{"id":"W2101465476","doi":"10.1093/molbev/msp123","title":"Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model","year":2009,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":132,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Phylogenetic tree; Lineage (genetic); Genome; Gene duplication; Evolutionary biology; Gene; Phylogenetics; Gene family; Horizontal gene transfer; Genetics; Genome evolution; Most recent common ancestor; Archaea","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":[0.001108844,0.0003329063,0.0005808807,0.001141976,0.0006347349,0.00122329,0.001307003,0.000930508,0.001072523],"category_scores_gemma":[0.003517836,0.0006569994,0.000957153,0.0007299877,0.000959761,0.0014386,0.0006996915,0.0007521596,0.0002824711],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00104678,"about_ca_system_score_gemma":0.0006262825,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004153199,"about_ca_topic_score_gemma":0.002804159,"domain_scores_codex":[0.9997953,0.00006468737,0.00001166557,0.00006268371,0.00003505359,0.00003070036],"domain_scores_gemma":[0.9988207,0.0007654353,0.00019666,0.00008116962,0.00006199895,0.00007385632],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002358179,0.00004977839,0.02850675,0.0001175235,0.0001062131,0.0004627,0.0004212713,0.8692543,0.007509279,0.07809356,0.0004269085,0.01481592],"study_design_scores_gemma":[0.00001053006,0.0000163011,0.001703128,0.000007263542,0.00001907288,0.000119944,0.0000297929,0.9770173,0.0004430724,0.020329,0.0002890676,0.00001562156],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.650728,0.0004482788,0.3468205,0.0003956761,0.00001084368,0.00002430814,0.0002743637,0.0002077511,0.001090242],"genre_scores_gemma":[0.9606984,0.0004685368,0.03676292,0.00005360447,0.0000158036,0.00006130206,0.0003428451,0.0000717797,0.001524938],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004153199,"threshold_uncertainty_score":0.008258045,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00913600527797277,"score_gpt":0.2541046732775207,"score_spread":0.2449686679995479,"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."}}