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研究生:何瓊紋
研究生(外文):Chuan-WenHo
論文名稱:以多基因分析探討芒屬植物遺傳變異及種化模式
論文名稱(外文):Multilocus analysis of genetic variation and speciation model in Miscanthus (Poaceae)
指導教授:蔣鎮宇蔣鎮宇引用關係
指導教授(外文):Tzen-Yuh Chiang
學位類別:博士
校院名稱:國立成功大學
系所名稱:生命科學系碩博士班
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2013
畢業學年度:101
語文別:中文
論文頁數:106
中文關鍵詞:芒草基因組分歧種化初期多樣性天擇離群基因座基因流鄰域種化
外文關鍵詞:Miscanthusgenomic divergenceincipient speciationdiversifying selectionoutlier locigene flowparapatric speciation
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芒屬植物(Genus Miscanthus)是目前最重要的生質燃料作物之一,具有增長快速和高生物量的植物特性。中國芒/五節芒複合群(M. sinensis/floridulus species complex)由數個具型態歧異的變種組成,分布上沿海拔梯度由低至高並可適應不同的環境壓力。這種在最近才產生分歧的物種複合群能提供有關植物新物種的形成與地域性適應的相關遺傳證據。在本研究中,應用最新組裝的中國芒轉錄體數據,隨機挑選80個基因探討中國芒/五節芒複合群的基因組分歧狀況與推測可能的種化模式。標準的異域種化(allopatric speciation)中,祖先群被分隔為兩個地理群後即沒有後續的基因交流,但在本研究的多基因分析中則呈現中國芒/五節芒複合群在種間與變種間皆具有頻繁的基因交流,且在比例上無法支持單一顯著的物種親緣關係。這個與物種親緣關係不一致的狀況不能完全以祖先的多型性來解釋,影響更多的是物種形成之後的基因交流。然而,透過等位基因重覆採樣模擬重建的親緣關係卻可以得到一個顯著支持的親緣關係,這顯示必定有一個外在的凝聚力量抵銷掉了頻繁的基因交流。以找出離群基因座(outlier loci)的方法發現,相較於可能傳遞基因交流資訊的中性演化基因座(neutral loci),離群基因座只佔一小部分(3.75-15%)但因受到多樣性天擇的影響使得中國芒/五節芒複合群開始分化,並且顯示出較高的單位點多型性(SNP)的連鎖不平衡,這樣的模式較符合鄰域種化(parapatric speciation)。總結中國芒/五節芒複合群的種化模式應由少數受到多樣性天擇的基因開始,之後再慢慢擴散到附近的染色體,隨著分歧時間拉長,基因體的分歧也愈明顯。
Miscanthus, is one of the most important biofuel plants with characteristics of fast growth and high biomass. M. sinensis/floridulus are composed of morphologically distinct intraspecific taxa that are distributed along an altitudinal gradient and respond to various environmental stresses. This species complex which diverged only recently can provide insight into the formation of new species and local adaptation. In this study, 80 DNA markers were developed based on newly assembled transcriptome data, and were used to explore the divergence in Miscanthus floridulus/sinensis species complex. In the standard model of allopatric speciation, the ancestral population was split into two geographically regional populations with no subsequent gene flow. In the study, multi-locus population genetic analyses revealed frequent gene flow both between species and among intraspecific taxa of M. sinensis. Furthermore, none of the nuclear loci supported the species phylogeny. Statistical analyses showed that such systematic inconsistency cannot be explained solely by the ancestral polymorphisms, while was caused by gene flow after speciation. Nevertheless, phylogenetic simulations via allele resampling were able to uncover the identity of species and intraspecific taxa, suggesting that there must exist some extrinsic cohesive forces counteracting the genetic exchanges between species. Compared to neutral background loci that were likely mediated with gene flow, outlier loci of a small proportion of the loci selected (3.75-15.0%) differentiated Miscanthus species/ races, and displayed higher linkage disequilibrium between SNP sites, agreeing with a model of parapatric speciation. The speciation of Miscanthus, was likely triggered by diversifying selection at few outlier loci, followed by widening divergence hitchhiking along chromosomes.
中文摘要……………………………………………………………………………… Ⅰ
英文摘要……………………………………………………………………………… Ⅱ
誌謝…………………………………………………………………………………… Ⅲ
目錄…………………………………………………………………………………… Ⅳ
表目錄………………………………………………………………………………… Ⅵ
圖目錄………………………………………………………………………………… Ⅶ
附錄目錄……………………………………………………………………………… Ⅷ

第壹章 緒言
第一節 芒屬植物……………………..…………………………..………………. 1
第二節 芒草相關研究概述……………………………………….………………. 3
第三節 近代基因體學應用於芒草之相關研究..………………….…………….. 7
第四節 以多基因分析探討種化機制...…..………………………..…………….. 9
第五節 研究目的….……………………………………………………………… 11
第貳章 材料與方法
第一節 研究材料………….……………………………………………………… 12
第二節 實驗方法………….……………………………………………………… 13
第三節 資料分析………….……………………………………………………… 16
第參章 結果
第一節 80基因座之遺傳變異……………….……………..…………………… 19
第二節 以核醣體去氧核醣核酸轉錄區間(nrITS)序列建構親緣關係假說…… 20
第三節 使用序列重新取樣的方法建構芒草的物種樹………………………… 21
第四節 離群基因座之鑑別……………………………………………………… 22
第五節 STRUCTURE 族群遺傳結構分析………….………….……………… 24
第六節 IMa2 分析…………………………………….……………………….… 26
第七節 族群遺傳分化分析…………………………….………………………… 27
第肆章 討論
第一節 中國芒/五節芒複合群之初始種化…………….……….…………….… 28
第二節 離群基因座貢獻物種間與變種間的遺傳分化………….……………… 30
第三節 種化過程存在基因交流與多樣性天擇:生殖隔離並非種化的必要條件............................................................................................................................... 33
第伍章 結論……………………………………………………………………….… 35
第陸章 參考文獻…………………………………………………………………… 36
表…………………………………………………………...………………………… 46
圖………………………………………………………...…………………………… 53
附錄……………………………………………………...…………………………… 67

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