栎属（Quercus L.）是北半球物种数目最多的森林类群之一，大约有435种，广泛分布于北美、中美洲以及欧亚大陆。因为种间杂交频繁，栎属物种被认为是研究物种进化的重要模式物种。杂交渐渗和不完全谱系分选（incomplete lineage sorting，ILS）是影响栎属物种进化历史的两个重要因素。杂交渐渗可以促进物种的扩散、分化以及适应性进化等，而不完全谱系分选影响了种间系统发育关系的分析。关于栎属物种进化历史的研究引起了广泛的关注，但针对东亚白栎组（section Quercus）物种进化历史的研究仍然有限。基于此，本研究首先以在东亚广泛分布的三个白栎组近缘物种，蒙古栎（Q. mongolica var. mongolica）、辽东栎（Q. liaotungensis）和日本栎（Q. mongolica var. crispula）组成的蒙古栎复合体为研究对象，利用全基因组重测序数据，通过D统计量（ABBA-BABA）来检验种间杂交和基因流，并结合隔离-迁移（Isolation with Migration）模型（IMa3）推断蒙古栎复合体各支系的种群进化历史，进一步检测基因流是否造成了种间适应性渐渗，探讨杂交渐渗在白栎组物种进化过程中所起到的作用。最后，将研究对象扩大到整个东亚白栎组物种支系，构建了东亚白栎组物种的系统发育树及系统发育网络，并系统地分析了杂交渐渗和不完全谱系分选对东亚白栎组物种系统发育关系构建的影响。主要结果如下：

（1）蒙古栎复合体已经分化成了4个独特的支系：西部辽东栎（Q. liaotungensis_NW-NC）、东北辽东栎（Q. liaotungensis_NEC）、蒙古栎以及日本栎。蒙古栎和西部辽东栎的亲缘关系比它与日本栎的更远，如果日本栎不被鉴定为蒙古栎的变种，而是按照某些研究者的观点提升为一个单独物种（Q. crispula），那么辽东栎的分类地位更应为一个物种。

（2）种群进化历史分析的结果表明，东北辽东栎起源于蒙古栎而不是西部辽东栎，同时检测到西部辽东栎和蒙古栎均对东北辽东栎有显著的基因流，且来自西部辽东栎的基因流强度更高。叶绿体基因组建树的结果显示东北辽东栎的叶绿体嵌套于蒙古栎之中。综合以上研究结果，推测东北辽东栎可能是西部辽东栎花粉湮没蒙古栎的一个产物。

（3）通过查找种间的高分化基因，并对这些基因进行选择和建树分析以推测其可能的系统发育过程。结果表明，蒙古栎的铜转运蛋白6（copper transporter 6-like）基因受到了选择，而该基因起源于日本栎，因此推测蒙古栎的铜转运蛋白6基因是从日本栎渐渗而来，杂交渐渗为蒙古栎的适应性进化提供了原材料。

（4）MYB6转录因子在西部辽东栎和蒙古栎中都受到了选择，在该基因的系统发育树中，西部辽东栎和蒙古栎的个体都各自聚成了单系，因此推测 MYB6转录因子可能受到了歧化选择。MYB6转录因子可能与黄酮类次生代谢产物的合成有关，推测其分化是由于西部辽东栎和蒙古栎地理分布不同而各自适应了不同的生境。

（5）对东亚白栎组物种系统发育关系重建的结果显示，使用串联SNP数据构建的最大似然（Maximum Likelihood, ML）树和使用SVDquartets构建的多物种溯祖树，与考虑了杂交渐渗和不完全谱系分选的PhyloNet构建的多物种溯祖网络的拓扑结构不一致。这提示了在分析栎属组内物种间的系统发育关系时，应考虑杂交渐渗和不完全谱系分选对拓扑结构的影响，否则会得到错误的结论。多物种溯祖网络、ML树和多物种溯祖树的结果均显示，锐齿槲栎（Q. aliena var. acuteserrata）与槲栎（Q. aliena var. aliena）没有聚成单系，推测锐齿槲栎可能并非槲栎的一个变种。

The genus Quercus L., as one of the largest genera in the northern hemisphere, has about 435 species widely distributed in North America, Central America, and Eurasia. Oaks are considered to be an important model species for studying evolution history due to frequent interspecies hybridization. Interspecific hybridization and incomplete lineage sorting (ILS) are two important factors affecting oak evolutionary history. Hybridization and introgression could promote disperesal, diversification, and adaptive evolution, while ILS could affects the phylogenetic analysis. The evolutionary history of Quercus has been studied in lots of research. However, up to date there has been few research on the evolutionary history of the East Asian White oaks (section Quercus). Based on this, we used the whole-genome resequencing data of East Asian white oaks to explore the role of hybridization and introgression in the oak evolutionary history. First, we focused on four groups within Mongolian oak complex, detected interspecific hybridization and gene flow among these groups using D statistics (ABBA-BABA), and inferred their evolutionary history under the Isolation with Migration model. Then, we detected whether gene flow had promoted adaptive introgression among these groups. Finally, by comparing the ML (Maximum Likelihood) tree of all sampled individuals, SVDquartets species tree and phylonetwork (PhyloNet) of the East Asian white oaks, we explored the influence of hybrid introgression and ILS on phylogenetic analysis. The main results are as follows:

(1) The four groups of the Mongolian oak complex, Q. liaotungensis_NW-NC, Q. liaotungensis_NEC, Q. mongolica var. mongolica and Q. mongolica var. crispula are found to be genetically distinct. The phylogenetic relatedness between Q. mongolica var. mongolica and Q. mongolica var. crispula is closer than that between Q. mongolica var. mongolica and Q. liaotungensis_NW-NC. As Q. mongolica var. crispula is sometimes identified as a distinct species Q. crispula, we suggested Q. liaotungensis should be identified as a different species rather than a variety of Q. mongolica.

(2) The results of evolutionary history showed that Q. liaotungensis_NEC originated from Q. mongolica var. mongolica, not Q. liaotungensis_NW-NC, and both Q. mongolica var. mongolica and Q. liaotungensis_NW-NC had significant introgression into Q. liaotungensis_ NEC, with the gene flow from Q. liaotungensis_ NW-NC being significantly higher. The result of chloroplast phylogenetic tree showed that the chloroplasts of Q. liaotungensis_ NEC were nested within Q. mongolica var. mongolica. Based on the above results, we suggested that Q. liaotungensis_ NEC is the result of asymmetric introgression from Q. liaotungensis_NW-NC to Q. mongolica var. mongolica via substantial pollen flow.

(3) We found several high-differentiated genes between species, and tested whether these genes have been subject to positive selection and inferred their possible phylogenetic origin by means of tree building. The results showed that the copper transporter 6-like gene of Q. mongolica var. mongolica has been selected, possibly promoting its resistance to heavy metal stress, and it was transferred from Q. mongolica var. crispula. We suggested that the copper transporter-6 gene of Q. mongolica var. mongolica is an example of adaptive introgression, which provided raw material for natural selection.

(4) MYB6 transcription factors has been selected both in Q. liaotungensis_NW-NC and Q. mongolica var. mongolica, and individuals of the two groups clustered into monophyletic clades in the gene tree. We suggested that MYB6 transcription factors might have been divergently selected between Q. liaotungensis_NW-NC and Q. mongolica var. mongolica. MYB6 transcription factor may control the differentiation of the synthesis of flavonoid secondary metabolites, and the differentiation of this gene is probably caused by differential adaptation of Q. liaotungensis_NW-NC and Q. mongolica var. mongolica to their own respective habitats.

(5) The ML tree of the East Asian white oak individuals based on concatenated SNP datasets and the multispecies coalescent tree constructed by SVDquartets, showed different topology with multispecies coalescent network constructed PhyloNet with considering ILS and hybridization introgression. This suggests that we may get wrong conclusions if ignoring the influence of hybrid introgression in phylogenetic analysis. The multispecies coalescent network, ML tree and the multispecies coalescent tree all showed that Q. aliena var. acuteserrata and Q. aliena var. aliena did not cluster into a monophyletic clade, indicated Q. aliena var. acuteserrata presumably was not a variety of Q. aliena.