A starting gene set was composed from of the human RefSeq [28] , UCSC Known Genes [29] , and VEGA [30] annotations (downloaded from UCSC Feb. 19, 2007) . Transcripts that lacked annotated coding regions (CDSs), that had CDSs of ,100 bp, or that had CDSs whose lengths were not multiples of three were discarded, leaving 88,879 nonredundant transcripts. These transcripts were grouped by same-stranded CDS overlap into 21,115 genes (transcript clusters). All transcripts were mapped from human to each of the other five mammalian species via the syntenic alignments, then subjected to a series of filters designed to minimize the impact of annotation errors, sequence quality, and changes in gene structure on subsequent analyses. Briefly, each human transcript was required (1) to map to the non-human genome via a single chain of sequence alignments including $80% of its CDS; (2) after mapping to a non-human species, to have #10% of its CDS in sequencing gaps or low quality sequence; (3) to have no frame-shift indels, unless they were compensated for within 15 bases; (4) to have no in-frame stop codons and to have all splice sites conserved. To allow for genes that are mostly conserved but whose start or stop codons have shifted, incomplete transcripts-with ,10% of bases removed from the 59 and 39 ends of the CDS-were also considered. The final collection of ortholog sets was obtained by selecting, for each gene, the (complete or incomplete) transcript that successfully mapped to the largest number of non-human species. In the case of a tie, the transcript with the greatest total CDS length was selected. This procedure resulted in 17,489 genes with $2 non-human orthologs, averaging ,5 species per gene (including human; see Table 1 ).