{"id":"W4307233207","doi":"10.1038/s41559-022-01871-3","title":"Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact","year":2022,"lang":"en","type":"letter","venue":"Nature Ecology & Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":false,"ca_institutions":"Dalhousie University","funders":"Vetenskapsrådet; Nederlandse Organisatie voor Wetenschappelijk Onderzoek","keywords":"Phylogenetic tree; Alpha (finance); Biology; Phylogenetics; Evolutionary biology; Computational biology; Genetics; Medicine; Gene","routes":{"ca_aff":true,"ca_fund":false,"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","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.0001237773,0.0003462651,0.0003963887,0.000134655,0.0002715024,0.000009269541,0.0002412526,0.001573368,0.00007740036],"category_scores_gemma":[0.00003497399,0.0003252147,0.00009734832,0.0001132046,0.0002246058,0.00000176427,0.0002188519,0.0009218054,0.000001288432],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006395809,"about_ca_system_score_gemma":0.0001739125,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002797777,"about_ca_topic_score_gemma":0.0002186589,"domain_scores_codex":[0.9982643,0.0001742091,0.0002796924,0.0007414694,0.000204009,0.0003362793],"domain_scores_gemma":[0.9989521,0.00002996013,0.0003424041,0.0004645667,0.000167699,0.00004325745],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003997547,0.0001777012,0.04021262,0.0001541526,0.0008344745,0.00001887231,0.000307438,0.0001832922,0.2283995,0.00005120181,0.7287928,0.0004681269],"study_design_scores_gemma":[0.001130001,0.00527495,0.3333383,0.00001606278,0.0004092358,0.0001079099,0.00009707751,0.0000516197,0.007359453,0.0004745911,0.6510315,0.0007092765],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9644755,0.008183155,0.00003263615,0.02562501,0.0007199737,0.0004837321,0.000322275,0.000006967287,0.0001508178],"genre_scores_gemma":[0.9651322,0.000567112,0.0006636803,0.03037838,0.001465706,0.00009484395,0.001115309,0.00005333433,0.0005293998],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2931257,"threshold_uncertainty_score":0.99992,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005985931128755465,"score_gpt":0.2191640056203972,"score_spread":0.2131780744916418,"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."}}