Data from: Pervasive phylogenomic incongruence underlies evolutionary relationships in eyebrights (Euphrasia, Orobanchaceae)

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.