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dc.contributor.authorGagnon, Edeline
dc.contributor.authorHilgenhof, Rebecca
dc.contributor.authorOrejuela, Andrés
dc.contributor.authorMcDonnell, Angela J.
dc.contributor.authorSablok, Gaurav
dc.contributor.authorAubriot, Xavier
dc.contributor.authorGiacomin, Leandro
dc.contributor.authorGouvêa, Yuri
dc.contributor.authorBragionis, Thamyris
dc.contributor.authorStehmann, João Renato
dc.contributor.authorBohs, Lynn
dc.contributor.authorDodsworth, Steven
dc.contributor.authorMartine, Christopher
dc.contributor.authorPoczai, Péter
dc.contributor.authorKnapp, Sandra
dc.contributor.authorSärkinen, Tiina
dc.identifier.citationGagnon E, Hilgenhof R, Orejuela A, McDonnell A, Sablok G, Aubriot X, Giacomin L, Gouvêa Y, Bragionis T, Stehmann JR, Bohs L, Dodsworth S, Martine C, Poczai P, Knapp S, Särkinen T (2022) 'Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum', American Journal of Botany, 109 (4), pp.580-601.en_US
dc.description.abstractPremise: Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). Results: While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. Conclusions: We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.en_US
dc.description.sponsorshipThis work was supported by the Fonds de recherche du Québec en Nature et Technologies postdoctoral fellowship and a grant from the Department of Biological Sciences of the University of Moncton to E.G., the Sibbald Trust fellowship to R.H., the Ceiba Foundation to A.O., CNPq Conselho Nacional de Desenvolvimento Científico e Tecnológico awards 479921/2010-54 and 427198/2016-0 and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior CAPES/FAPESPA award 88881.159124/2017-01 to L.L.G., NSF through grant DEB-0316614 “PBI Solanum: a worldwide treatment” to S.K. and L.B., the Calleva Foundation & Sackler Trust (Plant and Fungal Trees of Life Project at Kew), the LUOMUS Trigger and Systematics Research Fund to P.P., the OECD CRP and Eötvös Research Grant (MAEÖ−00074-002/2021). Field sampling was supported by the Northern Territory Herbarium (Palmerston, Northern Territory, Australia), and the David Burpee Endowment at Bucknell University (Lewisburg, Pennsylvania, USA) and National Geographic Society Northern Europe Award GEFNE49-12 (Peru, TS). Peruvian specimens were collected and sequenced under the permission of Ministerio de Agricultura, Dirección General Forestal y de Fauna Silvestre (collection permits 084-2012-AG-DGFFSDGEFFS and 096-2017-SERFOR/DGGSPFFS, and genetic resource permit 008-2014-MINAGRI-DGFFS/DGEFFS).en_US
dc.publisherJohn Wiley and Sons Incen_US
dc.rightsGreen - can archive pre-print and post-print or publisher's version/PDF
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International*
dc.subjectmultilocus phylogenetic treesen_US
dc.subjectshort backbone branchesen_US
dc.subjectincomplete lineage sortingen_US
dc.subjecthard polytomyen_US
dc.subjecttarget captureen_US
dc.subjectnuclear-plastid discordancesen_US
dc.subjectSubject Categories::C400 Geneticsen_US
dc.titlePhylogenomic discordance suggests polytomies along the backbone of the large genus Solanumen_US
dc.contributor.departmentRoyal Botanic Garden Edinburghen_US
dc.contributor.departmentUniversity of Edinburghen_US
dc.contributor.departmentChicago Botanic Gardenen_US
dc.contributor.departmentUniversity of Helsinkien_US
dc.contributor.departmentUniversité Paris‐Saclayen_US
dc.contributor.departmentUniversidade Federal do Oeste do Paráen_US
dc.contributor.departmentUniversidade Federal de Minas Gerais—UFMGen_US
dc.contributor.departmentUniversity of Utahen_US
dc.contributor.departmentUniversity of Bedfordshireen_US
dc.contributor.departmentRoyal Botanic Gardens, Kewen_US
dc.contributor.departmentBucknell University Lewisburgen_US
dc.contributor.departmentUniversity of Helsinkien_US
dc.contributor.departmentNatural History Museumen_US
dc.identifier.journalAmerican Journal of Botanyen_US
dc.description.notegold open access

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