{"id":"W2560156108","doi":"10.1016/j.meegid.2016.12.003","title":"Ascaris phylogeny based on multiple whole mtDNA genomes","year":2016,"lang":"en","type":"article","venue":"Infection Genetics and Evolution","topic":"Parasite Biology and Host Interactions","field":"Environmental Science","cited_by":32,"is_retracted":false,"has_abstract":false,"ca_institutions":"Centre Hospitalier Universitaire Sainte-Justine","funders":"Danish Agency for Science and Higher Education; National Health and Medical Research Council; Forsknings- og Innovationsstyrelsen; University of Surrey; Natural History Museum; Australian Research Council; Wellcome Trust; Medical Research Council; Wellcome","keywords":"Biology; Coalescent theory; Ascaris; Phylogenetic tree; Ascaris suum; Phylogenetics; Evolutionary biology; Population; Mitochondrial DNA; Haplotype; Ascaris lumbricoides; Genome; Most recent common ancestor; Genetics; Zoology; Gene; Helminths; Genotype","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":[0.00007174176,0.00007646345,0.00005339681,0.00004092237,0.0001799241,0.000009599678,0.00003002429,0.00007849257,0.0003747432],"category_scores_gemma":[0.00003099985,0.00005600462,0.00003218669,0.00006751118,0.00009535767,0.00005527763,0.00002457471,0.00004587411,0.0005464339],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001277849,"about_ca_system_score_gemma":0.000005256359,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000154763,"about_ca_topic_score_gemma":0.0002047664,"domain_scores_codex":[0.9994931,0.00003859309,0.00008849514,0.0001860188,0.00006751996,0.0001262661],"domain_scores_gemma":[0.9997184,0.00006702048,0.0000393651,0.000116068,0.000008014847,0.0000511237],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00001568255,0.00004361326,0.8825377,7.234495e-7,0.000004248966,2.017692e-7,0.00001014738,0.0009516806,0.09286044,0.00002292924,0.000372882,0.02317973],"study_design_scores_gemma":[0.0002441153,0.0001421502,0.9303437,0.000005280838,0.000007517129,0.000003269362,0.000002074524,0.005564061,0.002558659,0.0002277154,0.06081801,0.00008349284],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9799511,0.00004796613,0.01608288,0.0002406475,0.0002869221,0.00008517101,0.00001937031,0.00003319238,0.003252778],"genre_scores_gemma":[0.9989196,0.00007958931,0.0001840512,0.0001092164,0.00006145126,0.00001445446,0.000004822005,0.000005110131,0.0006217044],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09030178,"threshold_uncertainty_score":0.7023485,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009995853178964521,"score_gpt":0.2627488951248512,"score_spread":0.2527530419458867,"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."}}