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A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).ORCID iD: 0000-0002-2515-6509
Number of Authors: 732025 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 245, no 2, p. 818-834Article in journal (Refereed) Published
Abstract [en]

Grasses (Poaceae) comprise c. 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a newly inferred 910-tip plastome tree. We recovered most of the tribes and subfamilies previously established, despite pervasive incongruence among nuclear gene trees. The early diversification of the PACMAD clade could represent a hard polytomy. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly. Nuclear-plastome incongruence is rare, with very few cases of supported conflict. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.

Place, publisher, year, edition, pages
2025. Vol. 245, no 2, p. 818-834
Keywords [en]
Angiosperms353, genome, incongruence, phylogenomics, plastome, Poaceae, target capture, transcriptomics
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:su:diva-249619DOI: 10.1111/nph.20263ISI: 001457410600036PubMedID: 39568153Scopus ID: 2-s2.0-85210070130OAI: oai:DiVA.org:su-249619DiVA, id: diva2:2013613
Available from: 2025-11-13 Created: 2025-11-13 Last updated: 2025-11-13Bibliographically approved

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Humphreys, Aelys M.

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