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dc.contributor.authorGarrett, Steven
dc.contributor.authorBecher, Hannes
dc.contributor.authorGussarova, Galina
dc.contributor.authordePamphilis, C. W.
dc.contributor.authorNess, R. W.
dc.contributor.authorGopalakrishnan, S.
dc.contributor.authorTwyford, A.D.
dc.date.accessioned2022-11-22T12:41:36Z
dc.date.available2022-11-22T12:41:36Z
dc.date.issued2022-05-27
dc.description.abstractDisentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and polyploidy. Here, we perform a phylogenomic analysis of eyebrights (Euphrasia), a group renowned for taxonomic complexity, with the aim of documenting the extent of phylogenetic discordance at both deep and at shallow phylogenetic scales. We generate whole-genome sequencing data and integrate this with prior genomic data to perform a comprehensive analysis of nuclear genomic, nuclear ribosomal (nrDNA), and complete plastid genomes from 57 individuals representing 36 Euphrasia species. The species tree analysis of 3,454 conserved nuclear scaffolds (46 Mb) reveals that at shallow phylogenetic scales postglacial colonization of North Western Europe occurred in multiple waves from discrete source populations, with most species not being monophyletic, and instead combining genomic variants from across clades. At a deeper phylogenetic scale, the Euphrasia phylogeny is structured by geography and ploidy, and partially by taxonomy. Comparative analyses show Southern Hemisphere tetraploids include a distinct subgenome indicative of independent polyploidy events from Northern Hemisphere taxa. In contrast to the nuclear genome analyses, the plastid genome phylogeny reveals limited geographic structure, while the nrDNA phylogeny is informative of some geographic and taxonomic affinities but more thorough phylogenetic inference is impeded by the retention of ancestral polymorphisms in the polyploids. Overall our results reveal extensive phylogenetic discordance at both deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal. This suggests that Euphrasia species either have polytopic origins or are maintained by narrow genomic regions in the face of extensive homogenizing gene flow. Moreover, these results suggest genome skimming will not be an effective extended barcode to identify species in groups such as Euphrasia, or many other postglacial species groups.en_US
dc.identifier.citationGarrett, Becher, Gussarova, dePamphilis, Ness, Gopalakrishnan, Twyford. Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae). Frontiers in Plant Science. 2022;13en_US
dc.identifier.cristinIDFRIDAID 2053137
dc.identifier.doi10.3389/fpls.2022.869583
dc.identifier.issn1664-462X
dc.identifier.urihttps://hdl.handle.net/10037/27467
dc.language.isoengen_US
dc.publisherFrontiers Mediaen_US
dc.relation.journalFrontiers in Plant Science
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/EXCELLENT SCIENCE/765000/Norway/Molecular Identification of Plants/Plant-ID/en_US
dc.rights.accessRightsopenAccessen_US
dc.rights.holderCopyright 2022 The Author(s)en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)en_US
dc.titlePervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)en_US
dc.type.versionpublishedVersionen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's license is described as Attribution 4.0 International (CC BY 4.0)