台灣刺柏 (Juniperus formosana Hayata ) 在台灣呈現高、低海拔間斷分布的現象，大量族群分布在中央山脈兩千五百公尺以上的地區，是台灣高山的常見植物；低海拔族群則生長於花蓮清水斷崖區域，僅有少量族群分布。從臘葉標本資料和研究採集樣本比較，在兩種不同棲地生長的台灣刺柏於形態上相似。環境差異造成的天擇，在此間斷分布族群間可能誘發對當地環境的適應，而產生了種內分化現象。本研究利用Next-Generation Sequencing (NGS) 技術，取得台灣刺柏高低海拔族群的轉錄基因體 (transcriptome)。利用3組葉綠體片段、20組細胞核基因座，分析高海拔族群、低海拔族群及武夷山族群 (大陸)共74個樣本。並由表現量差異與對抗逆境相關基因進行篩選並設計專用引子，利用PCR取得序列並進行序列分析，利用中性基因座與天擇基因座的遺傳變異分析族群分化、族群動態、親緣關係與天擇檢測。在STRUCTURE的分群及network分析中顯示，高海拔和低海拔族群以及台灣刺柏變種有明顯的地域分群現象，並擁有獨立的基因型。族群動態Mismatch及Bayesian skyline 結果顯示台灣族群高、低海拔在過往都有擴張之歷史。IMa分析葉綠體和細胞核資料，顯示遷移方向為大陸往台灣，Most Recent Common Ancestor (TMRCA) 時間約為202~332萬年(細胞核) 和358~428萬年(葉綠體)前。BEAST yule model 顯示低海拔族群與武夷山族群及高海拔族群分歧時間為19萬年前，武夷山變種與高海拔分歧時間為14萬年前，在台灣壟起後經歷多次冰河，推測在冰期入侵台灣，族群大量擴張，冰期結束後大量個體往高海拔遷移，因高海拔地質的脆弱，棲地破碎化導致高海拔擁有一些獨特的基因型，而低海拔族群因困留在低海拔而與高海拔產生遺傳分化，台灣刺柏因適應環境的差
異，產生適應性演化，形成不同的譜系。

In Taiwan, Juniperus formosana Hayata is distributed at different altitudes. There are huge populations at altitudes over 2500 meters in the Central Mountains and they can be easily spotted in the high mountains in Taiwan.Only a small amount is distributed in the low-altitude regions around Chin-Shui Cliff. The morphologies of J. formosana Hayata growing in the two different habitats are similar when the data of herbarium specimens and the collection of specimens in this study are compared. However, the difference in environment causes environmental selection, which may induce local adaption among these discontinuously distributed populations, and thus produces intraspecific differentiation. In this study, Next-generation sequencing (NGS) is supplied to obtain the transcriptions of J. formosana Hayata from high and low altitudes. Three sets of chloroplast spacers and twenty sets of nuclear loci were used to analyse 74 specimens of different populations from high altitude regions, low altitude regions and the WuYi Mountains (China). We selected and designed specific primers according to the different expression and stress-related of genes to amplification by PCR then DNA sequencing analysis. The difference in gene between neutral loci and candidate loci was then used to analyse population differentiation, population dynamics, phylogenetics and positive selection. In the grouping of STRUCTURE and the analysis of networks, there is an obvious phenomenon of geographic clustering, coupled with a unique gene. The result of the analysis of population dynamics by Mismatch and Bayesian methods shows that both the high altitude and low altitude populations in Taiwan expanded in the past. According to IMa, in the direction of migration, China to Taiwan. And most recent common ancestor (TMRCA) was about 2.02-3.32mya (nrDNA) and 3.58-4.28 mya (cpDNA). A BEAST yule model shows that the low-altitude populations and WuYi Mountain populations and the divergence time of the high-altitude populations is 0.19 mya. Between WuYi Mountain populations and high-altitude populations has a divergence time of 0.14 mya. After the elevation of the island, Taiwan experienced various periods of glaciation. We think that that these populations invaded Taiwan during the glaciation periods, and they then hugely expanded. Some of the high-altitude populations have kept the unique genes, when habitat fragmentation. While the low-altitude populations were trapped in the low altitude regions in Taiwan. Due to ecological adaptation, J. formosana Hayata developed into various lineages to adapt to environmental variety.

目錄
致謝 ii
中文摘要 iii
英文摘要 iv
目錄 v
表目錄 viii
圖目錄 x
第一章 前言 1
1.1 台灣刺柏介紹及分布 1
1.2 台灣地質形成與第四紀的氣候變化 2
1.2.2第四紀冰河期 3
1.3 高低海拔環境差異的環境壓力 5
1.4 生態基因體學 6
1.5 多基因族群遺傳 8
1.6 胞器與細胞核基因體之遺傳特性 9
1.7 中性假說與天擇下適應性演化機制 10
1.8 台灣刺柏族群過往研究歷史 12
1.9 假說與研究目標 12
第二章 材料與方法 14
2.1 研究材料與製備 15
2.1.1高、低海拔刺柏及外群的採樣 15
2.1.2台灣刺柏DNA的萃取 15
2.1.3台灣刺柏RNA的萃取 15
2.2 利用次世代定序 (NGS) 取得刺柏高、低海拔之功能性表現基因組 16
2.2.1 次世代定序 (Next Generation Sequencing, NGS) 17
2.2.2轉錄體分析與表現量差異 17
2.3 核基因分子標記實驗方法 18
2.3.1 引子設計 18
2.3.2 聚合酵素連鎖反應 (polymerase chain reaction, PCR) 20
2.4 基因選殖（gene cloning） 21
2.5 多基因序列資料分析 23
2.5.1 序列比對與排列 (Alignment) 23
2.5.2 遺傳變異分析 23
2.5.3中性測試 24
2.5.4天擇檢測 25
2.5.5親緣演化樹之譜系關係 26
2.5.6族群變異分布分析 (Mismatch distribution) 27
2.5.7分群分析 (Assignment test) 28
2.5.8 基因交流 29
2.6 共同祖先時間 (TMRCA) 與分歧時間 (Divergence time) 30
第三章結果 32
3.1 台灣刺柏次世代定序之轉錄體基因組 32
3.1.1分子標記開發 33
3.2多基因序列分析 34
3.2.1遺傳歧異度分析與中性測試 34
3.2.2天擇檢測 35
3.2.3 TCS 37
3.2.4歸群分析 37
3.3親緣關係的重建 39
3.3.1最大簡約親緣樹 39
3.3.2 Neighbor joinig 近鄰結合法親緣樹 40
3.3.3 Mrbayes貝氏譜系分析樹 41
3.4 族群動態歷史推測 41
3.4.1 Mismatch distribution 41
3.4.2Bayesian skyline 42
3.5有效族群大小與基因交流評估 42
第四章 討論 46
4.1 台灣刺柏遺傳多樣性與親緣關係探討 46
4.2遺傳結構之分群結果 47
4.3中性檢測與天擇檢測之探討 49
4.4族群動態與遷移 50
4.5分歧時間與過去氣候變遷的關係 51
第五章 結論 53
參考文獻 55

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