{"id":"W2145611979","doi":"10.1093/molbev/msh235","title":"The Evolutionary Implications of knox-I Gene Duplications in Conifers: Correlated Evidence from Phylogeny, Gene Mapping, and Analysis of Functional Divergence","year":2004,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Plant Gene Expression Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":71,"is_retracted":false,"has_abstract":true,"ca_institutions":"GDG Environnement","funders":"Genome Canada","keywords":"Biology; Nonsynonymous substitution; Phylogenetic tree; Gene; Genetics; Negative selection; Monophyly; Phylogenetics; Sister group; Genome; Evolutionary biology; Molecular evolution; Rate of evolution; Synonymous substitution; Clade; Codon usage bias","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0001847404,0.0001119658,0.0001910298,0.0001764198,0.0001406538,0.000004334457,0.0001381173,0.000179364,0.000007380635],"category_scores_gemma":[0.0001734203,0.00009617923,0.00009294129,0.000537244,0.0003415762,0.000006672281,0.00013006,0.00007200146,9.945657e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002952048,"about_ca_system_score_gemma":0.00008765971,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003983754,"about_ca_topic_score_gemma":0.0001977744,"domain_scores_codex":[0.998974,0.000120392,0.0003304456,0.0003612571,0.0000715576,0.0001423239],"domain_scores_gemma":[0.999224,0.00006041111,0.0001939468,0.0003256408,0.0001481122,0.00004786779],"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":[0.0000451782,0.00003345194,0.1976319,0.000001942154,0.0003609285,3.149802e-7,0.00002338485,0.003665205,0.7973595,0.0007223808,0.00004657222,0.0001092624],"study_design_scores_gemma":[0.0002752716,0.00005618772,0.9046839,0.00001459844,0.000275622,0.000006303651,0.00004050763,0.001522811,0.09088746,0.0020527,0.00008000073,0.000104658],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.859724,0.008789202,0.130876,0.0002590545,0.00003269397,0.0001075465,0.0001918315,0.00000422189,0.00001550703],"genre_scores_gemma":[0.9955798,0.002186211,0.001302545,0.00003616176,0.00001339755,0.00003085453,0.0008284739,0.000004468522,0.00001809246],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.707052,"threshold_uncertainty_score":0.3922075,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01189047082601127,"score_gpt":0.2552427346853717,"score_spread":0.2433522638593605,"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."}}