{"id":"W4403854157","doi":"10.1093/sysbio/syae060","title":"Complex Hybridization in a Clade of Polytypic Salamanders (Plethodontidae: <i>Desmognathus</i> ) Uncovered by Estimating Higher-Level Phylogenetic Networks","year":2024,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genetic diversity and population structure","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"National Museum of Natural History; National Science Foundation","keywords":"Biology; Clade; Evolutionary biology; Phylogenetic tree; Introgression; Sympatric speciation; Range (aeronautics); Ecology; Gene; Genetics","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":[],"consensus_categories":[],"category_scores_codex":[0.0003113498,0.0001968439,0.000410483,0.0001162465,0.00004406216,0.0000272568,0.0002100009,0.0002980634,0.00003416432],"category_scores_gemma":[0.00009232337,0.000177958,0.00009634274,0.0002616263,0.00009797861,0.000003938448,0.0001095646,0.0001172461,0.000004059613],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002148401,"about_ca_system_score_gemma":0.0000578364,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000420595,"about_ca_topic_score_gemma":0.00002936085,"domain_scores_codex":[0.9983281,0.0003890559,0.0005618807,0.0003809398,0.00009700753,0.0002429445],"domain_scores_gemma":[0.9993441,0.00008270825,0.000188988,0.0002804005,0.00005498542,0.00004882782],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001081009,0.00009446503,0.05109378,0.01806158,0.0004966262,0.00001002443,0.0004826334,0.03925263,0.8807977,0.004742574,0.003824845,0.001035024],"study_design_scores_gemma":[0.008881265,0.002731923,0.1712442,0.01576868,0.00125296,0.0002994201,0.001642449,0.7265069,0.05077637,0.01284068,0.003865084,0.00418997],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.799612,0.00400554,0.1941782,0.0001277107,0.001063288,0.0006636531,0.000113873,0.00002955051,0.0002061377],"genre_scores_gemma":[0.9928693,0.00002525665,0.006193406,0.0001362428,0.00009865523,0.00001786442,0.0005120919,0.00001799515,0.0001291816],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8300213,"threshold_uncertainty_score":0.7256916,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02985144924104458,"score_gpt":0.2739927164527405,"score_spread":0.244141267211696,"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."}}