發(fā)布時(shí)間：2018-06-08 10:07

  本文選題：香果樹 + 親緣地理�。� 參考：《浙江大學(xué)》2016年博士論文

【摘要】：香果樹(Emmenopterys hnryi Oliv.)隸屬茜草科(Rubiaceae)康達(dá)明族(Condamineeae)香果樹屬(Emmenopterys),為中國(guó)特有的單種屬植物。香果樹祖先類群在始新世到中新世曾廣泛分布于北半球,目前僅分布于中國(guó)亞熱帶地區(qū)(北至秦嶺北坡,南至云南文山麻栗坡)海拔400-2200米處的溝谷或山坡谷地的暖溫帶落葉闊葉林中,香果樹的野外資源量有限,現(xiàn)已被列入我國(guó)二級(jí)重點(diǎn)保護(hù)植物。該物種在中國(guó)的分布范圍廣,是一個(gè)很好的檢驗(yàn)地理隔離、景觀隔離以及自然選擇在譜系分化中相對(duì)作用模式系統(tǒng)。此外,解析香果樹的中性與適應(yīng)性遺傳多樣性的空間分布,將為該物種的科學(xué)保護(hù)提供理論指導(dǎo)與技術(shù)支持。由于葉綠體基因組的遺傳變異更多反映古歷史事件所遺留的印跡,而核基因組的遺傳信息則能反映近期發(fā)生的基因流過(guò)程和狀況,因此,本研究利用葉綠體DNA(cpDNA)片段(psbA-trnH,trnL-trnF,trnT-trnL).細(xì)胞核核糖體DNA的內(nèi)轉(zhuǎn)錄間隔區(qū)(ITS)序列以及AFLPs分子標(biāo)記聯(lián)合分析香果樹分布區(qū)內(nèi)38個(gè)群體的遺傳多樣性、遺傳結(jié)構(gòu)以及譜系地理結(jié)構(gòu)。基于系統(tǒng)發(fā)生學(xué)、親緣地理學(xué)、群體遺傳學(xué)及景觀遺傳學(xué)等分析方法,解析了物種與譜系進(jìn)化歷史和譜系分化的生態(tài)與地理因素。主要結(jié)果如下：(1)葉綠體與核糖體DNA的遺傳多樣性與遺傳結(jié)構(gòu)基于cpDNA和ITS的系統(tǒng)發(fā)生分析結(jié)果表明,香果樹大致以長(zhǎng)江流域?yàn)榻绶譃閮纱笞V系,即南部譜系和北部譜系。在種水平,香果樹遺傳多樣性非常高(cpDNA:hT=0.928, πT=0.271×10-2；ITS:hT=0.675；πT=0.195×10-2),而群體水平的遺傳多樣性較低(hs=0.291,πs=0.054×10-2;ITS:hs=0.347,πs=0.083×10-2),因此群體間分化大(cpDNA: FST=0.779:ITS:FST=0.558).南部譜系的遺傳多樣性(cpDNA:hT=0.889,πT=0.215×10-2;ITS:hT=0.687,πT=0.220×10-2)高于北部譜系(cpDNA:hT=0.818,πT=0.196×10-2;ITS:hTT=0.561,πT=0.085×10-2).此外,南部譜系的群體遺傳分化(cpDNA:FST= 0.823；ITS:FST=0.558)明顯大于北部譜系(cpDNA:FST=0.551:ITS:FST=0.184).基于葉綠體片段的SAMOVA分析,南、北譜系又各自進(jìn)一步分為東、西兩個(gè)地理組,即東南地理組、中部-西南地理組、東北地理組和西北地理組。香果樹在種水平(GST/NST=0.704/0.802,P0.01)和南部譜系(GST/NST=0.757/0.868,P0.05)具有明顯的譜系地理結(jié)構(gòu),并在種內(nèi)(r=0.237,P=0.001)和南北譜系內(nèi)(北部譜系：r=0.506,P=0.001；南部譜系：r=0.293,P=0.001)均檢測(cè)到距離隔離效應(yīng)(Isolation-by-Distance, IBD)。(2)譜系分化與群體動(dòng)態(tài)歷史分析基于葉綠體單倍型數(shù)據(jù),使用松散分子鐘的貝葉斯系統(tǒng)進(jìn)化分析方法,由BEAST軟件估算得到：香果樹南北譜系分化的時(shí)間約為5.06百萬(wàn)年前(Ma)(95% HPD:1.68-8.91Ma),譜系內(nèi)的分化時(shí)間分別約為3.64Ma(南部譜系,95%HPD:1.18-6.42 Ma)和3.42Ma(北部譜系,95%HPD:0.99-6.40 Ma),因此譜系分化與中新世／上新世的氣候波動(dòng)導(dǎo)致物種的氣候避難所隔離有關(guān)。通過(guò)中性檢驗(yàn)和失配分布分析得到,東南、東北和西北3個(gè)地理組符合空間擴(kuò)張模型,其擴(kuò)張時(shí)間分別為：東南地理組c.0.23Ma(95%CI:0.000-0.811 Ma)；東北地理組c.0.19Ma(95%CI:0.111-0.314Ma);西北地理組c.0.26 Ma (95% CI:0.133-0.376 Ma),均在倒數(shù)第二個(gè)冰期[里斯冰期(c.0.12-0.35 Ma)]區(qū)間內(nèi)。(3)物種生態(tài)位模型模擬與譜系生態(tài)位分化分析采用香果樹的114個(gè)分布記錄點(diǎn)的地理信息,以6個(gè)生物氣候指標(biāo)為環(huán)境因子,使用MAXENT軟件對(duì)香果樹過(guò)去[末次間冰期(LIG;c.130-140 kyaBP)、末次盛冰期(LGM；c.21 kya BP)]、當(dāng)代(1950—2000)以及未來(lái)(2080)的潛在分布區(qū)做出預(yù)測(cè)。結(jié)果表明,盡管目前的分布預(yù)測(cè)很好的代表了該種的現(xiàn)存分布區(qū),但有些預(yù)測(cè)地區(qū)并沒有該種的分布記錄(如青藏高原的東南部以及臺(tái)灣地區(qū))。與現(xiàn)代的分布區(qū)相比：在LIG時(shí)期,香果樹具有很窄的潛在分布區(qū)范圍,特別是華中及華北地區(qū)(比如,四川盆地的北部以及秦嶺-大巴山系)：在LGM時(shí)期,香果樹的潛在分布區(qū)大幅地拓展,占據(jù)了中國(guó)亞熱帶大片低地區(qū)域。但是,在將來(lái)的2080年,除了北方秦嶺-大巴山系之外,香果樹其他的潛在分布區(qū)(特別是長(zhǎng)江以南地區(qū))急劇壓縮。譜系生態(tài)位分化分析表明,香果樹南北譜系的生態(tài)位存在明顯的分化,與其相關(guān)的主導(dǎo)因子是與降水相關(guān)的生物氣候因子。(4) AFLPs的遺傳多樣性與遺傳結(jié)構(gòu)篩選了9對(duì)AFLP引物組合,對(duì)394個(gè)香果樹群體的遺傳變異進(jìn)行了分析。9對(duì)AFLP引物共擴(kuò)增出了457條帶峰值清晰、可重復(fù)、可判讀的條帶,其中431條(94.31%)為多態(tài)性條帶。香果樹具有較高的種內(nèi)遺傳多樣性(HE=0.217,I=0.394),較低的群體內(nèi)遺傳多樣性(HE=0.117,I=0.176),因此群體間遺傳分化較大(FST=0.344)�；贐ayesian模型的BAPS聚類分析表明：cpDNA北部譜系單獨(dú)聚為1個(gè)群簇,而cpDNA南部譜系則由9個(gè)群簇組成。PCoA(principal coordinate analysis)分析、NJ(neighbour-joining)樹的結(jié)果與BAPS總體一致,但在南部cpDNA譜系,PCoA分析和NJ樹都支持分成西南地理組和中部-東南部地理組。盡管,cpDNA南部與北部譜系具有相似的遺傳多樣性水平(南部：HE=0.212,I=0.323；北部：HE=0.203,I=0.338),但cpDNA南部譜系的遺傳分化(FsT=0.416)顯著大于北部譜系(FST=0.175)。(5)空間遺傳分化的生態(tài)與地理因素采用基因組掃描(genome scanning,GS)與多元線性回歸方法(multiple linear regression,MLR)檢測(cè)了AFLPs的outlier位點(diǎn)以及與適應(yīng)相關(guān)的潛在位點(diǎn),并進(jìn)一步用單變量回歸分析(univariate regressions, UR)解析了導(dǎo)致香果樹群體局域適應(yīng)的環(huán)境因素。由Mcheza和BayeScan v.2.0軟件分別測(cè)到67個(gè)和16個(gè)AFLPs的outlier位點(diǎn),有6個(gè)outlier位點(diǎn)被兩個(gè)軟件同時(shí)檢測(cè)出。通過(guò)MLR分析發(fā)現(xiàn),6個(gè)位點(diǎn)中的4個(gè)位點(diǎn)(L128、L144、L294、L305,占總數(shù)的0.88%)受環(huán)境因子選擇。進(jìn)一步用UR分析得到平均日較差溫度(BI02:Mean Diurnal Range)、季節(jié)溫度(BIO4:Temperature Seasonality)、最熱月最高溫(BI05:Max Temperature of Warmest Month)、年降水(BIO12:Annual Precipitation)和季節(jié)降水(BIO15:Precipitation Seasonality)這5個(gè)環(huán)境因子與上述6個(gè)outlier位點(diǎn)具有最強(qiáng)的相關(guān)性�；谥行缘腁FLPs數(shù)據(jù),運(yùn)用隨機(jī)多重矩陣回歸分析(Multiple Matrix Regression with Randomization, MMRR)和結(jié)構(gòu)方程建模(Structural Equation Modelling, SEM)等景觀遺傳學(xué)統(tǒng)計(jì)方法研究了環(huán)境阻力、地理隔離及自然選擇在空間遺傳分化中的作用,結(jié)果表明：地理隔離效應(yīng)(IBD)對(duì)香果樹空間遺傳分化的促進(jìn)作用(MMRR:0.307; SEM:0.360±0.037)大于環(huán)境阻力效應(yīng)(Isolation-by-Environment;IBE) (MMRR:0.247; SEM:0.181士0.151)。通過(guò)環(huán)境變量貢獻(xiàn)分析得到環(huán)境阻力中貢獻(xiàn)度最大的是季節(jié)性溫度(BI04：Temperature Seasonality)和溫度年較差(BIO7:Temperature Annual Range);其次是年均溫(BIO1:Annual Mean Temperature)、最熱月最高溫(BIO5:Max Temperature of Warmest Month)及最干季平均溫(BIO9:Max Temperature of Warmest Month);而坡度、土壤類型及年降水量貢獻(xiàn)度最小。因此地理隔離、環(huán)境阻力及自然選擇共同塑造了香果樹近代的空間遺傳結(jié)構(gòu)。綜上所述,香果樹在種水平具有較高的遺傳多樣性和明顯的譜系地理結(jié)構(gòu),譜系分化與中新世/上新世的氣候波動(dòng)導(dǎo)致物種的氣候避難所隔離有關(guān),當(dāng)代的群體間地理隔離與環(huán)境阻力對(duì)群體間的基因流也產(chǎn)生了明顯的阻隔效應(yīng),同時(shí)自然選擇導(dǎo)致的局域適應(yīng)性則進(jìn)一步加速了群體間分化。本研究所揭示的香果樹群體遺傳多樣性和遺傳結(jié)構(gòu),對(duì)香果樹群體的保護(hù)具有重要的理論指導(dǎo)作用,同時(shí),有助于理解晚第三紀(jì)氣候變化對(duì)東亞溫帶植物進(jìn)化歷史和分布的影響。
[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.
【學(xué)位授予單位】：浙江大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：Q943
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本文編號(hào)：1995432