白刺花(豆科)谱系地理学研究
范邓妹
学位类型博士
导师孙航
2010-05
学位授予单位中国科学院研究生院
学位专业植物学
摘要白刺花是我国干旱河谷分布最为广泛的乡土优势灌木之一,集中分布于喜马拉雅横断山区、云贵高原、秦岭和黄土丘陵沟壑区。虽然以往关于我国高山植物的谱系地理学研究很多,但迄今对干旱河谷生境下植物物种居群的动态变化以及物种的进化历史仍缺乏了解,包括影响居群遗传结构的因素以及物种第四纪冰期的可能避难所等。本研究首先运用细胞学的方法,对白刺花居群进行染色体数目和倍性确定及核型分析,然后结合母系遗传的叶绿体基因片段和双亲遗传的核基因片段的序列数据,运用谱系地理学方法,探讨了白刺花的居群遗传多样性和居群的动态历史及影响白刺花居群遗传结构的各种因素,并推测了白刺花第四纪冰期的避难所和冰期后的扩张过程,还理清了白刺花变种间遗传关系。主要研究结果如下:1. 白刺花细胞地理学研究,对白刺花14个居群的染色体数目及核型进行了研究。结果表明白刺花种内不存在染色体倍性变化,均为二倍体,中期染色体数目为2n = 18。白刺花间期核属于复杂染色体中央粒型,分裂前期染色体属于中间型。14个居群中有7个居群的材料具有随体,但各居群随体的位置和数目不同。不同变异类型具有多样性核型,细胞遗传学的趋异主要不是染色体数目或倍性的变化,而在于染色体组织结构上的重组。白刺花倍性水平与西南山地高原的抬升没有明显的相关性。2. 谱系地理分析-来自叶绿体序列的证据:从10个叶绿体片段中筛选出2个适合白刺花居群遗传分析的片段,对40个居群400个个体进行了序列分析。结果显示rpl32-trnL和trnH-psbA两段序列联合分析后呈现了22个单倍型类型。叶绿体DNA居群遗传特征上表现为:总的遗传多样性较高(hT = 0.857),居群内平均遗传多样性低(hS = 0.171),居群分化指数(NST = 0.924,GST = 0.801)高,谱系地理结构(NST > GST,P < 0.05)明显。根据叶绿体单倍型空间分布可将所有的居群划分为7个组,其中前六个组间,它们的居群分布没有重叠区域:组1中10个居群占据白刺花分布范围的东北部地区(中国华北);组2中22个居群占据白刺花分布范围的东南部地区(云贵高原及华中);组3,4,5,6中共15个居群占据了白刺花分布范围的西部地区,并分别占据金沙江、澜沧江、雅砻江和大渡河上游4个河谷,我们将这4组作为西部地区的4个亚组来处理。Amova的分析结果也显示遗传变异主要存在于三个地理分区之间(82.43%)。白刺花居群间遗传距离和地理距离有显著的相关性(r = 0.540,P < 0.001),表明地理隔离对居群的分化有较大的影响。我们根据cpDNA序列变异所作的network网状图及系统发育树表明,其种内单倍型形成东西两大聚类簇,白刺花在东西两地区间的遗传分化,反映了田中-楷永线东侧与西侧或中国日-本植物亚区和中国-喜马拉雅植物亚区的物理环境异质性,使得东西两侧间出现隔离。伴随青藏高原的隆升,中国喜马拉雅地区的主要水系发生了改道和袭夺等重大变迁事件,导致了白刺花由过去间断分布居群变连续分布(金沙江上游/下游与雅砻江/大渡河),过去连续的分布变成间断(如怒江与红河)。这些河谷居群间单倍型的分化或联系均反映出了河流袭夺前古河流的格局以及对古老多态性的保留,而现今河流格局尚未对这些居群间的遗传结构产生明显影响。东西谱系分化后,东部分支中的南北居群发生了分化,分别固定C3或C5两种单倍型,我们推测伴随着瓶颈效应而出现的遗传漂变是导致这种居群间强烈分化的主要原因。白刺花在西部横断山区的居群具有高的遗传多样性和遗传分化,表明白刺花在该地区可能存在多个不同的第四纪冰期避难所。东部单倍型多样性较低,结合东部单倍型网状关系图呈星状分布及失配分析所得到的单峰曲线,我们推断冰期后东部避难所(金沙江中下游)居群(21,22,23)可能经历了两个不同阶段的近期扩张,并且推测扩张时间为37 ~ 303 kya。一个是含单倍型C5的祖先居群沿红河、南盘江、金沙江下游和长江流域的扩张,另一个是含单倍型C3的居群冰期后的向北再次入侵或扩张过程。在这个过程中由于瓶颈效应和奠基者效应造成了单倍型在居群中高频率的随机固定,从而使东部居群遗传多样性下降。3. 谱系地理分析-来自核基因序列的证据:从7个核基因片段中筛选出了ncpGS片段,对白刺花40个居群进行了序列分析,结果检测到23个单倍型。与叶绿体数据相比,核基因DNA居群遗传特征上表现为居群间的分化(NST = 0.470,GST = 0.338)和三个地理分区间遗传变异对总变异量的贡献(37.10%)都较低,这说明核基因单倍型分布的地理格局不如叶绿体明显。与叶绿体数据类似,核基因的遗传矩阵与地理矩阵之间具有显著的正相关关系,但这种遗传分化随地理距离增加而增大的趋势不如叶绿体明显。所有这些由cpDNA和nDNA两种标记揭示的居群遗传结构的差异主要是因为长距离的花粉扩散使核基因组比叶绿体基因组具有更大的基因流。核基因单倍型分布也表明西部地区的单倍型比较丰富,遗传多样性及遗传分:化明显地高于东南部(云贵高原及华中)和东北部地区(中国华北)。东部独特单倍型H1的存在也表现出了田中-楷永线东侧和西侧的分化。后两个地区单倍型多样性的降低在一定程度上同样反映了奠基者效应的影响。但是,我们检测到居群内核基因遗传多样性保持在较高水平(hS = 0.559),这主要是因为不同区域间或区域内高水平的花粉交流足以抵制居群由奠基者效应引起的遗传结果。4. 白刺花变种间的系统关系:谱系地理分析结果显示,叶绿体单倍型被分成两个聚类簇,分别对应于白刺花原变种和川西白刺花变种,并且前者具有后者所没有的核基因单倍型H1。白刺花原变种和凉山白刺花变种在一个谱系分支中。这两个变种与川西白刺花变种之间的遗传分化可能与形态上叶片大小差异有关,而变种间表型分异反映了对环境改变的表型可塑性。因此,它们在叶片形态上的差异是由地理隔离产生的种子传播限制和在降水及海拔上的环境异质性或二者共同作用所造成的。总之,伴随喜马拉雅隆升产生的一系列地质、水系变迁及区系特征差异对白刺花居群遗传格局的影响为进一步探讨我国植物区系的起源和分布格局的变迁提供了一个新的思路。白刺花的遗传多样性和居群遗传结构对我们推测其冰期避难所,阐明种内关系提供了重要依据。它独特的居群结构和动态历史对进一步制定相应的保护措施具有重要的参考价值。首先在保护时应将其东西两地区的居群作为两个独立的“显著进化单元”(ESU)。对于居群遗传多样性较高的“避难地”是优先保护的热点地区,由于高度遗传分化,在迁地保护和取样时,应该在尽可能多的群体中取样,而且要在每个群体中取足够多的个体来进行繁殖。秦岭以北地区尤其是北方黄土丘陵沟壑区生态环境破坏比较严重,该区域内白刺花居群单倍型单一,遗传多样性非常低,因此该地区保护应加强重视。
资助项目Sophora davidii (Franch.) Skeels is an endemic species to China, and widely distributed in the dry valleys of the Himalayan-Hengduan Mountain Systems, the Yungui Plateau, the Qinling Mountain, the Loess Plateau and other places of China. Previous studies of plant phylogeography have focused mainly on some taxa from the mountainous areas of China, relatively few studies have been conducted on plant taxa from the river valleys. The population dynamics and evolutionary history of species in such habitat remain less unknown, including the factors affecting the population genetic structure and its potential refugia in glaciation. In this study, we first determine the chromosome number, ploidy and karyotype of most populations we sampled. Then, based on sequence data from two maternally inherited cpDNA and one biparentally inherited nuclear DNA fragments, our study revealed the genetic diversity and population genetic structure of S. davidii and factors affecting them. The demographic history and potential refugia of this speices were investigated and the genetic relationship among three varieties was also clarified. The main results are summarized as follows:1. Cytogeography,The chromosome number and karyotypes of 14 S. davidii populations have been studied. The results showed that the choromosome number of all the populations is 2n = 18. The interphase nuclei and prophase chromosomes of the species were found to be of the complex chromosome type and interstitial type. The results of karyotype analysis showed that 7 of 14 materials has satellites, and the number and position of satellites differ among populations, and thus revealed a series of diversified karyotypes. With most populations being of ploidy, cytogenetical divergence within the species lied mainly in chromosome size and structure. The fact that polyploidization did not occur very often for variations in Southwest China was against viewpoint that polyploidization level in this area is higher than that of other distribution areas due to the elevation of mountains and plateau. 2. Phylogeographic analysisbased on chloroplast sequence,We sequenced two cpDNA fragments rpl32-trnL(UAG)intergenic spacer and trnH-psbA spacer in 40 populations sampled, recovering 22 chlorotypes. The average with-in population diversity (hS = 0.171) was much lower than total genetic diversity (hT = 0.857). Population differentiation was high (NST = 0.924, GST = 0.801) indicating low levels of seed-based gene flow and significant phylogeographical stucture (NST > GST, P < 0.05) were exhibited by this species. The SAMOVA revealed seven diverging groups of related chlorotypes, six of them had distinct nonoverlapping geographical ranges: one in the northeast comprising 10 populations, a second with a southeast distribution comprising 22 populations, and the remaning four groups comprising 15 populations located in the west part of the species’ range along different river valleys. The genetic clustering of populations into three regions was also supported by analysis of molecular variance, which showed that most genetic variation (82.43%) was found among these three regions. Two clusters were distinguished by both phylogenetic analysis and genealogical analysis of chlorotypes, one consisting of chlorotypes from the western region and the second consisting of those from the eastern region. Significant genetic differences between the two regions might be attributed to vicariance and restricted gene flow, and this vicariance could be explained by the physical environmental heterogeneity on each side of the Tanaka-Kaiyong Line. Following the uplift of the Tibetan Plateau, the reorganization of the major river drainages was primarily caused by river separation and capture events. These historical events could change the distribution of S. davidii from fragmented to continuous (Upper/Lower Jinshajiang and Yalongjiang/Daduhe), and from continuous to fragmented (Nujiang and Jinshajiang/Honghe). However, spatial and temporal patterns of phylogeographic divergence are strongly associated with historical disjunction rather than modern drainage connections. Moreover, the following north-south split in the eastern region and effective isolation with their genetic diversity were essentially modelled by genetic drift. The higher chlorotype richness and genetic divergence for populations in western region compared with other two regions suggests that there were multipe refugia or in situ survival of S. davidii in the Himalayan-Hengduan Mountain region. Fixation of chlorotypes in the northeastern region and near fixation in the southeastern region suggest a recent colonization of these areas. We further found that this species underwent past range expansion around 37-303 thousand years ago (kya). The southeastern populations likely experienced a demographic expansion via unidirectional gene flow along rivers, while northeastern populations underwent a more northward expansion, both from initial populations (s) (21, 22, 23) preserved on eastern refugia (Jinshajiang). This process might have been accompanied with a series of founder effects or bottlenecks making populations genetically impoverished. 3. Phylogeographic analysisbased on nuclear sequence,We sequenced the nuclear (ncpGS) region in all populations sampled, recovering 23 nuclear haplotypes. Compared to cpDNA, both NST (0.470) and GST (0.338) were relatively lower, but NST was also significantly larger than GST. 37.10% of the total variation was distributed among regions which was much lower than that shown by chlorotypes. Thus, more extensive distribution of nuclear haplotypes was exhibited across the geographical range instead of the strong population subdivision observed in chlorotypes. Similarly to the chloroplast data, we found that genetic differentiation of nDNA was positively correlated with the geographical distance, but the increase in the geographical distance between populations did not increase the genetic differentiation of nDNA as rapidly as that of cpDNA. These contrasting levels between the chloroplast and nuclear genomes of S. davidii are likely due to limited gene flow of cpDNA by seeds vs. the extensive gene flow of nDNA by wind-mediated pollen in the population history. We also determined from nuclear markers that haplotype diversity was reduced in the southeastern and northeastern regions due to the loss of rare haplotypes in western region. This reduction of gene diversity is also a signature of founder events or recent bottleneck during post-glacial colonization. However, nuclear diversity within populations remains high. This provides evidence that regionally pollen flow might be sufficiently high to blur the genetic identity of founder populations over a reasonably large spatial scale.3. Relationships among three varieties,The phylogenetic analysis identified two phylogroups of chlorotypes, corresponding to S. davidii var. davidii and var. chuansinesis. The former was distinguished by the abscence of predonminant nuclear haplotype H1 of the latter. The monophyletic group of chlorotypes in var. davidii and var. liangshanesis showed their relatively close relationship. And their genetic divergence from the third variety appears to be relative to their slight morphological difference in leaf size and the divergent environmental niche spaces they occupy. Thus, the observed differences in morphological characters between var. chuansinesis and other two varieties can be explained by the seed dispersal limitation illustrated above (as inferred by geographical separation) and by environmental heterogeneity (as inferred by precipitation or elevation) or by a combination of both. After all, the geological changes, drainage reorganization, and floristic differences following the Himalayan uplift have been suggested to affect the genetic structure of S. davidii. These results provide new insights into the phylogeographic pattern of plants in China. In addition, the unique population genetic structure found in S. davidii has provided important insights into the evolutionary history of this species. The genetic profile uncovered in this study is also critical for its conservation management. Our study has uncovered the existence of at least two ‘evolutionary significant units’ independent units within S. davidii, corresponding to var. davidii from eastern region and var. chuansinensis from western region. The conservation efforts should first focus on most western populations and on the southeastern ones exhibiting high levels of genetic diversity, while the genetically homogeneous northeastern populations located in the degraded Loess Plateau should require much greater conservation efforts.
语种中文
文献类型学位论文
条目标识符http://ir.kib.ac.cn/handle/151853/16192
专题昆明植物所硕博研究生毕业学位论文
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范邓妹. 白刺花(豆科)谱系地理学研究[D]. 中国科学院研究生院,2010.
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