{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008428835,0.0001878155,0.0002359117,0.0003987825,0.0003005026,0.0004649832,0.0001650924,0.0003062547,0.0005822831],"category_scores_gemma":[0.0003111811,0.000130951,0.0002188714,0.000389228,0.0002373481,0.0002851901,0.000473918,0.0004846462,0.0002571977],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001666134,"about_ca_system_score_gemma":0.0001384817,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006134199,"about_ca_topic_score_gemma":0.001347445,"domain_scores_codex":[0.9999076,0.000005767309,0.00000974511,0.0000484516,0.00001661266,0.00001185335],"domain_scores_gemma":[0.9997416,0.00005388984,0.00006864573,0.0000501669,0.00003006699,0.00005564484],"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":[0.0001690345,0.00001010838,0.01298414,0.00006767435,0.00002547247,0.000200933,0.0003883312,0.0001036352,0.9817345,0.0001251191,0.00004474009,0.004146278],"study_design_scores_gemma":[0.00004046372,0.0003048046,0.7988418,0.00006246682,0.0002116206,0.004533643,0.001177218,0.001569027,0.1764031,0.0007886744,0.01601953,0.00004751278],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9973393,0.0004844316,0.0006667122,0.00003981061,0.000004283972,0.00000493951,0.0009984997,0.00002890577,0.0004331504],"genre_scores_gemma":[0.9912515,0.0005104216,0.002453065,0.0001179266,0.000006620658,0.00001484696,0.004953672,0.00005043838,0.00064142],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0006134199,"threshold_uncertainty_score":0.001947939,"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."}}