Supplemental Table 1: Strain list
Strain
Identifier
(see Tables
1, 2)
Genotype
Species
Notes
Strain background
YMD139
lys2Δ0/+ +/ura3-167 MATa/MATα
cer
GRF167 x S288C
YMD140
lys2Δ0/+ +/ura3-167 MATa/MATα
cer
YMD129
HOΔ::kanMX/HOΔ::kanMX lys21/+ +/ura3-167 MATa/MATα
HOΔ::kanMX/HOΔ::kanMX lys21/+ +/ura3-167 (high Ty)
MATa/MATα
HOΔ::kanMX /HOΔ::kanMX lys21/+ ura3Δ::cloNAT/+
MATa/MATα
hybrid
Ancestor of S. cerevisiae
evolved diploids (high
Ty)
Ancestor of S. cerevisiae
evolved diploids
Ancestor of evolved
hybrids
Ancestor of evolved
hybrids (high Ty)
uva
Ancestor of S. uvarum
evolved diploids
CBS7001
uva
uva
cer
cer
cer
cer
hybrid
hybrid
hybrid
hybrid
hybrid
hybrid
uva
uva
cer
cer
hybrid
hybrid
hybrid
uva
uva
cer
cer
cer
cer
hybrid
hybrid
hybrid
hybrid
hybrid
hybrid
hybrid
cer
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Phosphate limitation
Glucose limitation
Glucose limitation
Glucose limitation
Glucose limitation
Glucose limitation
Glucose limitation
Glucose limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
Sulfate limitation
2 preferred S. cerevisiae
alleles at PHO84
2 un-preferred S.
cerevisiae alleles at
PHO84
CBS7001
CBS7001
GRF167 x S288C
GRF167 x S288C
GRF167 x S288C
GRF167 x S288C
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
CBS7001
CBS7001
GRF167 x S288C
GRF167 x S288C
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
CBS7001
CBS7001
GRF167 x S288C
GRF167 x S288C
GRF167 x S288C
GRF167 x S288C
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
GRF167 x CBS7001
YMD130
YMD366
YMD35
YMD92
YMD18
YMD77
YMD66
YMD98
YMD30
YMD39
YMD90
YMD101
YMD741
YMD744
YMD723
YMD725
YMD34
YMD23
YMD726
YMD737
YMD739
YMD720
YMD721
YMD31
YMD83
YMD105
YMD21
YMD751
YMD752
YMD754
YMD747
YMD749
YMD858
YMD861
CSH98
CSH100
CSH119
Pu1
Pu2
Pc3
Pc1
Pc4
Pc2
Ph1
Ph2
Ph3
Ph5
Ph4
Ph6
Gu1
Gu2
Gc2
Gc1
Gh1
Gh2
Gh3
Su1
Su2
Sc3
Sc2
Sc1
Sc4
Sh2
Sh3
Sh4
Sh1
Sh7
Sh5
Sh6
ura3-167/+ MATa/MATα
PHO84Δ::ScPHO84(un-preferred
allele)/PHO84Δ::ScPHO84(unpreferred allele) ura3-167/+
MATa/MATα
PHO84Δ::ScPHO84(un-preferred
hybrid
cer
cer
1 preferred, 1 un-
GRF167 x S288C
GRF167 x CBS7001
GRF167 x CBS7001
CSH123
CSH125
CSH93
CSH59
YMD129
CSH126
CSH130
CSH94
CSH81
CSH108
YMD1459
allele)/PHO84Δ::ScPHO84(unpreferred allele) ura3-167/+
MATa/MATα
ura3-167/ura3-167 +pIL37-PHO84URA3
ura3-167/ura3-167 +pIL37-URA3
preferred S. cerevisiae
allele at PHO84
cer
cer
ura3-167/+ +/ lys2-1
ScPHO84Δ::SuPHO84/+
ura3-167/+ +/lys2-1
+/SuPHO84Δ::ScPHO84(unpreferred allele)
HOΔ::kanMX/HOΔ::kanMX lys21/+ +/ura3-167 MATa/MATα
hybrid
HOΔ::HYGb/HOΔ::kanMX lys21/+ ura3Δ::cloNAT/ura3-167
PHO84∆::kanMX/+
+pIL37-PHO84-URA3
HOΔ::kanMX/HOΔ::kanMX lys21/+ +/ura3-167 MATa/MATα
+pIL37-PHO84-URA3
HOΔ::kanMX/HOΔ::kanMX lys21/+ +/ura3-167 MATa/MATα
+pIL37-URA3
HO∆::natMX-GFP/+ lys2-1/+
+/ura3-167 MATa/MATα
HO∆::natMX-GFP/+ lys2-1/+
+/ura3-167 MATa/MATα (high Ty)
HO∆::natMX-GFP/ HOΔ::kanMX
ura3Δ::cloNAT/+ lys2-1/+
MATa/MATα
HO∆::kanMX-GFP/+ MATa/MATα
hybrid
hybrid
hybrid
hybrid
hybrid
hybrid
hybrid
uva
cer
3+ preferred S. cerevisiae
alleles at PHO84
2 preferred S. cerevisiae
alleles at PHO84 +
empty plasmid
2 S. uvarum alleles at
PHO84
1 preferred, 1 unpreferred S. cerevisiae
allele at PHO84
1 preferred S. cerevisiae,
1 S. uvarum allele at
PHO84
2+ preferred S. cerevisiae
alleles at PHO84
2+ preferred S.
cerevisiae, 1 S. uvarum
alleles at PHO84
1 preferred S. cerevisiae,
1 S. uvarum allele at
PHO84 + empty plasmid
GFP competitor strain
for hybrids
GFP competitor strain
for hybrids (high Ty)
GFP competitor strain
for S. uvarum
GFP competitor strain
for S. cerevisiae
Clones are identified by nutrient (G: glucose-limitation, P: phosphate-limitation, and S: sulfate-limitation), by species (“h” denotes a
hybrid, “c” denotes S. cerevisiae, “u” denotes S. uvarum), and the number indicates its derivation from independent populations.
The strain number in the Dunham lab strain database is listed for each.
Supplemental Table 2: Sequencing coverage
Strain
YMD140
YMD130
YMD366
YMD35
YMD92
YMD18
YMD77
YMD66
YMD98
YMD30
YMD39
YMD90
YMD101
YMD741
YMD744
YMD723
YMD725
YMD34
YMD23
YMD726
YMD737
YMD739
YMD720
YMD721
YMD31
YMD83
YMD105
YMD21
YMD751
YMD752
YMD754
YMD747
YMD749
YMD858
YMD861
Clone (see
Table 1, 2)
Pu1
Pu2
Pc3
Pc1
Pc4
Pc2
Ph1
Ph2
Ph3
Ph5
Ph4
Ph6
Gu1
Gu2
Gc2
Gc1
Gh1
Gh2
Gh3
Su1
Su2
Sc3
Sc2
Sc1
Sc4
Sh2
Sh3
Sh4
Sh1
Sh7
Sh5
Sh6
Average
Coverage
174.1
65.5/107.9
176.7
288.3
60.2
389.8
82.0
57.1
100.5
32.4/28.15
39.9/34.1
38.4/32.4
19.13/17.8
63.2/57.5
37.4/69.4
94.3
80.5
72.2
104.0
25.6/47.8
35.4/30.9
21.2
43.6
74.3
77.4
90.9
81.6
133.7
59.8
31.7/29.4
33.7/33.0
100.1
27.6
33.5/34.9
39.2/35.1
Mean sequencing coverage is reported from GATK DepthOfCoverage for each evolved clone and ancestor. For hybrids, sequencing
depth was sometimes calculated separately for each genome, and follows the format “cer/uva”.
Supplemental Table 3: Primers used
Primer name
ScPHO84_URA3homF
SCER_chr13_23602_PHO84F
Primer sequence
CGGAGACAATCATATGGGAGAAGCAATTGGAAGATAGAAAAAAGGTACTCGGTACATAAA
GTAACCTGACAGTATTTATA
TGGAGGAAGTTTGAGAGGGCTTATCGCAATGGTTGTAATGGTTTAAAACTCTTTTTCGAT
CCATATTATTATGAAAAGAC
TGTCCCACAGGTGCCATTGGTTG
SCER_chr13_24217_PHO84R
CGCCTTATTCATGTTGTTGGGTATCTTCAC
Purpose
Replace S. cerevisiae PHO84 with K.
lactis URA3
Replace S. cerevisiae PHO84 with K.
lactis URA3
Confirm loss of S. cerevisiae PHO84,
gain of URA3
Confirm loss of S. cerevisiae PHO84
SCER_URA3gain_5primeR
GGCCCAATCACAACCACATCTTAGATAGTTG
Confirm gain of K. lactis URA3
SCER_chr13_26112_PHO84F
GCCTTTCACACGACATTTGGTGCATAAC
Confirm loss of S. cerevisiae PHO84
SCER_chr13_26652_PHO84R
GACTTCAAACGACTCGGTATACTCTGCC
SCER_URA3gain_3primeF
GAAATGCTGGATGGGAAGCGTACC
Confirm loss of S. cerevisiae PHO84,
gain of URA3
Confirm gain of K. lactis URA3
SCER_PHO84amp_chr13_23928F
GTAACCTGACAGTATTTATAGATTATGTAAGGGGTTT
SCER_PHO84amp_chr13_26478R
CCATATTATTATGAAAAGACACAACCGGAAGGGG
SUVA_PHO84amp_SCERhomF
SUVA_lossPHO84_5primeF
ACAGGATGGCAGAGAGATGTGAGGAAATAATGAAATTAAAAGAAATTATCGAATAAATAT
GTATAATAAATATGTAGCCT
GAAACTAATTTATCAGCCGCTCGTTTATCAACCGTTATACCAAATTATGAATAAAAAAA
CTATAGAGCAGAATAATAGA
CGCAATCAAACATACCGTTGATACTGATGAC
Amplify the S. cerevisiae PHO84
allele
Amplify the S. cerevisiae PHO84
allele
Replace S. cerevisiae PHO84 with S.
uvarum PHO84
Replace S. cerevisiae PHO84 with S.
uvarum PHO84
Confirm loss of S. uvarum PHO84
SUVA_new_lossPHO84_5primeR
GAACGATGTCGAATCTTCTTCTCCATCTC
Confirm loss of S. uvarum PHO84
SUVA_new_lossPHO84_3primeF
CGTGGGCTATAACGACGCTACTG
Confirm loss of S. uvarum PHO84
SUVA_lossPHO84_3primeR
ATCACCAATCACGTGATCTAGTTTACCC
Confirm loss of S. uvarum PHO84
SUVA_PHO84ampF
GTATAATAAATATGTAGCCTGACAGTATTTATAGATTATGTACGT
Amplify the S. uvarum PHO84 allele
SUVA_PHO84ampR
CTATAGAGCAGAATAATAGACACAACCGGCG
Amplify the S. uvarum PHO84 allele
Suva_PHO84_KANMX_F
AGTTTCTCATTGAAACTTTTTTGAAATTGATTCAGTAAGC CGACATGGAGGCCCAGAATA
Suva_PHO84_KANMX_R
CAGTAAGCCACAACAAACAAACAACAAGAATACATCAAAG CAGTATAGCGACCAGCATTC
pIL37_cerPHO84F
GCCCGGGGGATCTCGTAACCTGACAGTATTTATAGATTATG
pIL37_cerPHO84R
GAACTAGTGGATCTCGCCATATTATTATGAAAAGACACAAC
IL429
IL430
30_chrIV_1055864F
GTGAGCGCGCGTAATACGACTC
CACACAGGAAACAGCTATGACCATG
CAAGAGGCAGTGGCAGACTTGC
Replace S. uvarum PHO84 with
kanMX
Replace S. uvarum PHO84 with
kanMX
Cloning S. cerevisiae PHO84 into
pIL37 plasmid
Cloning S. cerevisiae PHO84 into
pIL37 plasmid
Confirm insertion in pIL37 plasmid
Confirm insertion in pIL37 plasmid
Confirm SNP in evolved hybrid
ScPHO84_URA3homR
SUVA_PHO84amp_SCERhomR
30_chrIV_1055864R
39_chrV_432778F
39_chrV_432778R
741_chrVII_555885F
741_chrVII_555885F
741_chrX_246208F
741_chrX_246208R
744_chrVII_972813F
744_chrVII_972813R
726_chrXIII_852028F
726_chrXIII_852028R
737_chrIV_111919F
737_chrIV_111919R
737_chrIII_51593F
737_chrIII_51593R
749_chrII_238875F
749_chrII_238875R
749_chrXVI_490631F
749_chrXVI_490631R
749_chrXVI_86106F
749_chrXVI_86106R
751_chrVII_936384F
751_chrVII_936384R
752_chrVI_162998F
752_chrVI_162998R
754_chrXIV_666675F
754_chrXIV_666675R
754_chrXV_800832F
754_chrXV_800832R
754_chrIV_259517F
754_chrIV_259517R
861_chrV_269392F
861_chrV_269392R
861_chrXIV_746688F
861_chrXIV_746688R
39_uva_chrVII_9524F
39_uva_chrVII_9524R
39_uva_chrXVI_232879F
39_uva_chrXVI_232879R
39_uva_chrXIII_194496F
39_uva_chrXIII_194496R
CCGTGGAACGGGATTTGGCAG
GGACTCACAACCAGTTGACGTTG
CGGCTATCTCGACATATGAGTAGGC
GGATGGGTTGTCAGTAGACGGTG
GTCGCCCTATGCCTGGATTG
GTTGGTATTCAAGAATGGCGCACC
GACTCCGAGTGAGCTTCGACATC
GCGGTGGCATCAATGTAGTCAACC
GATTCTCCAGGTATGAATGCCGCTG
CGGGTAACGAAGAATCGACTCTCGC
GCGGAATAACCTAACACGTGGAGG
GATACGACAGGTAGCATACGAACCCC
GTGATTCCTCCAGCACCTACCTG
GGATGTCGTGCAATTGTACCAGGAG
GCTTGAGCTCATTATCGAAGGACCC
GCAAGAAGATCTGGCAAGCTACAAGG
CGTCGCTACAGAAGGCTTTGGTTG
CCAATGCAGGTGGCTTATTGGTTG
GGCGAAAGTAAGTCCAGCACTGAG
CTGGTAGTCAACCATCCCGAGATG
GGGCAGCAACCCTAAACTGCTG
CATGCTCGTTTCCCATATGACCAGG
GCATAGAACTTCGGAGGTCAATGGG
GGAATTGACCGGTGATACGTCCAAG
GCCCACAAGACCATATCTGTGACC
GAATTGAGCTCTCAGTCTTTAAGCGACC
CTGGGACGATATCAACGAGCAATCC
CTGCTGTTGGCACTGATATGCC
CCCAGCAAGGCGATGATTCTAACTTC
CCTTAGCCTGCTTCACTACTTAGAAGTTG
CCAGCTCTGTTTGAATGTGCCTCC
TACGTCGTCTACAGTTGGACAGGC
GTGGTTCCAGATGTGCCAACTGTG
AACTGGTCTTTGGCAAATGGCTCC
CAGACACAGTTTTTCAGCGATGCCC
GGCGCCTAATGTGGAAGAAGATGAC
GTCTTGTATGCTGGTAGGCAGGTG
CTAAGACCGTTCCCGTTCCTAAGC
GCCACCAGTTTAGCTATATCTTTCGCTG
GATTCACCACGCCTAAGCTCTTGAG
GTTGTCAAGGAATTGCCAAAGCC
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
39_uva_chrIV_244399F
39_uva_chrIV_244399R
101_uva_chrXIII_231731F
101_uva_chrXIII_231731R
741_uva_chrXIII_324121F
741_uva_chrXIII_324121R
749_uva_chrII_273296F
749_uva_chrII_273296R
752_uva_chrXIV_495890F
752_uva_chrXIV_495890R
754_uva_chrV_342563F
754_uva_chrV_342563R
754_uva_chrX_769768F
754_uva_chrX_769768R
754_uva_chrX_990873F
754_uva_chrX_990873R
754_uva_chrXII_192491F
754_uva_chrXII_192491R
754_uva_chrXIV_19697F
754_uva_chrXIV_19697R
858_uva_chrIV_310881F
858_uva_chrIV_310881R
858_uva_chrVIII_16911F
858_uva_chrVIII_16911R
861_uva_chrIV_413046F
861_uva_chrIV_413046R
739_uva_chrII_889421F
739_uva_chrII_889421R
GAACCGACCTAGCTTCAACCCTTC
ATACGATGTCAGCCTCGCAGGAG
GGATCATCGAAGGCGGTAGATCG
CACAAACCCTCCTGCACACCTTTC
GTCCATAGCACGCTGTGCTTCTG
GAGCATGGTAGACTGAACCAGTTCAG
GTGGCTTGTCCATGAGATGCAACAG
CCACTCCGTGAGACCCAATCTTC
GTGACGGTACATGTGGTACGAACC
CGCGACTATGATTACACAGGCCATAC
GCCAATTCGGTACTTCCTTCTGAGC
GAATCGAGTGCCTAGCGAGAGC
CTGTCCTGGAGACTTTCAGATTCGG
GCTGTCTTCGCCTTCGTCTGTAC
CACCATGACTGTCGCTATGTCAAACG
CACATTTGGTACATGGTTCTGGTGCTC
AAAGCAGTACTCGACATGCGGC
CTGACAGGGATGCTGGTGACAAG
CGGGTCGTTCCCTCAAGAGTC
GGGACAGATTTGACAGGTTCATTGAAGG
CAACAGGGGAAGGTTGCCTATGAC
CAATGTCGGTAAGTGAACAGGACCC
GCCTCCTTCATAGCCCTGCTTTC
CCCGAATCCACCCTCTTACCATAC
GTTAGACCGATCCAGCAGGAGC
GAACCTATTCCTAAGCAGGGTCCG
GAAGGTCGAGGCAGATCTATCCACC
GCGTAGGTGCAGAAACCACCC
Primers used for allele replacements and SNP confirmation in evolved hybrid clones.
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
Confirm SNP in evolved hybrid
A
Supplementary Figure 1
Gc2
copy number
Gc1
B
Pc2
copy number
Pc1
copy number
Pc3
Genomic Position (bp)
Pc4
C
Sc2
Sc3
Sc4
copy number
copy number
Sc1
Genomic Position (bp)
Supplementary Figure 2
Gu1
Gu2
Pu1
Pu2
Su1
Su2
copy number
A
copy number
B
copy number
C
Genomic Position (bp)
Supplementary Figure 3
Copy number
A
B
Genomic position
Copy number
C
Genomic position
Copy number
Genomic position
Copy number
Genomic position
Supplementary Figure 4
A
B
C