{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00328369,0.0004107885,0.0007279738,0.0007054177,0.0005718817,0.00176421,0.0005070628,0.000479528,0.0008297687],"category_scores_gemma":[0.007393773,0.0002449857,0.0003876592,0.001248973,0.00127337,0.002078634,0.0009654334,0.001253542,0.0001425063],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004724692,"about_ca_system_score_gemma":0.0004987321,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002691154,"about_ca_topic_score_gemma":0.003990477,"domain_scores_codex":[0.9994671,0.0002288409,0.00003906689,0.0001641316,0.00004651651,0.00005446417],"domain_scores_gemma":[0.997341,0.001430186,0.000493828,0.0003839022,0.0002133844,0.0001376891],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0007507465,0.00007740664,0.6464503,0.0007224652,0.0009916632,0.001016231,0.005514147,0.06197986,0.08766586,0.02842334,0.001658845,0.1647491],"study_design_scores_gemma":[0.00003726405,0.0002480211,0.7970807,0.0003565084,0.0006322307,0.0008359982,0.004854115,0.1228591,0.005984245,0.0507268,0.01624797,0.000137091],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9583347,0.003582322,0.03442466,0.001708421,0.0000362716,0.00000946102,0.0003355315,0.00007141555,0.001497237],"genre_scores_gemma":[0.9936255,0.001298217,0.004466219,0.0001917514,0.00003058199,0.000007170892,0.000216993,0.00005065314,0.0001128565],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00328369,"threshold_uncertainty_score":0.01736605,"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."}}