The pattern of amino acid substitution does not differ between sequences derived from duplicate gene pairs (“Double-copy”; from A2′) and single-copy sequences (“Single-copy”; from A1′) either prior to the WGD (branch X), immediately after the WGD (branch Y), or in modern sequences (since the divergence of S. cerevisiae and S. bayanus; branch Z)
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The branches X, Y, and Z are labeled in Figure 1A, bottom, right. Note that because the residues present at the time of duplicate gene divergence on T1′ (black dot in Fig. 1A, top, right) cannot be reconstructed, branch Y on T1′ was treated as extending from the divergence of pre-WGD and post-WGD lineages to the divergence of S. castellii. P-values were calculated using a χ2 test of homogeneity.
