{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:06:17Z","timestamp":1789171577031,"version":"build-2803163510"},"reference-count":105,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:00:00Z","timestamp":1775520000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100012542","name":"Sichuan Provincial Science and Technology Support Program","doi-asserted-by":"publisher","award":["2025ZNSFSC1129"],"award-info":[{"award-number":["2025ZNSFSC1129"]}],"id":[{"id":"10.13039\/100012542","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32100180"],"award-info":[{"award-number":["32100180"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Cladistics"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Phylogenomics with abundant informative sites offers a powerful means for elucidating complex diversification history. Here, we collected 22 samples from 18 populations representing all species of subgenus\n                    <jats:italic>Caloscordum<\/jats:italic>\n                    (\n                    <jats:italic>Allium<\/jats:italic>\n                    ). Using transcriptome and whole\u2010genome resequencing data, we generated 1755 low\u2010copy nuclear genes and 81 plastid genes. By integrating morphological and phylogenomic evidence, we clarified the subgenus's complex evolutionary histories and speciation patterns. A total of 18 morphological characteristics were analysed, with a taxonomic framework established. Our analyses resolved robust species relationships despite detecting extensive phylogenetic discordances, which were attributed to incomplete lineage sorting (ILS) and hybridization. Specifically, our results suggest that\n                    <jats:italic>A. inutile<\/jats:italic>\n                    originated via rapid budding speciation from the widespread\n                    <jats:italic>A. tubiflorum<\/jats:italic>\n                    . This process likely coincided with mid\u2010Pleistocene glacial\u2013interglacial cycles and may have been reinforced by geographic isolation and ecological adaptation. In contrast, the sole tetraploid species,\n                    <jats:italic>A. peikingense<\/jats:italic>\n                    , was confirmed to be of hybrid origin, derived from\n                    <jats:italic>A. neriniflorum<\/jats:italic>\n                    and\n                    <jats:italic>A. tubiflorum<\/jats:italic>\n                    . This allopolyploidization event appears to have been facilitated by secondary contact between the parent species, which was likely associated with climatic oscillations within the 35\u00b0\u2009N\u201345\u00b0\u2009N arid belt. Overall, our findings elucidate the intricate speciation patterns within\n                    <jats:italic>Caloscordum<\/jats:italic>\n                    and highlight how the interplay of polyploidization, ecological isolation, and tectonic uplift\u2010driven aridification has shaped plant diversity in East Asia.\n                  <\/jats:p>","DOI":"10.1111\/cla.70035","type":"journal-article","created":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T04:49:37Z","timestamp":1775623777000},"page":"425-446","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus\n                    <i>Caloscordum<\/i>\n                    (\n                    <i>Allium<\/i>\n                    , Amaryllidaceae)"],"prefix":"10.1111","volume":"42","author":[{"given":"Rui\u2010Yu","family":"Cheng","sequence":"first","affiliation":[{"name":"Southwest Bio\u2010Resources R&amp;D Key Laboratory of Sichuan Province, Chengdu Botanical Garden\u2010Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences Sichuan University  Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin\u2010Yue","family":"Zhang","sequence":"additional","affiliation":[{"name":"Southwest Bio\u2010Resources R&amp;D Key Laboratory of Sichuan Province, Chengdu Botanical Garden\u2010Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences Sichuan University  Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin\u2010Bo","family":"Tan","sequence":"additional","affiliation":[{"name":"Southwest Bio\u2010Resources R&amp;D Key Laboratory of Sichuan Province, Chengdu Botanical Garden\u2010Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences Sichuan University  Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4561-5258","authenticated-orcid":false,"given":"Jia\u2010Hui","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao\u2010di Herbs, National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Sciences  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1161-8573","authenticated-orcid":false,"given":"Song\u2010Dong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Southwest Bio\u2010Resources R&amp;D Key Laboratory of Sichuan Province, Chengdu Botanical Garden\u2010Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences Sichuan University  Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2064-0112","authenticated-orcid":false,"given":"Xing\u2010Jin","family":"He","sequence":"additional","affiliation":[{"name":"Southwest Bio\u2010Resources R&amp;D Key Laboratory of Sichuan Province, Chengdu Botanical Garden\u2010Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences Sichuan University  Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9244-456X","authenticated-orcid":false,"given":"Deng\u2010Feng","family":"Xie","sequence":"additional","affiliation":[{"name":"Southwest Bio\u2010Resources R&amp;D Key Laboratory of Sichuan Province, Chengdu Botanical Garden\u2010Sichuan University Joint Laboratory for Ex Situ Conservation and Resource Utilization of Mountain Plants, College of Life Sciences Sichuan University  Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,4,7]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13015-019-0159-2"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2013.2980"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw082"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syaa083"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13742-015-0047-8"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_2_9_11_1","first-page":"39","article-title":"Effects of mountain uplift and climatic oscillations on phylogeography and species divergence of Notholirion (Liliaceae)","volume":"137","author":"Cheng R.Y.","year":"2025","journal-title":"J. Hered."},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-025-06982-0"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.11646\/phytotaxa.720.3.2"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.18.00967"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-020-01687-4"},{"key":"e_1_2_9_16_1","first-page":"1342","volume-title":"An Encyclopaedia of Plants (New Edition)","author":"Don G.","year":"1855"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592-005-9073-x"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msr048"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1832-y"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2025.04.009"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2024.12.005"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.5642\/aliso.20062201.31"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/jbi.12658"},{"key":"e_1_2_9_24_1","first-page":"560","article-title":"Subgenus Caloscordum (Herb.) R.M. Fritsch","volume":"49","author":"Fritsch R.M.","year":"1994","journal-title":"Kew Bull."},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1079\/9780851995106.0005"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts565"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-022-03993-z"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2013.04.026"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2008.04.005"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.20432"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1883"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.17786"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2013.084"},{"key":"e_1_2_9_34_1","first-page":"1","article-title":"Cenozoic climate change in eastern Asia: Part I","volume":"510","author":"Hanlie H.","year":"2018","journal-title":"Palaeogeogr. Palaeoclimatol. Palaeoecol."},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2017.05.010"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2023.12.002"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-3169-7"},{"key":"e_1_2_9_38_1","doi-asserted-by":"crossref","unstructured":"Helfrich P. Rieb E. Abrami G. L\u00fccking A.andMehler A. 2018.TreeAnnotator: Versatile visual annotation of hierarchical text relations. Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018).","DOI":"10.63317\/2kvui6d689hn"},{"key":"e_1_2_9_39_1","first-page":"66","article-title":"Caloscordum","volume":"30","author":"Herbert W.","year":"1844","journal-title":"Edwards's Bot. Reg."},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2015.11.004"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw046"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj030"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/sys062"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2023.06.009"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02154-5"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4285"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.30848\/PJB2021-5(1)"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-023-02183-1"},{"key":"e_1_2_9_50_1","first-page":"772","article-title":"PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses","volume":"34","author":"Lanfear R.","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"e_1_2_9_51_1","first-page":"28","article-title":"Study on the introduction and chromosomes of Allium sect. Caloscordum","volume":"16","author":"Li R.J.","year":"1996","journal-title":"Acta Bot. Boreali\u2010Occident. Sin."},{"key":"e_1_2_9_52_1","first-page":"288","article-title":"Studies on karyotype and phylogenetic relationship of the Allium sect. Caloscordum from China","volume":"34","author":"Li R.J.","year":"1996","journal-title":"Acta Phytotax. Sin."},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcq177"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.5194\/cp-15-405-2019"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15407"},{"key":"e_1_2_9_56_1","doi-asserted-by":"publisher","DOI":"10.1111\/cla.12491"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcab140"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.13905"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2025.108422"},{"key":"e_1_2_9_60_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcr291"},{"key":"e_1_2_9_61_1","first-page":"952","article-title":"Comparative study on leaf micromorphology characteristics of Allium tubiflorum and Allium neriniflorum","volume":"53","author":"Lu L.D.","year":"2016","journal-title":"J. Sichuan Univ. Nat. Sci. Ed."},{"key":"e_1_2_9_62_1","first-page":"104","article-title":"Allium (Schoenoprasum) inutile Makino sp. nov","volume":"12","author":"Makino T.","year":"1898","journal-title":"Bot. Mag. (Tokyo)"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13265"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1086\/323280"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2010.11.036"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2023.107869"},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcl148"},{"key":"e_1_2_9_68_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"e_1_2_9_69_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syaf012"},{"key":"e_1_2_9_70_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.0906-7590.2008.5203.x"},{"key":"e_1_2_9_71_1","unstructured":"Rambaut A. 2014.FigTree: A graphical viewer of phylogenetic trees version 1.4.2. Institute of Evolutionary Biology University of Edinburgh UK."},{"key":"e_1_2_9_72_1","first-page":"42","article-title":"Notes on Allium","volume":"44","author":"Rendle A.B.","year":"1906","journal-title":"J. Bot."},{"key":"e_1_2_9_73_1","doi-asserted-by":"publisher","DOI":"10.1111\/jeb.12849"},{"key":"e_1_2_9_74_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa868"},{"key":"e_1_2_9_75_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ers288"},{"key":"e_1_2_9_76_1","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhae330"},{"key":"e_1_2_9_77_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcae141"},{"key":"e_1_2_9_78_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syab006"},{"key":"e_1_2_9_79_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-015-0423-0"},{"key":"e_1_2_9_80_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.palaeo.2023.111951"},{"key":"e_1_2_9_81_1","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/vey016"},{"key":"e_1_2_9_82_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40645-016-0080-y"},{"key":"e_1_2_9_83_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-322"},{"key":"e_1_2_9_84_1","doi-asserted-by":"publisher","DOI":"10.1086\/323880"},{"key":"e_1_2_9_85_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syac011"},{"key":"e_1_2_9_86_1","doi-asserted-by":"publisher","DOI":"10.1002\/evl3.77"},{"key":"e_1_2_9_87_1","article-title":"Allium inutile, a new record species to China","volume":"21","author":"Wang X.H.","year":"1999","journal-title":"Acta Bot. Yunnan."},{"key":"e_1_2_9_88_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-63331-3"},{"key":"e_1_2_9_89_1","doi-asserted-by":"publisher","DOI":"10.1111\/cla.70012"},{"key":"e_1_2_9_90_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.70167"},{"key":"e_1_2_9_91_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syy015"},{"key":"e_1_2_9_92_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43017-022-00331-7"},{"key":"e_1_2_9_93_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcaa024"},{"key":"e_1_2_9_94_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2024.108182"},{"key":"e_1_2_9_95_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13924"},{"key":"e_1_2_9_96_1","first-page":"165","volume-title":"Flora of China","author":"Xu J.M.","year":"2000"},{"key":"e_1_2_9_97_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2024.10.003"},{"key":"e_1_2_9_98_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.4338"},{"key":"e_1_2_9_99_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2023.1124277"},{"key":"e_1_2_9_100_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syad029"},{"key":"e_1_2_9_101_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1059412"},{"key":"e_1_2_9_102_1","doi-asserted-by":"publisher","DOI":"10.1093\/pcp\/pcg121"},{"key":"e_1_2_9_103_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2129-y"},{"key":"e_1_2_9_104_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.13096"},{"key":"e_1_2_9_105_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pld.2023.07.004"},{"key":"e_1_2_9_106_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.673200"}],"container-title":["Cladistics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/cla.70035","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/cla.70035","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/cla.70035","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T23:13:37Z","timestamp":1789168417000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/cla.70035"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,7]]},"references-count":105,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["10.1111\/cla.70035"],"URL":"https:\/\/doi.org\/10.1111\/cla.70035","archive":["Portico"],"relation":{},"ISSN":["0748-3007","1096-0031"],"issn-type":[{"value":"0748-3007","type":"print"},{"value":"1096-0031","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,7]]},"assertion":[{"value":"2026-01-05","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-03-16","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-07","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}