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Nemo has a small fin because of a genetic loss of the gene Pitx1. This loss of gene activity is compensated for on the left side by the activity of a similar gene, called Pitx2. This breaks the symmetry and leaves the fish with only one hypomorph fin.

For further reference in a related species see

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Shapiro MD, Marks ME, Peichel CL, Blackman BK, Nereng KS, Jónsson B, Schluter D, Kingsley DM. Nature. 2004 Apr 15;428(6984):717-23.

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