本研究筛选了2个叶绿体基因间序列psbA-trnH和trnQ-rps16，一个核基因ITS序列对百花蒿28个居群进行了序列变异分析。从两个cpDNA联合序列分析中检测到6个单倍型，从核基因ITS序列检测到31个核单倍型。cpDNA以及核基因遗传特征上分析结果表明：从物种水平上，百花蒿的cpDNA显示较高的遗传多样性(cpDNA: π = 0.0020, h = 0.794, HT = 0.820)，核基因上显示出遗传多样性相对较高(ITS: π = 0.0040, h = 0.870, HT = 0.817)。根据cpDNA数据，百花蒿居群之间存在显著地遗传分化(cpDNA: GST = 0.976, NST = 0.986, NST > GST, P > 0.05)，表明居群之间存在高的遗传分化和低水平的种子介导的基因流，但是对于cpDNA数据来说，百花蒿居群之间不存在明显的谱系地理结构，可能与单倍型H5广泛存在于三个沙漠有关。然而，根据核基因ITS数据，百花蒿居群之间的分化水平为中等水平(ITS: GST = 0.244, NST = 0.053, NST > GST, P < 0.05)，表明对于核基因来说，百花蒿居群之间存在广泛花粉介导的基因流而且存在显著谱系地理结构，这可能与地理隔离导致的限制性基因流有关。百花蒿居群间遗传距离和地理距离有显著的相关性(cpDNA: r = 0.304, P < 0.05; ITS: r = 0.288, P < 0.05)，表明地理隔离对居群的分化有较大影响。在居群水平上，每个居群（除YBA和YBB）仅固定一个cpDNA单倍型，核基因主导单倍型R1广泛分布于多个居群中。基于SAMOVA分析将所有叶绿体单倍型分为4组并与4个谱系分支相对应，谱系I主要位于腾格里-巴丹吉林沙漠，谱系II位于库布齐沙漠，谱系III位于毛乌素沙漠，谱系IV主要位于乌兰布和沙漠。谱系I和谱系IV在地理分布上有重合，表明可能在腾格里沙漠和乌兰布和沙漠之间存在一个谱系交汇区。因此，推测百花蒿现有的遗传结构可能是由生境片段化以及生态隔离导致基因流受限导致。根据错配分析（多峰曲线）、中性检验(Tajima’s D = 1.956, P = 0.970; Fu’s Fs = 5.793, P > 0.05)以及Mantel test的分析结果，我们认为百花蒿现存的异域分布模式可能与腾格里沙漠、乌兰布和沙漠、库不齐沙漠和毛乌素沙漠形成与演化的地质事件相关。基于叶绿体平均替换速率，我们推测四个不同谱系分支的分化时间大约在0.5-1.2Ma之间，这个时间段与现有的地质学文献关于本文涉及到沙漠的形成和演化时间相一致，而沙漠的形成与演化与青藏高原的青藏-黄河运动和第四纪气候周期波动息息相关，因此我们认为百花蒿的遗传分化受到地质运动和第四纪冰期的共同影响。基于居群的遗传多样性分布格局和每个谱系地理组的独特性，对整个分布区划分了四个进化显著单元并提出了相应的保护策略。
本研究选取蒙古高原特有类群绵刺研究其谱系地理结构，选择两个叶绿体DNA片段trnL-trnF和psbA-trnH来研究绵刺13个居群共131个个体的序列测定。结果共检测到2个变异位点，共得到3个单倍型。H1普遍存在，占所有样本的71%，而且在简约性网络图中处于中心位置，因此推测H1可能是比较古老的单倍型。总的遗传多样性HT = 0.493，平均遗传多样性HS = 0.186，GST = 0.622，NST = 0.467，P > 0.05，无显著性，缺乏一个明显的谱系结构，可能与绵刺具有克隆的营养繁殖方式有关。将绵刺地理分布人为分为：中心组和边缘组，发现中心组居群内具有较高水平的单倍型多样性，边缘组居群内单倍型单一，符合中心-边缘假说。分子方差分析（AMOVA）结果表明，绵刺居群间遗传变异为47.1%，居群内遗传变异为52.9%，居群遗传分化系数FST为0.4710。这表明绵刺遗传变异主要来源于居群内部，但居群间也出现一定程度分化。绵刺居群间遗传距离和空间距离的Mantel test检验结果显示并没有相关性。错配分析呈单峰分布，表明绵刺居群历史上发生过居群动态扩张。根据绵刺的遗传分布格局，我们建议在绵刺的中心分布区建立保护区，有利于保护该物种的遗传多样性。|
|其他摘要||The formation of flora in the arid land of Northwest China is closely related a variety of historical events, such as the uplift of QTP, Paleotethys retreat due to the Indian Plate collided with the Eurasian Plate, the formation and development of deserts and climate change in glacial epoch. Of great interest is to unravel the mechanisms for the species differentiation in this region. In this study, three representative endemic species (Zygophyllum xanthoxylon, Stilpnolepis centiflora and Potaninia mongolica) were selected to study the mechanism of their phylogeographical pattern. The main findings and conclusions are summarized as follows.
1. Phylogeography of Zygophyllum xanthoxylon
Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.
2. Phylogeography of Stilpnolepis centiflora
The nucleotide sequences from two chloroplast DNA (cpDNA) regions (trnQ-5’rps16 intergenic spacer and psbA-trnH intergenic spacer) and one nuclear gene (ITS) were selected to characterize the genetic structure and phylogeography of S. centiflora. Twenty-eight populations were sampled across the distribution range of S. centiflora. Based on cpDNA and nDNA dates, six haplotypes and thirty-one ribotypes were recovered, respectively. High levels of cpDNA genetic diversity were found in this species and low genetic diversity within population (cpDNA: π = 0.0020, h = 0.794, HT = 0.820, HS = 0.02), while the high levels of genetic diversity in this species and within populations revealed by the nuclear gene ITS were found (ITS: π = 0.0040, h = 0.870, HT = 0.817, HS = 0.617). High genetic differentiation for cpDNA markers were detected at the wide-species level (cpDNA: GST = 0.976, NST = 0.986, NST > GST, P > 0.05), indicating that the limited gene flow through seeds was presented among populations and no significant phylogeographical structure caused by H5 shared among three deserts. However, the detection of a moderate nrDNA population subdivision (ITS: GST = 0.244, NST = 0.053, NST > GST, P < 0.05) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure, which may be caused by restricted gene flow with isolation by distance. There are significant correlation between genetic distance and geography distance for all populations of S. centiflora, which mean that isolation by distance has a great influence to genetic differentiation among populations. Almost every population except the population YBA and YBB was fixed for one cpDNA haplotype, causing no variation within the populations. Several nuclear haplotypes were distributed widely in most populations. These results may be mainly explained by long-term fragmentation and the limited gene flow caused by geographic isolation among populations. The analysis of genetic structure using SAMOVA showed that the number of population groups equaled four, and all the haplotypes can be divided into four groups, corresponding to the four lineages found in the network and phylogeny tree: (lineage I) Tengger-Badain Jaran Desert; (lineage II) Kubuqi Desert; (lineage III) Mu Us Desert; (lineage IV) Ulan Buh Desert. There is a overlap region between lineage I and lineage IV, which indicated there was a contact zone between Tengger Desert and Ulan Buh Desert. Mismatch distribution (multimodal curve) and neutral tests (Tajima’s D = 1.956, P = 0.970; Fu’s Fs = 5.793, P > 0.05) provided no evidence of recent demographic population growth. We suggest that modern allopatric distribution of cpDNA haplotypes in S. centiflora, result from vicariance caused by ecological isolation betweent deserts. By assuming a common mutation rate of the cpDNA-IGS regions, our inferred timings of these events (0.5-1.2 Mya) broadly agrees with previous geological estimated time of the origin and evolution of the deserts in this region, which were close relationship with the Kun-Huang Motion of Qinghai Tibet Plateau uplift and a glacial event (Naynayxungla) during the Mid-Late Pleistocene. So we conclude that the evolutionary dynamics of the species appear to have been driven by geological movement and climate change. Based on the phylogenetic analyses, SAMOVA analyses, network analyses and uniqueness of the populations, four evolutionary significant units (ESU) were identified and conservation strategies are discussed for this endangered species.
3. Phylogeography of Potaninia mongolica
We choose the chloroplast DNA psbA-trnH and trnL-trnF for sequencing 131 individuals from 13 natural populations of P. mongolica. The result showed that there were 2 variation sites and 3 haplotypes in combined sequence. Among the three haplotypes, H1 exists in uniquity, 71% of total samples. In the parsimony network, H1 was the root haplotype in all of haplotypes, which mean that H1 was the ancestral haplotype. Total gene variability HT = 0.493 is larger than gene diversity within population HS = 0.186. Genetic differentiation indicated no significant phylogeographic structure (GST = 0.622, NST = 0.467, P > 0.05)， which may be related to the clonal propagation characteristics of P. mongolica. The analysis of molecular variation (AMOVA) result suggested 47.1% of total variation between the populations, and 52.9% within population. The fixation index was 0.4710, which indicated that the differentiation of P. mongolica mainly came from within population and the differentiation among populations was relatively low. The mismatch distribution analysis suggested that the population of P. mongolica experienced population expansion. The result of Mantel test showed that there are no correlation between genetic distance and geographic distance. According to the distribution pattern of P. mongolica, we artificially divided it into two parts: the central region and the marginal region. We found the level of genetic diversity of P. mongolica was relatively higher in the central region than the marginal region, so we recommended the local government should establish nature reserves in the central region of P. mongolica.|