{"id":"W2894893973","doi":"10.1186/s12862-018-1261-7","title":"Environmentally-driven gene content convergence and the Bacillus phylogeny","year":2018,"lang":"en","type":"article","venue":"BMC Evolutionary Biology","topic":"Bacillus and Francisella bacterial research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":30,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University","funders":"Canadian Institutes of Health Research; Consejo Nacional de Ciencia y Tecnología","keywords":"Biology; Polyphyly; Phylogenetics; Monophyly; Phylogenetic tree; Clade; Convergent evolution; Bacillus (shape); Evolutionary biology; Zoology; Gene; Genetics","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":[0.000227776,0.0002292578,0.0002916744,0.001236289,0.0003445799,0.0005755145,0.0002308602,0.0004329873,0.000773162],"category_scores_gemma":[0.0007005836,0.00016045,0.0001931822,0.001047322,0.0003778158,0.0002777247,0.0004563082,0.0003898194,0.0003191458],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000272007,"about_ca_system_score_gemma":0.0002280374,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005859503,"about_ca_topic_score_gemma":0.0005352377,"domain_scores_codex":[0.9997595,0.00003904688,0.00001627617,0.00007272745,0.00005998524,0.0000524471],"domain_scores_gemma":[0.9994096,0.0001609924,0.0001863096,0.00003555696,0.0001192651,0.00008837017],"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":[0.0007741582,0.0000924683,0.1533122,0.0002200905,0.00007171284,0.000239152,0.0006415907,0.00130641,0.8267263,0.0005381085,0.00009415701,0.01598359],"study_design_scores_gemma":[0.00001395793,0.0003650526,0.9459946,0.00005522322,0.00007187363,0.000920639,0.0005410503,0.004896245,0.04442066,0.0009477937,0.001749905,0.00002303322],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979575,0.0002117406,0.001017125,0.0000237707,0.000001740701,0.00000522782,0.0001924844,0.00001578373,0.0005746282],"genre_scores_gemma":[0.9970027,0.0001722178,0.001957836,0.00001475659,0.000003671923,0.00001146169,0.0006656303,0.00001139783,0.0001603837],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001236289,"threshold_uncertainty_score":0.002586484,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02609273497945524,"score_gpt":0.24883666908632,"score_spread":0.2227439341068647,"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."}}