Using the latest human, chimpanzee, macaque, mouse, rat, and dog genome assemblies, we identified 17,489 human genes with high-confidence orthologs in at least two of the remaining five species. These ortholog sets (human genes and non-human orthologs) were identified by an automatic pipeline that made use of syntenic whole-genome alignments, sequence quality scores, and other data (see Methods). Briefly, the pipeline began with 21,115 human genes drawn from the RefSeq [28] , UCSC Known Genes [29] , and VEGA [30] gene sets. These genes were mapped to the other genomes via syntenic pairwise alignments, then passed through a series of rigorous filters to ensure correct mapping, high sequence quality, and only minimal changes between species in gene structure. This approach exploits the fact that gene structures are generally well-conserved between mammalian species [22] and avoids any dependency on the non-human gene annotations, which-with the exception of mouse-are significantly less accurate and complete than those for human. Because low-quality sequence can produce a spurious signal for positive selection (e.g., [8] ), all bases with low quality scores (Phred quality ,20) were masked out for subsequent analyses. Masking (or truncation at the 59 or 39 end) was also used to exclude regions of genes in which minor differences in gene structure were apparent. Genes that showed signs of substantial disruptions to their exon-intron structures or open reading frames in one or more species (perhaps indicating pseudogenization) were masked out completely in those species. All masked bases were treated as missing data in the subsequent analysis of positive selection. This masking approach allowed the number of genes to be maximized while ensuring that the analyzed alignments were of high quality (Table 1) .