Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose

Copy-number and point mutations form the basis for most evolutionary
novelty through the process of gene duplication and divergence. While a
plethora of genomic sequence data reveals the long-term fate of diverging
coding sequences and their cis-regulatory elements, little is
known about the early dynamics around the duplication event itself. In
microorganisms, selection for increased gene expression often drives the
expansion of gene copy-number mutations, which serves as a crude
adaptation, prior to divergence through refining point mutations. Using a
simple synthetic genetic system that allows us to distinguish copy-number
and point mutations, we study their early and transient adaptive dynamics
in real-time in Escherichia coli. We find two qualitatively
different routes of adaptation depending on the level of functional
improvement selected for: In conditions of high gene expression demand,
the two types of mutations occur as a combination. Under low gene
expression demand, negative epistasis between the two types of mutations
renders them mutually exclusive. Thus, owing to their higher frequency,
adaptation is dominated by copy-number mutations. Ultimately, due to high
rates of reversal and pleiotropic cost, copy-number mutations may not only
serve as a crude and transient adaptation but also
constrain sequence divergence over evolutionary time scales.