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Both comparative genomics and experimental evolution are powerful tools that can be used to make inferences about evolutionary processes. Together, these approaches provide the opportunity to observe evolutionary adaptation over millions of generations where selective history is largely unknown, and over short timescales under controlled selective pressures in the laboratory. Comparative experimental evolution combines these disciplines to determine whether different species adapt in similar ways when faced with new environments, and to explore what features of genetic background modulate evolutionary potential and path. We performed laboratory evolution experiments of multiple populations of Saccharomyces cerevisiae and Saccharomyces uvarum for ~200-500 generations of sulfate-limited continuous culture. S. cerevisiae cultures repeatedly take advantage of a single, high fitness gene amplification of the high affinity sulfate transporter SUL1. Surprisingly, however, in S. uvarum, we identified a copy number increase at the paralogous SUL2 locus, which codes for a lower affinity sulfate transporter in S. cerevisiae. In order to better understand divergence of these paralogs across the sensu stricto genus, laboratory evolution experiments in sulfate-limitation was performed in interspecific hybrids between S. uvarum and S. cerevisiae and in two other species of the sensu stricto clade: S. paradoxus and S. mikatae. Amplification of the SUL1 locus was detected both in the hybrids and for both species, with no amplification of the SUL2 locus. Our data show evidence of differential sub-functionalization among the sulfur transporters across the sensu stricto clade through recent changes in noncoding sequence. This study highlights differential evolutionary adaptations between multiple diverged yeast species and presents a method for tracking evolutionary path differences in microorganisms. |