Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

Significance Unexpected evolutionary innovations that lead to qualitatively new traits may result from complex genetic and ecological interactions that develop over long timescales. In a 25-y evolution experiment withEscherichia coli , a rare metabolic innovation arose that allowed a previously untapped resource to be exploited. By dissecting the genetics of this trait using a recursive genomewide recombination and sequencing method (REGRES), we identified a key mutation that converts a rudimentary form of the innovation into a refined trait that confers a decisive competitive advantage. The effects of this mutation demonstrate how improvement of an emergent trait can be as important to its eventual success as earlier mutations or environmental conditions that may have been necessary for it to evolve in the first place.