{"id":"W2971513102","doi":"10.7554/elife.46497","title":"Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade","year":2019,"lang":"en","type":"article","venue":"eLife","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":155,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Biomedical Imaging and Bioengineering; Natural Sciences and Engineering Research Council of Canada; University of Chicago; Marine Biological Laboratory","keywords":"Subclade; Biogeography; Evolutionary biology; Biology; Genetics; Computational biology; Clade; Phylogenetics; Paleontology; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009587167,0.0001416916,0.000148148,0.00001523056,0.00007194924,0.00001151905,0.0002610855,0.00009358292,0.00001761724],"category_scores_gemma":[0.00004942033,0.0001045032,0.00009794899,0.0001646764,0.0001164909,0.000001135777,0.0001755768,0.00004158083,0.0000140128],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009065586,"about_ca_system_score_gemma":0.00009835219,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002519874,"about_ca_topic_score_gemma":0.00002031622,"domain_scores_codex":[0.9991485,0.00003373589,0.0001639978,0.000272277,0.0001674613,0.0002140231],"domain_scores_gemma":[0.9993861,0.00001431145,0.0001055369,0.0003148667,0.000138595,0.00004056412],"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":[0.00007437282,0.00008888107,0.4549601,0.00004953815,0.0001499,7.601309e-7,0.00005232759,0.000009379281,0.5416058,0.0000896898,0.002229528,0.0006897022],"study_design_scores_gemma":[0.0005539416,0.0005056057,0.79493,0.00002805225,0.00004978668,0.00002389739,0.0002222933,0.00001578497,0.1764732,0.0002450551,0.02669114,0.0002611385],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9853887,0.01206619,0.00002434021,0.0002275048,0.0002073462,0.0002017392,0.0001560532,0.000003979171,0.001724131],"genre_scores_gemma":[0.9985051,0.0004767312,0.0004066158,0.0003267521,0.0001454435,0.00001220842,0.00003126251,0.00001048089,0.00008547466],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3651326,"threshold_uncertainty_score":0.4261517,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01349770276866736,"score_gpt":0.2210992887297382,"score_spread":0.2076015859610709,"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."}}