In this study, a phylogeographic scenario of the coal tit (Periparus ater) was reconstructed based on a fragment of the mitochondrial control region, and within- and between-population genetic diversity was analysed with a focus on the western Palearctic breeding range. We inferred a first pan-European
delimitation of a postulated secondary contact zone among coal tits from the north-eastern Palearctic ater subspecies group and those from the south-western Palearctic abietum group. Generally, between population differentiation was greatest in the Mediterranean range, which was explained by a greater
separation in multiple Pleistocene refuge areas compared to the lower differentiation across the northeastern Palearctic range. Genetic diversity indices were lowest on Mediterranean island populations
as compared to continental populations. Pairwise ˚ST values were highest among island populations and the Eurasian continent on the one hand and among the continental north-eastern ater and southwestern
abietum group on the other. Local co-occurrence of ater and abietum haplotypes was found all across Germany and in one Greek population. Molecular dating suggested that these two major subspecies
groups separated from each other and from two further North African and Middle Eastern coal tit lineages during the early to mid-Pliocene. Successively, the Mediterranean region remained a centre of mainly insular diversification until late Pleistocene times including a long period of steady population
growth. At the same time, at least four distinct genetic lineages emerged in eastern Eurasia, the nominate ater subspecies group being one of them. Finally, during the Holocene extant wide-range secondary
contact in Europe was established via rapid westward range expansion from an East Asian refuge and via northeastward expansion from Mediterranean refuges.