Wildenberg, Murray Supplementary File 1 Strain name yGW 461 yGW E6 yGW E15 yGW 5A7 yGW 501 yGW 556 Genetic change MATa BUD4 HIS3∆::PACT1-ymCherry-tADH1-HIS3MX6 PFLO1::PFLO1-ymCitrine-tADH1 pol3-L523D leu2-3,112 ura3∆0 can1-100 Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations PACT1-ymCerulan-tADH1 MATalpha lys2∆::Hygror yGW 451 Ancestor with wild type POL3 yGW 992 MATa BUD4 HIS3∆::PACT1-ymCherry-tADH1- HIS3∆::MX6 PFLO1::PFLO1-ymCitrine-tADH1 leu2-3,112 ura3∆0 can1-100 hbn1 ids2 pet127 scw11 sir4 vps5 whi2-100 yjl070c hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 Ancestor genotype: evolved 360 generations hml∆:: Ca.URA3 Ancestor genotype: evolved 360 generations hml∆::Ca.URA3 hbn1∆:: KANr ids2∆:: KANr pet127∆:: KANr scw11∆:: KANr sir4∆:: KANr vps5∆:: KANr whi2-100∆:: KANr yjl070c∆:: KANr Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations yGW 861 yGW 1A1 yGW 903 yGW 1G1 yGW 905 yGW 5A1 yGW 900 yGW 5C5 yGW 898 yGW 1B2 yGW 896 yGW 1C3 yGW 894 yGW 1D10 yGW 907 yGW 1E7 yGW 893 yGW 936 yGW 932 yGW 924 yGW 926 yGW 928 yGW 934 yGW 923 yGW930 yGW E6/1A9 yGW E6/5A5 yGW E6/1B8 yGW E6/1B12 yGW E6/1C3 yGW E6/1D10 yGW E6/1H6 yGW E6/5A11 yGW E6/5B4 yGW E6/5B8 yGW E6/5B12 yGW E15/1A7 yGW E15/1E1 yGW E15/1E3 yGW E15/1F6 yGW E15/1G9 Additional Information Ancestor Evolved population: 6% selection Evolved population: 15% selection E6-1 evolved clone from 6% evolved population E6-1 + CFP Mating type switched Ancestor used for crossing to E6-1 and bulk segregant analysis Lab strain used to introduce clock alleles: direct descendant of ancestor prior to introduction of pol3-L523D Complete recreated clock strain with all 8 mutations E6-1 with hml∆ E6-2 clone E6-2 hml∆ E6-3 clone E6-3 hml∆ E6-4 clone E6-4 hml∆ E6-5 clone E6-5 hml∆ E15-1 clone E15-1 hml∆ E15-2 clone E15-2 hml∆ E15-3 clone E15-3 hml∆ E15-4 clone E15-4 hml∆ E6-1 hbn1∆ E6-1 ids2∆ E6-1 pet127∆ E6-1 scw11∆ E6-1 sir4∆ E6-1 vps5∆ E6-1 whi2∆ E6-1 yjl070c∆ E6-6 E6-7 E6-8 E6-9 E6-10 E6-11 E6-12 E6-13 E6-14 E6-15 E6-16 E15-5 E15-6 E15-7 E15-8 E15-9 yGW E15/2A1 yGW E15/2B6 yGW E15/2C7 yGW E15/2D8 yGW E15/2E3 yGW E15/2F6 Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations Ancestor genotype: evolved 360 generations E15-10 E15-11 E15-12 E15-13 E15-14 E15-15