Phylogeography of Oaks in the Crimea Reveals Pleistocene Refugia and Migration Routes

Chloroplast DNA variability was examined in 872 trees of pedunculate oak (Q. robur L.), sessile oak (Q. petraea (Matt.) Liebl.) and downy oak (Q. pubescens Willd.) on the Crimean Peninsula, in the Western Caucasus and in the Balkan region in order to study phylogeography and interaction of these species in the Black Sea region. Sequencing of five fragments with a total length of more than 10,000 base pairs revealed 12 haplotypes of chloroplast DNA. For the haplotype typing in the studied populations, chloroplast microsatellites (cpSSR), sequencing, and restriction analysis were used. Haplotypes detected belong to several divergent phylogenetic lineages. The studied species almost do not differ from each other in the composition of haplotypes and the geographical structure of variability, which demonstrates a certain level of gene flow between them in mixed populations. The haplotypes of the Balkan region are closely related to the haplotypes of previously studied populations from Eastern Europe and the western part of the Russian Plain, and are not found in the Crimea and the Caucasus. On the Crimean Peninsula, two geographical groups of populations are distinguished, which differ sharply in the composition of haplotypes. The difference between the western part of the peninsula and the eastern part is shown, which suggests a multiple origin of oak populations in the Crimea as a result of migrations from two sources, which could be facilitated by fluctuations in the Black Sea level and its desalination, which repeatedly occurred in the Pleistocene and Holocene. The predominance of two divergent haplotypes in the western part of the peninsula, similar to the haplotypes of Asia Minor, indicates the penetration of oak from this region and the presence of an isolated refugium in the mountainous forest regions of Crimea during the last glacial maximum. At the same time, haplotypes common with the Western Caucasus are spread in the east of the mountain-forest part of the Eastern Crimea. The sharp boundary between the areas of distribution of “western” and “eastern” haplotypes in the Eastern Crimea indicates a relatively recent time of the formation of a secondary contact zone between local and Caucasian oak populations as a result of postglacial colonization.