To summarize, primers were designed from single-copy, orthologous protein-coding nuclear genes as described in ref. 16. We made pairwise alignments for 5,274 putative orthologues from D. melanogaster and H. sapiens identified using the InParanoid method31, and further reduced them to
595 genes with .55% sequence identity between D. melanogaster and H. sapiens (sequences from C. elegans were added to the alignments when suitable16). Our primers amplified messenger RNAs encoded by 62 distinct genes from most of the 80 taxa in this study (Supplementary Table 1) and many Bilateria (C.W.C., unpublished results). The primers were completely degenerate with respect to the amino-acid code.