蘇鐵在地質歷史上高度多樣性約在侏羅紀至白堊紀，近代研究顯示現生物種的分歧約少於一千兩百萬年。蘇鐵屬(Cycas)為蘇鐵科(Cycadaceae)唯一的屬，分為6組(section)。本研究以其中4組(東方蘇鐵組、攀枝花蘇鐵組、叉葉蘇鐵組與韋德蘇鐵組)共15物種，利用4個葉綠體片段、24核基因座與AFLP基因座進行親緣演化研究。
遺傳歧異度顯示分佈在中國物種(含海南島)的核苷酸歧異皆大於島嶼分佈物種，但其遺傳組成不複雜，可將物種歸併成2至5群，AFLP的5分群大致與地理分布相關。物種推測由近代的輻射適應演化而來，因而在親緣分析中呈現多分支(polytomy)，結合分群結果將物種分為6群，分別為ASI分群(球蘇鐵與台東蘇鐵)、TAG分群(台灣蘇鐵)、PAN分群(攀枝花蘇鐵)、STA分群(貴州蘇鐵、仙湖蘇鐵、海南蘇鐵、葫蘆蘇鐵、四川蘇鐵、叉孢蘇鐵、台灣蘇鐵1個體TA05、銹毛蘇鐵、石山蘇鐵與滇南蘇鐵)、CWG分群(韋德蘇鐵)與CUG分群(C. curranii)。
以BEAST及IMa2推估蘇鐵屬內物種的分歧時間不超過6百萬年。以IMa2估算有效族群大小及分群間的遷移率，顯示現生有效族群大小約200萬個至1,700萬個個體，各分群間有不對等的基因交流存在。結合RASP的分析，推測現今物種分布與第四紀冰河期變動相關，以中國西南地區為多樣性中心，分為二路徑分別向南擴散至海南島和向東南擴散到中國東南地區而至台灣及琉球。海南島兩物種推測因在地質上較晚才與中國大陸分離，而使之遺傳組成呈現與大陸物種相似，且遺傳歧異度大於其他島嶼分布物種。

Cycads are ancestral lineage but recent diversification within 12 Mya. Cycas is the only genus recognized in the family Cycadaceae, and divides into six sections. In this study, we use multilocus analyses to evaluate the nucleotide diversity, phylogenetic relationship, Bayesian clustering analysis, divergence time, and Dispersal-Vicariance model among 15 cycad taxa from four sections of Asiorientales, Panzhihuanses, Stangerioides, and Wadeanae. In total, 125 samples were sampled and 4 chloroplast DNA fragments, 24 nuclear DNA loci, and 425 AFLP loci were used for phylogenetic estimation.
Genetic diversity of the continental species is higher than the island taxa. In the Bayesian clustering analysis, the best grouping numbers, respectively, is inferred as 2, 4, and 2 in plastid DNA, 24 nuclear DNA, and 425 AFLP loci, respectively, and the second fit number of grouping is inferred as 3 and 5 in plastid DNA and 425 AFLP loci, respectively. In addition, the second fit number of grouping based on AFLP loci is congruent with geographical distribution. Due to recent diversification, phylogenetic relationships revealed paraphyly or polyphyly within sections and may be resulting by incomplete lineage sorting. ASI group is composed of 2 species, C. revolute and C. taitungensis. TAG group contains the single species C. taiwaniana. PAN group contains the single species C. panzhihuaensis. STA group contains 9 species in section Stangerioides and one individual of C. taitungensis. CWG group contains the single species C. wadei. CUG group contains the single species C. curranii.
Using models of isolation with migration and BEAST sofeware to estimate the divergence time are not older than 6 Mya. The extant population sizes is extremely large (1.77×〖10〗^6~1.69×〖10〗^7), and the gene flows are asymmetry between groups. Current species distribution is affected by the oscillation of glaciation and the southwest China is the cycad biodiversity hotspot. Two migrate routes are start at the hotspot. The first migrate route is dispersal from southwest China to south China and Hainan Island. The second route is migrated from hotspot to southeast China and followed to Taiwan and Ryukyu Archipelago. The genetic components between taxa distributed on Hainan Island and mainland China are similar, but the genetic diversity for taxa distributed on Hainan Island is higher than other island taxa due to isolation from mainland China.

論文審定書 i
誌謝 ii
中文摘要 iii
Abstract iv
目錄 vi
圖目錄 viii
表目錄 x
第一章 前言 1
1.1 蘇鐵物種介紹及其分類與分布 1
1.2 親緣關係學 4
1.3 親緣地理學 6
1.4 物種形成與種化機制 8
1.5 地質歷史 9
1.6 研究動機與目的 11
第二章 材料與方法 12
2.1研究材料 12
2.1.1樣本採集 12
2.2實驗方法 12
2.2.1 DNA萃取 13
2.2.2 EST基因片段比對、註解及引子設計 13
2.2.3聚合酵素連鎖反應 15
2.2.4純化及定序 16
2.2.5 基因選殖 17
2.2.6擴增片段長度多型性(AFLP) 19
2.3資料分析 21
2.3.1 序列比對與排序 21
2.3.2 遺傳歧異度分析 21
2.3.3 遺傳結構分析 22
2.3.4中性測試 23
2.3.5基因天擇檢測 24
2.3.6 親緣關係重建 26
2.3.7 物種分歧時間評估 27
2.3.8 族群變動分析 29
2.3.9擴散-隔離分化分析 31
第三章 結果 33
3.1跨物種之適用性基因座 33
3.2 遺傳歧異度分析與中性測試 33
3.2.1 葉綠體片段與核基因座的遺傳歧異度分析、中性檢測及基因天擇檢測 33
3.2.2 物種與地理分群的遺傳歧異度分析 36
3.2.3 AFLP遺傳歧異度分析 38
3.3 遺傳結構分析 39
3.3.1 主座標分析 39
3.3.2 貝氏歸群分析 39
3.4 親緣演化關係推論 41
3.5 分歧時間評估 44
3.6 有效族群大小與基因交流評估 45
3.7 擴散與隔離分化之推測 48
第四章 討論 50
4.1 蘇鐵族群遺傳歧異度與親緣關係探討 50
4.2 親緣關係不一致性探討 52
4.3 分歧時間與地質歷史及過去氣候變遷的關係 54
第五章 結論 58
第六章 參考文獻 60

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