Fig. 3
From: Recurrent sequence evolution after independent gene duplication
Asymmetric divergence of duplicated genes. Two primary categories of quartets are sampled: those with a single duplication and those with independent duplications (top). As an example, two quartets from Fig. 1 are shown. Within the subset of positions that supports the predicted fates (R in the case of human and yeast), asymmetry captures the difference in congruity between the two fates, i.e. are only Human_a and Yeast_c similar at a number of positions (t=ABAC) or are Human_b and Yeast_d similar as well (u=ABCB)? From the asymmetry (A), its significance ZA can be calculated in the same manner as ZF (see Material and Methods and Suppl. Figure S3). The bottom panels show the percentage of quartets with |ZA|>1.96 (i.e. significant asymmetry) as a fraction of quartets with significant fate similarity (|ZF|>1.96). Bars display averages; error bars give standard errors of the proportions; sample sizes are indicated beneath the categories. Note that duplications represented in Other quartets are likely substantially older than those in WGD quartets which only contain the vertebrate 2R and 3R WGD and the yeast WGD (∼500, 350 and 150 Mya)