{"id":"W2439262910","doi":"10.1186/s12864-016-2643-0","title":"Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution","year":2016,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Microbial infections and disease research","field":"Immunology and Microbiology","cited_by":83,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; U.S. Geological Survey; Universiteit Gent; Western Canada Research Grid; Compute Canada; Canadian Wildlife Health Cooperative; Université de Montréal; Biotechnology and Biological Sciences Research Council; BC Oil and Gas Research and Innovation Society; Killam Trusts; University of Calgary; Weyerhaeuser Company","keywords":"Biology; Erysipelothrix rhusiopathiae; Clade; Phylogenetic tree; Evolutionary biology; Population; Genome; Host (biology); Biological dispersal; Genetic diversity; Phylogenetics; Multilocus sequence typing; Genetics; Gene; Genotype","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":[0.0002645053,0.0002662519,0.0002007021,0.000892397,0.0002010383,0.0003345148,0.0001546598,0.0002902259,0.0005022608],"category_scores_gemma":[0.0005370979,0.00009344735,0.0003330529,0.0008194291,0.0002046524,0.0002093942,0.0003261975,0.0003812161,0.0001969366],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001475909,"about_ca_system_score_gemma":0.0001409965,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006780958,"about_ca_topic_score_gemma":0.001050142,"domain_scores_codex":[0.9997938,0.0000247761,0.00002268826,0.00008207553,0.00004406589,0.00003264811],"domain_scores_gemma":[0.9995286,0.0001375782,0.000207119,0.00003858681,0.00004567655,0.00004251753],"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":[0.0004207336,0.00009381714,0.1442928,0.0002401719,0.0001197704,0.0005392742,0.0008296256,0.000695792,0.8336405,0.0001346887,0.00007597022,0.01891687],"study_design_scores_gemma":[0.0000102714,0.0002888385,0.9620448,0.00002551453,0.00009642059,0.001540924,0.0004621488,0.001597348,0.03242403,0.0000946177,0.001402313,0.00001268027],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9969265,0.0002199569,0.001804876,0.00001611459,0.000002221203,0.00001643153,0.0005923084,0.00001547527,0.0004060858],"genre_scores_gemma":[0.9941207,0.000169038,0.003711313,0.00002134606,0.000003592075,0.00001360867,0.001734036,0.000007083587,0.000219418],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.000892397,"threshold_uncertainty_score":0.001680195,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02238851587019232,"score_gpt":0.2553317491864754,"score_spread":0.2329432333162831,"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."}}