Diagrammatic summary of the morphological defects induced by pharmacological treatments and gene knockdown in the developing amphioxus pharynx. The effects are described in the pharynx of larvae at 36 hours post fertilization (hpf), which are characterized by a well-developed mouth (gray circle), an endostyle (anterior dotted lines), a club-shaped gland (posterior dotted lines) and two gill slit primordia (yellow ovals) with two gill slits (gray oval). Indicated are the results obtained from treatments with the Cyp26 inhibitor R115866, with retinoic acid (RA) at different developmental stages and at different concentrations, from injections of a Tbx1/10-specific antisense morpholino oligonucleotide (MO) and from the combination of RA treatments with the injection of a Hox1-specific MO. Mispatterned gill slit primordia with malformed gill slits are indicated as oval structures with brown centers. The results obtained with the retinoic acid receptor (RAR) antagonist BMS009 are not shown.