DOI: 10.5061/dryad.jh9w0vtd3
title: Data from: Pervasive phylogenomic incongruence underlies evolutionary relationships in eyebrights (Euphrasia, Orobanchaceae)

description: Disentangling the phylogenetic relationships of taxonomically complex
 plant groups is often mired by challenges associated with recent
 speciation, hybridisation, complex mating systems and polyploidy. Here, we
 perform the first global phylogenomic analysis of eyebrights (Euphrasia),
 a group renowned for taxonomic complexity, with the aim of understanding
 the evolutionary processes underlying phylogenetic discordance. 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 species sampled across the genus. The species
 tree analysis of 3454 conserved nuclear scaffolds (46 Mb) is structured by
 geography and ploidy, and partially by taxonomy, and indicates that post
 glacial colonisation of North Western Europe occurred in multiple waves
 from discrete source populations. However, most species are not
 monophyletic, and combine genomic variants from across clades. Comparative
 analyses confirm the close relationship between Northern Hemisphere
 allotetraploids and diploids, while Southern Hemisphere tetraploids
 include a distinct subgenome history indicative of independent polyploidy
 events. 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
 polymorphim in tetraploids. 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 homogenising 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.
description: Our phylogenomic analyses included a total of 58 samples, 56
 samples from 36 <em>Euphrasia </em>species and two outgroup
 species, <em>Bartsia alpina </em>and
 <em>Neobartsia</em> <em>chilensis</em>. This
 included a combination of newly sequenced samples and previously generated
 data. Short-read Illumina data for each sample was used for de novo
 plastid genome assembly using Novoplasty or GetOrganelle, nuclear
 ribosomal DNA array assembly using Novoplasty, and nuclear genome analysis
 based on mapping to the Euphrasia arctica genome.
description: # Pervasive phylogenomic incongruence underlies evolutionary relationships
 in eyebrights (Euphrasia, Orobanchaceae)
 [https://doi.org/10.5061/dryad.jh9w0vtd3](https://doi.org/10.5061/dryad.jh9w0vtd3) ## Description of the data and file structure Our phylogenomic analyses included a total of 58 samples, 56 samples from 36 *Euphrasia* species and two outgroup species, *Bartsia alpina* and *Neobartsia* *chilensis*. This included a combination of newly sequenced samples and previously generated data. Short-read Illumina data for each sample was used for de novo plastid genome assembly using Novoplasty or GetOrganelle, nuclear ribosomal DNA array assembly using Novoplasty, and nuclear genome analysis based on mapping to the Euphrasia arctica genome.  ### Files and variables #### File: ConservedScaffolds.tree **Description:** Sequence analysis of conserved nuclear genome scaffolds, used to make Figure 3 in the paper. #### File: mash\_NJ.treefile **Description:** Neighbor-joining trees generated from raw sequence reads using MASH, used to make Figure S1 in the paper. #### File: nrDNA.tree **Description:** Phylogenetic relationships inferred from nuclear ribosomal DNA sequences for global *Euphrasia* species, used in Figure 2 in the paper. #### File: Plastid.tree **Description:** Phylogenetic relationships inferred from complete plastid genome sequences for global *Euphrasia* species, used in Figure 1 in the paper. #### File: plotTangle.R **Description:** Tanglegram comparing the species tree from the conserved nuclear scaffolds and the maximum likelihood phylogeny for the plastid genome used in Figure 5 in the paper. #### File: nrDNA\_alignment.fasta **Description:** Alignment of nuclear ribosomal DNA sequences for global *Euphrasia* species, used in Figure 2 in the paper. #### File: Plastid\_alignment.fasta **Description:** Alignment of complete plastid genome sequences for global *Euphrasia* species, used in Figure 2 in the paper. ## Access information Other publicly accessible locations of the data: * n/a Data was derived from the following sources: * n/a