{"id":"W4392126416","doi":"10.1016/j.syapm.2024.126499","title":"Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus","year":2024,"lang":"en","type":"article","venue":"Systematic and Applied Microbiology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":false,"ca_institutions":"McMaster University","funders":"Natural Sciences and Engineering Research Council of Canada; Ontario Research Foundation","keywords":"Biology; Clade; Phylogenetic tree; Phylogenetics; Genome; Evolutionary biology; Indel; Genus; Genetics; Zoology; Gene; Single-nucleotide polymorphism; 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":[0.0008094496,0.0003115279,0.0006395303,0.000133448,0.0002630237,0.00002753361,0.0002147663,0.0001890523,0.000003275925],"category_scores_gemma":[0.00008454955,0.0002050002,0.0001337086,0.0001470832,0.001069896,0.000003735537,0.0001714418,0.0001773104,0.000001409895],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000328256,"about_ca_system_score_gemma":0.00007029434,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001048232,"about_ca_topic_score_gemma":0.00003804753,"domain_scores_codex":[0.9980364,0.0002513674,0.0008536932,0.0004917856,0.0001122944,0.0002544748],"domain_scores_gemma":[0.998886,0.0003120016,0.0002427346,0.0003968894,0.0001148443,0.00004749567],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000118897,0.0000303718,0.0006128566,0.003600877,0.0007507364,0.000001149518,0.002257472,0.001040177,0.9800997,0.01123843,0.0002022434,0.00004703669],"study_design_scores_gemma":[0.002814505,0.001524645,0.1904854,0.003291316,0.002197348,0.0002301184,0.03930763,0.001159548,0.7510354,0.002777368,0.003483933,0.001692822],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9733577,0.02287859,0.00126616,0.0005111906,0.0002005103,0.001243305,0.0003980643,0.000005167275,0.0001392773],"genre_scores_gemma":[0.9980567,0.001090173,0.0003030225,0.00007574446,0.00008217245,0.0001018252,0.0000517394,0.00002653659,0.0002121317],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2290643,"threshold_uncertainty_score":0.8359666,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03045709156874354,"score_gpt":0.2261350816898822,"score_spread":0.1956779901211387,"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."}}