Tertiary remnants and Holocene colonizers: Genetic structure and phylogeography of Scots pine reveal higher genetic diversity in young boreal than in relict Mediterranean populations and a dual colonization of Fennoscandia

AIM: Scots pine is one of the dominant tree species in forest ecosystems of the temperate and boreal zones in Eurasia. Since the Tertiary, it has persisted also in the Mediterranean region, forming relict populations. In this study, we investigate range‐wide genetic diversity of Scots pine, aiming to provide comprehensive information on the phylogeography and genetic resources of the species. LOCATION: Europe and Asia. METHODS: Thirteen paternally inherited chloroplast microsatellite (cpSSR) loci were used to investigate the genetic structure of 62 populations from Fennoscandia and 30 populations from the Mediterranean. We also surveyed variability of two maternally inherited mitochondrial DNA (mtDNA) regions and additionally included literature data from 156 populations (248 populations in total). RESULTS: Scots pine retains an overall high genetic diversity in the chloroplast genome but, unexpectedly, the historically younger populations from Fennoscandia showed statistically higher mean intrapopulation diversity than the Mediterranean stands (0.807 and 0.750, respectively). The latter also contained a lower number of private cpSSR haplotypes. Population differentiation with respect to mtDNA was higher (GST = 0.628) than at cpSSR (GST = 0.015) indicating an efficient pollen‐mediated gene flow among refugial populations of the species. One novel haplotype mtDNA was found, increasing the number of known mitotypes for the species from 4 to 5. The geographic distribution of mitotypes was structured into four groups corresponding to the main refugial areas of the species. MAIN CONCLUSIONS: Genetic impoverishment of the Mediterranean populations may enhance their vulnerability to future environmental changes. The spatial distribution of two mitotypes in Fennoscandia, featuring predominance of mitotype a in Norway and Sweden and mitotype b in Finland, gives strong support for dual colonization of that region from south‐eastern (Finland) and south‐western (Sweden) directions. These results thus provide new insights into both Holocene expansion of Scots pine and the present distribution of species' genetic resources.