Fig 1.
An overview of the computational process used to infer PPI networks for each of the 5 yeast species, and to generate the simulated null model.
Molecular evolutionary parameters were inferred under the M0 model in PAML, and were used to generate simulated datasets using INDELible. PIPE was used to infer PPI networks for both the real and simulated datasets.
Fig 2.
Phylogeny of the five yeast species studied here.
Fig 3.
Distribution of the change in protein-protein interaction across the phylogeny.
The distribution of γ, which represents the total number of interaction changes (gains or losses) over the entire phylogeny. The majority of proteins experience relatively few changes in interaction across the phylogeny with a small number of proteins experiencing many changes.
Fig 4.
Comparing the change in protein-protein interaction to protein degree and rate of sequence change across the phylogeny.
Comparison of changes in PPIs across the phylogeny (γ) to degree (A) or to rate of substitution across the phylogeny (ω) (B). A protein’s γ is correlated with its degree in the network (see regression line in panel A), but not with its overall rate of substitution.
Table 1.
Number of interactions in the predicted interactomes for four yeast species, inferred from real and simulated datasets.
Fig 5.
Proteins which experience a lower or higher number of changes in PPIs in the real data compared to the simulated interactomes.
Proteins which experience a lower (A) or higher (B) number of changes in inferred PPIs in the real data in comparison to the simulated interactomes. Each protein’s real γ is plotted in red and the range of γ observed in the null model are plotted in black.
Table 2.
A comparison of proteins and enriched GO processes that were identified through conservation or rapid evolution of sequence or of inferred PPIs.
Table 3.
Enriched GO terms for proteins with lower than expected γ not identified when analyzing slowly evolving protein sequences.
Table 4.
Enriched GO terms for proteins with higher than expected γ not identified when analyzing positively selected protein sequences.
Table 5.
Summary of the enriched GO Terms of the proteins participating in conserved PPIs.
Table 6.
Significant protein clusters and GO term enrichment analysis results found in each of the four non-cerevisaie species.
Table 7.
Enriched GO terms in S. kudriavzevii cluster 113.