Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

Natural environments are rarely static; rather selection can fluctuate on
time scales ranging from hours to centuries. However, it is unclear how
adaptation to fluctuating environments differs from adaptation to constant
environments at the genetic level. For bacteria, one key axis of
environmental variation is selection for planktonic or biofilm modes of
growth. We conducted an evolution experiment with Burkholderia
cenocepacia, comparing the evolutionary dynamics of populations evolving
under constant selection for either biofilm formation or planktonic growth
with populations in which selection fluctuated between the two
environments on a weekly basis. Populations evolved in the fluctuating
environment shared many of the same genetic targets of selection as those
evolved in constant biofilm selection, but were genetically distinct from
the constant planktonic populations. In the fluctuating environment,
mutations in the biofilm-regulating genes wspA and rpfR rose to high
frequency in all replicate populations. A mutation in wspA first rose
rapidly and nearly fixed during the initial biofilm phase but was
subsequently displaced by a collection of rpfR mutants upon the shift to
the planktonic phase. The wspA and rpfR genotypes coexisted via negative
frequency-dependent selection around an equilibrium frequency that shifted
between the environments. The maintenance of coexisting genotypes in the
fluctuating environment was unexpected. Under temporally fluctuating
environments coexistence of two genotypes is only predicted under a narrow
range of conditions, but the frequency-dependent interactions we observed
provide a mechanism that can increase the likelihood of coexistence in
fluctuating environments.