For the both the WGD- and LGD-derived duplicates, significantly different BLAST hits were retrieved (supplementary figs. S7.1 S7.3, Supplementary Material online).
In nine of the eleven organisms, duplicates significantly increase chances of survival upon gene deletion (P-value ≤ 0.05), but only by up to 13%.
Duplicates significantly and positively contribute to survival in nine of the eleven organisms, but have noticeable effects only in six (>5%; H. pylori, M. tuberculosis, P. aeruginosa, E. coli, yeast, worm; Figure 2).
The observation that death rates in relocalized duplicates was significantly lower than nonrelocalized duplicate pairs at a Ks ≤ 0.05 for 34% of the species we examined, suggests that PSR may influence paralog retention during the earlier stages of duplication in some eukaryotic species.
However, for the nondevelopmental duplicates, we found that the age distribution of duplicates differs significantly between the genome set and KO set.
The duplication span of young human gene duplicates is significantly greater than the human gene length (Wilcoxon Rank Sum Test, W = 2,102,894, p = 0.0015) as well as the length of the coding region for protein-coding genes (Wilcoxon Rank Sum Test, W = 2,367,542, p = 7.61 × 10−11) (Fig. 7).
A Kruskal-Wallis test demonstrated that the three structural categories of gene duplicates differ significantly with respect to their distributions of duplication span (H = 6.3047; p-value = 0.0428) with structurally heterogeneous gene duplicates (partial and chimeric) possessing diminished duplication spans relative to homogeneous/ complete duplicate pairs.
A small P-value implies that duplicates are significantly enriched amongst non-essential genes compared to random and vice versa.
The result shows that, the sequence identity of tandem duplicates is significantly higher than that of retrogenes (human: p = 0.021, mouse: p = 0.034, rank sum test).
In fact, in this case, we found no instances in which nonrelocalized duplicates had significantly higher retention (supplementary table S4, Supplementary Material online).
