Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes

The impact of fitness landscape features on evolutionary outcomes has
attracted considerable interest in recent decades. However, evolution
often occurs under time-dependent selection in so-called fitness seascapes
where the landscape is under flux. Fitness seascapes are an inherent
feature of natural environments, where the landscape changes owing both to
the intrinsic fitness consequences of previous adaptations and extrinsic
changes in selected traits caused by new environments. The complexity of
such seascapes may curb the predictability of evolution. However,
empirical efforts to test this question utilising a comprehensive set of
regimes are lacking. Here we employed an in vitro microbial model system
to investigate differences in evolutionary outcomes between time-invariant
and -dependent environments, including all possible temporal permutations,
with three subinhibitory antimicrobials and a viral parasite (phage) as
selective agents. Expectedly, time-invariant environments caused stronger
directional selection for resistances compared to time-dependent
environments. Intriguingly, however, multidrug resistance outcomes in both
cases were largely driven by two strong selective agents (rifampicin and
phage) out of four agents in total. These agents either caused
cross-resistance or obscured the phenotypic effect of other resistance
mutations, modulating the evolutionary outcome overall in time-invariant
environments and as a function of exposure epoch in time-dependent
environments. This suggests that identifying strong selective agents and
their pleiotropic effects is critical for predicting evolution in fitness
seascapes, with ramifications for evolutionarily informed strategies to
mitigate drug resistance evolution.