Genome-wide differentiation by geography not species in taxonomically complex eyebrights (<i>Euphrasia</i>)

Most studies investigating the genomic nature of species differences anticipate monophyletic species with genome-wide differentiation. However, this may not be the case at the earliest stages of speciation where reproductive isolation is weak and homogenizing gene flow blurs species boundaries. We investigate genomic differences between species in a postglacial radiation of eyebrights (Euphrasia), a taxonomically complex plant group with variation in ploidy and mating system. We use genotyping-by-sequencing and spatially aware clustering methods to investigate genetic structure across 378 populations from 18 British and Irish Euphrasia species. We find only northern Scottish populations of the selfing heathland specialist E. micrantha demonstrate genome-wide divergence from other species. Instead of genetic clusters corresponding to species, all other clusters align with geographic regions, such as a genetic cluster on Shetland that includes 10 tetraploid species. Recent divergence and extensive gene flow between putative species are supported by a lack of species-specific single-nucleotide polymorphisms or clear outlier loci. We anticipate a similar lack of association between genomic clusters and species identities may occur in other recent postglacial groups. Where new species emerge this is associated with a transition in mating system or novel ecological preferences.