Genetic differentiation between two subspecies of Emberiza schoeniclus and open forest bunting's evolution inferred from mitogenomes

The reed bunting, Emberiza schoeniclus (Linnaeus 1758), is the only member of the genus adapted to Mediterranean wetlands, where some subspecies are critically endangered. The first complete mitogenome of the eastern Iberian reed bunting ( E. s. witherbyi ) is presented here and compared with an unpublished mitogenome obtained in northeast Asia (most likely E. s. pyrrhulina ). Genetic distance analyses are consistent with the new reed bunting data corresponding to two distinct lineages of E. schoeniclus . A new fossil‐calibrated phylogeny suggests that open forest buntings have suffered two rapid speciation events from Late Miocene to Pleistocene, that seem to be correlated with major climatic changes and habitat shifts. Adaptation to a new ecological niche (i.e. wetlands) could have favoured the reed bunting expansion across the Palearctic. The high intraspecific variation observed today could result from the establishment of resident populations within small areas, potentially acting as a climatic refuge.