{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:23:19Z","timestamp":1791822199256,"version":"4.3.4"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T00:00:00Z","timestamp":1732233600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CAS \u2018Light of West China\u2019 Program, Yunnan Provincial Science and Technology Mission","award":["202404BI090014"],"award-info":[{"award-number":["202404BI090014"]}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"strategic priority research program of Kunming Institute of Botany, Chinese Academy of Sciences","award":["32471734 and 32360336"],"award-info":[{"award-number":["32471734 and 32360336"]}]},{"name":"strategic priority research program of Kunming Institute of Botany, Chinese Academy of Sciences","award":["KIBXD202401"],"award-info":[{"award-number":["KIBXD202401"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Incomplete lineage sorting (ILS) and introgression\/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination. Here, we addressed these shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining ILS and IH indices to quantify ILS and IH, this tool can detect the extent of ILS and IH among lineages with high reliability, and can visualize them based on the gene tree topology patterns constructed using ASTRAL. We tested Phytop extensively using both simulated and real data, and found that it enables users to quickly and conveniently estimate the extent of ILS and IH, thus clarifying the phylogenetic uncertainty. Phytop is available at https:\/\/github.com\/zhangrengang\/phytop and is expected to contribute to the intuitive and convenient inference of genetic relationships among lineages in future research.<\/jats:p>","DOI":"10.1093\/hr\/uhae330","type":"journal-article","created":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T19:32:30Z","timestamp":1732217550000},"source":"Crossref","is-referenced-by-count":63,"title":["Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6886-7810","authenticated-orcid":false,"given":"Hong-Yun","family":"Shang","sequence":"first","affiliation":[{"name":"Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 101408 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8134-5830","authenticated-orcid":false,"given":"Kai-Hua","family":"Jia","sequence":"additional","affiliation":[{"name":"Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences , Jinan, Shandong 250100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nai-Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences , Nanjing 210014 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Jie","family":"Zhou","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 101408 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Yang","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 101408 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Ling","family":"Tian","sequence":"additional","affiliation":[{"name":"College of characteristic plant research, Guiyang Institute of Humanities and Technology , Guiyang 550025 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7725-3677","authenticated-orcid":false,"given":"Yong-Peng","family":"Ma","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ren-Gang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming, Yunnan 650201 ,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing 101408 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,21]]},"reference":[{"key":"2025030502252761900_ref1","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1038\/s41467-022-29643-4","article-title":"Genomic evidence for homoploid hybrid speciation between ancestors of two different genera","volume":"13","author":"Wang","year":"2022","journal-title":"Nat Commun"},{"key":"2025030502252761900_ref2","doi-asserted-by":"crossref","first-page":"6929","DOI":"10.1038\/s41467-021-26931-3","article-title":"The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms","volume":"12","author":"Ma","year":"2021","journal-title":"Nat Commun"},{"key":"2025030502252761900_ref3","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1111\/jipb.13415","article-title":"Phylogenomics and the flowering plant tree of life","volume":"65","author":"Guo","year":"2023","journal-title":"J Integr Plant Biol"},{"key":"2025030502252761900_ref4","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1016\/j.cell.2022.03.034","article-title":"Incomplete lineage sorting and phenotypic evolution in marsupials","volume":"185","author":"Feng","year":"2022","journal-title":"Cell"},{"key":"2025030502252761900_ref5","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1093\/sysbio\/syaa049","article-title":"Out of sight, out of mind: widespread nuclear and plastid-nuclear discordance in the flowering plant genus Polemonium (Polemoniaceae) suggests widespread historical gene flow despite limited nuclear signal","volume":"70","author":"Rose","year":"2021","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref6","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1093\/sysbio\/syaa083","article-title":"The perfect storm: gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales","volume":"70","author":"Cai","year":"2021","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref7","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1146\/annurev.arplant.043008.092039","article-title":"The role of hybridization in plant speciation","volume":"60","author":"Soltis","year":"2009","journal-title":"Annu Rev Plant Biol"},{"key":"2025030502252761900_ref8","doi-asserted-by":"crossref","first-page":"2337","DOI":"10.1111\/mec.13557","article-title":"A genomic perspective on hybridization and speciation","volume":"25","author":"Payseur","year":"2016","journal-title":"Mol Ecol"},{"key":"2025030502252761900_ref9","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.tree.2009.01.009","article-title":"Gene tree discordance, phylogenetic inference and the multispecies coalescent","volume":"24","author":"Degnan","year":"2009","journal-title":"Trends Ecol Evol"},{"key":"2025030502252761900_ref10","article-title":"Insights into the superrosids phylogeny and flavonoid synthesis from the telomere-to-telomere gap-free genome assembly of Penthorum chinense Pursh","volume":"11","author":"Wang","year":"2024","journal-title":"Hortic Res"},{"key":"2025030502252761900_ref11","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1111\/1755-0998.13833","article-title":"Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids","volume":"23","author":"Liu","year":"2023","journal-title":"Mol Ecol Resour"},{"key":"2025030502252761900_ref12","doi-asserted-by":"crossref","first-page":"2451","DOI":"10.1093\/molbev\/msz112","article-title":"Phylogenomics reveals an ancient hybrid origin of the persian walnut","volume":"36","author":"Zhang","year":"2019","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref13","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1002\/ajb2.1468","article-title":"Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages","volume":"107","author":"Stull","year":"2020","journal-title":"Am J Bot"},{"key":"2025030502252761900_ref14","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1038\/s41467-023-37939-2","article-title":"Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes","volume":"14","author":"Zhang","year":"2023","journal-title":"Nat Commun"},{"key":"2025030502252761900_ref15","article-title":"Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations","volume":"25","author":"Zhang","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025030502252761900_ref16","doi-asserted-by":"crossref","first-page":"1250092","DOI":"10.1126\/science.1250092","article-title":"Ancient hybridizations among the ancestral genomes of bread wheat","volume":"345","author":"Marcussen","year":"2014","journal-title":"Science"},{"key":"2025030502252761900_ref17","doi-asserted-by":"crossref","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":"Syst Biol"},{"key":"2025030502252761900_ref18","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/sysbio\/syab008","article-title":"Gene tree discord, simplex plots, and statistical tests under the coalescent","volume":"71","author":"Allman","year":"2022","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref19","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1111\/1755-0998.13265","article-title":"Dsuite - fast D-statistics and related admixture evidence from VCF files","volume":"21","author":"Malinsky","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2025030502252761900_ref20","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1093\/molbev\/msx307","article-title":"Bayesian inference of species networks from multilocus sequence data","volume":"35","author":"Zhang","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref21","doi-asserted-by":"crossref","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":"2025030502252761900_ref22","doi-asserted-by":"crossref","first-page":"3292","DOI":"10.1093\/molbev\/msx235","article-title":"PhyloNetworks: a package for phylogenetic networks","volume":"34","author":"Sol\u00eds-Lemus","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref23","doi-asserted-by":"crossref","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":"2025030502252761900_ref24","doi-asserted-by":"crossref","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":"2025030502252761900_ref25","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1093\/sysbio\/syaa092","article-title":"Comparative performance of popular methods for hybrid detection using genomic data","volume":"70","author":"Kong","year":"2021","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref26","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13015-019-0159-2","article-title":"NANUQ: a method for inferring species networks from gene trees under the coalescent model","volume":"14","author":"Allman","year":"2019","journal-title":"Algorithms Mol Biol"},{"key":"2025030502252761900_ref27","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2164-16-S10-S10","article-title":"A maximum pseudo-likelihood approach for phylogenetic networks","volume":"16","author":"Yu","year":"2015","journal-title":"BMC Genomics"},{"key":"2025030502252761900_ref28","doi-asserted-by":"crossref","first-page":"16448","DOI":"10.1073\/pnas.1407950111","article-title":"Maximum likelihood inference of reticulate evolutionary histories","volume":"111","author":"Yu","year":"2014","journal-title":"Proc Natl Acad Sci"},{"key":"2025030502252761900_ref29","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005896","article-title":"Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting","volume":"12","author":"Sol\u00eds-Lemus","year":"2016","journal-title":"PLoS Genet"},{"key":"2025030502252761900_ref30","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/sysbio\/syad077","article-title":"Detection of ghost introgression requires exploiting topological and branch length information","volume":"73","author":"Pang","year":"2024","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref31","doi-asserted-by":"crossref","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":"2025030502252761900_ref32","article-title":"Phylogenomic approaches to detecting and characterizing introgression","volume":"220","author":"Hibbins","year":"2022","journal-title":"Genetics"},{"key":"2025030502252761900_ref33","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/sysbio\/syx085","article-title":"Coestimating reticulate phylogenies and gene trees from multilocus sequence data","volume":"67","author":"Wen","year":"2018","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref34","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s12862-015-0423-0","article-title":"Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants","volume":"15","author":"Smith","year":"2015","journal-title":"BMC Evol Biol"},{"key":"2025030502252761900_ref35","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.ympev.2018.01.019","article-title":"DiscoVista: interpretable visualizations of gene tree discordance","volume":"122","author":"Sayyari","year":"2018","journal-title":"Mol Phylogenet Evol"},{"key":"2025030502252761900_ref36","doi-asserted-by":"crossref","first-page":"4949","DOI":"10.1093\/bioinformatics\/btac620","article-title":"ASTRAL-pro 2: ultrafast species tree reconstruction from multi-copy gene family trees","volume":"38","author":"Zhang","year":"2022","journal-title":"Bioinformatics"},{"key":"2025030502252761900_ref37","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.aav9188","article-title":"Pervasive hybridizations in the history of wheat relatives","volume":"5","author":"Gl\u00e9min","year":"2019","journal-title":"Sci Adv"},{"key":"2025030502252761900_ref38","doi-asserted-by":"crossref","DOI":"10.1101\/2024.06.06.597697","article-title":"The accuracy of species tree inference under gene tree dependence","author":"He","year":"2024"},{"key":"2025030502252761900_ref39","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msad049","article-title":"Recombination variation shapes phylogeny and introgression in wild diploid strawberries","volume":"40","author":"Feng","year":"2023","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref40","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1038\/s41586-024-07324-0","article-title":"Phylogenomics and the rise of the angiosperms","volume":"629","author":"Zuntini","year":"2024","journal-title":"Nature"},{"key":"2025030502252761900_ref41","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1186\/s12915-021-01166-2","article-title":"Plastid phylogenomic insights into relationships of all flowering plant families","volume":"19","author":"Li","year":"2021","journal-title":"BMC Biol"},{"key":"2025030502252761900_ref42","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41597-021-00997-6","article-title":"The world checklist of vascular plants, a continuously updated resource for exploring global plant diversity","volume":"8","author":"Govaerts","year":"2021","journal-title":"Sci Data"},{"key":"2025030502252761900_ref43","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1111\/jipb.13455","article-title":"Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets","volume":"65","author":"Hu","year":"2023","journal-title":"J Integr Plant Biol"},{"key":"2025030502252761900_ref44","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/sysbio\/syab035","article-title":"A comprehensive phylogenomic platform for exploring the angiosperm tree of life","volume":"71","author":"Baker","year":"2022","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref45","doi-asserted-by":"crossref","first-page":"6930","DOI":"10.1038\/s41467-021-26922-4","article-title":"Chloranthus genome provides insights into the early diversification of angiosperms","volume":"12","author":"Guo","year":"2021","journal-title":"Nat Commun"},{"key":"2025030502252761900_ref46","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1038\/s41477-021-00990-2","article-title":"Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome","volume":"7","author":"Qin","year":"2021","journal-title":"Nat Plants"},{"key":"2025030502252761900_ref47","first-page":"20181012","article-title":"Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms","volume":"2018","author":"Ran","year":"1881","journal-title":"Proc R Soc B Biol Sci"},{"key":"2025030502252761900_ref48","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1002\/ajb2.1048","article-title":"Plastid phylogenomic analysis of green plants: a billion years of evolutionary history","volume":"105","author":"Gitzendanner","year":"2018","journal-title":"Am J Bot"},{"key":"2025030502252761900_ref49","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1038\/s42003-021-02697-8","article-title":"Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production","volume":"4","author":"Song","year":"2021","journal-title":"Commun Biol"},{"key":"2025030502252761900_ref50","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/s41477-022-01129-7","article-title":"The Cycas genome and the early evolution of seed plants","volume":"8","author":"Liu","year":"2022","journal-title":"Nat Plants"},{"key":"2025030502252761900_ref51","doi-asserted-by":"crossref","first-page":"0126","DOI":"10.1038\/s41559-017-0126","article-title":"Contentious relationships in phylogenomic studies can be driven by a handful of genes","volume":"1","author":"Shen","year":"2017","journal-title":"Nat Ecol Evol"},{"key":"2025030502252761900_ref52","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1093\/sysbio\/syac002","article-title":"On the need for new measures of phylogenomic support","volume":"71","author":"Thomson","year":"2022","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref53","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1093\/sysbio\/syab024","article-title":"Most genomic loci misrepresent the phylogeny of an avian radiation because of ancient gene flow","volume":"70","author":"Zhang","year":"2021","journal-title":"Syst Biol"},{"key":"2025030502252761900_ref54","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1093\/bioinformatics\/btr124","article-title":"Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios","volume":"27","author":"Laurent","year":"2011","journal-title":"Bioinformatics"},{"key":"2025030502252761900_ref55","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1111\/tpj.15399","article-title":"Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation","volume":"107","author":"Ma","year":"2021","journal-title":"Plant J"},{"key":"2025030502252761900_ref56","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2025030502252761900_ref57","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025030502252761900_ref58","doi-asserted-by":"crossref","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":"Standley","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref59","doi-asserted-by":"crossref","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":"2025030502252761900_ref60","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Gutierrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2025030502252761900_ref61","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref62","doi-asserted-by":"crossref","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":"2025030502252761900_ref63","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref64","doi-asserted-by":"crossref","first-page":"1669","DOI":"10.1093\/bioinformatics\/btq243","article-title":"The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell","volume":"26","author":"Junier","year":"2010","journal-title":"Bioinformatics"},{"key":"2025030502252761900_ref65","article-title":"Robust identification of orthologous synteny with the Orthology index and its applications in reconstructing the evolutionary history of plant genomes","author":"Zhang","year":"2024"},{"key":"2025030502252761900_ref66","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac215","article-title":"Weighting by gene tree uncertainty improves accuracy of quartet-based species trees","volume":"39","author":"Zhang","year":"2022","journal-title":"Mol Biol Evol"},{"key":"2025030502252761900_ref67","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1093\/molbev\/msw046","article-title":"ETE 3: reconstruction, analysis, and visualization of phylogenomic data","volume":"33","author":"Huerta-Cepas","year":"2016","journal-title":"Mol Biol Evol"}],"container-title":["Horticulture Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hr\/advance-article-pdf\/doi\/10.1093\/hr\/uhae330\/60781215\/uhae330.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/12\/3\/uhae330\/60781215\/uhae330.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/12\/3\/uhae330\/60781215\/uhae330.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T21:26:08Z","timestamp":1741123568000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hr\/article\/doi\/10.1093\/hr\/uhae330\/7906583"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,21]]},"references-count":67,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,2,28]]}},"URL":"https:\/\/doi.org\/10.1093\/hr\/uhae330","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.09.02.610893","asserted-by":"object"}]},"ISSN":["2052-7276"],"issn-type":[{"value":"2052-7276","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,3]]},"published":{"date-parts":[[2024,11,21]]},"article-number":"uhae330"}}