Chloroplast DNA Markers on the Phylogeography Study of Roburoid Oaks (Quercus L. sect. Quercus, Fagaceae) in the Crimean-Caucasian Region.

The variability of five fragments of chloroplast DNA (ASq, CDq, TFq, trnH-psbA, and trnK-matK) with a total length of more than 10 000 bp in three species of roburoid oaks of the Crimean-Caucasian region (Q. robur, Q. petraea, and Q. pubescens) has been studied. A total of 11 haplotypes were found in 290 individuals from 20 populations, ten of which differed from the haplotypes of the main range. The results show a pronounced structure of the geographical distribution of haplotypes in roburoid oaks in the Crimea and the Caucasus, and the chloroplast haplotypes of the region belong to several divergent phylogenetic lineages. A comparison with data from other studies was carried out, with an assessment of the degree of effectiveness of using various chloroplast fragments and markers. The isolated phylogenetic position of the haplotypes from the Crimean-Caucasian populations and deep differences from the haplotypes of the main area allow us to conclude that roburoid oaks have historically been isolated for a long time in the Caucasus and Crimea. At the same time, the presence of common haplotypes indicates closer historical ties between the Crimean-Caucasian populations with Asia Minor and the Balkans. All haplotypes are identified by three fragments (ASq, CDq, and TFq), with a sufficient level of variability and suitable for solving problems of oak phylogeography in the Crimean-Caucasian region. The trnH-psbA and trnK-matK markers had a low level of variability and did not reveal additional haplotypes. Optimized genotyping options have been proposed, including both stepwise sequencing and a combination of analysis of chloroplast DNA microsatellite loci (cpSSR), restriction analysis (PCR-RFLP), and sequencing. To assess the variability of markers in a larger taxonomic range, representatives of other sections of the genus Quercus were included in the analysis. It was shown that the oak-specific primers proposed for ASq, CDq, and TFq fragments are suitable for species of other sections. [ABSTRACT FROM AUTHOR]