For this study, we chose to avoid recently duplicated gene families and to focus on 1:1 orthologs. This simplified the analysis, allowed for parameter sharing across genes (see Methods), and eliminated an important source of error by avoiding the need for a separate tree reconstruction for each gene family. (All ortholog sets were assumed to obey the species tree shown in Figure 1 ; because only an unrooted tree is needed, the topology is well accepted.) It was therefore necessary to discard any genes that showed evidence of recent duplication. This was accomplished in a pairwise fashion, by examining each human gene and orthologous non-human gene, and determining-based on BLAST matches to other genes and gene predictions in the same genome-whether either gene had a paralog that was more similar to it than the two orthologs