{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005437069,0.0001957361,0.0003859791,0.0001777019,0.0003585258,0.00001996262,0.0004331038,0.0001734615,0.0002883248],"category_scores_gemma":[0.0002389759,0.0001000638,0.0003590047,0.000674332,0.0009068684,0.00006605319,0.0001953127,0.0001549178,0.0001169411],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001199257,"about_ca_system_score_gemma":0.0002485658,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001251837,"about_ca_topic_score_gemma":0.00216467,"domain_scores_codex":[0.9983423,0.0004254408,0.0004775163,0.000363549,0.00007745541,0.0003137444],"domain_scores_gemma":[0.997939,0.0003160364,0.0004646562,0.0007744133,0.0004710733,0.00003481568],"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":[0.0002593222,0.0001494299,0.1296404,0.00002096005,0.0005060557,8.673169e-7,0.00009569441,0.0001370541,0.8670921,0.001678605,0.0001279759,0.0002915449],"study_design_scores_gemma":[0.001676245,0.0003153069,0.8827503,0.0001004026,0.001359196,0.00003982435,0.0003442437,0.00008699259,0.1083462,0.001114383,0.003551605,0.0003152653],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9932966,0.001508918,0.00332512,0.0002606654,0.0001330297,0.0005895358,0.000768441,0.00001623148,0.0001014189],"genre_scores_gemma":[0.998244,0.0005703812,0.0001145715,0.00008103505,0.00001509671,0.00003442464,0.0001851819,0.00001768259,0.0007375777],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7587459,"threshold_uncertainty_score":0.4080482,"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."}}