{"id":"W4416794297","doi":"10.1093/nsr/nwaf542","title":"Horizontal gene transfer and gene loss drove the divergent evolution of host dependency in Micrarchaeota","year":2025,"lang":"en","type":"article","venue":"National Science Review","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Institute of Infection and Immunity","funders":"National Natural Science Foundation of China; John Templeton Foundation; National Science Foundation","keywords":"Horizontal gene transfer; Archaea; Gene; Genome; Phylogenetics; Lineage (genetic); Host (biology); Metabolic pathway; Gene pool","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":[0.00056413,0.00006048006,0.00009446612,0.0000391873,0.00008706241,0.000004686146,0.0001882584,0.00002364812,0.000003296578],"category_scores_gemma":[0.00009044915,0.00004302059,0.00003538998,0.0002279112,0.0002795499,0.000001507771,0.0001182623,0.00003208257,5.754262e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003867182,"about_ca_system_score_gemma":0.0002661167,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000392719,"about_ca_topic_score_gemma":0.00008046738,"domain_scores_codex":[0.9993222,0.00002606183,0.0001599198,0.0001964145,0.0001896091,0.0001057808],"domain_scores_gemma":[0.9997034,0.00001190707,0.00002350074,0.0000917387,0.000149542,0.00001988175],"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":[0.000005868922,0.00002715388,0.01230064,0.0001016405,0.00001579102,2.634162e-7,0.00002936429,0.000008099715,0.9779246,0.005412959,0.00003851762,0.004135061],"study_design_scores_gemma":[0.0006442615,0.000193414,0.6840754,0.0004221525,0.00007031361,0.00002686436,0.00005443931,0.00009019883,0.2919929,0.005329266,0.01681459,0.0002862512],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8120798,0.1859057,0.000363856,0.0009064091,0.00007206146,0.0002343809,0.00002778662,4.595339e-7,0.0004095844],"genre_scores_gemma":[0.9242553,0.07536576,0.000166198,0.0001477662,0.00001958686,0.00001527685,0.00000340587,0.000001454604,0.00002522873],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6859317,"threshold_uncertainty_score":0.1754329,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008607275721482118,"score_gpt":0.2704692063762918,"score_spread":0.2618619306548097,"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."}}