{"doi":"10.1101/571505","title":"Chromosomal barcoding of\n                  <i>E. coli</i>\n                  populations reveals lineage diversity dynamics at high resolution","abstract":"<jats:p>\n                  Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages have so far prevented a detailed elucidation of evolutionary dynamics in large bacterial populations. Here, we overcome this hurdle by developing a chromosomal barcoding technique that allows simultaneous tracking of ∼450,000 distinct lineages in\n                  <jats:italic>E. coli.</jats:italic>\n                  We used this technique to gather insights into the evolutionary dynamics of large (&gt;10\n                  <jats:sup>7</jats:sup>\n                  cells)\n                  <jats:italic>E. coli</jats:italic>\n                  populations propagated for ∼420 generations in the presence of sub-inhibitory concentrations of common antibiotics. By deep sequencing the barcodes, we reconstructed trajectories of individual lineages at high frequency resolution (&lt; 10\n                  <jats:sup>−5</jats:sup>\n                  ). Using quantitative tools from ecology, we found that populations lost lineage diversity at distinct rates corresponding to their antibiotic regimen. Additionally, by quantifying the reproducibility of these dynamics across replicate populations, we found that some lineages had similar fates over independent experiments. Combined with an analysis of individual lineage trajectories, these results suggest how standing genetic variation and new mutations may contribute to adaptation to sub-inhibitory antibiotic levels. Altogether, our results demonstrate the power of high-resolution barcoding in studying the dynamics of bacterial evolution.\n                </jats:p>","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":null,"id":33787,"datarank":0.2615978181952956,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.05365366402731196,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.05365366402731196,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":3,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":176107,"name":"Michael Manhart","orcid":"0000-0003-3791-9056","position":1,"is_corresponding":false},{"id":176108,"name":"Weronika Jasinska","orcid":null,"position":2,"is_corresponding":false},{"id":176109,"name":"Louis Gauthier","orcid":null,"position":3,"is_corresponding":false},{"id":176110,"name":"Adrian W.R. Serohijos","orcid":"0000-0001-8369-982X","position":4,"is_corresponding":false},{"id":176111,"name":"Shimon Bershtein","orcid":"0000-0003-4322-1025","position":5,"is_corresponding":false},{"id":176106,"name":"Jesse Lerner","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24523987","pmcid":null,"openalex_id":"https://openalex.org/W2920061786","authors":[],"funders":[{"funder_name":"Natural Sciences and Engineering Research Council of Canada","grant_id":"unidentified","title":"unidentified"},{"funder_name":"Swiss National Science Foundation","grant_id":"180147","title":"Molecular mechanisms and evolutionary consequences of pleiotropy and single-cell variation in microbial growth"},{"funder_name":"National Institutes of Health","grant_id":"1F32GM116217-01","title":"Characterizing the Co-evolution of Protein-protein and Regulatory Interactions"}],"total_grants":3,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2020,"count":3}],"oa_status":"closed","license":"Springer Nature TDM","oa_locations":[{"url":"https://syndication.highwire.org/content/doi/10.1101/571505","host_type":"publisher"},{"url":"https://doi.org/10.1101/571505","host_type":"repository"},{"url":"https://doi.org/10.1038/s41559-020-1103-z","host_type":""},{"url":"https://www.research-collection.ethz.ch/bitstream/20.500.11850/404463/3/Manuscript.pdf","host_type":""},{"url":"https://dx.doi.org/10.3929/ethz-b-000404463","host_type":""},{"url":"https://pubmed.ncbi.nlm.nih.gov/32094541","host_type":""},{"url":"https://dx.doi.org/10.1101/571505","host_type":""},{"url":"https://dx.doi.org/10.1038/s41559-020-1103-z","host_type":""},{"url":"https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37374290","host_type":""},{"url":"http://hdl.handle.net/20.500.11850/404463","host_type":""},{"url":"http://dx.doi.org/10.1101/571505","host_type":""},{"url":"https://doi.org/https://doi.org/10.1101/571505","host_type":""}],"fields_of_study":["Evolution and Genetic Dynamics","Genomics and Phylogenetic Studies","CRISPR and Genetic Engineering","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Lineage (genetic)","Biology","Evolutionary dynamics","Evolutionary biology","Adaptation (eye)","Experimental evolution","Dynamics (music)","Genetic diversity","Mutation rate","Genetics","Gene","Population","Evolution, Molecular","570","Population genetics","Mutation","Escherichia coli","Molecular evolution","Evolutionary ecology","Anti-Bacterial Agents"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T16:55:24.559701Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}