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研究生:陳盈先
研究生(外文):Chen,Ying-Xian
論文名稱:細葉山螞蝗親緣地理
論文名稱(外文):The Phylogeography of Desmodium gracillimum Hemsl.
指導教授:謝宗欣謝宗欣引用關係
指導教授(外文):Hsieh, Tsung-Hsin
口試委員:曾登裕林弘都
口試委員(外文):Tseng, Deng-YuLIN, HONG-DU
口試日期:2014-06-27
學位類別:碩士
校院名稱:國立臺南大學
系所名稱:生態科學與技術學系環境生態碩士班
學門:環境保護學門
學類:環境資源學類
論文種類:學術論文
論文出版年:2014
畢業學年度:102
語文別:中文
論文頁數:67
中文關鍵詞:細葉山螞蝗親緣地理遺傳歧異度特有種
外文關鍵詞:Desmodium gracillimumphylogeographygenetic diversityendemic species
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本研究是使用台灣的特有種細葉山螞蝗進行親緣地理研究,其分佈在北回歸線以南,100-550 m低海拔濕性及半陰性次生林及灌叢中。此研究於台灣採集7個族群包含62株個體,使用cpDNA的兩個trnL-trnF與trnS-trnG的非編碼區域(noncoding region)研究細葉山螞蝗的遺傳變異與親緣地理。分析結果顯示為:於1,403 bp中,發現7個有效變異位點,包含6個突變,1段InDel(17個鹼基),共得7個單倍基因型(Haplotype)。本研究細葉山螞蝗h值為0.599,π值為0.00057,雖然單倍基因型歧異度有達到高程度,但細葉山螞蝗與台灣植物相關研究互相比較,不管是木本植物或是草本植物,本研究的單倍基因型歧異度值與核苷酸歧異度偏低。族群間的分化指數高,推測可能原因為本研究的花粉與種子都並非具有長距離散播能力,由AMOVA與SAMOVA作的分組方式和距離隔離分化模型(IBD)推估,形成高分化程度且影響基因交流,也可能是生育地破碎化的阻隔所引起。由單倍基因型網狀圖(network)與單倍基因型於台灣分佈的樣貌,可推測出祖先型為Hap B,再加上Migrate做出的遷移率,可以察覺細葉山螞蝗並非有方向性的散播族群,推論出當時細葉山螞蝗曾經廣泛的分布於台灣南部,中間出現阻隔,比如生育地破碎化且發生選擇作用(如瓶頸效應),將它們阻隔開成為目前所見到的格局。在族群變動分析中,由一個單峰的分布的序列變異分佈測驗結果與中性檢測結果,表示細葉山螞蝗整體族群是位在擴張的邊緣狀態,未發生擴張的現象。
Desmodium gracillimum Hemsl., distributed in wet and semi-shaded place under secondary forest or margin of thicket, is an endemic species and located at elevation below 550 meters in south Taiwan. The aim of this study is to evaluate the phylogeography of Desmodium gracillimum Hemsl. The cpDNA variation was used to infer the temporal dynamics of distributional and demographic history of Desmodium gracillimum Hemsl. In this study, 62 individuals from seven populations were examined by sequencing two noncoding region using cpDNA universal primers trnL-trnF and trnS-trnG. The results show, of the aligned 1,403 base pairs (bp) sequence, there are 7 valid of polymorphic site, include six singleton and one insertion∕deletion (InDel) fragments (17 base pairs ), and 7 haplotypes in total. The Desmodium gracillimum Hemsl. is high in haplotype diversity and low in nucleotide diversity (h: 0.599∕π: 0.00057 ). But, comparison on cpDNA genetic feature Vascular plant and Desmodium gracillimum Hemsl., no matter it's herbaceous plant or woody plant, in this study, nucleotide diversity and haplotype diversity lower than other species's in Taiwan. The index of genetic differentiation within populations is high, it may due to the pollen and seed of this species without specialized long-distance dispersal mechanism. The results of AMOVA, SAMOVA and IBD show the cause of high level of differentiation influence gene flow, could be habitat fragmented separate. According to the distribution of haplotypes and haplotype network in populations, the ancestral haplotype Hap B is proposed, plus the immigration rates sugguest that is not direction of dispersal of Desmodium gracillimum Hemsl. They were widely distributed in south Taiwan in past, but the habitats fragmented and bottleneck effect, so become the phylogeographical pattern we saw today. According to unimodal pattern of the mismatch distribution and Neutral theory test, suggests that the all populations of Desmodium gracillimum Hemsl are not in expansion.
中文摘要 v
英文摘要 vi
誌謝 viii
目錄 ix
表目錄 xii
圖目錄 xiv
第壹章 前言 1
一、研究物種介紹-細葉山螞蝗 1
(一)分類地位與地理分布 1
(二)形態特徵 1
二、研究背景理論 2
(一)親緣地理學 2
(二)族群遺傳學 4
(三)植物的基因交流 6
(四)分子技術在物種親緣及族群遺傳的應用 7
(五)葉綠體的去氧核醣核酸(cpDNA)之遺傳性質 8
三、研究目的 10
第貳章 材料與方法 11
一、研究材料:野外採樣 11
二、實驗方法: 11
(一)去氧核醣核酸萃取(DNA extraction) 11
(二)去氧核醣核酸定量(DNA Quantification ) 12
(三)引子(primer)的選擇 13
(四)PCR程序-聚合酶連鎖反應(Polymerase Chain Reaction, PCR) 13
(五)電泳(Electrophoresis) 13
(六)定序(Sequencing) 13
三、資料分析: 14
(一)、序列整理 14
(二)、核苷酸鹼基組成分析 14
(三)、遺傳歧異度分析(Analysis of genetic diversity): 15
(四)、親緣分析(phylogenetic analysis) 16
(五)、族群遺傳結構分析(Analysis of genetic structure): 17
(六)、族群變動分析 19
第參章 結果 21
ㄧ、核苷酸鹼基組成分析 21
二、單倍基因型的組成與分布 21
三、遺傳歧異度分析(Analysis of genetic diversity) 22
四、親緣分析(phylogenetic analysis) 24
(一)親緣關係樹狀圖 24
(二)單倍基因型網狀圖 24
五、族群遺傳結構分析(Analyses of genetic structure) 24
(一)族群分化分析(Analysis of Population differentiation) 24
(二)基因交流(gene flow) 25
(三)AMOVA(Analysis of MOlecular VAriance, 分子變異分析) 26
(三)SAMOVA(Spatial Analysis of MOlecular VAriance, 分子變異空間分析) 28
(四)距離隔離分化(Isolation by distance, IBD)模型 29
六、族群變動分析結果 29
第肆章 討論 31
一、細葉山螞蝗的遺傳組成 31
二、細葉山螞蝗族群的遺傳變異 32
三、細葉山螞蝗親緣關係 35
四、細葉山螞蝗族群分化與基因交流 36
五、細葉山螞蝗的族群變動 38
第伍章 結論 40
第陸章 文獻 41
第柒章 表與圖 49
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