{"id":"W4414160406","doi":"10.1111/nph.70557","title":"The pitfalls of r<scp>DNA</scp>‐based <scp>AMF</scp> identification: a comparative analysis of r<scp>DNA</scp> and protein‐coding genes","year":2025,"lang":"en","type":"article","venue":"New Phytologist","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"Agriculture and Agri-Food Canada","keywords":"Phylogenetic tree; Clade; Paraphyly; Gene; Ribosomal DNA; Phylogenetics; DNA sequencing; Genome; Ribosomal RNA","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001886273,0.0003774214,0.0003956757,0.00118968,0.0003763809,0.0009275321,0.0004694345,0.0006568034,0.0008217616],"category_scores_gemma":[0.003367967,0.0001975652,0.0004001349,0.0008037289,0.0008499488,0.000674419,0.0005252971,0.00103362,0.0008917787],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001926385,"about_ca_system_score_gemma":0.0003701788,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005424031,"about_ca_topic_score_gemma":0.001161472,"domain_scores_codex":[0.9985208,0.0004687737,0.0001340687,0.0002978582,0.0004771732,0.0001013193],"domain_scores_gemma":[0.9969941,0.001490147,0.0005248418,0.0002942751,0.0005688721,0.0001277673],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001512967,0.00003415247,0.01900382,0.0005264631,0.00007001647,0.0006167664,0.0005092715,0.0003574574,0.9153199,0.0006166056,0.0003584719,0.06243585],"study_design_scores_gemma":[0.00001803953,0.00061618,0.2546865,0.0003858144,0.000268486,0.009674523,0.002269026,0.0123914,0.6862964,0.004624731,0.02867366,0.00009520114],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9298339,0.005659514,0.05729108,0.001091004,0.00008003079,0.00008139435,0.0007864368,0.0002782329,0.004898506],"genre_scores_gemma":[0.9320241,0.001749936,0.0636277,0.0005491117,0.00007736578,0.00008334649,0.0009858813,0.0001551606,0.0007475197],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001886273,"threshold_uncertainty_score":0.009975731,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02410013771055275,"score_gpt":0.2823271736741287,"score_spread":0.258227035963576,"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."}}