{"id":"W4409984056","doi":"10.1128/msystems.00301-25","title":"Heterogeneity in recombination rates and accessory gene co-occurrence distinguish <i>Pseudomonas aeruginosa</i> phylogroups","year":2025,"lang":"en","type":"article","venue":"mSystems","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Agriculture and Agri-Food Canada","funders":"National Institute of General Medical Sciences; National Institutes of Health","keywords":"Biology; Genome; Genetics; Gene; Gammaproteobacteria; Pseudomonas aeruginosa; Homologous recombination; Phylogenetic tree; Recombination; Population; Evolutionary biology; Bacteria; 16S ribosomal RNA","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002611998,0.0002551205,0.0002202348,0.001235232,0.0001579339,0.0004693287,0.0001686585,0.0002541273,0.001362217],"category_scores_gemma":[0.00087387,0.0001114424,0.0002202337,0.0008117448,0.0002051909,0.0002995224,0.0004247279,0.0002486719,0.0003555067],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001196543,"about_ca_system_score_gemma":0.00009311228,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00101558,"about_ca_topic_score_gemma":0.0006615442,"domain_scores_codex":[0.9997117,0.00004758514,0.00002717937,0.00009173955,0.00003770435,0.00008415204],"domain_scores_gemma":[0.9990793,0.0001977364,0.0004068176,0.00006435497,0.0001276721,0.0001240411],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005033027,0.000052726,0.5985156,0.00007083113,0.00007292187,0.00009047291,0.0004497235,0.000225712,0.3930737,0.0001100179,0.0001022658,0.006732802],"study_design_scores_gemma":[0.000003956298,0.0001094547,0.9901204,0.000008314514,0.00002172209,0.0002865563,0.0003464812,0.000711518,0.007887369,0.00008101366,0.0004164141,0.000006837591],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9991234,0.000116365,0.0002957279,0.000006246164,9.868786e-7,0.00000423037,0.0002435628,0.000006170533,0.0002032592],"genre_scores_gemma":[0.9989828,0.00004159838,0.0003114608,0.000005767771,0.00000275207,0.000004320425,0.0005450267,0.000004225291,0.000101943],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001362217,"threshold_uncertainty_score":0.004557014,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0127883318481898,"score_gpt":0.2973917341737315,"score_spread":0.2846034023255418,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}