{"id":"W4391361973","doi":"10.1101/2024.01.29.577868","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":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genetic diversity and population structure","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"National Museum of Natural History; George Washington University; Smithsonian Institution; National Science Foundation","keywords":"Biology; Introgression; Evolutionary biology; Clade; Sympatric speciation; Phylogenetic tree; Range (aeronautics); Convergent evolution; Ecology; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000830038,0.0002116191,0.0002522659,0.001667444,0.0004514442,0.0008125203,0.0004141599,0.0005437054,0.0007115232],"category_scores_gemma":[0.003477728,0.0002041658,0.0003447222,0.0008356678,0.0003583278,0.0007256085,0.0006063778,0.0003879912,0.0001165238],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003971457,"about_ca_system_score_gemma":0.000202466,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002142879,"about_ca_topic_score_gemma":0.004690801,"domain_scores_codex":[0.9996008,0.0001686962,0.00002186323,0.0001388515,0.00004027739,0.00002959106],"domain_scores_gemma":[0.9984459,0.0008950817,0.0003715504,0.0001332055,0.00008532978,0.00006888543],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001480263,0.00009199092,0.8196714,0.00016035,0.0003276575,0.0001722463,0.0008176191,0.1211832,0.02372409,0.003200846,0.0002781189,0.03022446],"study_design_scores_gemma":[0.000008280749,0.00005120165,0.3060985,0.00002899226,0.00006804154,0.000155093,0.0004926642,0.6855003,0.001764511,0.0052978,0.0005139781,0.00002059415],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9903679,0.00005057092,0.009058289,0.00002716551,8.827517e-7,0.000009087669,0.0001354248,0.00002842765,0.0003222478],"genre_scores_gemma":[0.9938586,0.00002195276,0.005822957,0.000005675126,0.000002196021,0.000007818248,0.0002386281,0.000003745181,0.00003836302],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002142879,"threshold_uncertainty_score":0.004389703,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02100720813656594,"score_gpt":0.2335746009053263,"score_spread":0.2125673927687604,"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."}}