The constructive black queen hypothesis: new functions can evolve under conditions favouring gene loss

Abstract

Duplication is a major route for emergence of new gene functions. However, emergence of new gene function via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because under an emerging Black Queen dynamic there is high gene redundancy, spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede fixation of new function. Our results expand the mechanisms by which new gene function can emerge in prokaryotic systems.