{"id":"W4408846260","doi":"10.1093/sysbio/syaf021","title":"Massive Inter-species Introgression Overwhelms Phylogenomic Relationships Among Jaguar, Lion, and Leopard","year":2025,"lang":"en","type":"article","venue":"Systematic Biology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"Natural Environment Research Council; Biotechnology and Biological Sciences Research Council","keywords":"Jaguar; Leopard; Biology; Introgression; Panthera; Evolutionary biology; Coalescent theory; Phylogenetic tree; Monophyly; Phylogenetics; Clade; Topology (electrical circuits); Zoology; Genetics; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003700471,0.0002047389,0.000398199,0.0001033139,0.0001922837,0.00003109813,0.0001811452,0.0002439777,0.000005622613],"category_scores_gemma":[0.0002936456,0.0001610788,0.00008180855,0.00008517811,0.0002688125,0.000001065573,0.0003741008,0.0001221676,0.000006307827],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002095866,"about_ca_system_score_gemma":0.00003896161,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001424807,"about_ca_topic_score_gemma":0.00005856884,"domain_scores_codex":[0.9985572,0.0003316657,0.0004477769,0.00039807,0.00003960351,0.0002257486],"domain_scores_gemma":[0.9991888,0.00009373795,0.0001996358,0.0003780886,0.00009046461,0.00004928048],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00004780895,0.0000368261,0.5291466,0.00239183,0.0004214984,0.000001643869,0.0003496328,0.00002781774,0.4587656,0.008187075,0.0004434266,0.0001802995],"study_design_scores_gemma":[0.002503942,0.0009241051,0.9117277,0.003724767,0.0004811652,0.00004740908,0.004767819,0.0007688024,0.05253974,0.01878173,0.002558179,0.001174678],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9866809,0.008401564,0.002719814,0.0002602485,0.0003950307,0.0005867072,0.00001730842,0.000008365133,0.0009301155],"genre_scores_gemma":[0.9984808,0.0002421537,0.0004036298,0.00009641518,0.00009334787,0.0001266646,0.00002578088,0.00001108394,0.0005201244],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4062258,"threshold_uncertainty_score":0.6568601,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01484577405183628,"score_gpt":0.242617631952506,"score_spread":0.2277718579006697,"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."}}