{"id":"W4414434373","doi":"10.1101/2025.09.22.677722","title":"Placing very long branch taxa in the plant tree of life: a case study with Dioscoreales mycoheterotrophs","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Plant Diversity and Evolution","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Biotechnology and Biological Sciences Research Council; Korea University; Western Canada Research Grid; Compute Canada; Natural Sciences and Engineering Research Council of Canada; James Hutton Institute","keywords":"Phylogenetic tree; Taxon; Phylogenetics; Tree of life (biology); Range (aeronautics); Phylogenomics; Sister group; Convergent evolution","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":[0.001085644,0.0004086223,0.0003974078,0.0009669652,0.002603601,0.001006624,0.0006105292,0.0007985823,0.001101574],"category_scores_gemma":[0.002080441,0.0001812746,0.0002745096,0.001344864,0.001009463,0.0007696563,0.001305931,0.0009526209,0.0002055653],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008229908,"about_ca_system_score_gemma":0.0005356041,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.007532352,"about_ca_topic_score_gemma":0.02459327,"domain_scores_codex":[0.9995204,0.000160135,0.00003051261,0.0001202433,0.00006406238,0.0001045715],"domain_scores_gemma":[0.9987029,0.0006087656,0.0002802395,0.0001003786,0.00008752726,0.0002202541],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005079814,0.0001762616,0.8361046,0.0002590391,0.00008572489,0.08077646,0.01728183,0.00121201,0.01906962,0.002322513,0.0008971225,0.04130692],"study_design_scores_gemma":[0.00002116817,0.000453277,0.8424542,0.0002883011,0.0001702879,0.08648928,0.03997285,0.004469363,0.004129886,0.005198504,0.01626364,0.00008920664],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982414,0.0003657573,0.0005926269,0.0001159141,0.000003566649,0.000008964401,0.00005142913,0.000005573985,0.000614808],"genre_scores_gemma":[0.9970406,0.0002805779,0.002218196,0.00008782452,0.000009201135,0.000005147851,0.00008421832,0.000009611601,0.0002647207],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007532352,"threshold_uncertainty_score":0.01497704,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02265237723715186,"score_gpt":0.1926563232873964,"score_spread":0.1700039460502446,"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."}}