Table 1.
Mutations and Fitness of Evolved Hybrid Clones.
| Clone | Location | Gene(s) | Mutation | Species | Generations | Relative Fitness ± SE (condition) |
|---|---|---|---|---|---|---|
| Gh1 | chrXIII: 852028 | Intergenic | cer | 125 | 26.80 ± 0.98 (G); 0.35 ± 1.60 (S); −1.18 (P) | |
| chrII: 911866..917272 | HXT6/7 | CNV (amplification) | uva | |||
| Gh2 | chrIV: 111919 | SNF3 | Nonsynonymous: D114Y | cer | 100 | 28.17 ± 2.18 (G); 10.48 ± 0.78 (S); 11.23 (P) |
| chrIII: 51593 | GLK1 | Synonymous: T252T | cer | |||
| chrIV: 884801..912119 | 13 genes including IRC3 | LOH, CNV | uva lost | |||
| chrII: 912143..917470 | HXT6/7 | CNV (amplification) | uva | |||
| chrIV | 836 genes | CNV (amplification) | cer | |||
| Gh3 | chrII: 889421 | IRC3 | nonsynonymous: M333I | uva | 124 | 18.65 ± 0.47 (G); 17.68 ± 3.67 (S); −10.46 (P) |
| chrII: 912416..917778 | HXT6/7 | CNV (amplification) | uva | |||
| Ph1 | chrV: 269392 | Intergenic | cer | 103 | 29.18 ± 1.37 (P); −1.68 ± 0.78 (G); 0.08 ± 0.43 (S) | |
| chrXIV: 746688 | Intergenic | cer | ||||
| chrIV: 1055864 | MHR1 | Nonsynonymous: T218R | cer | |||
| chrIX | 241 genes | LOH, CNV | uva lost, cer amp | |||
| Ph2 | chrV: 432778 | GLC7 | Intron | cer | 124 | 25.34 ± 0.24 (P); 15.12 ± 4.66 (G); −2.45 ± 1.16 (S) |
| chrVII: 9524 | PDR11 | Nonsynonymous: L383* | uva | |||
| chrXVI: 232879 | MRPL40 | Nonsynonymous: V149E | uva | |||
| chrXIII: 194496 | YML037C | Nonsynonymous: P306S | uva | |||
| chrIV: 244399 | YDL114W | Nonsynonymous: G119C | uva | |||
| chr IV | 836 genes | CNV (amplification) | cer | |||
| Ph3 | chrIV: 1055864 | MHR1 | Nonsynonymous: T218R | cer | 167 | 30.03 ± 4.31 (P); 21.39 ± 6.25 (G); NA (S) |
| chrIX: 30830..33084 | YIL166C | CNV (amplification) | cer | |||
| chrXIII: 0..24562 | 10 genes including PHO84 | LOH, CNV | uva lost, cer amp | |||
| chrIV | 836 genes | CNV (amplification) | cer | |||
| Ph4 | chrVII: 555885 | RPL26B | Intron | cer | 131 | 27.02 ± 3.62 (P); 0.68 ± 4.10 (G); 20.46 ± 8.60 (S) |
| chrX: 246208 | PHS1 | Nonsynonymous: K206N | cer | |||
| chrXIII: 324121 | EIS1 | Nonsynonymous: E349* | uva | |||
| chrIII:0..82687 | 49 genes | LOH, CNV | cer lost | |||
| chrXIII:0..221753 | 112 genes, including PHO84 | LOH, CNV | uva lost, cer amp | |||
| Ph5 | chrXIII: 231731 | PPZ1 | Nonsynonymous: A63S | uva | 122 | 30.24 ± 8.32 (P); −8.20 ± 0.34 (G); 18.20 ± 2.91 (S) |
| chrXIII: 0..234112 | 120 genes, including PHO84 | LOH, CNV | uva lost, cer amp | |||
| chrIX:370117..439888 | 45 genes | LOH, CNV | cer lost | |||
| Ph6 | chrVII: 972813 | PFK1 | Nonsynonymous: G308S | cer | 111 | 25.52 ± 3.32 (P); 5.22 ± 2.81 (G); NA (S) |
| chrIV | 836 genes | CNV (amplification) | cer | |||
| Sh1 | chrII:511362..644974; 696397.. 813184 | 74 genes; 63 genes including SUL1 | LOH,CNV | cer lost; cer amp | 126 | 33.86 ± 4.60 (S); 3.81 ± 1.17 (G); −15.48 ± 8.55 (P) |
| chIV: 680386.. 866667; 866667.. 983774 | 104 genes; 63 genes | LOH, CNV | uva amp; uva lost | |||
| chrXVI: 847000.. 948066 | 49 genes | LOH, CNV | cer lost | |||
| Sh2 | chrVII: 936384 | MRPL9 | Nonsynonymous: D167G | cer | 268 | 19.64 ± 4.30 (S); −6.19 ± 1.21 (G); −1.43 ± 6.37 (P) |
| chrXVI: 572308 | ICL2 | Nonsynonymous: M247I | uva | |||
| chrVIII: 116661 | ERG11 | Nonsynonymous: S286C | uva | |||
| chrII:787389..813,184 | 11 genes including SUL1 | CNV (amplification) | cer | |||
| Sh3 | chrVI: 162998 | GCN20 | Nonsynonymous: D171Y | cer | 132 | 21.84 ± 1.53 (S); −6.07 ± 1.11 (G); 5.55 ± 4.81 (P) |
| chrXIV: 495890 | FKH2 | Synonymous: S418S | uva | |||
| chrII:786584..813,184 | 11 genes including SUL1 | CNV (amplification) | cer | |||
| Sh4 | chrXIV: 666675 | ARE2 | Nonsynonymous: I446T | cer | 285 | 27.19 ± 4.33 (S); −6.17 ± 0.51 (G); −20.55 ± 3.30 (P) |
| chrXV: 800832 | APC5 | 5’-upstream | cer | |||
| chrIV: 25917 | TRM3 | Synonymous: S201S | cer | |||
| chrV: 342563 | Intergenic | uva | ||||
| chrX: 769768 | SPO77 | Nonsynonymous: D418G | uva | |||
| chrX: 990873 | LEU3 | 5’-upstream | uva | |||
| chrXII: 192491 | Intergenic | uva | ||||
| chrXIV: 25138 | EGT2 | Synonymous: T168T | uva | |||
| chrII: 770311..813184 | 22 genes, including SUL1 | CNV (amplification) | cer | |||
| chrVIII | 321 genes | CNV (amplification) | uva | |||
| Sh5 | chrIV: 310881 | RXT3 | Nonsynonymous: P87T | uva | 263 | 46.52 ± 4.94 (S); 6.79 ± 1.35 (G); 3.72 ± 7.23 (P) |
| chrVIII: 16911 | Intergenic | uva | ||||
| chrII: 786040..813184 | 11 genes including SUL1 | CNV (amplification) | cer | |||
| Sh6 | chrV: 269392 | Intergenic | cer | 273 | 47.52 ± 3.69 (S); 2.60 ± 1.25 (G); 4.47 ± 6.04 (P) | |
| chrXIV: 746688 | Intergenic | cer | ||||
| chrIV: 413046 | Intergenic | uva | ||||
| chrII:778942..813,184 | 14 genes including SUL1 | CNV (amplification) | cer | |||
| Sh7 | chrII: 238875 | Intergenic | cer | 129 | 31.44 ± 0.49 (S); −1.87 ± 1.99 (G); 8.74 ± 9.22 (P) | |
| chrXVI: 490631 | SVL3 | Nonsynonymous: A245V | cer | |||
| chrXVI: 86106 | YPL245W | Nonsynonymous: A174D | cer | |||
| chrII: 273296 | Intergenic | uva | ||||
| chrII:737875..813184 | 42 genes, including SUL1 | CNV (amplification) | cer |
Point mutations, copy number variants (CNVs), and loss of heterozygosity events (LOH) are recorded for each evolved hybrid clone. Clones are identified by nutrient (G: glucose limitation, P: phosphate limitation, and S: sulfate limitation), an “h” denotes hybrid, and the number indicates its derivation from independent populations. Genes in underline have been found to have point mutations in prior experiments. Note that mutations in the S. uvarum genome use S. uvarum chromosomes and coordinates. All break points were called by visual inspection of sequencing reads and are thus approximate. Relative fitness is reported with standard error (SE) and the condition the clone was evolved in listed first, followed by the two alternative conditions; several clones are reported without SE due to technical difficulties with replicates.