臺灣博碩士論文加值系統

為了獲取更多關於百合屬物種間之系統分類的訊息與更進一步瞭解百合屬的演化歷史，本研究重建屬下各組(sections)的物種親緣。利用台灣百合(Lilium formosanum)、鐵炮百合(Lilium longiflorum)EST序列設計之引子，擴增多基因(包括8個葉綠體DNA片段及22個細胞核DNA基因)，進行遺傳變異及親緣分析，透過核酸變異提供的資訊與重建20個近緣物種親緣樹狀圖，探討百合屬每個組間以及物種間之親緣關係。
本研究顯示細胞核DNA之nrITS與葉綠體母系DNA重建的物種親緣與傳統分類學的處理吻合，尤其在移除不一致性高的蘭州百合(L.davidii var.willmottiae)之後。可能的原因來自胞器DNA缺乏基因重組以及nrITS的concerted evolution共同提供的親緣訊息，因此本研究以nrITS與葉綠體母系結合所建構之物種親緣樹狀圖作為本研究的假設物種樹，共計有三個群聚被鑑定，即Cluster A (Sect. Leucolirion、Archelirion與Daurolirion)、Cluster B (Sinomartagon、Archelirion)以及Cluster C (Pseudolirium、Liriotypus、Martagon、Leucolirion、Sinomartagon)，顯然地Leucolirion與Sinomartagon為側系群。相對於cpDNA及nrITS，多數的核基因存在著高度的systematic inconsistency，利用DnaSP分析亦顯示約有17個核基因(85%)有較高的遺傳重組，且在百合屬組內與組間由於長時間的遺傳分化，顯示物種間存在高度的基因交流，也因此造成組與組之間界限的模糊，並破壞物種間之親緣型式。因此多基因分析不僅提供物種親緣分群的訊息，同時顯現基因漸滲造成種間親緣的不確定。

To understand the evolutionary history and phylogeny of Lilium, a multilocus analysis was conducted on eight chloroplast genes and 22 nuclear loci, which were PCR amplified and sequenced based on EST libraries of Lilium formosanum and L. longiflorum. Phylogenies based on the maternally inherited cpDNA, which is merited with low or no genetic recombination, and nrDNA, a gene family regulated by concerted evolution, were consistent with the taxonomy of Lilium sections, especially after removing L. davidii var. willmottiae that caused systematic inconsistency. The tree based on the combined evidence of cpDNA genes and nrITS was deemed as the hypothetical species tree, which uncovered three groups, i.e., Cluster A (Sect. Leucolirion, Archelirion and Daurolirion), Cluster B (Sinomartagon and Archelirion), and Cluster C (Pseudolirium, Liriotypus, Martagon, Leucolirion, and Sinomartagon). Apparently, Sect. Leucolirion and Sinomartagon are paraphyletic. Nevertheless, most of the nuclear loci, up to 17 genes (85%), displayed various tree topologies inconsistent with the species tree. Given a long time period for genetic divergence, frequent systematic inconsistency is likely attributable to genetic exchanges between species / sections, as further indicated by the high levels of genetic recombination detected in the nuclear genes. Such rampant gene flow blurred the taxonomic boundaries of sections in Lilium. Nevertheless, multilocus analysis not only provide phylogenetic informations about species split, but also the status of gene flow between species.

中文摘要................................................I
英文摘要................................................II
致 謝................................................III
目 錄................................................IV
表目錄..................................................V
圖目錄..................................................VI
附錄目錄................................................VII


第壹章 緒言.............................................1
一、百合與其近緣物種的相關研究與材料背景介紹...................1
二、分子生物學在物種親緣、溯祖理論的應用.......................8
三、親緣基因體學的發展與應用................................13
四、研究動機與目的........................................17
第貳章 材料與方法........................................18
一、研究材料.............................................18
二、實驗方法.............................................19
三、資料分析.............................................24
第參章 結果.............................................27
一、建構物種親緣假說.......................................27
二、百合屬的分子親緣.......................................29
三、百合近緣種間基因交流的模式...............................36
四、物種間之遺傳變異分析(π)與重組率(Rm)的估算..................37
五、不同物種在同基因發生Indels的事件.........................38
第肆章 討論.............................................40
一、百合屬Section的定義和分子資訊的落差......................40
二、推估百合屬內近緣物種間之雜交與基因流之可能性................44
三、百合屬內七個組間與組內物種親緣與分類地位之探討...............47
四、不同物種於相同基因上之變異點與物種親緣相關性之探討............ 57
第伍章 結論..............................................60
第陸章 參考文獻...........................................61

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