
Paris, since her expression was certainly enhanced quite nicely.