{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T14:04:59Z","timestamp":1790345099545,"version":"4.1.0"},"reference-count":113,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100032203","name":"Danish Data Science Academy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100032203","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF21SA0069429"],"award-info":[{"award-number":["NNF21SA0069429"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF23OC0081468"],"award-info":[{"award-number":["NNF23OC0081468"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008398","name":"Villum Fonden","doi-asserted-by":"publisher","award":["40516"],"award-info":[{"award-number":["40516"]}],"id":[{"id":"10.13039\/100008398","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background and Aims<\/jats:title>\n                    <jats:p>Complex genomic histories shaped by hybridization and polyploidy can influence traits related to plant defence, stress tolerance and toxicity, particularly in Amaranthaceae, which includes crops such as quinoa and spinach. Within this family, white goosefoot (Chenopodium album), a widespread agricultural weed and traditional food resource, belongs to a diploid\u2013polyploid aggregate with extensive phylogenetic discordance. Clarifying its evolutionary history provides context for interpreting ecologically and agronomically relevant trait variation across the aggregate. Building on the established genome-lineage framework, we tested whether discordance persists when constituent genome-lineage components are represented separately and whether the remaining signal is compatible with reticulate evolution.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analysed 2298 conserved nuclear BUSCO families across 27 assembly-level terminals using tree- and network-based approaches. Genome-lineage-aware analyses used 2156 families after separating polyploid Chenopodium into A\u2013H components, with Dysphania ambrosioides as an outgroup. HyDe tested site-pattern asymmetry under global false-discovery-rate correction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Key Results<\/jats:title>\n                    <jats:p>Assembly-level analyses grouped the Danish C. album aggregate accession Ca6-1 with hexaploid C. album sensu stricto dcCheAlbu1.1, whereas relationships among surrounding Chenopodium taxa were less stable. Genome-lineage-aware analyses recovered the expected B-, C- and D-affinity relationships, but substantial gene-family heterogeneity persisted. Reticulate network models fitted the assembly-level data better than bifurcating models, although inferred patterns differed between methods. HyDe detected significant site-pattern asymmetry in a small subset of loci, with most retained signal shared between the focal assemblies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Gene-tree discordance persists in the C. album aggregate after genome-lineage separation. The established genome-lineage framework captures the dominant phylogenomic structure, while residual heterogeneity is compatible with both tree-like and reticulate processes without identifying direct progenitors or a unique hybridization history. This framework supports future analyses of lineage-specific and trait-associated loci related to plant defence, food quality and toxicity in C. album and related Amaranthaceae.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/aob\/mcag290","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T10:12:04Z","timestamp":1788948724000},"source":"Crossref","is-referenced-by-count":0,"title":["Phylogenomics reveals persistent gene-tree discordance in the\n                    <i>Chenopodium album<\/i>\n                    aggregate"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-6517-1521","authenticated-orcid":false,"given":"Kate","family":"Escobar","sequence":"first","affiliation":[{"name":"Department of Plant and Environmental Sciences, University of Copenhagen , Frederiksberg 1871 ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6009-9581","authenticated-orcid":false,"given":"Josefin","family":"Stiller","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Copenhagen , Copenhagen N 2200 ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4141-2410","authenticated-orcid":false,"given":"Pablo D","family":"C\u00e1rdenas","sequence":"additional","affiliation":[{"name":"Department of Plant and Environmental Sciences, University of Copenhagen , Frederiksberg 1871 ,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092509461379300_mcag290-B1","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.envexpbot.2012.07.004","article-title":"Salt tolerance mechanisms in quinoa (Chenopodium quinoa Willd.)","volume":"92","author":"Adolf","year":"2013","journal-title":"Environmental and Experimental Botany"},{"key":"2026092509461379300_mcag290-B2","first-page":"215","volume-title":"Springer series in statistics","author":"Akaike","year":"1974"},{"key":"2026092509461379300_mcag290-B3","first-page":"149","volume-title":"Methods in molecular biology","author":"Altenhoff","year":"2019"},{"key":"2026092509461379300_mcag290-B4","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1111\/j.1365-3180.2010.00836.x","article-title":"Evaluation of changes in weed flora in arable fields of nordic countries\u2014based on Danish long-term surveys","volume":"51","author":"Andreasen","year":"2011","journal-title":"Weed Research"},{"key":"2026092509461379300_mcag290-B5","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/j.gde.2007.09.001","article-title":"A genomic view of introgression and hybrid speciation","volume":"17","author":"Baack","year":"2007","journal-title":"Current Opinion in Genetics & Development"},{"key":"2026092509461379300_mcag290-B6","doi-asserted-by":"publisher","first-page":"5357","DOI":"10.1007\/s11356-018-04104-y","article-title":"A global perspective on the biology, impact and management of Chenopodium album and Chenopodium murale: two troublesome agricultural and environmental weeds","volume":"26","author":"Bajwa","year":"2019","journal-title":"Environmental Science and Pollution Research International"},{"key":"2026092509461379300_mcag290-B7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0241206","article-title":"The major satellite DNA families of the diploid Chenopodium album aggregate species: arguments for and against the \"library hypothesis\"","volume":"15","author":"Belyayev","year":"2020","journal-title":"PLoS One"},{"key":"2026092509461379300_mcag290-B8","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/s13100-020-00219-7","article-title":"Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome","volume":"11","author":"Belyayev","year":"2020","journal-title":"Mobile DNA"},{"key":"2026092509461379300_mcag290-B9","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1093\/sysbio\/syy023","article-title":"Hyde: a python package for genome-scale hybridization detection","volume":"67","author":"Blischak","year":"2018","journal-title":"Systematic Biology"},{"key":"2026092509461379300_mcag290-B10","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1126\/science.1252076","article-title":"Genomic signatures of specialized metabolism in plants","volume":"344","author":"Chae","year":"2014","journal-title":"Science"},{"key":"2026092509461379300_mcag290-B11","first-page":"47","article-title":"Interspecific relationships and intraspecific variation of Chenopodium album L. in Britain 1. 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