{"doi":"10.1101/2025.08.13.669769","title":"Not So Mosaic After All? The Core Genomes of IncP-1 Plasmids Evolve Predominantly Through Vertical Transmission","abstract":"Abstract Broad-host-range plasmids of the incompatibility group IncP-1 play an important role in bacterial evolution by disseminating genes between diverse bacteria. This includes the notable spread of antibiotic resistance genes to bacterial pathogens that increasingly threaten human health. A better understanding of the evolution of genetic elements like IncP-1 plasmids that underwrite bacterial adaptation is required to counter this threat. Here we examined the evolutionary history of IncP-1 plasmids by utilizing the large increase in published genomes and advancing techniques for lineage-based detection of microbial recombination. We specifically tested whether IncP-1 backbone genes evolve primarily (1) through vertical transmission, or (2) horizontally through homologous recombination between distinct plasmids. Our key finding is the IncP-1 plasmid backbone evolves predominantly through vertical transmission, which was supported by a nucleotide-level mapping of backbone recombination. We also showed via a phylogeny of 187 IncP-1 plasmids that established subgroup categories are well-supported. Finally, we examined factors that are potentially associated with IncP-1 subgroup diversification, including a gene related to plasmid-host adaptation and accessory genes like antibiotic and resistance metals. While some IncP-1 subgroups do correlate with certain categories of accessory genes, it remains unknown if these are causes or consequences of subgroup diversification.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":572789,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.945,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":807787,"name":"Clinton A. Elg","orcid":"0000-0001-5468-395X","position":1,"is_corresponding":false},{"id":465326,"name":"Jack Sullivan","orcid":"0000-0003-0216-6867","position":2,"is_corresponding":false},{"id":344992,"name":"Eva M. Top","orcid":"0000-0002-6380-8782","position":3,"is_corresponding":false},{"id":466446,"name":"David Sneddon","orcid":null,"position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:57:27.876396Z","pmid":"41332546","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":[]}