中国特有第三纪孑遗植物香果树（Emmenopterys henryi）的亲缘地理学和景观遗传学研究

发布时间：2018-06-08 10:07

  本文选题：香果树 + 亲缘地理　； 参考：《浙江大学》2016年博士论文

【摘要】：香果树(Emmenopterys hnryi Oliv.)隶属茜草科(Rubiaceae)康达明族(Condamineeae)香果树属(Emmenopterys),为中国特有的单种属植物。香果树祖先类群在始新世到中新世曾广泛分布于北半球,目前仅分布于中国亚热带地区(北至秦岭北坡,南至云南文山麻栗坡)海拔400-2200米处的沟谷或山坡谷地的暖温带落叶阔叶林中,香果树的野外资源量有限,现已被列入我国二级重点保护植物。该物种在中国的分布范围广,是一个很好的检验地理隔离、景观隔离以及自然选择在谱系分化中相对作用模式系统。此外,解析香果树的中性与适应性遗传多样性的空间分布,将为该物种的科学保护提供理论指导与技术支持。由于叶绿体基因组的遗传变异更多反映古历史事件所遗留的印迹,而核基因组的遗传信息则能反映近期发生的基因流过程和状况,因此,本研究利用叶绿体DNA(cpDNA)片段(psbA-trnH,trnL-trnF,trnT-trnL).细胞核核糖体DNA的内转录间隔区(ITS)序列以及AFLPs分子标记联合分析香果树分布区内38个群体的遗传多样性、遗传结构以及谱系地理结构。基于系统发生学、亲缘地理学、群体遗传学及景观遗传学等分析方法,解析了物种与谱系进化历史和谱系分化的生态与地理因素。主要结果如下：(1)叶绿体与核糖体DNA的遗传多样性与遗传结构基于cpDNA和ITS的系统发生分析结果表明,香果树大致以长江流域为界分为两大谱系,即南部谱系和北部谱系。在种水平,香果树遗传多样性非常高(cpDNA:hT=0.928, πT=0.271×10-2；ITS:hT=0.675；πT=0.195×10-2),而群体水平的遗传多样性较低(hs=0.291,πs=0.054×10-2;ITS:hs=0.347,πs=0.083×10-2),因此群体间分化大(cpDNA: FST=0.779:ITS:FST=0.558).南部谱系的遗传多样性(cpDNA:hT=0.889,πT=0.215×10-2;ITS:hT=0.687,πT=0.220×10-2)高于北部谱系(cpDNA:hT=0.818,πT=0.196×10-2;ITS:hTT=0.561,πT=0.085×10-2).此外,南部谱系的群体遗传分化(cpDNA:FST= 0.823；ITS:FST=0.558)明显大于北部谱系(cpDNA:FST=0.551:ITS:FST=0.184).基于叶绿体片段的SAMOVA分析,南、北谱系又各自进一步分为东、西两个地理组,即东南地理组、中部-西南地理组、东北地理组和西北地理组。香果树在种水平(GST/NST=0.704/0.802,P0.01)和南部谱系(GST/NST=0.757/0.868,P0.05)具有明显的谱系地理结构,并在种内(r=0.237,P=0.001)和南北谱系内(北部谱系：r=0.506,P=0.001；南部谱系：r=0.293,P=0.001)均检测到距离隔离效应(Isolation-by-Distance, IBD)。(2)谱系分化与群体动态历史分析基于叶绿体单倍型数据,使用松散分子钟的贝叶斯系统进化分析方法,由BEAST软件估算得到：香果树南北谱系分化的时间约为5.06百万年前(Ma)(95% HPD:1.68-8.91Ma),谱系内的分化时间分别约为3.64Ma(南部谱系,95%HPD:1.18-6.42 Ma)和3.42Ma(北部谱系,95%HPD:0.99-6.40 Ma),因此谱系分化与中新世／上新世的气候波动导致物种的气候避难所隔离有关。通过中性检验和失配分布分析得到,东南、东北和西北3个地理组符合空间扩张模型,其扩张时间分别为：东南地理组c.0.23Ma(95%CI:0.000-0.811 Ma)；东北地理组c.0.19Ma(95%CI:0.111-0.314Ma);西北地理组c.0.26 Ma (95% CI:0.133-0.376 Ma),均在倒数第二个冰期[里斯冰期(c.0.12-0.35 Ma)]区间内。(3)物种生态位模型模拟与谱系生态位分化分析采用香果树的114个分布记录点的地理信息,以6个生物气候指标为环境因子,使用MAXENT软件对香果树过去[末次间冰期(LIG;c.130-140 kyaBP)、末次盛冰期(LGM；c.21 kya BP)]、当代(1950—2000)以及未来(2080)的潜在分布区做出预测。结果表明,尽管目前的分布预测很好的代表了该种的现存分布区,但有些预测地区并没有该种的分布记录(如青藏高原的东南部以及台湾地区)。与现代的分布区相比：在LIG时期,香果树具有很窄的潜在分布区范围,特别是华中及华北地区(比如,四川盆地的北部以及秦岭-大巴山系)：在LGM时期,香果树的潜在分布区大幅地拓展,占据了中国亚热带大片低地区域。但是,在将来的2080年,除了北方秦岭-大巴山系之外,香果树其他的潜在分布区(特别是长江以南地区)急剧压缩。谱系生态位分化分析表明,香果树南北谱系的生态位存在明显的分化,与其相关的主导因子是与降水相关的生物气候因子。(4) AFLPs的遗传多样性与遗传结构筛选了9对AFLP引物组合,对394个香果树群体的遗传变异进行了分析。9对AFLP引物共扩增出了457条带峰值清晰、可重复、可判读的条带,其中431条(94.31%)为多态性条带。香果树具有较高的种内遗传多样性(HE=0.217,I=0.394),较低的群体内遗传多样性(HE=0.117,I=0.176),因此群体间遗传分化较大(FST=0.344)。基于Bayesian模型的BAPS聚类分析表明：cpDNA北部谱系单独聚为1个群簇,而cpDNA南部谱系则由9个群簇组成。PCoA(principal coordinate analysis)分析、NJ(neighbour-joining)树的结果与BAPS总体一致,但在南部cpDNA谱系,PCoA分析和NJ树都支持分成西南地理组和中部-东南部地理组。尽管,cpDNA南部与北部谱系具有相似的遗传多样性水平(南部：HE=0.212,I=0.323；北部：HE=0.203,I=0.338),但cpDNA南部谱系的遗传分化(FsT=0.416)显著大于北部谱系(FST=0.175)。(5)空间遗传分化的生态与地理因素采用基因组扫描(genome scanning,GS)与多元线性回归方法(multiple linear regression,MLR)检测了AFLPs的outlier位点以及与适应相关的潜在位点,并进一步用单变量回归分析(univariate regressions, UR)解析了导致香果树群体局域适应的环境因素。由Mcheza和BayeScan v.2.0软件分别测到67个和16个AFLPs的outlier位点,有6个outlier位点被两个软件同时检测出。通过MLR分析发现,6个位点中的4个位点(L128、L144、L294、L305,占总数的0.88%)受环境因子选择。进一步用UR分析得到平均日较差温度(BI02:Mean Diurnal Range)、季节温度(BIO4:Temperature Seasonality)、最热月最高温(BI05:Max Temperature of Warmest Month)、年降水(BIO12:Annual Precipitation)和季节降水(BIO15:Precipitation Seasonality)这5个环境因子与上述6个outlier位点具有最强的相关性。基于中性的AFLPs数据,运用随机多重矩阵回归分析(Multiple Matrix Regression with Randomization, MMRR)和结构方程建模(Structural Equation Modelling, SEM)等景观遗传学统计方法研究了环境阻力、地理隔离及自然选择在空间遗传分化中的作用,结果表明：地理隔离效应(IBD)对香果树空间遗传分化的促进作用(MMRR:0.307; SEM:0.360±0.037)大于环境阻力效应(Isolation-by-Environment;IBE) (MMRR:0.247; SEM:0.181士0.151)。通过环境变量贡献分析得到环境阻力中贡献度最大的是季节性温度(BI04：Temperature Seasonality)和温度年较差(BIO7:Temperature Annual Range);其次是年均温(BIO1:Annual Mean Temperature)、最热月最高温(BIO5:Max Temperature of Warmest Month)及最干季平均温(BIO9:Max Temperature of Warmest Month);而坡度、土壤类型及年降水量贡献度最小。因此地理隔离、环境阻力及自然选择共同塑造了香果树近代的空间遗传结构。综上所述,香果树在种水平具有较高的遗传多样性和明显的谱系地理结构,谱系分化与中新世/上新世的气候波动导致物种的气候避难所隔离有关,当代的群体间地理隔离与环境阻力对群体间的基因流也产生了明显的阻隔效应,同时自然选择导致的局域适应性则进一步加速了群体间分化。本研究所揭示的香果树群体遗传多样性和遗传结构,对香果树群体的保护具有重要的理论指导作用,同时,有助于理解晚第三纪气候变化对东亚温带植物进化历史和分布的影响。
[Abstract]:Emmenopterys hnryi Oliv., belonging to the Condamineeae (Emmenopterys) of the alizaraceus (Rubiaceae) Kangda (Condamineeae), is a single species of single species in China. The ancestors of fragrant fruit trees were widely distributed in the Northern Hemisphere from Eocene to Miocene and are currently distributed only in subtropical regions of China (north to North Qinling Mountains, South to Wenshan in Yunnan). Malipo) in the warm temperate deciduous broad-leaved forest of the valley or hillside Valley at 400-2200 meters above sea level, the wild resources of the fruit tree are limited. It has been listed as the two key protected plant in China. The species is widely distributed in China. It is a good test of geographical isolation, landscape isolation and natural selection in the differentiation of genealogical differentiation. In addition, the spatial distribution of the neutral and adaptive genetic diversity of the fruit tree will provide theoretical guidance and technical support for the scientific protection of the species. As the genetic variation of the chloroplast genome is more reflected in the legacy of the ancient historical events, the genetic information of the nuclear gene group can reflect the recent gene. Flow processes and conditions, therefore, this study uses the chloroplast DNA (cpDNA) fragment (psbA-trnH, trnL-trnF, trnT-trnL), the nuclear ribosome DNA internal transcriptional spacer (ITS) sequence and the AFLPs molecular marker to analyze the genetic diversity, genetic structure and genealogical structure of 38 populations in the fruit tree distribution area. The main results are as follows: (1) the genetic diversity and genetic structure of the chloroplast and ribosome DNA and the phylogenetic analysis of the genetic structure based on cpDNA and ITS indicate that the fruit tree is roughly in the Yangtze River flow. The domain is divided into two lineages, that is, the southern pedigree and the northern pedigree. At the seed level, the genetic diversity of the fruit tree is very high (cpDNA:hT=0.928, PI T=0.271 x 10-2; ITS:hT=0.675; PI T=0.195 x 10-2), and the genetic diversity of the population is low (hs=0.291, PI s=0.054 x 10-2; ITS:hs=0.347, PI s=0.083 x 10-2), so the population differentiation is large (cpDNA:). FST=0.779:ITS:FST=0.558). The genetic diversity of the southern pedigree (cpDNA:hT=0.889, PI T=0.215 x 10-2; ITS:hT=0.687, PI T=0.220 x 10-2) is higher than the northern pedigree (cpDNA:hT=0.818, PI T=0.196 x 10-2; ITS:hTT=0.561, PI T=0.085 x 10-2). In addition, the genetic differentiation of the southern pedigree (cpDNA:FST= 0.823; ITS:FST=0.558) is obviously larger than the northern lineage (cpD). NA:FST=0.551:ITS:FST=0.184). Based on the SAMOVA analysis of chloroplast fragments, the southern and Northern pedigrees are further divided into two eastern and western geographical groups, namely, the southeast geographic group, the central - Southwest geographic group, the Northeast geographic group and the northwest geographic group. The fruit tree is at the level of GST/NST=0.704/ 0.802, P0.01 and the southern pedigree (GST/NST=0.757/0.868, P0.05). The distinct genealogical structure and the detection of distance isolation effect (Isolation-by-Distance, IBD) in r=0.237 (r=0.237, P=0.001) and North and South pedigree (r=0.506, P=0.001; r=0.293, P=0.001) in the southern part of the genealogy. (2) pedigree differentiation and population dynamic historical analysis based on the chloroplast haplotype data and the use of a loose molecular clock. The Juliu phylogenetic analysis method was estimated by BEAST software: the differentiation time of the north and South pedigree of the fruit tree was about 5 million 60 thousand years ago (Ma) (95% HPD:1.68-8.91Ma), and the differentiation time in the pedigree was about 3.64Ma (Southern pedigree, 95%HPD:1.18-6.42 Ma) and 3.42Ma (the northern pedigree, 95%HPD:0.99-6.40 Ma), so the pedigree differentiation and the Miocene / Miocene The climate fluctuations in the Pliocene lead to the isolation of the species' climatic shelters. Through the neutral test and mismatch distribution analysis, the 3 geo groups in the southeast, northeast and northwest are in accordance with the spatial expansion model, and their expansion time is c.0.23Ma (95%CI:0.000-0.811 Ma) of the southeast geographic group, the Northeast Geographic group c.0.19Ma (95%CI:0.111-0.314Ma), and the northwest. The geographic group c.0.26 Ma (95% CI:0.133-0.376 Ma) was within the second glacial period [Rees glacial (c.0.12-0.35 Ma)] interval. (3) the species niche model simulation and pedigree niche differentiation analysis adopted the geographical information of 114 distribution points of the fruiter tree, with 6 bioclimatic indicators as environmental factors and MAXENT software for the fruit tree. The last interglacial (LIG; c.130-140 kyaBP), the last glacial period (LGM; c.21 kya BP), the contemporary (1950 - 2000) and future (2080) potential distribution areas were predicted. The results showed that although the current distribution forecast represented the extant distribution of the species well, some of the predicted regions did not have the distribution records of the species (such as the Qinghai Tibet Plateau. In the southeast and Taiwan areas. Compared with the modern distribution area: in the LIG period, the fragrant fruit tree has a very narrow potential distribution area, especially in central and North China (for example, the north of the Sichuan basin and the Qinling Mountains - DBA mountain system): in the LGM period, the potential distribution area of the fruit tree was greatly expanded and occupied a large subtropical low land in the subtropical region of China. However, in the future, in 2080, in addition to the northern Qinling Mountains Daba mountain system, the other potential areas of the fruit tree (especially in the south of the Yangtze River) are sharply compressed. The analysis of pedigree niche differentiation shows that the niche of the north and South pedigree of the fragrant fruit tree has obvious differentiation, and the leading factor related to it is the biologic climate related to the precipitation. (4) the genetic diversity and genetic structure of AFLPs were screened by 9 pairs of AFLP primers, and the genetic variation of 394 fruit tree populations was analyzed by.9. 457 bands with clear, repeatable and readable bands were amplified by AFLP primers, of which 431 (94.31%) were polymorphic bands. Fruit trees had higher intraspecific genetic diversity (HE= 0.217, I=0.394), the genetic diversity in the lower population (HE=0.117, I=0.176), so the genetic differentiation among the populations was larger (FST=0.344). The BAPS cluster analysis based on the Bayesian model showed that the pedigree of the northern part of cpDNA was individually clustered into 1 clusters, and the genealogical lineage of the Southern cpDNA was composed of 9 clusters of.PCoA (principal coordinate analysis). Oining) the result of the tree is the same as that of the BAPS, but in the southern cpDNA pedigree, the PCoA analysis and the NJ tree are all supported into the southwest geographic group and the central and southeastern geographic group. Although the southern and Northern pedigree of the southern part of the cpDNA have similar genetic diversity (South: HE=0.212, I=0.323; North: HE=0.203, I=0.338), but the genetic score of the southern pedigree of cpDNA. (FsT=0.416) was significantly greater than the northern pedigree (FST=0.175). (5) the ecological and geographical factors of spatial genetic differentiation were detected by genome scanning (GS) and multivariate linear regression (multiple linear regression, MLR) to detect outlier loci of AFLPs and the potential sites associated with adaptation, and further use single variable regression analysis. Univariate regressions, UR) analyzed the environmental factors that led to local adaptation to the fruit tree population. The outlier loci of 67 and 16 AFLPs were measured by Mcheza and BayeScan v.2.0 software, 6 outlier loci were detected by two software. 4 of the 6 loci were found by MLR analysis (L128, L144, 0.8, 0.8). 8%) by the environmental factors, the average daily temperature (BI02:Mean Diurnal Range), the seasonal temperature (BIO4:Temperature Seasonality), the most hot month temperature (BI05:Max Temperature of Warmest Month), the annual precipitation (BIO12:Annual) and seasonal precipitation are obtained by UR analysis. The factor has the strongest correlation with the above 6 outlier loci. Based on the neutral AFLPs data, the landscape genetic statistical methods such as random multiple matrix regression analysis (Multiple Matrix Regression with Randomization, MMRR) and structural equation modeling (Structural Equation Modelling, SEM) are used to study environmental resistance, geographical isolation and The effect of natural selection on spatial genetic differentiation showed that the effect of geographic isolation effect (IBD) on spatial genetic differentiation of fragrant fruit trees (MMRR:0.307; SEM:0.360 + 0.037) was greater than environmental resistance effect (Isolation-by-Environment; IBE) (MMRR:0.247; SEM: 0.181 0.151). The environmental resistance was analyzed by the contribution of environmental variables to environmental resistance. The largest contribution is the seasonal temperature (BI04:Temperature Seasonality) and the temperature range (BIO7:Temperature Annual Range), followed by Nian Junwen (BIO1:Annual Mean Temperature), the hottest month's highest temperature (BIO5:Max Temperature of Warmest) and the dry season average temperature; and the slope, soil Therefore, geographical isolation, environmental resistance and natural selection jointly mold the modern spatial genetic structure of the fruit tree. To sum up, the fruit tree has a high genetic diversity and a distinct genealogical structure at the level of seed, and the climatic fluctuation of the pedigree and the Miocene / Pliocene leads to the species. The geographical isolation and environmental resistance of the present population also have obvious barrier effect on the gene flow among the population, while the local adaptability caused by natural selection further accelerates the interpopulation differentiation. The diversity and genetic structure of the fruit tree population in this study are revealed to the fruit tree population. Conservation has important theoretical guidance and helps to understand the impact of late third climatic changes on the evolution and distribution of plants in temperate temperate zone of East Asia.
【学位授予单位】：浙江大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q943
，

本文编号：1995432