Data from: Genomic analysis of a key innovation in an experimental Escherichia coli population

Evolutionary novelties have been important in the history of life, but
their origins are usually difficult to examine in detail. We previously
described the evolution of a novel trait, aerobic citrate utilization
(Cit+), in an experimental population of Escherichia coli. Here we analyze
29 genomes to investigate the history and genetic basis of this trait. At
least three distinct clades coexisted for more than 10,000 generations
prior to its emergence. The Cit+ trait originated in one clade by a tandem
duplication that captured an aerobically-expressed promoter for the
expression of a previously silent citrate transporter. The clades varied
in their propensity to evolve this novel trait, although genotypes able to
do so existed in all three clades, implying that multiple potentiating
mutations arose during the population’s history. Our findings illustrate
the importance of promoter capture and altered gene regulation in
mediating the exaptation events that often underlie evolutionary
innovations.