{"id":"W4410183734","doi":"10.1002/ajb2.70039","title":"Disentangling serial chloroplast captures in willows","year":2025,"lang":"en","type":"article","venue":"American Journal of Botany","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"","keywords":"Biology; Chloroplast; Chloroplast DNA; Nuclear gene; Genome; Introgression; Lineage (genetic); Phylogenetic tree; Phylogenetics; Phylogenomics; Evolutionary biology; Genetics; Gene; Clade","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001182803,0.00008884333,0.0001983553,0.00005859822,0.00003031056,0.00001150263,0.0001313181,0.0000254304,0.000002874373],"category_scores_gemma":[0.00005073685,0.00007719691,0.00008495757,0.0001196141,0.0001100274,6.940032e-7,0.00005631573,0.00007570519,4.813338e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001645302,"about_ca_system_score_gemma":0.00007758781,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002305098,"about_ca_topic_score_gemma":0.0001025601,"domain_scores_codex":[0.9993993,0.00003285269,0.0002526981,0.0001077136,0.00006647127,0.0001409742],"domain_scores_gemma":[0.9996283,0.00001404449,0.0001551706,0.0001045454,0.0000588312,0.0000390782],"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":[0.0004831772,0.00007425027,0.1800389,0.000005801303,0.0002072987,0.00002735334,0.0002166417,0.0006136079,0.7981899,0.00006581793,0.0008704928,0.01920675],"study_design_scores_gemma":[0.006071529,0.003946734,0.6370511,0.0002904505,0.0002331503,0.0002820666,0.01005292,0.0001656294,0.187167,0.001118264,0.15257,0.001051107],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9964406,0.002174311,0.0001213321,0.000257573,0.0003925582,0.00003775537,0.000004300335,5.783332e-7,0.0005709402],"genre_scores_gemma":[0.9981948,0.0005498306,0.0006425486,0.000273793,0.0002450339,0.000001435145,5.314828e-7,0.000007104194,0.00008499061],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6110229,"threshold_uncertainty_score":0.3147998,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00356201152212568,"score_gpt":0.2303262119005381,"score_spread":0.2267642003784124,"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."}}