{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003080445,0.00009001778,0.0001416854,0.00006606884,0.00005972279,0.0000133024,0.0001282091,0.0001415494,0.000007377625],"category_scores_gemma":[0.0001637343,0.00005275009,0.00006071236,0.0001084947,0.0001889032,0.00002257902,0.00006071524,0.0004012627,0.000001835699],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002652509,"about_ca_system_score_gemma":0.0002477171,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002698788,"about_ca_topic_score_gemma":0.00001668669,"domain_scores_codex":[0.9991024,0.00005127858,0.0001966836,0.0001525638,0.0003381184,0.0001590099],"domain_scores_gemma":[0.9992356,0.000158958,0.00007229742,0.0003065162,0.0001452824,0.0000813346],"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":[0.0008014375,0.0001374318,0.01798026,0.0009133249,0.0005151115,0.00001211533,0.005777332,0.0001273619,0.7974832,0.001031651,0.02768859,0.1475322],"study_design_scores_gemma":[0.0006185593,0.0004030032,0.8512875,0.0001136448,0.0002412139,0.00003547249,0.0001961081,0.00665457,0.006189764,0.001399872,0.1327213,0.000138975],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8620321,0.1347407,0.00009622885,0.00168283,0.0002626435,0.0004232328,0.00003774528,0.00001530171,0.0007092716],"genre_scores_gemma":[0.992342,0.005791769,0.000255415,0.00007827719,0.0001194984,0.000003326402,0.00003148534,0.00001543533,0.00136282],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8333072,"threshold_uncertainty_score":0.2151086,"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."}}