{"id":"W4319594984","doi":"10.1038/s41467-023-36139-2","title":"Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces","year":2023,"lang":"en","type":"article","venue":"Nature Communications","topic":"Fermentation and Sensory Analysis","field":"Agricultural and Biological Sciences","cited_by":59,"is_retracted":false,"has_abstract":true,"ca_institutions":"Natural Resources Canada; Université de Montréal; Université Laval","funders":"National Institute of General Medical Sciences; Great Lakes Bioenergy Research Center; Office of Science; National Institutes of Health; National Institute of Food and Agriculture; Division of Graduate Education; Wisconsin Alumni Research Foundation; Generalitat Valenciana; European Commission; Universitat de València; Biological and Environmental Research; National Natural Science Foundation of China; University of Wisconsin-Madison; Norges Forskningsråd; Natural Sciences and Engineering Research Council of Canada; U.S. Department of Agriculture; National Science Foundation","keywords":"Biology; Evolutionary biology; Phylogenetic tree; Lineage (genetic); Genome; Phylogenetics; Saccharomyces; Population; Genetic diversity; Biodiversity; Genus; Saccharomyces cerevisiae; Genetics; Gene; Ecology","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":[0.0001451302,0.00003489802,0.00005480024,0.00001877567,0.0003019086,0.000008303882,0.0004251899,0.00005196711,0.00001657837],"category_scores_gemma":[0.00001716476,0.00001349882,0.00003141787,0.0004673327,0.00007503615,0.00004707224,0.0002210876,0.0001419672,0.000004391548],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005691953,"about_ca_system_score_gemma":0.000002609817,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004979295,"about_ca_topic_score_gemma":0.00175536,"domain_scores_codex":[0.9996229,0.00008783137,0.00007677943,0.00006573548,0.00008928694,0.00005749246],"domain_scores_gemma":[0.999706,0.0001498533,0.00003070396,0.00007183752,0.00002789348,0.00001376727],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0000788391,0.0009173218,0.4601716,0.00003560054,0.0001937244,0.000007399955,0.02721249,0.002150457,0.2513169,0.07963671,0.01852241,0.1597565],"study_design_scores_gemma":[0.00004538858,0.00000848709,0.9869918,0.000002517659,0.00001050479,0.000001098839,0.002278956,0.00755011,0.00002067602,0.0009985595,0.002053272,0.00003869548],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9907809,0.001025217,4.50907e-7,0.007319397,0.000004867237,0.00006422595,0.0000829817,0.00001499229,0.0007069525],"genre_scores_gemma":[0.9984346,0.001005577,0.0001305722,0.0002496046,0.000006355037,0.000004362379,0.00008015881,1.850662e-7,0.0000886065],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5268201,"threshold_uncertainty_score":0.2322068,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05199305415678124,"score_gpt":0.2717363981059259,"score_spread":0.2197433439491447,"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."}}