The postglacial history of <i>Euphrasia micrantha</i> in Scotland: evidence from genome skimming

The flora of Northern Europe has a complex glacial history, with species recolonising via different migration routes. However, traditional genetic markers have often struggled to resolve subtle population structure arising from closely located or cryptic refugia. This study investigated the phylogeography of the widespread plant species <i>Euphrasia micrantha</i> in Scotland, using genome skimming to detect complex patterns of recolonisation. We recovered complete plastid genomes and partial nuclear ribosomal DNA arrays for 145 individuals of <i>E. micrantha</i> and sympatric species. Phylogeographic histories are inferred from comparative phylogenetics and haplotype diversity measures. We identified a plastid haplotype group unique to <i>E. micrantha</i>, and present only in northern Scotland, while two other genetic clusters were intermixed with co-occurring species. Within the unique plastid lineage, we detected subtle east–west genetic divergence. <i>E. micrantha</i> recolonised Scotland from multiple distinct refugia, potentially including cryptic northern refugia. The genetic distinctiveness of northern Scottish <i>E. micrantha</i> suggests a cryptic lineage, and/or this species’ distinct ecology and mating system maintain population differences. Genome skimming is likely to be useful in many other phylogeographic studies requiring dense population sampling.