{"id":"W4415758378","doi":"10.1101/2025.10.30.685713","title":"Phylogenomics and species delimitation in the brown snake <i>Storeria dekayi</i> (Natricidae)","year":2025,"lang":"","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Amphibian and Reptile Biology","field":"Environmental Science","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Subspecies; Paraphyly; Phylogenomics; Phylogenetic tree; Population; Phylogenetics","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000258836,0.0001520796,0.0002184896,0.001208717,0.0005146394,0.0004492291,0.0001717195,0.0002350352,0.001142075],"category_scores_gemma":[0.0002871249,0.0001012635,0.0002354328,0.0008931872,0.0002695609,0.0001448929,0.0004678362,0.0004093947,0.0001782174],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003140176,"about_ca_system_score_gemma":0.000198375,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002794377,"about_ca_topic_score_gemma":0.006505305,"domain_scores_codex":[0.9998603,0.00002053458,0.00000846198,0.00006874514,0.00002092525,0.00002095885],"domain_scores_gemma":[0.9998323,0.00004161585,0.00006972288,0.000009826928,0.00002415794,0.00002236683],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005839317,0.000153399,0.7218161,0.0002068464,0.0001939913,0.0004081005,0.002115998,0.002310198,0.229142,0.001058827,0.0007565487,0.04125409],"study_design_scores_gemma":[0.0000133,0.00006207355,0.9906772,0.00003171607,0.00004795286,0.0002291798,0.0007705427,0.002977537,0.002212121,0.0001929396,0.002775122,0.00001026582],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9983889,0.0001497092,0.0005803206,0.00002503097,0.000002163746,0.000005757171,0.0004072268,0.00001427501,0.0004265643],"genre_scores_gemma":[0.9963686,0.00008054423,0.001621731,0.00003216686,0.000002539603,0.0000133075,0.001629259,0.00001057178,0.0002411956],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002794377,"threshold_uncertainty_score":0.005556226,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01300307527846554,"score_gpt":0.2010596107536977,"score_spread":0.1880565354752322,"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."}}