{"id":"W4288038235","doi":"10.1093/sysbio/syac051","title":"Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations","year":2022,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Fish biology, ecology, and behavior","field":"Environmental Science","cited_by":37,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Museum of Nature; Royal Ontario Museum; University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; Grantová Agentura České Republiky; Universität Basel; University of Michigan; American Museum of Natural History; Nature; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Biology; Cichlid; Phylogenetic tree; Phylogenomics; Evolutionary biology; Coalescent theory; Phylogenetics; Supertree; Supermatrix; Clade; Gene; Genetics; Fish <Actinopterygii>","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":[0.002301947,0.0001188889,0.0004299011,0.00005037382,0.0004623957,0.000005003315,0.0002935111,0.00007786221,0.00009471326],"category_scores_gemma":[0.0003732444,0.00006307085,0.00006142766,0.0001867709,0.00147898,0.00001897404,0.0001579426,0.0002205451,0.000001415563],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005207306,"about_ca_system_score_gemma":0.00002915376,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009710022,"about_ca_topic_score_gemma":0.0002797487,"domain_scores_codex":[0.9971213,0.001842982,0.0005495027,0.0002354808,0.00007964378,0.0001711155],"domain_scores_gemma":[0.9970613,0.001827647,0.0007027377,0.0003667358,0.00001933218,0.00002229577],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002322637,0.0001354723,0.9596041,0.001647849,0.0002581232,0.000002015259,0.01168967,0.004364023,0.01411542,0.007491885,0.00001819965,0.000440996],"study_design_scores_gemma":[0.004193715,0.001700572,0.8389208,0.00042128,0.0008531417,0.0003762598,0.1314831,0.01352349,0.001628885,0.006215294,0.00005440613,0.0006290321],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9960825,0.0009442259,0.0000689818,0.001270434,0.0001007688,0.0009469432,0.00003304396,0.00001419414,0.0005388869],"genre_scores_gemma":[0.9990578,0.00002684158,0.0005359309,0.00005019326,0.00001101576,0.0002993978,0.000005475888,0.000007559798,0.00000581886],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1206832,"threshold_uncertainty_score":0.5449364,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0311947281632158,"score_gpt":0.2191032125537023,"score_spread":0.1879084843904865,"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."}}