Measurement of Proxy-Ancestral Evolutionary Rate

To calculate proxy ancestral rates of evolution (fig. 1b and supplementary fig. S3, Supplementary Material online), we extracted the aligned singleton gibbon and macaque sequences from the multiple sequence alignment and used them in the calculation of d_N/d_S. By extracting the alignment of just these genes, we prevent PAML from allowing evolutionary rate calculations dependent on the evolution of the genes after duplication to interfere with or otherwise affect the inference of the rate when they are singletons. Any effects of gene conversion postduplication, for example, cannot then interfere with ancestral rate estimation. We estimated d_N, d_S, and d_N/d_S as above. Gene trees with d_N/d_S values > 10 or d_S values < 0.01 were excluded from further analysis (as per Villanueva-Cañas et al. 2013), as low d_S values may artificially inflate d_N/d_S.