{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T12:23:21Z","timestamp":1789129401820,"version":"build-2803163510"},"reference-count":120,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T00:00:00Z","timestamp":1788566400000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"JSPS KAKENHI","award":["26K08749"],"award-info":[{"award-number":["26K08749"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group\u2014a model for plant speciation and domestication\u2014the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.<\/jats:p>","DOI":"10.1093\/gbe\/evag191","type":"journal-article","created":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T11:24:31Z","timestamp":1785151471000},"source":"Crossref","is-referenced-by-count":1,"title":["Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild\n                    <i>Oryza<\/i>\n                    AA-Genome Species With Widely Separated Contemporary Distributions"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1615-5077","authenticated-orcid":false,"given":"Kanako O","family":"Koyanagi","sequence":"first","affiliation":[{"name":"Faculty of Information Science and Technology, Hokkaido University , Sapporo 060-0814 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuta","family":"Kotoku","sequence":"additional","affiliation":[{"name":"Graduate School of Agriculture, Hokkaido University , Sapporo 060-8589 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0942-3371","authenticated-orcid":false,"given":"Yuji","family":"Kishima","sequence":"additional","affiliation":[{"name":"Research Faculty of Agriculture, Hokkaido University , Sapporo 060-8589 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,5]]},"reference":[{"key":"2026091107172342200_evag191-B1","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1111\/j.1420-9101.2012.02599.x","article-title":"Hybridization and speciation","volume":"26","author":"Abbott","year":"2013","journal-title":"J Evol Biol"},{"key":"2026091107172342200_evag191-B2","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1186\/s12864-025-11246-0","article-title":"The genomes of the most diverse AA genome rice species provide a resource for rice improvement and studies of rice evolution and domestication","volume":"26","author":"Abdullah","year":"2025","journal-title":"BMC Genomics"},{"key":"2026091107172342200_evag191-B3","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1126\/science.1209202","article-title":"The shaping of modern human immune systems by multiregional admixture with archaic humans","volume":"334","author":"Abi-Rached","year":"2011","journal-title":"Science"},{"key":"2026091107172342200_evag191-B4","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2026091107172342200_evag191-B5","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1002\/j.1537-2197.1938.tb09237.x","article-title":"Hybridization in Tradescantia. III. The evidence for introgressive hybridization","volume":"25","author":"Anderson","year":"1938","journal-title":"Am J Bot"},{"key":"2026091107172342200_evag191-B6","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.plantsci.2013.10.007","article-title":"Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?","volume":"215\u2013216","author":"Atwell","year":"2014","journal-title":"Plant Sci"},{"key":"2026091107172342200_evag191-B7","doi-asserted-by":"publisher","first-page":"2071","DOI":"10.5194\/cp-14-2071-2018","article-title":"Climate evolution across the mid-brunhes transition","volume":"14","author":"Barth","year":"2018","journal-title":"Clim Past"},{"key":"2026091107172342200_evag191-B8","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/sysbio\/syz056","article-title":"Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data","volume":"69","author":"Blair","year":"2020","journal-title":"Syst Biol"},{"key":"2026091107172342200_evag191-B9","doi-asserted-by":"publisher","first-page":"e1006650","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"Bouckaert","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2026091107172342200_evag191-B10","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1023\/A:1005825519998","article-title":"Alien introgression in rice","volume":"35","author":"Brar","year":"1997","journal-title":"Plant Mol Biol"},{"key":"2026091107172342200_evag191-B11","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1111\/pbi.12674","article-title":"Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice","volume":"15","author":"Brozynska","year":"2017","journal-title":"Plant Biotechnol J"},{"key":"2026091107172342200_evag191-B12","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1111\/pbi.12454","article-title":"Genomics of crop wild relatives: expanding the gene pool for crop improvement","volume":"14","author":"Brozynska","year":"2016","journal-title":"Plant Biotechnol J"},{"key":"2026091107172342200_evag191-B13","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1007\/BF00041576","article-title":"The origin, evolution, cultivation, dissemination, and diversification of Asian and African rices","volume":"25","author":"Chang","year":"1976","journal-title":"Euphytica"},{"key":"2026091107172342200_evag191-B14","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1266\/ggs.77.323","article-title":"Evolutionary relationships among rice species with AA genome based on SINE insertion analysis","volume":"77","author":"Cheng","year":"2002","journal-title":"Genes Genet Syst"},{"key":"2026091107172342200_evag191-B15","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1093\/sysbio\/syp054","article-title":"Species trees from highly incongruent gene trees in rice","volume":"58","author":"Cranston","year":"2009","journal-title":"Syst Biol"},{"key":"2026091107172342200_evag191-B16","doi-asserted-by":"publisher","first-page":"2274","DOI":"10.1016\/j.cub.2018.05.066","article-title":"The rise and fall of African rice cultivation revealed by analysis of 246 new genomes","volume":"28","author":"Cubry","year":"2018","journal-title":"Curr Biol"},{"key":"2026091107172342200_evag191-B17","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/s10528-006-9062-x","article-title":"Phylogenetic analysis of AA-genome Oryza species (Poaceae) based on chloroplast, mitochondrial, and nuclear DNA sequences","volume":"45","author":"Duan","year":"2007","journal-title":"Biochem Genet"},{"key":"2026091107172342200_evag191-B18","doi-asserted-by":"publisher","first-page":"2239","DOI":"10.1093\/molbev\/msr048","article-title":"Testing for ancient admixture between closely related populations","volume":"28","author":"Durand","year":"2011","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B19","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1007\/978-1-0716-0199-0_2","article-title":"Processing and analyzing multiple genomes alignments with MafFilter","volume":"2090","author":"Dutheil","year":"2020","journal-title":"Methods Mol Biol"},{"key":"2026091107172342200_evag191-B20","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1146\/annurev-genet-021821-020805","article-title":"Prevalence and adaptive impact of introgression","volume":"55","author":"Edelman","year":"2021","journal-title":"Annu Rev Genet"},{"key":"2026091107172342200_evag191-B21","doi-asserted-by":"publisher","first-page":"737","DOI":"10.3732\/ajb.1400024","article-title":"Is gene flow the most important evolutionary force in plants?","volume":"101","author":"Ellstrand","year":"2014","journal-title":"Am J Bot"},{"key":"2026091107172342200_evag191-B22","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1111\/eva.13565","article-title":"Identifying and addressing methodological incongruence in phylogenomics: a review","volume":"16","author":"Fleming","year":"2023","journal-title":"Evol Appl"},{"key":"2026091107172342200_evag191-B23","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1093\/molbev\/msz296","article-title":"A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis","volume":"37","author":"Flouri","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B24","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.1038\/s41588-025-02183-5","article-title":"Oryza genome evolution through a tetraploid lens","volume":"57","author":"Fornasiero","year":"2025","journal-title":"Nat Genet"},{"key":"2026091107172342200_evag191-B25","doi-asserted-by":"publisher","first-page":"1981","DOI":"10.1007\/s00122-019-03332-1","article-title":"Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication","volume":"132","author":"Fujino","year":"2019","journal-title":"Theor Appl Genet"},{"key":"2026091107172342200_evag191-B26","doi-asserted-by":"publisher","first-page":"10274","DOI":"10.1073\/pnas.93.19.10274","article-title":"Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL","volume":"93","author":"Gaut","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026091107172342200_evag191-B27","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/s10725-020-00597-1","article-title":"Genetic relatedness among Ethiopian Oryza longistaminata populations and other AA genome Oryza species","volume":"91","author":"Getachew","year":"2020","journal-title":"Plant Growth Regul"},{"key":"2026091107172342200_evag191-B28","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1104\/pp.16.01340","article-title":"Hybridization in plants: old ideas, new techniques","volume":"173","author":"Goulet","year":"2017","journal-title":"Plant Physiol"},{"key":"2026091107172342200_evag191-B29","doi-asserted-by":"crossref","first-page":"205","DOI":"10.7312\/gran92318-018","volume-title":"Plant speciation","author":"Grant","year":"1981"},{"key":"2026091107172342200_evag191-B30","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1126\/science.1188021","article-title":"A draft sequence of the Neandertal genome","volume":"328","author":"Green","year":"2010","journal-title":"Science"},{"key":"2026091107172342200_evag191-B31","doi-asserted-by":"publisher","first-page":"giaf074","DOI":"10.1093\/gigascience\/giaf074","article-title":"Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation","volume":"14","author":"Guang","year":"2025","journal-title":"Gigascience"},{"key":"2026091107172342200_evag191-B32","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1038\/s41586-025-08883-6","article-title":"A pangenome reference of wild and cultivated rice","volume":"642","author":"Guo","year":"2025","journal-title":"Nature"},{"key":"2026091107172342200_evag191-B33","doi-asserted-by":"publisher","first-page":"767635","DOI":"10.3389\/fpls.2022.767635","article-title":"Reticulate evolution in AA-genome wild rice in Australia","volume":"13","author":"Hasan","year":"2022","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B34","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/nature11041","article-title":"Butterfly genome reveals promiscuous exchange of mimicry adaptations among species","volume":"487","author":"Heliconius Genome Consortium","year":"2012","journal-title":"Nature"},{"key":"2026091107172342200_evag191-B35","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1146\/annurev-earth-032320-104209","article-title":"The mid-pleistocene climate transition","volume":"51","author":"Herbert","year":"2023","journal-title":"Annu Rev Earth Planet Sci"},{"key":"2026091107172342200_evag191-B36","doi-asserted-by":"publisher","first-page":"bav096","DOI":"10.1093\/database\/baw053","article-title":"Ensembl comparative genomics resources","volume":"2016","author":"Herrero","year":"2016","journal-title":"Database"},{"key":"2026091107172342200_evag191-B37","doi-asserted-by":"publisher","first-page":"iyab173","DOI":"10.1093\/genetics\/iyab173","article-title":"Phylogenomic approaches to detecting and characterizing introgression","volume":"220","author":"Hibbins","year":"2022","journal-title":"Genetics"},{"key":"2026091107172342200_evag191-B38","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B39","doi-asserted-by":"publisher","author":"Htut","year":"2021","DOI":"10.21203\/rs.3.rs-717529\/v1"},{"key":"2026091107172342200_evag191-B40","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nature11532","article-title":"A map of rice genome variation reveals the origin of cultivated rice","volume":"490","author":"Huang","year":"2012","journal-title":"Nature"},{"key":"2026091107172342200_evag191-B41","doi-asserted-by":"publisher","first-page":"2669","DOI":"10.1038\/s41467-026-69076-x","article-title":"Digitaria genome analyses indicate introgression may drive local adaptation and herbicide resistance","volume":"17","author":"Huang","year":"2026","journal-title":"Nat Commun"},{"key":"2026091107172342200_evag191-B42","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1038\/nature13408","article-title":"Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA","volume":"512","author":"Huerta-S\u00e1nchez","year":"2014","journal-title":"Nature"},{"key":"2026091107172342200_evag191-B43","doi-asserted-by":"publisher","first-page":"1529","DOI":"10.1093\/pcp\/pcac073","article-title":"Reloading DNA history in rice domestication","volume":"63","author":"Izawa","year":"2022","journal-title":"Plant Cell Physiol"},{"key":"2026091107172342200_evag191-B44","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.pbi.2013.02.014","article-title":"The international Oryza map alignment project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question","volume":"16","author":"Jacquemin","year":"2013","journal-title":"Curr Opin Plant Biol"},{"key":"2026091107172342200_evag191-B45","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1270\/jsbbs.60.518","article-title":"The species of the genus Oryza and transfer of useful genes from wild species into cultivated rice, O. sativa","volume":"60","author":"Jena","year":"2010","journal-title":"Breed Sci"},{"key":"2026091107172342200_evag191-B46","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"2026091107172342200_evag191-B47","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B48","author":"Khush","year":"2001"},{"key":"2026091107172342200_evag191-B49","doi-asserted-by":"publisher","first-page":"308","DOI":"10.5897\/AJB2005.000-3060","article-title":"Contrasting genetic diversity among Oryza longistraminata (a. Chev et Roehr) populations from different geographic origins using AFLP","volume":"4","author":"Kiambi","year":"2005","journal-title":"Afr J Biotechnol"},{"key":"2026091107172342200_evag191-B50","doi-asserted-by":"publisher","first-page":"15655","DOI":"10.1038\/srep15655","article-title":"Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species","volume":"5","author":"Kim","year":"2015","journal-title":"Sci Rep"},{"key":"2026091107172342200_evag191-B51","doi-asserted-by":"publisher","first-page":"bar030","DOI":"10.1093\/database\/bar030","article-title":"Ensembl BioMarts: a hub for data retrieval across taxonomic space","volume":"2011","author":"Kinsella","year":"2011","journal-title":"Database"},{"key":"2026091107172342200_evag191-B52","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.ympev.2013.09.011","article-title":"Bacoca\u2014a heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions","volume":"70","author":"K\u00fcck","year":"2014","journal-title":"Mol Phylogenet Evol"},{"key":"2026091107172342200_evag191-B53","doi-asserted-by":"publisher","first-page":"msac174","DOI":"10.1093\/molbev\/msac174","article-title":"TimeTree 5: an expanded resource for species divergence times","volume":"39","author":"Kumar","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B54","doi-asserted-by":"publisher","first-page":"1278196","DOI":"10.3389\/fpls.2023.1278196","article-title":"Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa","volume":"14","author":"Labroo","year":"2023","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B55","doi-asserted-by":"publisher","first-page":"1769","DOI":"10.1007\/s10722-020-01080-6","article-title":"Genetic diversity of African wild rice (Oryza longistaminata Chev. et Roehr) at the edge of its distribution","volume":"68","author":"Lakew","year":"2021","journal-title":"Genet Resour Crop Evol"},{"key":"2026091107172342200_evag191-B56","doi-asserted-by":"publisher","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2026091107172342200_evag191-B57","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1111\/cla.12491","article-title":"Seeing through the hedge: phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for tertiary relict flora","volume":"38","author":"Li","year":"2022","journal-title":"Cladistics"},{"key":"2026091107172342200_evag191-B58","doi-asserted-by":"publisher","first-page":"1652","DOI":"10.1111\/pbi.14294","article-title":"Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata","volume":"22","author":"Lian","year":"2024","journal-title":"Plant Biotechnol J"},{"key":"2026091107172342200_evag191-B59","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/s12862-015-0459-1","article-title":"Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene","volume":"15","author":"Lin","year":"2015","journal-title":"BMC Evol Biol"},{"key":"2026091107172342200_evag191-B60","doi-asserted-by":"publisher","first-page":"125","DOI":"10.3389\/fpls.2018.00125","article-title":"Function of plant DExD\/H-box RNA helicases associated with ribosomal RNA biogenesis","volume":"9","author":"Liu","year":"2018","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B61","first-page":"51","volume-title":"Grasses: systematics and evolution","author":"Lu","year":"2000"},{"key":"2026091107172342200_evag191-B62","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1002\/bies.201500149","article-title":"How reticulated are species?","volume":"38","author":"Mallet","year":"2016","journal-title":"Bioessays"},{"key":"2026091107172342200_evag191-B63","doi-asserted-by":"publisher","first-page":"943","DOI":"10.4314\/tjs.v49i5.2","article-title":"Gene flow between the wild rice species (Oryza longistaminata) and two varieties of cultivated rice (Oryza sativa) in Kilombero district, Tanzania","volume":"49","author":"Mangosongo","year":"2024","journal-title":"Tanzan J Sci"},{"key":"2026091107172342200_evag191-B64","doi-asserted-by":"publisher","first-page":"e00138","DOI":"10.1016\/j.sciaf.2019.e00138","article-title":"Genetic diversity and differentiation of the African wild rice (Oryza longistaminata chev. et roehr) in Ethiopia","volume":"6","author":"Melaku","year":"2019","journal-title":"Sci Afr"},{"key":"2026091107172342200_evag191-B65","doi-asserted-by":"publisher","first-page":"2727","DOI":"10.1093\/molbev\/msaa106","article-title":"New methods to calculate concordance factors for phylogenomic datasets","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B66","doi-asserted-by":"publisher","first-page":"4360","DOI":"10.1002\/ece3.3989","article-title":"Diversity and evolution of rice progenitors in Australia","volume":"8","author":"Moner","year":"2018","journal-title":"Ecol Evol"},{"key":"2026091107172342200_evag191-B67","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/j.ympev.2018.05.002","article-title":"Chloroplast phylogeography of AA genome rice species","volume":"127","author":"Moner","year":"2018","journal-title":"Mol Phylogenet Evol"},{"key":"2026091107172342200_evag191-B68","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1186\/s12870-020-02689-6","article-title":"Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production","volume":"20","author":"Moner","year":"2020","journal-title":"BMC Plant Biol"},{"key":"2026091107172342200_evag191-B69","doi-asserted-by":"publisher","first-page":"109761","DOI":"10.1016\/j.isci.2024.109761","article-title":"OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata","volume":"27","author":"Myint","year":"2024","journal-title":"iScience"},{"key":"2026091107172342200_evag191-B70","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/pcp\/pcv205","article-title":"OryzaGenome: genome diversity database of wild Oryza species","volume":"57","author":"Ohyanagi","year":"2016","journal-title":"Plant Cell Physiol"},{"key":"2026091107172342200_evag191-B71","doi-asserted-by":"publisher","first-page":"2366","DOI":"10.1093\/bioinformatics\/btw137","article-title":"chromPlot: visualization of genomic data in chromosomal context","volume":"32","author":"Or\u00f3stica","year":"2016","journal-title":"Bioinformatics"},{"key":"2026091107172342200_evag191-B72","doi-asserted-by":"publisher","first-page":"e2000012","DOI":"10.1002\/bies.202000012","article-title":"Ghost introgression: spooky gene flow in the distant past","volume":"42","author":"Ottenburghs","year":"2020","journal-title":"Bioessays"},{"key":"2026091107172342200_evag191-B73","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1093\/sysbio\/syaa102","article-title":"A comprehensive approach to detect hybridization sheds light on the evolution of earth's largest lizards","volume":"70","author":"Pav\u00f3n-V\u00e1zquez","year":"2021","journal-title":"Syst Biol"},{"key":"2026091107172342200_evag191-B74","first-page":"7","article-title":"CODA: convergence diagnosis and output analysis for MCMC","volume":"6","author":"Plummer","year":"2006","journal-title":"R News"},{"key":"2026091107172342200_evag191-B75","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst Biol"},{"key":"2026091107172342200_evag191-B76","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/s42003-018-0171-y","article-title":"Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species","volume":"1","author":"Reuscher","year":"2018","journal-title":"Commun Biol"},{"key":"2026091107172342200_evag191-B77","first-page":"65","article-title":"Phylogenetic consequences of cytoplasmic gene flow in plants","volume":"5","author":"Rieseberg","year":"1991","journal-title":"Evol Trends Plant"},{"key":"2026091107172342200_evag191-B78","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/BF00279649","article-title":"Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21","volume":"236","author":"Ronald","year":"1992","journal-title":"Mol Gen Genet"},{"key":"2026091107172342200_evag191-B79","doi-asserted-by":"publisher","first-page":"1261705","DOI":"10.3389\/fpls.2023.1261705","article-title":"Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species","volume":"14","author":"Saito","year":"2023","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B80","doi-asserted-by":"publisher","first-page":"e6","DOI":"10.1093\/pcp\/pcs183","article-title":"Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics","volume":"54","author":"Sakai","year":"2013","journal-title":"Plant Cell Physiol"},{"key":"2026091107172342200_evag191-B81","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1016\/j.molp.2023.08.003","article-title":"A complete assembly of the rice nipponbare reference genome","volume":"16","author":"Shang","year":"2023","journal-title":"Mol Plant"},{"key":"2026091107172342200_evag191-B82","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1046\/j.1469-8137.2003.00699.x","article-title":"Gene flow from cultivated rice to the wild species Oryza rufipogon under experimental field conditions","volume":"157","author":"Song","year":"2003","journal-title":"New Phytol"},{"key":"2026091107172342200_evag191-B83","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1038\/s41576-023-00620-x","article-title":"Incongruence in the phylogenomics era","volume":"24","author":"Steenwyk","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2026091107172342200_evag191-B84","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/s41588-018-0040-0","article-title":"Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza","volume":"50","author":"Stein","year":"2018","journal-title":"Nat Genet"},{"key":"2026091107172342200_evag191-B85","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1016\/j.ympev.2008.05.015","article-title":"Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa)","volume":"48","author":"Struck","year":"2008","journal-title":"Mol Phylogenet Evol"},{"key":"2026091107172342200_evag191-B86","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1111\/tpj.16142","article-title":"Deep reticulation: the long legacy of hybridization in vascular plant evolution","volume":"114","author":"Stull","year":"2023","journal-title":"Plant J"},{"key":"2026091107172342200_evag191-B87","doi-asserted-by":"publisher","first-page":"20170688","DOI":"10.1098\/rsbl.2017.0688","article-title":"Adaptive introgression: a plant perspective","volume":"14","author":"Suarez-Gonzalez","year":"2018","journal-title":"Biol Lett"},{"key":"2026091107172342200_evag191-B88","doi-asserted-by":"publisher","first-page":"W609","DOI":"10.1093\/nar\/gkl315","article-title":"PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments","volume":"34","author":"Suyama","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2026091107172342200_evag191-B89","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1186\/1471-2105-13-209","article-title":"Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython","volume":"13","author":"Talevich","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2026091107172342200_evag191-B90","doi-asserted-by":"publisher","first-page":"19333","DOI":"10.1073\/pnas.1213199109","article-title":"Estimating divergence times in large molecular phylogenies","volume":"109","author":"Tamura","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026091107172342200_evag191-B91","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2026091107172342200_evag191-B92","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1016\/j.ympev.2009.08.007","article-title":"Phylogeny and biogeography of the rice tribe (Oryzeae): evidence from combined analysis of 20 chloroplast fragments","volume":"54","author":"Tang","year":"2010","journal-title":"Mol Phylogenet Evol"},{"key":"2026091107172342200_evag191-B93","doi-asserted-by":"publisher","first-page":"W122","DOI":"10.1093\/nar\/gkx382","article-title":"agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update","volume":"45","author":"Tian","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026091107172342200_evag191-B94","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1016\/j.tig.2020.06.002","article-title":"Molecular clocks without rocks: new solutions for old problems","volume":"36","author":"Tiley","year":"2020","journal-title":"Trends Genet"},{"key":"2026091107172342200_evag191-B95","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s12284-023-00630-7","article-title":"Can the wild perennial, rhizomatous rice species Oryza longistaminata be a candidate for de novo domestication?","volume":"16","author":"Tong","year":"2023","journal-title":"Rice"},{"key":"2026091107172342200_evag191-B96","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1111\/tpj.13803","article-title":"Overcoming the species hybridization barrier by ploidy manipulation in the genus Oryza","volume":"93","author":"Tonosaki","year":"2018","journal-title":"Plant J"},{"key":"2026091107172342200_evag191-B97","doi-asserted-by":"publisher","first-page":"1776","DOI":"10.1111\/j.0014-3820.2003.tb00585.x","article-title":"A model for chloroplast capture","volume":"57","author":"Tsitrone","year":"2003","journal-title":"Evolution"},{"key":"2026091107172342200_evag191-B98","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1270\/jsbbs.55.113","article-title":"On the phylogeny and biogeography of the genus Oryza","volume":"55","author":"Vaughan","year":"2005","journal-title":"Breed Sci"},{"key":"2026091107172342200_evag191-B99","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1016\/j.plantsci.2008.01.016","article-title":"The evolving story of rice evolution","volume":"174","author":"Vaughan","year":"2008","journal-title":"Plant Sci"},{"key":"2026091107172342200_evag191-B100","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/S1369-5266(03)00009-8","article-title":"Diversity in the Oryza genus","volume":"6","author":"Vaughan","year":"2003","journal-title":"Curr Opin Plant Biol"},{"key":"2026091107172342200_evag191-B101","doi-asserted-by":"publisher","first-page":"2392","DOI":"10.1093\/bioinformatics\/btx155","article-title":"IcyTree: rapid browser-based visualization for phylogenetic trees and networks","volume":"33","author":"Vaughan","year":"2017","journal-title":"Bioinformatics"},{"key":"2026091107172342200_evag191-B102","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1016\/j.molp.2022.03.009","article-title":"Twenty years of rice genomics research: from sequencing and functional genomics to quantitative genomics","volume":"15","author":"Wang","year":"2022","journal-title":"Mol Plant"},{"key":"2026091107172342200_evag191-B103","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s41586-018-0063-9","article-title":"Genomic variation in 3,010 diverse accessions of Asian cultivated rice","volume":"557","author":"Wang","year":"2018","journal-title":"Nature"},{"key":"2026091107172342200_evag191-B104","doi-asserted-by":"publisher","first-page":"534","DOI":"10.1111\/1755-0998.12469","article-title":"HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data","volume":"16","author":"Ward","year":"2016","journal-title":"Mol Ecol Resour"},{"key":"2026091107172342200_evag191-B105","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1093\/sysbio\/syy015","article-title":"Inferring phylogenetic networks using PhyloNet","volume":"67","author":"Wen","year":"2018","journal-title":"Syst Biol"},{"key":"2026091107172342200_evag191-B106","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/S0065-2113(02)78004-8","article-title":"Polyploidy and the evolutionary history of cotton","volume":"78","author":"Wendel","year":"2003","journal-title":"Adv Agron"},{"key":"2026091107172342200_evag191-B107","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"Ggplot2: elegant graphics for data analysis","author":"Wickham","year":"2016","edition":"2nd ed."},{"key":"2026091107172342200_evag191-B108","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1534\/genetics.116.190173","article-title":"Challenges in species tree estimation under the multispecies coalescent model","volume":"204","author":"Xu","year":"2016","journal-title":"Genetics"},{"key":"2026091107172342200_evag191-B109","doi-asserted-by":"publisher","first-page":"100728","DOI":"10.1016\/j.xplc.2023.100728","article-title":"Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus","volume":"5","author":"Xu","year":"2024","journal-title":"Plant Commun"},{"key":"2026091107172342200_evag191-B110","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/j.gene.2011.01.013","article-title":"Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison","volume":"477","author":"Yang","year":"2011","journal-title":"Gene"},{"key":"2026091107172342200_evag191-B111","doi-asserted-by":"publisher","first-page":"D996","DOI":"10.1093\/nar\/gkab1007","article-title":"Ensembl genomes 2022: an expanding genome resource for non-vertebrates","volume":"50","author":"Yates","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026091107172342200_evag191-B112","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1266\/ggs.14-00063","article-title":"Inconsistent diversities between nuclear and plastid genomes of AA genome species in the genus Oryza","volume":"90","author":"Yin","year":"2015","journal-title":"Genes Genet Syst"},{"key":"2026091107172342200_evag191-B113","doi-asserted-by":"publisher","first-page":"E4954","DOI":"10.1073\/pnas.1418307111","article-title":"Rapid diversification of five Oryza AA genomes associated with rice adaptation","volume":"111","author":"Zhang","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026091107172342200_evag191-B114","doi-asserted-by":"publisher","first-page":"908342","DOI":"10.3389\/fpls.2022.908342","article-title":"Understanding the nature of hybrid sterility and divergence of Asian cultivated rice","volume":"13","author":"Zhang","year":"2022","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B115","doi-asserted-by":"publisher","first-page":"5249","DOI":"10.1016\/j.cell.2025.06.034","article-title":"Ancient hybridization underlies tuberization and radiation of the potato lineage","volume":"188","author":"Zhang","year":"2025","journal-title":"Cell"},{"key":"2026091107172342200_evag191-B116","doi-asserted-by":"publisher","first-page":"932737","DOI":"10.3389\/fpls.2022.932737","article-title":"Interspecific hybridization is an important driving force for origin and diversification of Asian cultivated rice Oryza sativa L","volume":"13","author":"Zhou","year":"2022","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B117","doi-asserted-by":"publisher","first-page":"1535880","DOI":"10.3389\/fpls.2025.1535880","article-title":"Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated rice Oryza sativa L","volume":"16","author":"Zhou","year":"2025","journal-title":"Front Plant Sci"},{"key":"2026091107172342200_evag191-B118","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1016\/j.ympev.2013.10.008","article-title":"Phylogenetic relationships and genome divergence among the AA-genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions","volume":"70","author":"Zhu","year":"2014","journal-title":"Mol Phylogenet Evol"},{"key":"2026091107172342200_evag191-B119","doi-asserted-by":"publisher","first-page":"R49","DOI":"10.1186\/gb-2008-9-3-r49","article-title":"Analysis of 142 genes resolves the rapid diversification of the rice genus","volume":"9","author":"Zou","year":"2008","journal-title":"Genome Biol"},{"key":"2026091107172342200_evag191-B120","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1111\/nph.12230","article-title":"Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus","volume":"198","author":"Zou","year":"2013","journal-title":"New Phytol"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/18\/9\/evag191\/70939266\/evag191.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/18\/9\/evag191\/70939266\/evag191.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T11:17:28Z","timestamp":1789125448000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evag191\/8781030"}},"subtitle":[],"editor":[{"given":"Vincent","family":"Castric","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":120,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,2]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evag191","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,9]]},"article-number":"evag191"}}