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Fig. S1 Fluorescent images (A-C) of lateral views of 48 hours post fertilization Tg(foxp2.A:EGFP)zc42 embryos demonstrate the isolation of a novel transgenic insertion, resulting in the sox9a:EGFP expression domain. The initial stable line of Tg(foxp2.A:EGFP)zc42 had two expression domains: brain and pharyngeal arches (A). These two domains independently segregated in offspring (B,C). Using inverse PCR, the genomic location of the insertion site of the pharyngeal arch expression domain was identified as being approximately 120kb upstream of the sox9a transcriptional start site in a 400kb stretch of the genome devoid of known genes (D). The official name of this transgenic line is sox9azc81Tg, which we refer to as zc81Tg in the atlas, and for clarity in this paper sox9a:EGFP Abbreviations: b=brain; pa=pharyngeal arches.