We analyzed the phenotype of Cre transgene-negative embryos carrying wild-type shha alleles, heterozygous mutagenic alleles, or homozygous mutagenic alleles. Pectoral fin development was normal in all wild-type embryos (all five analyzed fish were normal) and most heterozygous mutants (six of seven fish were normal), but severely hampered in all homozygous mutants (all three analyzed fish were abnormal) (Figure 3—figure supplement 2C). We also performed semi-qRT-PCR analysis of shha expression in these embryos (Figure 3—figure supplement 2D). Densitometric quantification of the PCR result demonstrated that shha expression was reduced in a concentration-dependent manner with the mutagenic allele (Figure 3—figure supplement 2E). Together with the observation from the Cre DNA injection experiment (Figure 3A–C), we believe these results strongly support our conclusion that the inverted shhactallele is a loss-of-function allele of shha. We have described this result in the revised manuscript as follows: