{"id":"W4410267570","doi":"10.1093/ismejo/wraf091","title":"Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy","year":2025,"lang":"en","type":"article","venue":"The ISME Journal","topic":"Legume Nitrogen Fixing Symbiosis","field":"Agricultural and Biological Sciences","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"H2020 Marie Skłodowska-Curie Actions; HORIZON EUROPE Framework Programme; Okinawa Institute of Science and Technology Graduate University; Queen's University; Queen's University Belfast; UK Research and Innovation","keywords":"Plasmid; Biology; Gene; Genetics; Chromosome; Genome; Phenotype; Ecological niche; Ecology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003126275,0.0001393748,0.000230957,0.00001798801,0.0003775774,0.0000711313,0.0005889644,0.0001466291,0.0006858543],"category_scores_gemma":[0.00007765747,0.00004055561,0.0002101425,0.0002910272,0.0001574131,0.00008124258,0.0001293219,0.0003465591,0.00001381274],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003966615,"about_ca_system_score_gemma":0.00003908462,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004912128,"about_ca_topic_score_gemma":0.00007649454,"domain_scores_codex":[0.9988418,0.0001454743,0.0003272891,0.0001553952,0.0002496568,0.0002803709],"domain_scores_gemma":[0.9993895,0.0002161883,0.0001719577,0.00005752591,0.0001001655,0.00006470254],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00007231061,0.0002096212,0.01646906,0.00001042829,0.0001219259,0.00001456635,0.000394871,0.00001176165,0.9571372,0.00155716,0.003566817,0.02043431],"study_design_scores_gemma":[0.0005684424,0.0006949487,0.67429,0.0001308189,0.0001762097,0.0003005269,0.001814793,0.00005950138,0.2959309,0.0152908,0.01034957,0.0003935039],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9874339,0.0007619665,0.000003102332,0.009900354,0.0004790776,0.00009255243,0.00002380925,0.00002080626,0.001284459],"genre_scores_gemma":[0.9984924,0.00007021018,0.0001286365,0.0003358504,0.0005698671,0.000003448696,0.000004261129,8.290764e-7,0.0003945347],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6612063,"threshold_uncertainty_score":0.7509623,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01291712473444952,"score_gpt":0.2251541163931384,"score_spread":0.2122369916586889,"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."}}