**2. Identifying duplicated genes that resulted from the FSGD event throughout the teleost genomes**

We obtained 23,155 gene families from the database HOMOLENS version 4 (ftp://pbil.univ-lyon1.fr/databases/homolens4.php) (Penel et al. 2009), which is based on the Ensembl release 49. We chose HOMOLENS, because it allowed us to reliably retrieve sets of orthologous genes for our evolutionary analysis. HOMOLENS is devoted to metazoan genomes from Ensembl and contains gene families from complete animal genomes found in Ensembl. HOMOLENS has the same architecture as HOVERGEN (Duret et al. 1994), in which genes are organized in families and include precalculated alignments and phylogenies. In HOMOLENS 4, alignments are computed using MUSCLE (Edgar 2004) with default parameters; phylogenetic trees are computed with PHYML, using the JTT amino acid substitution model (Jones et al. 1992). Phylogenies are computed based on conserved blocks of the alignments selected with Gblocks (Castresana 2000). Each phylogenetic tree is reconciled with a species tree using the program RAP (Dufayard et al. 2005), which, combined with the tree pattern search functionality, allows detection of ancient gene duplications or selection of orthologous genes (Penel et al. 2009). Several studies on duplicated gene evolution have been performed with data retrieved from HOMOLENS (Brunet et al. 2006; Studer et al. 2008).

We employed a topology-based method to identify duplicated genes that resulted from the FSGD event in the five teleost genomes we study. Briefly, if two teleosts have been subject to the same whole genome duplication event, a gene *X* that has been duplicated in this event and retained in both genomes, should form two gene lineages ''*Xa*'' and ''*Xb*'' (Figure 1A). We identified gene trees with the topology shown in Figure 1A using the TreePattern functionality (Dufayard et al. 2005) of the FamFetch client for HOMOLENS. We required duplicated genes to exist in at least two species to increase the likelihood that they result from the FSGD event (Figure 1B). In total, we identified 1,500 gene families with duplicated genes in this way.
