{"id":"W2077573210","doi":"10.1016/j.ympev.2013.11.013","title":"Sampling strategies for improving tree accuracy and phylogenetic analyses: A case study in ciliate protists, with notes on the genus Paramecium","year":2013,"lang":"en","type":"article","venue":"Molecular Phylogenetics and Evolution","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Guelph","funders":"","keywords":"Biology; Phylogenetic tree; Coalescent theory; Monophyly; Phylogenetics; Evolutionary biology; Phylogenomics; Subgenus; Protist; Tree (set theory); Genus; Taxon; Genetics; Zoology; Gene; Clade; Ecology; Mathematics","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":[0.0002078649,0.0002618784,0.000192143,0.00007857331,0.0002583657,0.0001547842,0.0001408242,0.0001174792,0.000001928844],"category_scores_gemma":[0.0000950926,0.0001949018,0.00005090698,0.0001335715,0.000139508,0.000008996558,0.0001266923,0.000114686,0.000001034977],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002118019,"about_ca_system_score_gemma":0.00007849112,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009399554,"about_ca_topic_score_gemma":0.0008967099,"domain_scores_codex":[0.9986759,0.0001272064,0.0002111836,0.0005261739,0.0001315978,0.0003278826],"domain_scores_gemma":[0.999274,0.00006983752,0.000108825,0.0003493988,0.000115795,0.00008221018],"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":[0.0002336912,0.0003197896,0.1094355,0.0001177704,0.00020207,0.0001193467,0.0005679555,0.003583742,0.8711917,0.0004100976,0.00001073291,0.01380758],"study_design_scores_gemma":[0.006597301,0.01054392,0.8482662,0.0001008525,0.0005781916,0.0007443087,0.01325034,0.01602618,0.09641617,0.00547287,0.000137979,0.001865721],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9748036,0.001299912,0.02156308,0.00008098599,0.00002397779,0.002175998,0.00002435262,0.000007025943,0.00002105604],"genre_scores_gemma":[0.9977352,0.00003390759,0.001635284,0.0001114132,0.00004481896,0.0003909167,0.00001942514,0.00002331196,0.000005698902],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7747755,"threshold_uncertainty_score":0.7947867,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03570407063811577,"score_gpt":0.2870252248471614,"score_spread":0.2513211542090456,"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."}}