**4. Molecular evolution of duplicated genes**

We next wished to study patterns of sequence evolution in the 1,500 duplicate gene families we had identified. To this end, we downloaded both nucleic acid and amino acid sequences for genes in these families. For each species, we retained only one gene copy in each duplicated clade (Figure 1B) for further analysis, and discarded all other copies in those gene families where additional duplications have occurred after the FSGD event. We then aligned the amino acid sequences within each gene family with MUSCLE (Edgar 2004), and calculated DNA alignments from protein alignments with RevTrans (Wernersson and Pedersen 2003). The following computations were then done on the new DNA alignments. We estimated the nucleic acid evolutionary distance between fish genes and their human orthologs using the LogDet nucleotide substitution model (Tamura and Kumar 2002) in PHYLIP-3.6b (Felsenstein 2004).

Previous studies show that duplicated genes in yeast often diverge asymmetrically (Kellis et al. 2004), meaning that one copy evolves significantly faster than the other. We asked whether this is also the case for teleost duplicates. To this end, we compared evolutionary distances of duplicated genes with their human orthologs within the 1,500 gene families we had identified. There is indeed evidence for asymmetric evolution between duplicated gene pairs from the FSGD event (Table 2). Average evolutionary distances to the human homologue between members of duplicated gene pairs are significantly different for each of our five teleost species (paired *t*-test: *P* < 4.8 × 10—95). As all duplicated gene pairs stemming from the FSGD diverged at the same time from their human orthologs, we can directly convert differences between evolutionary distances into differences between evolutionary rates. Taken together, our observations suggest that duplicate genes tend not to accumulate sequence change at the same rate. Our results are consistent with previous works in teleosts (Brunet et al. 2006; Steinke et al. 2006) and yeast (Kellis et al. 2004), and confirm that asymmetric sequence evolution between duplicated genes is a frequent pattern of duplicated gene evolution after a genome duplication event.


Duplicate\_L: duplicated gene in each duplicate pair that has the larger distance to the human orthologue (distances averaged over all duplicate gene families); Duplicate\_S: duplicated gene in each duplicate pair that has the smaller distance to the human orthologue (distances averaged over all duplicate gene families). All means are ± one standard deviation. \* paired *t*-test

Table 2. Average evolutionary distances of duplicated genes in five teleost species to their human orthologs.
