{"id":"W2952835547","doi":"10.7717/peerj.6334","title":"The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates","year":2019,"lang":"en","type":"article","venue":"PeerJ","topic":"Evolution and Paleontology Studies","field":"Earth and Planetary Sciences","cited_by":52,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"National Center for Research Resources; National Institute of General Medical Sciences","keywords":"Prior probability; Molecular clock; Phylogenetic tree; Phylogenetics; Evolutionary biology; Biology; Bayesian probability; Diversification (marketing strategy); Inference; Bayesian inference; Lineage (genetic); Tree (set theory); Econometrics; Statistics; Computer science; Artificial intelligence; Mathematics; Genetics","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":[0.0001561052,0.00005853063,0.0001221274,0.00002474974,0.00008284481,0.000008882227,0.0001116429,0.00003055182,0.00006930631],"category_scores_gemma":[0.00007765466,0.00003245655,0.00002702045,0.00006940615,0.0001873998,0.00003296592,0.000008433094,0.00003566732,0.0000120646],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":6.002387e-7,"about_ca_system_score_gemma":0.00001617877,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007056749,"about_ca_topic_score_gemma":0.02585731,"domain_scores_codex":[0.9994912,0.00006894552,0.0001184747,0.0001076158,0.0001196508,0.0000941207],"domain_scores_gemma":[0.9992847,0.0004380842,0.00009777595,0.0001030099,0.00005645218,0.00001999622],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00002658571,0.000003815085,0.9880847,0.00002182831,0.00002582702,1.743365e-7,0.0002039826,0.00003009786,0.004210271,0.0002552617,0.0000149314,0.007122475],"study_design_scores_gemma":[0.0001675305,0.0001122965,0.9929433,0.000007052656,0.00001952693,3.841121e-7,0.0002542199,0.0004463402,0.005474637,0.000119725,0.0004092182,0.00004569604],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9930887,0.00380514,0.00001196459,0.0003860814,0.0001224894,0.0001190147,0.00002386319,0.000005499579,0.002437206],"genre_scores_gemma":[0.999309,0.0004054901,0.00007837425,0.00002362526,0.000008959251,4.538892e-7,0.000005786841,6.857991e-7,0.0001676106],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02515164,"threshold_uncertainty_score":0.9919183,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01793399615284594,"score_gpt":0.2462212138204466,"score_spread":0.2282872176676007,"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."}}