{"id":"W3167015799","doi":"10.1093/gbe/evab141","title":"Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments","year":2021,"lang":"en","type":"review","venue":"Genome Biology and Evolution","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":150,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Synonymous substitution; Biology; Nonsynonymous substitution; Genetics; Neutral mutation; Silent mutation; Neutral theory of molecular evolution; Genetic Fitness; Experimental evolution; Fitness landscape; Gene; Molecular evolution; Directed evolution; Mutation; Mutation rate; Codon usage bias; Adaptation (eye); Evolutionary biology; Mutant; Phylogenetics; Missense mutation; Population; Genome","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003160316,0.0004203589,0.0008156372,0.0001021385,0.0004065192,0.00002044861,0.0003060153,0.000803183,0.000007903571],"category_scores_gemma":[0.0004561822,0.0003412703,0.0004340466,0.0002267845,0.0005964506,0.000009972304,0.0002002886,0.0002072089,0.000008757151],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001944305,"about_ca_system_score_gemma":0.0006374013,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001610836,"about_ca_topic_score_gemma":0.0001275906,"domain_scores_codex":[0.9975742,0.0005647274,0.0006295784,0.0007672505,0.000094699,0.0003695741],"domain_scores_gemma":[0.9982949,0.0004024866,0.0004982473,0.0004606208,0.0002550663,0.00008866244],"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":[0.002059389,0.002736623,0.001429734,0.02136327,0.01276665,0.00003104909,0.001870469,0.001590232,0.6667881,0.0701999,0.006499868,0.2126647],"study_design_scores_gemma":[0.004722593,0.004275786,0.0103823,0.01031014,0.0114817,0.0004012091,0.0009309332,0.001057495,0.002660871,0.00503723,0.9448528,0.003886938],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.005011868,0.9237509,0.06823474,0.00002256137,0.000636923,0.0014125,0.0008902902,0.00001609743,0.00002414798],"genre_scores_gemma":[0.06851085,0.9247113,0.001374968,0.00003656588,0.0004926519,0.000514069,0.004077877,0.00003872834,0.0002429982],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9383529,"threshold_uncertainty_score":0.9999039,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04709467167788768,"score_gpt":0.336831654909981,"score_spread":0.2897369832320933,"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."}}