{"id":"W2100733246","doi":"10.1080/10635150802559265","title":"The Impact of Reticulate Evolution on Genome Phylogeny","year":2008,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":51,"is_retracted":false,"has_abstract":true,"ca_institutions":"Atlantic School of Theology; Dalhousie University","funders":"Genome Canada","keywords":"Biology; Genome; Phylogenetic tree; Evolutionary biology; Phylogenetics; Tree (set theory); Tree of life (biology); Reticulate; Horizontal gene transfer; Reticulate evolution; Set (abstract data type); Genome evolution; Genetics; Gene; Paleontology; Computer science","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":[0.000293011,0.0001477131,0.0002927161,0.00002925167,0.0001757452,0.000003876202,0.0002149887,0.0001216863,0.000002385767],"category_scores_gemma":[0.0001448507,0.00008173755,0.0002046708,0.00005863096,0.0002418048,2.049366e-7,0.0001009963,0.0000500249,0.00001139521],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002657868,"about_ca_system_score_gemma":0.00006202811,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003952934,"about_ca_topic_score_gemma":0.000005160301,"domain_scores_codex":[0.9989405,0.0002018676,0.0003660173,0.0002122888,0.0000567822,0.000222565],"domain_scores_gemma":[0.9990996,0.00005517044,0.000218253,0.0004859694,0.0001037024,0.00003730495],"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":[0.0000575035,0.000033885,0.0132421,0.0003142942,0.0003433781,9.320161e-7,0.0001081603,0.0005332201,0.9839653,0.001345576,0.00004515644,0.00001045706],"study_design_scores_gemma":[0.001574371,0.005750826,0.9366696,0.0004112962,0.0001390786,0.0003287152,0.0003919701,0.0006902107,0.04625927,0.006837488,0.0001641735,0.000782932],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9943023,0.004281272,0.0003529302,0.00002429453,0.0001258216,0.0004329652,0.00001989149,0.000002762982,0.0004577589],"genre_scores_gemma":[0.9994844,0.000215711,0.00006515727,0.0000152173,0.0000856044,0.00004780055,0.000009454719,0.00001047709,0.00006617156],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9377061,"threshold_uncertainty_score":0.3333161,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0139986834536393,"score_gpt":0.2552974969370502,"score_spread":0.2412988134834109,"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."}}