{"id":"W4411097965","doi":"10.1093/gbe/evaf117","title":"Divergent Plastid Genomes in the Deepest-Branching Apicomplexan Parasites","year":2025,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Japan Society for the Promotion of Science; Hokkaido University; Fundação para a Ciência e a Tecnologia; Gordon and Betty Moore Foundation","keywords":"Plastid; Biology; Apicoplast; Genome; Evolutionary biology; Lineage (genetic); Genome evolution; Phylogenetics; Phylogenomics; Genetics; Gene; Chloroplast; Clade","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":[0.0002008106,0.0001149612,0.0001153745,0.00004785734,0.0002037186,0.00001072785,0.0001440524,0.0001048978,0.000003697523],"category_scores_gemma":[0.00002549594,0.00008571239,0.00003742301,0.00008647185,0.0001201921,7.515339e-7,0.0001202185,0.00006839033,0.000003297135],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000147181,"about_ca_system_score_gemma":0.00002590913,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004467501,"about_ca_topic_score_gemma":0.0001343461,"domain_scores_codex":[0.9992642,0.00009303413,0.0001476297,0.0002610274,0.00002563808,0.0002085169],"domain_scores_gemma":[0.9997411,0.00002733295,0.00003482136,0.0001578448,0.00002005121,0.00001883165],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00005404156,0.00003471033,0.6241211,0.00001331068,0.00006758835,6.072881e-7,0.0002056672,0.0001217595,0.3675145,0.00625466,0.0001483244,0.00146374],"study_design_scores_gemma":[0.0003011787,0.0001154376,0.971082,0.000003712016,0.00001584039,0.000005104171,0.0002016716,0.00002834457,0.0004493786,0.004880155,0.02280833,0.0001088428],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9739584,0.02330958,0.001103224,0.0002865345,0.0001674433,0.0001518619,0.00001603857,0.000002719668,0.00100423],"genre_scores_gemma":[0.9979594,0.00129205,0.0001805177,0.0002926173,0.0001129069,0.00002884049,0.00004995663,0.000003668258,0.0000799793],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3670651,"threshold_uncertainty_score":0.349525,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007891752681300516,"score_gpt":0.2449035845795524,"score_spread":0.2370118318982519,"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."}}