Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum
McDonnell, Angela J.
Stehmann, João Renato
AffiliationRoyal Botanic Garden Edinburgh
University of Edinburgh
Chicago Botanic Garden
University of Helsinki
Universidade Federal do Oeste do Pará
Universidade Federal de Minas Gerais—UFMG
University of Utah
University of Bedfordshire
Royal Botanic Gardens, Kew
Bucknell University Lewisburg
University of Helsinki
Natural History Museum
multilocus phylogenetic trees
short backbone branches
incomplete lineage sorting
Subject Categories::C400 Genetics
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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 Methods: A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.)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.
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.
PublisherJohn Wiley and Sons Inc
JournalAmerican Journal of Botany
SponsorsThis 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).
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