胡桃科 (Juglandaceae) 共11个属60多个物种，染色体基数 (x) 为16 (除化香树属x = 15)。胡桃科通常被分为三个亚科：马尾树亚科 (Rhoipteleoideae)；黄杞亚科 (Engelhardioideae)，黄杞族 (Tribe Engelhardieae)；胡桃亚科 (Juglandoideae)，包括化香树族 (Tr. Platycaryeae)、胡桃族 (Tr. Juglandeae) 和山核桃族 (Tr. Hicorieae)。早期核型研究揭示胡桃科的四倍体起源 (Tetraploid) 可能与杨梅科 (Myricaceae, x = 8) 有关。胡桃属 (Juglans) 和山核桃属 (Carya) 的全基因组数据表明两个属共享近期的全基因组加倍(Whole-genome duplication, WGD) 且加倍后两个亚基因组 (Subgenome) 之间存在有偏分镏现象 (Biased fractionation)，表明此次WGD可能是异源多倍化 (Allopolyploidization)。异源多倍化涉及种间杂交和基因组加倍，然而胡桃科WGD涉及到的亲本尚不清楚。杂交包括杂交物种形成 (Hybrid speciation) 和渐渗杂交 (Introgressive hybridization或Introgression)，其不仅是遗传变异的重要来源而且是物种形成和作物驯化重要途径。已有研究表明胡桃科物种之间的杂交事件非常普遍，然而对于整个胡桃科网状进化关系的研究较少。另外，杂交和渐渗在核桃和铁核桃的驯化中起到的作用也知之甚少。
本研究从三个尺度 (科、族、种) 探究胡桃科进化历史。首先，从头组装胡桃科最基部类群—马尾树 (Rhoiptelea chiliantha) 以及黄杞亚科黄杞 (Alfaropsis roxburghiana) 染色体水平的基因组。然后，利用胡桃科7个物种 (涉及到所有的亚科和族) 的全基因组数据，采用三种方法检测全基因组加倍事件，发现所有物种近期都经历了WGD。基因组共线性以及系统发生树的结果表明所有物种共享近期的WGD事件。WGD后保留的两个亚基因组之间存在有偏分馏现象以及在早期的核型观察中发现减数分裂中期存在次级配对现象，推测胡桃科近期的WGD是异源多倍化。由于异源多倍化涉及到杂交成种，传统的二叉树无法反映真实的网状进化关系。因而我们对胡桃科7个物种进行亚基因组拆分，分别获得显性亚基因组 (Dominant subgenome) 和隐性亚基因组 (Recessive subgenome)，每个亚基因组可代表多倍化的一个亲本谱系。同时下载壳斗目 (Fagales) 5个近期除γ-WGT (Whole-genome triplication) 外没有经历其他全基因组加倍的物种作为外类群，利用受基因流干扰较小的全基因组结构变异信息构建亚基因组水平的系统发生树，结果表明杨梅科或者与杨梅科亲缘关系较近的物种可能是胡桃科多倍化的一个亲本，另一个亲本已经灭绝或者没有取到样。另外，在胡桃科亚基因组水平的系统发生树中发现黄杞和化香树是姊妹类群，这与早期的形态学证据吻合，然而与DNA序列得到的结果存在冲突。
为了解决这一问题，我们在前面用到的7个胡桃科物种的基础上又增加5个物种，并对其进行亚基因组划分，获得12个物种隐性亚基因组和12个物种显性亚基因组的直系同源基因。使用D统计量和D3检验发现化香树与山核桃族和胡桃族之间存在基因流，DIP检验支持化香树给山核桃族和胡桃族有单向基因流。进一步使用PhyloNet软件包中的DeepCoalCount_network比较了4种可能的网络拓扑，结果支持在物种树拓扑 ((黄杞族, 化香树族), (山核桃族，胡桃族)) 中，化香树分别给山核桃族和胡桃族单向基因流，且化香树族与山核桃族之间的基因流事件发生时间早于化香树族给胡桃族基因流的发生时间。
核桃和铁核桃作为重要的经济作物，为了探究杂交以及人工选择在两个物种的进化以及驯化历史中的作用，我们测序和下载87个分布在欧洲、伊朗、哈萨克斯坦、巴基斯坦和中国的核桃以及26个来自中国的铁核桃全基因组重测序数据。种群聚类分析结果表明核桃可以分成西部和东部支系，西部支系包括欧洲和伊朗，东部支系全部来自中国。东部和西部核桃支系在~80-40世代前种群快速下降，导致整个分布区的核桃样本只有两个几乎相同的叶绿体单倍型。IMa3估计铁核桃和核桃两个种的分化时间约为85万年，东部核桃支系给铁核桃有单向基因流。另外，铁核桃从20世代前开始出现严重的种群瓶颈。猜测是驯化的核桃传入中国之后与铁核桃之间存在基因流，使得铁核桃获得了重要的驯化性状，如薄壳、大果实等，促进铁核桃近期的驯化。
本研究利用全基因组数据揭示了胡桃科异源多倍化的起源及进化历史，初步解决了胡桃科四个族之间的网状进化关系。古老的杂交和渐渗会影响胡桃科的系统发生关系，在推断物种进化历史时不容忽视。另外，种群基因组分析揭示了核桃和铁核桃的驯化历史，为探讨多年生植物的驯化瓶颈提供了新思路。

The walnut family, Juglandaceae,  consist of ~11 genera and more than 60 species, with the base number of chromosomes (x) being 16 (except in Platycarya x = 15). Traditionally, Juglandaceae is classified into three subfamilies, i.e., Rhoipteleoideae, Engelhardioideae (Tribe Engelhardieae) and Juglandoideae (Tr. Platycaryeae, Tr. Juglandeae, Tr. Hicorieae). The early karyomorphological study indicated that Juglandaceae are probably of tetraploid origin from a common ancestor with Myricaceae (x = 8). The whole-genome sequence data showed that Juglans and Carya have recently experienced whole-genome duplication (WGD) and one parental subgenome often retains more genes than the other parental subgenome (biased fractionation), pointing to allopolyploidization. Allopolyploidy involves both interspecific hybridization and genome doubling. However, the parental lineages of Juglandaceae are unclear. Hybridization is not only an important source of genetic variation but also important for speciation and crop domestication. Previous studies have shown that hybridization events among lineages of Juglandaceae are greatly common, but less attention is given to the reticulated history of the whole family. In addition, the role of hybridization and introgression in the domestication of Persian walnut (J. regia) and Iron walnut (J. sigillata) is still unclear.
This thesis aimed to explore the evolutionary history of the Juglandaceae from three scales (family, tribe and species). Firstly, we assembled the chromosome-level genome of Rhoiptelea chiliantha, the most basal and monotypic clade of Juglandaceae, and Alfaropsis roxburghiana of Engelhardioideae. Using three methods to detect WGD in seven species representing  all four tribes of Juglandaceae, we found that all species had experienced a recent WGD event. The result of whole-genome microsynteny and phylogenetic trees suggested that all species share the recent WGD. Biased fractionation and early karyotype evidence indicated that the recent WGD was an allotetraploidization event. Because allotetraploidization involved hybridization speciation, the traditional bifurcated tree cannot reflect the evolution history of network. We detected two paleo-subgenomes (Dominant and Recessive subgenome) of 7 species of Juglandaceae, with each subgenome representing one parental lineage. Five species of Fagales were chosen as outgroups that have not experienced a more recent WGD than the γ-WGT common to the core eudicots. We used whole-genome structural variation information (more robust to introgression) to construct the phylogenetic trees of Juglandaceae at the subgenome level. The results showed that one of the parents of Juglandaceae was a species closely related to Myricaceae and another was extinct or unsampled. In addition, the phylogenetic trees of the Juglandaceae suggested that Alfaropsis roxburghiana and Platycarya strobilacea were sister groups, consistent with the morphology-based phylogeny but radically different from the one based on DNA sequence alignments.
To resolve the conflict, we used 12 Juglandaceae species and assigned paleo-subgenomes to obtain the orthologous genes of recessive and dominant subgenomes of the 12 species, respectively. The result of D statistic and D3 test showed massive gene flow between Tr. Platycaryeae and Tr. Juglandeae/Tr. Hicorieae. Using DeepCoalCount_network in the PhyloNet software package, we compared the four possible network topologies, and found the topology of ((Tr. Engelhardieae, Tr. Platycaryeae), (Tr. Juglandeae, Tr. Hicorieae)) to be more likely, with unidirectional gene flow from Tr. Platycaryeae to Tr. Hicorieae, and later from Tr. Platycaryeae to Tr. Juglandeae. 
Persian walnut and Iron walnut are important economic crops. To research the role of hybridization and artificial selection in the evolutionary history and domestication history of the two species, we sequenced and downloaded from the public database whole genome resequencing data of 87 Persian walnuts and 26 Iron walnuts. Population clustering analysis detected two main genetic groups of Persian walnuts, i.e., a western group  from Europe and Iran and an eastern group from China. The effective population size of the eastern and western Persian walnuts suffered a rapid population decline during the ~80-40 generations ago, resulting in only two very similar haplotypes of chloroplast. The divergence time of the two species was 0.85 Mya and unidirectional gene flow from eastern Persian walnut to Iron walnut was detected. In addition, the Iron walnut experienced a serious bottleneck beginning from 20 generations ago. Introgression of shell thickness and nut weight genes from introduced J. regia may have facilitated the domestication of J. sigillata. 
In this study, whole-genome data were successfully used to uncover the origin and evolutionary history of the Juglandaceae. A reticulated evolutionary history among the four tribes is preliminarily proposed. Ancient hybridization or introgression should no longer be ignored in evolutionary studies of Juglandaceae. In addition, the population genomic analyses revealed the domestication history of Persian walnut and Iron walnut, providing new fuels for the domestication bottleneck of perennial crop plants.