Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)

Abstract

Disentangling 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.

Genomic clustering by geography not species in taxonomically complex British and Irish eyebrights (Euphrasia)

“…This pattern of recolonisation from multiple refugia is common in many European plant groups and leaves a distinct genetic signature (Huck et al, 2009; Petit et al, 2002; Valtueña et al, 2012). In Euphrasia , previous phylogenetic studies using widespread European sampling showed that there were multiple waves of colonisation to Britain (Garrett et al, 2022; Gussarova et al, 2008), while studies of phylogeography in the Euphrasia minima complex found persistence in multiple refugia: one from North America where plants subsequently colonised Greenland/Iceland/Norway, and the other from the Russian Ural mountains where populations subsequently spread to Svalbard (Gussarova et al, 2012).…”

“…Species readily hybridise, with 71 hybrid combinations identified to date, based on morphology (Metherell & Fred, 2018). Phylogenomic analyses have revealed extremely close relationships between species, with British samples showing 99.8% pairwise sequence identity based on complete plastid genomes (Garrett et al, 2022).…”

“…Species readily hybridise, with 71 hybrid combinations identified to date, based on morphology (Metherell & Fred, 2018). Phylogenomic analyses have revealed extremely close relationships between species, with British samples showing 99.8% pairwise sequence identity based on complete plastid genomes (Garrett et al, 2022). British species vary in their mating system, from small flowered selfers through to large flowered mixed maters and outcrossers (French et al, 2004; Yeo, 1966).…”

Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone?

“…The high degree of tetraploid subgenome divergence (~5%; Becher et al, 2020 ) has benefits for genomic analyses, increasing confidence in the assignment of short reads to the appropriate subgenome. British tetraploids are thought to have a common origin in mainland Europe and to have subsequently colonized the British Isles (Garrett et al, 2022 ).…”