| Summary: | Immediately following a gene duplication event, if both gene copies are to be fixed into a species’ genome there is a period of enhanced selection acting on either one or both duplicates (paralogs) that results in some extent of functional divergence. However, as redundancy among extant duplicates is thought to confer genomic robustness, a consequent question is: how much functional overlap exists between duplicates that are retained over long spans of evolutionary time? To examine this issue I determined the extent of shared protein interactions and protein complex membership for paralogous gene pairs resulting from an ancient Whole Genome Duplication (WGD) event in yeast, finding retained functional overlap to be substantial among this group. Surprisingly however, I found paralogs existing within the same complex tended to maintain greater disparities in expression, suggesting the existence of previously proposed “transcriptional back-up” mechanisms. To test both for existence of such mechanisms and for any phenotypic manifestation of their shared functional overlap I surveyed for the presence of aggravating genetic interactions between 399 WGD-resultant paralog pairs. While these paralogs exhibited a high frequency (~30%) of epistasis, observed genetic interactions were not predictable based on protein interaction overlap. Further, exposure to a limited number of stressors confirmed that additional instances of epistasis were only observable under alternate conditions. As only a small number of stress conditions were tested, the high frequency of genetic interactions reported appears to be a minimum estimate of the true extent of epistasis among WGD paralogs, potentially explaining the lack of overlap with protein interaction data. As it is impossible to survey an infinite condition space, Synthetic Genetic Array (SGA) screening of yeast strains carrying double-deletions of paralog pairs was used to assess functional redundancy among a group of the remaining non-epistatic paralog pairs. The resulting interactions demonstrated functional relationships in non-epistatic paralogs only obvious upon ablation of both duplicates, suggesting that these interactions had initially been masked through redundant function. These findings ultimately suggest an advantage to retained functional overlap among whole genome duplicates that is capable of being stably maintained through millions of years of evolutionary time.
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