Single-molecule FISH in embryos reveals early embryonic expression dynamics of , and and possible differences between hyper-diverged strains.

Wild strains harbor natural variation in developmental pathways, but investigating these differences requires precise and well-powered phenotyping methods. Here we employ a microfluidics platform for single-molecule FISH to simultaneously visualize the transcripts of three genes in embryos of two distinct strains. We capture transcripts at high resolution by developmental stage in over one hundred embryos of each strain and observe wide-scale conservation of expression, but subtle differences in and abundance and rate of change. As both genes reside in a genomic interval of hyper-divergence, these results may reflect consequences of pathway evolution over long timescales.