Genome-wide differentiation by geography not species in taxonomically complex eyebrights (Euphrasia)

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 homogenising 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 ten tetraploid species. Recent
divergence and extensive gene flow between putative species is supported
by a lack of species-specific SNPs 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.