The genus Quercus L. is one of the most abundant and important genera of woody plants in the Northern Hemisphere as well as in Turkey. In the current study which is the most comprehensive study dealing with Turkish oaks, sequence variations of three noncoding regions (trnT^(UGU)-L^(UAA) IGS, trnL^(UAA)intron, trnL^(UAA)-F^(GAA) IGS) of chloroplast DNA (cpDNA) were used for phylogeographic and phylogenetic analysis on 319 individuals representing 23 taxa (17 species). The trnT^(UGU)-L^(UAA) region was found to be the most variable and parsimony informative region. Twenty-eight cpDNA haplotypes were identified based on 34 substitutions and 22 indels. High number of haplotypes and h_T > v_T observed in populations of oaks in Turkey indicated that the Anatolian Peninsula might have been a refugium at Glacial Periods. Phylogeographic construction and molecular variance analysis revealed that Quercus cpDNA haplotypes were geographically structured. Although local haplotype sharing among species from same infrageneric clades was common, levels of hybridization differ between species pairs. Haplotype analysis revealed four infrageneric clades, namely Section Quercus, Section Cerris and two clades corresponding to Section Ilex, namely “Ilex” and “Coccifera.” Furthermore, a Section Cerris haplotype was detected in the Aegean members of Q. ilex and Q. coccifera. Section Ponticae was placed in the Section Quercus cluster. In contrast to the phylogenetic reconstructions based on the nuclear DNA sequence data, Group Ilex seems to be polyphyletic based on plastome phylogeny. Chloroplast phylogeny of oaks reflects the traces of recent and ancient introgression events during diversification of species. In addition to this, incomplete linkage sorting may also explain this polymorphic assemblage. Therefore, further investigation is required to clarify the cpDNA phylogeny of oaks, especially for Section Ilex.

属栎属是在北半球，以及在土耳其木本植物最丰富的和重要的属之一。在目前最全面的研究土耳其橡树的研究中，三个非编码区域的序列变异（trnT ^(UGU) -L ^(UAA) IGS、trnL ^(UAA)内含子、trnL ^(UAA) -F ^(GAA) IGS）的叶绿体 DNA (cpDNA) 用于对代表 23 个分类群（17 个物种）的 319 个个体进行系统地理学和系统发育分析。该TRNT ^（UGU） -L ^（UAA）区域被发现是最可变和最简洁的信息区域。基于 34 个替换和 22 个插入缺失，鉴定了 28 个 cpDNA 单倍型。在土耳其橡树种群中观察到的大量单倍型和h _T  >  v _T表明安纳托利亚半岛可能是冰川时期的避难所。系统地理学构建和分子方差分析表明，栎属cpDNA 单倍型是地理结构的。尽管来自同一属下进化枝的物种之间的局部单倍型共享很常见，但物种对之间的杂交水平不同。单倍型分析揭示了四个属下进化枝，即 Quercus 科、Cerris 科和对应于冬青科的两个进化枝，即“Ilex”和“Coccifera”。此外，在Q. ilex和Q. coccifera的爱琴海成员中检测到了一个 Section Cerris 单倍型. Ponticae 部分被放置在 Quercus 部分集群中。与基于核 DNA 序列数据的系统发育重建相反，冬青组似乎是基于塑性体系统发育的多系。橡树的叶绿体系统发育反映了物种多样化过程中最近和古代基因渗入事件的痕迹。除此之外，不完全连锁排序也可以解释这种多态组合。因此，需要进一步调查以阐明橡树的 cpDNA 系统发育，尤其是冬青科。