We argue that the overall reduction of epistatic interaction for individual duplicate genes occurred as a result of subfunctionalization after gene duplication.
A unique record was created for each individual; duplicate reports were not included in the final datasets.
There is also an overall correlation between sequence similarity and combined interaction degree for individual duplicate gene pairs (supplementary table 1, Supplementary Material online).
For each individual, duplicate sequences were summarized into genotypes with two alleles retained for analysis.
Although epistatic interaction for individual duplicate gene is overall reduced, the sum of epistatic interactions for duplicate gene pairs is increased (fig. 1 A ).
Consistent with previous results (Costanzo et al. 2010), on average, individual duplicate genes have fewer epistatic interactions than single-copy genes (data not shown).
Biologically this would correspond to the hypothesis that the network organization can be seen by individual duplicate nodes only through their neighbours.
The buffering effect induced by a large number of duplicated genes leads to a higher variation in individual duplicated genes, a phenomenon also observed in polyploid plants [ 55].
In particular, unless the other player is completely insensitive to what an individual does (duplicating, in effect, the behavior of the non-iterated prisoner's dilemma), "always defect" is not a very attractive strategy.
In addition, a recent study in Paramecium shows that the maintenance or loss of protein-coding genes after whole-genome duplication is largely determined by dosage constraints (Gout and Lynch 2015), conforming to a model under which the expression level of individual duplicated genes can evolve neutrally as long as they maintain a roughly constant summed expression.
Furthermore, the evolutionary dynamics of individual duplicated genes is similar for the products of single genome and whole genome duplications.
