The postglacial history of Euphrasia micrantha in Scotland: evidence from genome skimming

The flora of northern Europe has been shaped by a complex history of glaciation, where species have recolonised from different refugia and spread via contrasting migration routes. Our understanding of plant phylogeography in northern Europe has been limited by the resolution of genetic markers that cannot detect subtle population structure arising from close or cryptic refugia. Here, we employ genome skimming to recover complete plastid genomes and partial nuclear ribosomal arrays in the widespread plant species Euphrasia micrantha. We focus on populations from Scotland, where cryptic and complex patterns of recent recolonisation may prove hard to resolve. Genome skimming from 145 individuals revealed a species specific plastid DNA lineage in Scotland and England, while two other genetic clusters were highly intermixed with co-occurring taxa. Within the distinct plastid DNA lineage we recover subtle genetic divergence corresponding to West-East differentiation. These findings suggest E. micrantha has recolonised from multiple distinct refugia, potentially including cryptic northern refugia.