Life Cycle Experiment

• Interactive Colgen Output Displays genealogies and propagated mutation information.
• Full dataset as a SQLite database (33MB)
• 🔗 Zenodo Record 11170876
• 🔗 Code repository on gitlab
• 🔗 Preprint on Biorxiv
• 🔗 Colgen

Tables

• Common mutations List of mutations identified in at least one ancestral genotype
• Sequencing Metadata for each sequenced genotype

Figures

• Figure 2 Proportion of surviving collectives in phase I and II for each cycle
• Figure 3 Lineage genealogies
• Figure 4 Nodes in the L-LCS- genealogy predicted to mark adaptive change
• Figure 5 Reconstruction of the number of mutations through time
• Figure 6 mutL and mutS mutations in the L-LCS- genealogy
• Figure 7 Probability and fitness estimate

Supplementary Figures

• Improvement all lineages Nodes in all lineages predicted to mark adaptive change
• MMR system mutations Identified mutations of the methyl-directed mismatch repair system in the sequenced genomes
• Number of mutations Estimated number of identified by direct sequencing.
• Number of mutations reconstructed by belief propagation. Estimated number of mutation reconstructed by belief propagation.
• Number of mutations within the genealogies Estimated number of mutation reconstructed by belief propagation displayed on the genealogies.
• Mutations on L-LCS- tree Mut mutations and number of mutations.
• Mutations on L-LCS+ tree Mut mutations and number of mutations.
• Mutations on S-LCS- tree Mut mutations and number of mutations.
• Mutations on S-LCS+ tree Mut mutations and number of mutations.
• MutL mutation origin using only the sequenced endpoints Mut mutations and number of mutations.
• MutL mutation origin using all sequencing data Mut mutations and number of mutations.
• Comparison of Ph. I survival Between colgen and fitness assays.
• Probabilities in S-LCS+ endpoints Results of fitness assays.
• Probabilities in S-LCS- endpoints Results of fitness assays.
• Probabilities in L-LCS+ endpoints Results of fitness assays.
• Probabilities in L-LCS- endpoints Results of fitness assays.

Notebooks

All outputs are generated by running the following Python notebooks:
• 01_genealogies.ipynb
• 02_tree_display.ipynb
• 03_survival.ipynb
• 04_sequencing.ipynb
• 05_mutation_propagation.ipynb
• 06_fitness_assays.ipynb
• 07_compare_fit.ipynb
• 08_illustrate_colgen.ipynb