Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments
- Department of Biology, Stanford University, United States
- Department of Organismic and Evolutionary Biology, Harvard University, United States
- Quantitative Biology Initiative, Harvard University, United States
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, United States
- Department of Genetics, Stanford University, United States
- Department of Physics, Stanford University, United States
- Department of Physics, Harvard University, United States
Figures
Figure 1 with 1 supplement
DNA double-barcoding strategy enables massively parallel bulk ‘common garden’ fitness remeasurements across many environments.
For both ploidies (1N and 2N) 12 pools of singly barcoded yeast were generated. A second, high complexity barcode was then introduced into each pool, creating 24 (12 haploid and 12 diploid) pools of …
Figure 1—figure supplement 1
Double barcoding system.
A Gal-Cre-NatMX cassette was homologously recombined into the YBF209W dubious open reading frame region in an S288C derivative, BY4709. The NatMX marker was replaced with a DNA fragment containing a …
Figure 2 with 1 supplement
Lineage tracking data for evolutions in clotrimazole, fluconazole, and glycerol/ethanol.
The lines correspond to 10,000 barcoded lineages (the 5000 lineages with highest abundance, and 5000 additional randomly chosen lineages). The intensity of the color of the line indicates the …
Figure 2—figure supplement 1
Lineage tracking for all evolutions.
(A) Lineage tracking data for each haploid experimental evolution. The lines correspond to barcoded lineages. Each row represents the home environment in which the evolution was conducted. Each …
Figure 3
Haploid and diploid mutational spectra.
For each focal condition, the mutations are grouped by the ploidy they were identified in: blue (haploids), yellow (diploids). The genes listed in the overlap region are genes that had acquired …
Figure 4 with 1 supplement
Heatmaps representing pleiotropic profiles of adaptive mutant lineages from populations evolved in fluconazole.
Each heatmap shows the lineages evolved in a particular condition and their fitness remeasurements in a specific bulk fitness assay. Each square on the heatmap shows the average fitness of the …
Figure 4—figure supplement 1
Heatmaps representing pleiotropic profiles of adaptive mutant lineages from populations evolved in clotrimazole.
Each heatmap shows the lineages evolved in a particular condition and their fitness remeasurements in a specific bulk fitness assay. Each square on the heatmap shows the average fitness of the …
Appendix 1—figure 1
Relative mutation rates of each of the six possible nucleotide changes for each condition and ploidy tested.
Appendix 1—figure 2
Lineage Tracking Data for Fitness Remeasurement Assays.
(A) Lineage tracking data of haploid bulk fitness assay (hBFA) for lineages evolved in fluconazole, clotrimazole, and glycerol/ethanol. Each column represents a replicate. The columns are grouped …
Appendix 1—figure 3
Comparison of replicates for each bulk fitness assay (BFA).
Each panel corresponds to a BFA and two replicates within that assay. Each row corresponds to a test environment. We plot the fitness of a lineage in one replicate against its fitness in another …
Appendix 1—figure 4
Heatmaps for all adaptive lineages with shared mutations.
These heatmaps show the fitnesses of all lineages including lineages that had the same mutation and were collapsed into a single row using the median fitnesses in Figure 4. The number at the end of …
Appendix 1—figure 5
Home environment compared to test environments for all adaptive lineages.
The columns are the home environments that lineages evolved in and the rows are the test environments in which their fitnesses were remeasured. X axis is the fitness of the lineages remeasured in …
Appendix 1—figure 6
Net effect of mutant haploid lineages evolved in glycerol/ethanol.
(A) Fitness measurements, s, of haploid lineages adapted to glycerol/ethanol. The colored lines represent lineages that have a mutation identified to be adaptive. The colors represent which gene the …
Appendix 1—figure 7
Distribution of fitness effects for fitness estimates of all adaptive diploid lineages remeasured in clotrimazole, fluconazole, and glycerol/ethanol.
The distribution of fitness effects for all adaptive diploid lineages remeasured in clotrimazole, fluconazole, and glycerol/ethanol. The gray vertical line delineates the fitness threshold of the …
Appendix 1—figure 8
Mutations in the same gene tend to lead to more similar pleiotropic profiles than in different genes for the same evolution condition.
(A) Correletions aggregated across all conditions. (B) Correlations by condition and ploidy. The fitnesses of lineages with candidate adaptive mutations in the same gene that arose in the same …
Appendix 1—figure 9
Heatmaps representing pleiotropic profiles of adaptive mutant lineages from populations evolved in glycerol/ethanol.
Each heatmap shows the lineages evolved in a particular condition and their fitness remeasurements in a specific bulk fitness assay. Each square on the heatmap shows the average fitness of the …
Appendix 1—figure 10
The mean frequency of putatively neutral barcodes with different minimum GC-contents.
The y axis represents the log10 of the mean frequency of the putatively neutral barcodes with different minimum GC-contents of a 26 bp sliding window measured across the barcode region. The ordering …
Tables
Table 1
Environmental conditions used in this study.
Evolution conditions used in this study, after how many generations clones were isolated, whether adaptive mutations were identified, and abbreviations used.
| Environment | Description | Evolution condition | Putative adaptation observed | Lineage tracking data available for evolution conditions | Fitness measurements available for bulk fitness assay pools | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Haploids | Diploids | Haploids | Diploids | Haploids | Diploids | hBFA | dBFA | cBFA | ||
| SC | Defined rich medium | ✓ | ✓ | X | X | X | ✓ | ✓ | ✓ | ✓ |
| CLM | Antifungal drug, 2 mg/L clotrimazole | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | X | ✓ | ✓ |
| FLC4 | Antifungal drug, 4 mg/L fluconazole | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| GlyEtOH | Nonfermentable carbon source and diluted every 48 hr, 2% glycerol + 2% ethanol | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| 0.2 M NaCl | Low salt concentration | ✓ | ✓ | X | X | ✓ | ✓ | X | ✓ | ✓ |
| 0.8 M NaCl | High salt concentration | ✓ | ✓ | X | X | ✓ | ✓ | X | X | X |
| 21°C | Low temperature | ✓ | ✓ | X | X | ✓ | ✓ | ✓ | ✓ | ✓ |
| 37°C | High temperature | ✓ | ✓ | X | X | X | ✓ | ✓ | ✓ | ✓ |
| pH 3.8 | Defined rich media buffered to pH 3.8 | ✓ | ✓ | X | X | X | ✓ | ✓ | ✓ | ✓ |
| pH 7.3 | Defined rich media buffered to pH 7.3 | ✓ | ✓ | X | X | X | ✓ | ✓ | ✓ | ✓ |
| 48 hr | Defined rich media, diluted every 48 hr | ✓ | ✓ | X | X | X | ✓ | X | X | X |
| YPD | Undefined rich medium, YP + 2% glucose | ✓ | ✓ | X | X | X | ✓ | ✓ | ✓ | ✓ |
Table 2
Summary of adaptive mutations.
Mutations are grouped by the home environment and the ploidy of the population in which they arose. The mutations are tabulated by gene. Genes are listed multiple times because mutations arose in …
| Home environment | Ploidy | Gene | Total mutations | Missense | Nonsense | Coding In/Del | Non-coding | List of unique mutations/amino acid change |
|---|---|---|---|---|---|---|---|---|
| CLM | 2N | PDR1 | 15 | 15 | 0 | 0 | 0 | +/E768G; F1047V; +/C862Y; +/T817K; +/K540E; +/G282V; +/E829K; +/N733Y; +/T1043K; +/F769L; +/Y864H; +/Q762K; +/L278V; +/A826E; +/R821G |
| PDR3 | 5 | 5 | 0 | 0 | 0 | +/S773I; +/L281F; +/G957D; +/L279S; +/K272N | ||
| CLM | 1N | PDR1 | 29 | 28 | 0 | 1 | 0 | N1050D; P261L; P261S; L868F; V871F; H751N; H751Q; S753SVYRSFAHYS; C862W; H723N; Y270S; K540Q; R959M; E688D; N1049H; A301S; Y864H; T358R; S814Y; F607L; R747P; L867F; L714R; G875A; E491D; F511V; A863G; S259G; V819I |
| PDR3 | 7 | 7 | 0 | 0 | 0 | R794S; C707F; F710L; L249V; L959Q; Y963H; A681E | ||
| FLC4 | 2N | CYC8 | 2 | 1 | 1 | 0 | 0 | +/Q610*; +/L370P |
| HAP1 | 1 | 1 | 0 | 0 | 0 | +/V638F | ||
| PDR1 | 1 | 1 | 0 | 0 | 0 | +/H689N | ||
| SSO2 | 2 | 1 | 0 | 0 | 1 | +/627963T>A; +/D233G | ||
| TUP1 | 3 | 1 | 0 | 1 | 1 | +/I416_fs; +/I704N; +/262515A>T | ||
| VPS35 | 2 | 1 | 0 | 0 | 1 | +/131054G>GT; +/S64T | ||
| YHK8 | 2 | 1 | 0 | 0 | 1 | +/N337T; +/203404T>C | ||
| FLC4 | 1N | CSG2 | 3 | 3 | 0 | 0 | 0 | S26F; E234D; G258C |
| CYC8 | 4 | 3 | 0 | 1 | 0 | G265C; NA729_fs; A384T; Y268D | ||
| HAP1 | 2 | 0 | 0 | 1 | 1 | 646403A>C; V1471ETHKFNCSNKRSEIDQTSSN | ||
| PDR1 | 2 | 2 | 0 | 0 | 0 | S832N; E675K | ||
| PDR3 | 2 | 2 | 0 | 0 | 0 | L249I; R210M | ||
| PDR5 | 4 | 4 | 0 | 0 | 0 | P943T; E169K; L790I; T912S | ||
| ROX1 | 3 | 1 | 2 | 0 | 0 | Q107*; K72T; M1T | ||
| SKN7 | 4 | 2 | 1 | 1 | 0 | D446E_fs; D446E; S486*; S411P | ||
| SUR1 | 11 | 4 | 6 | 1 | 0 | Y116_fs; Y116N; Y235C; E263*; Y104*; D141E; M1V; R218*; Y116*; H176Y; R360_fs | ||
| SXM1 | 3 | 0 | 1 | 2 | 0 | SS58_fs; E701*_fs; G259_fs | ||
| TUP1 | 1 | 1 | D699Y | |||||
| UPC2 | 3 | 3 | 0 | 0 | 0 | V419F; L876R; L876P | ||
| GlyEtOH | 2N | HAP1 | 3 | 2 | 0 | 1 | 0 | K1474E, V1485I/K1474E,V1485I; +/IYVTSI1483I |
| HEM2 | 2 | 1 | 1 | 0 | 0 | +/L338*; +/A248E | ||
| HEM3 | 7 | 5 | 1 | 1 | 0 | +/S20P; +/G10E; +/G130G_fs; +/C111F; +/Y261*; +/G157E; +/G211C | ||
| IRA1 | 1 | 1 | 0 | 0 | 0 | +/N66I | ||
| IRA2 | 1 | 1 | 0 | 0 | 0 | +/I1657N | ||
| NDI1 | 2 | 2 | 0 | 0 | 0 | +/I298S; +/R205G | ||
| WHI2 | 4 | 1 | 1 | 1 | 1 | +/S289P; +/G141*; +/410637A>T; +/VLREDLDYYC165_fs | ||
| GlyEtOH | 1N | GPB2 | 2 | 0 | 2 | 0 | 0 | Q602*; R509* |
| IRA1 | 19 | 3 | 9 | 7 | 0 | D1116_fs; L1429*; ILV1729I; P1827L; K2034_fs; Y2354*; L1549F_fs; E2440*; S1612*; G780_fs; G780*; S2966*; W2779L_fs; C2067*; I1862S; LLMRYLL2976_fs; Y1239*; L587*; G1716_fs | ||
| IRA2 | 9 | 4 | 3 | 2 | 0 | G2097*; I339R; E3063*; L598W; F2628S; R1852L; I1463_fs; E2558*; R2195_fs | ||
| SSK2 | 2 | 1 | 0 | 1 | 0 | G1275D; L968_fs | ||
| WHI2 | 1 | 0 | 0 | 0 | 1 | 410536G>A | ||
| YTA6 | 2 | 1 | 0 | 0 | 1 | K517R; 418169T>G |
Additional files
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Supplementary file 1
Table of isolation timepoints and bulk fitness assay (BFA) composition: The information regarding the BFA pools such as the number of isolated lineages and the evolutions and the timepoints from which they were isolated.
- https://cdn.elifesciences.org/articles/92899/elife-92899-supp1-v3.xlsx
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Supplementary file 2
Table of conditions and number of unique lineages sequenced: For each environment, the number of lineages with unique barcodes isolated is listed along with the number of lineages sequenced that had identifiable mutations.
- https://cdn.elifesciences.org/articles/92899/elife-92899-supp2-v3.xlsx
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Supplementary file 3
Table of mutations identified in each sequenced clone.
- https://cdn.elifesciences.org/articles/92899/elife-92899-supp3-v3.xlsx
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Supplementary file 4
Summary of clone fitnesses from each evolved population across test environments.
Lineages from each evolution are categorized according to whether their fitness is positive or negative or neutral in each test environment.
- https://cdn.elifesciences.org/articles/92899/elife-92899-supp4-v3.xlsx
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Supplementary file 5
Landing pad diploid strains – the sequences of each BC1 landing pad barcode, and the environment in which that barcoded population was evolved.
- https://cdn.elifesciences.org/articles/92899/elife-92899-supp5-v3.xlsx
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Supplementary file 6
Table of timepoints excluded from fitness estimation.
- https://cdn.elifesciences.org/articles/92899/elife-92899-supp6-v3.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/92899/elife-92899-mdarchecklist1-v3.docx
