{"id":"W4317499925","doi":"10.1038/s42003-022-04394-6","title":"Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis","year":2023,"lang":"en","type":"article","venue":"Communications Biology","topic":"Yersinia bacterium, plague, ectoparasites research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University Medical Centre; Canadian Institute for Advanced Research; McMaster University","funders":"Compute Canada; McMaster University; Social Sciences and Humanities Research Council of Canada; Government of Canada; Canadian Institute for Advanced Research","keywords":"Yersinia pestis; Plague (disease); Pandemic; Evolutionary biology; Biology; Phylogenetic tree; Phylogenetics; Molecular clock; Infectious disease (medical specialty); Population; Divergence (linguistics); Zoology; Genealogy; Geography; Demography; Disease; Coronavirus disease 2019 (COVID-19); Genetics; History; Virulence; Gene; Medicine","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":[0.0001823522,0.0001190369,0.0001672212,0.00003216831,0.0001754925,0.00001770688,0.0009800498,0.0001864414,0.00002018791],"category_scores_gemma":[0.0004645459,0.00009617419,0.00004651019,0.0002856161,0.0007453172,0.000003738229,0.0009235024,0.000127669,0.00004756863],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001551157,"about_ca_system_score_gemma":0.00006525263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005283686,"about_ca_topic_score_gemma":0.0002869332,"domain_scores_codex":[0.9989024,0.0003615516,0.0002072963,0.0002497665,0.00005916616,0.0002198529],"domain_scores_gemma":[0.9981646,0.0002857923,0.00007845584,0.001293769,0.0001196131,0.00005779155],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00005642632,0.00005954794,0.1459137,0.000005200484,0.0001136703,5.246841e-7,0.0001890727,8.910461e-7,0.8375267,0.001301815,0.01312721,0.001705272],"study_design_scores_gemma":[0.001099091,0.0005362739,0.4679104,0.00003346081,0.00006236263,0.00001844954,0.0004431171,0.000470108,0.05325837,0.002197675,0.4735888,0.000381854],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9807995,0.01338864,0.00004471062,0.004162306,0.00005356205,0.0001898866,0.00058881,0.00002234019,0.000750271],"genre_scores_gemma":[0.9887394,0.00789174,0.0008549594,0.0001883597,0.00004545674,0.00003127396,0.00212393,0.00001037318,0.0001144634],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7842683,"threshold_uncertainty_score":0.3921869,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02728569997487008,"score_gpt":0.3467836361181149,"score_spread":0.3194979361432448,"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."}}