{"id":"W4394823558","doi":"10.1038/s41588-024-01695-w","title":"The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars","year":2024,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Coffee research and impacts","field":"Medicine","cited_by":85,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Instituut voor Landbouw-, Visserij- en Voedingsonderzoek, Vlaamse Overheid; Vlaamse regering; Instituto Nacional de Ciência e Tecnologia do Café; Natural Sciences and Engineering Research Council of Canada; Fundação Araucária; Universiteit Gent; Fonds Wetenschappelijk Onderzoek; Institut de Recherche pour le Développement; Conselho Nacional de Desenvolvimento Científico e Tecnológico; Universitair Ziekenhuis Gent; Academy of Finland; Helsingin Yliopisto; Fundação de Amparo à Pesquisa do Estado de São Paulo; Nanyang Technological University; European Commission; Directorate for Biological Sciences; Canada Research Chairs; University at Buffalo; Universidade Tecnológica Federal do Paraná; National Science Foundation","keywords":"Biology; Coffea canephora; Coffea arabica; Domestication; Ploidy; Genomics; Genome; Population; Botany; Genetics; Gene","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":[0.0000973783,0.0001929124,0.0001347437,0.0005977112,0.0003126405,0.0003594951,0.0001125581,0.0002335617,0.002210935],"category_scores_gemma":[0.0003082299,0.00008945147,0.0002071388,0.0006676252,0.0001302974,0.000238897,0.0002874446,0.0003214476,0.0002480586],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002171045,"about_ca_system_score_gemma":0.0001100416,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002324385,"about_ca_topic_score_gemma":0.004050802,"domain_scores_codex":[0.9999533,0.000003865764,0.000002468852,0.00002763718,0.000006136008,0.000006640139],"domain_scores_gemma":[0.9998754,0.00002395141,0.00004525362,0.00001442684,0.00001457268,0.00002630543],"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":[0.0005334122,0.00003298343,0.07913934,0.0002647569,0.0001749077,0.0003581323,0.001486776,0.001014367,0.8735629,0.0007490575,0.0006964453,0.04198695],"study_design_scores_gemma":[0.000008795553,0.00006485462,0.9729875,0.00002960738,0.0001017432,0.0006166617,0.0004159189,0.001647004,0.0120341,0.0004826599,0.01159056,0.00002056667],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9948364,0.0008783951,0.001151536,0.00008265435,0.000007528,0.000004632142,0.001968854,0.00008128317,0.0009886601],"genre_scores_gemma":[0.993731,0.0003656127,0.001930173,0.0000619179,0.000008634272,0.000008840764,0.003065705,0.00004275242,0.0007852351],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002324385,"threshold_uncertainty_score":0.00739634,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0208827562971149,"score_gpt":0.2858889327256383,"score_spread":0.2650061764285234,"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."}}