{"id":"W4411599464","doi":"10.1101/2025.06.18.660443","title":"Phylogenomic timetree-calibrated speciation clocks for <i>Caenorhabditis</i> nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Reproductive isolation; Biology; Evolutionary biology; Molecular clock; Genetic algorithm; Caenorhabditis; Caenorhabditis elegans; Ecological speciation; Population; Genetics; Phylogenetics; Genetic variation; Gene","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":[0.0004342923,0.0002396192,0.0002341829,0.001005126,0.0005257557,0.0006324418,0.000284785,0.0003236527,0.001324133],"category_scores_gemma":[0.001233763,0.0002147179,0.0003786893,0.0007400841,0.0003023628,0.0005143716,0.0003488895,0.0005136247,0.0003131656],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004977761,"about_ca_system_score_gemma":0.0001856305,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00283288,"about_ca_topic_score_gemma":0.005278076,"domain_scores_codex":[0.9998364,0.00002779746,0.00001173833,0.00007752988,0.0000265795,0.00001992264],"domain_scores_gemma":[0.9992921,0.0001750113,0.0003020522,0.00007858402,0.0001030174,0.00004912066],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003750355,0.00003840742,0.4593145,0.0003968827,0.0005118074,0.0002273314,0.000717594,0.01421103,0.4959367,0.002298538,0.0006969594,0.02527511],"study_design_scores_gemma":[0.000009787836,0.00007767641,0.947522,0.00004237919,0.000128517,0.0003285604,0.0003650873,0.02791101,0.01941516,0.001148223,0.003007651,0.00004388269],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895958,0.0003420682,0.008092265,0.00003477082,0.000007685747,0.000005373787,0.0007953991,0.0001178712,0.001008712],"genre_scores_gemma":[0.9960834,0.00009072036,0.00294451,0.00001829505,0.000002632996,0.000005447132,0.00071717,0.00004395476,0.0000939215],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00283288,"threshold_uncertainty_score":0.005632818,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01391027865681741,"score_gpt":0.25217405723429,"score_spread":0.2382637785774726,"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."}}