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研究生: 黃秉宏
Huang, Bing-Hong
論文名稱: 地理與生態因子在島嶼上黃芩屬物種的族群分化與快速種化上的效應
The geographic and ecological effects on the population differentiation and rapid divergence of island Scutellaria (Lamiaceae)
指導教授: 廖培鈞
Liao, Pei-Chun
學位類別: 博士
Doctor
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2020
畢業學年度: 108
語文別: 中文
論文頁數: 95
中文關鍵詞: 黃芩快速種化棲位模擬ABC溯祖理論分析
英文關鍵詞: Scutellaria, rapid speciation, niche modeling, ABC coalescence simulation
DOI URL: http://doi.org/10.6345/NTNU202000542
論文種類: 學術論文
相關次數: 點閱:131下載:10
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  • 研究背景:
    島嶼物種的快速種化可以由隨機的力量、遷徙拓殖、基因交流以及天擇等力量驅動。然而島嶼面積不大,頻繁的物種接觸導致的基因交流理應減少物種或族群分化,現今我們常以生態力量趨動的生態種化解釋之,因為生態因子如環境氣候異質性等使族群間有區域性適應阻擋部分基因組的基因交流,區域性適應影響的基因組週邊區域因連鎖而產生搭便車效應加強了該區段的基因交流阻隔,而漸漸的這些阻隔區域增加以到一定程度並完全種化,這些力量可以共同作用以加快島嶼物種的分化速度。研究具高特有種比例的物種有助了解這些力量在祖先物種拓殖入島嶼後加快分化速度的相對重要性。台灣產的黃芩屬特有種比例比起其他東亞及東南亞的鄰近島嶼或陸塊都高上許多,全部共8種,即有6種為特有種。過去的研究指出台灣產黃芩屬的多樣性來自至少三次的拓殖事件以及島嶼在地的快速種化。而台灣產的黃芩利用分子定年計算出的最早分歧時間不過50萬年內,其中被命名作indica group的印度黃芩、布烈氏黃芩、田代氏黃芩及南台灣黃芩形成單一分支且分歧時間短於20萬年內,被認為可能是其中一次拓殖事件後的在地快速種化。我們想以台灣產黃芩屬成員作材料切入生態種化如何與台灣高特有性之關聯性。
    方法
    我們使用了微衛星體基因型檢測作為快速變異的遺傳資料進行分析。並輔以溯祖理論分析法及演化模型選擇找出最適合解釋台灣產黃芩是否一如生態種化之預測分化早期有基因交流。並以環境因子與遺傳分化進行關聯性分析,了解遺傳變異或族群分化是否與環境因子有關。
    結果
    我們優先了解這群物種來檢測indica group是否主要來自單次的快速種化,以利後續設計實驗了解台灣產黃芩的快速種化之因。然而,依據溯祖理論IMa3分析,我們發現indica group在分歧時伴隨旺盛的基因交流,然而在使用貝氏歸群分析時卻顯示這些近期分歧且鄰域物佈的物種甚少種間遺傳混雜,顯示物種明顯分化,考量過去旺盛的基因交流及台灣島面積不大,物種易接觸,這麼短的分歧時間實難分化出這麼多特有種,我們藉分歧時有種間基因交流的情形,再依生態種化的概念,推論生態因子可能參與在這些快速種化的黃芩的物種維持與分化。我們挑選兩組共域/鄰域分佈的特有種,分別是田代氏與布烈氏黃芩組,以及向天盞與台北黃芩組來問答這個議題。我們利用以approximate Bayesian computation的方法進行溯祖模型選擇,發現田代氏黃芩與布烈氏黃芩有強烈的祖先性基因交流,然而現今已有明顯的分化及基因交流的阻斷。兩個物種的分化都可以由在地環境異質性及多環境因子組合的棲位分化來解釋。而向天盞及台北黃芩則展現不同的結果,不論是溯祖模擬模型選擇、群聚分析及單套形的樹形/網狀分析都無法清楚的區分特有的台北黃芩及廣布於東亞的向天盞。而可供區別的形態特徵如小堅果外衣紋路及葉型,在觀測後也證實僅是採集植物個體發育時期不同所致,並非可供物種區分的特徵。組合台北黃芩及向天盞的族群後發現族群間有明顯的遺傳結構,這些遺傳結構以廣義線性模型及座標軸分析等方法發現夏秋降雨量在族群的差異與族群遺傳分化有關。
    結論
    因此,無論是向天盞/台北黃芩組,或是布烈氏黃芩/田代氏黃芩組都發現明顯的族群尺度分化,這些分化都可以由氣候異質性及區域性適應解釋。換言之,氣候異質性及區域性適應均能促進台灣產黃芩屬成員讓族群分化,更可能加速種化以讓多樣性速率提升。

    Background:
    Species diversification within an island can be invoked by stochastic process (eg. drift or geographic isolation), migration (or gene flow) and ecological factors (eg. divergent selection lead population differentiation). However, gene flow is often considered to homogenize the genetic component between populations or species as area of island may be so small that species may contact to each other. The ecological factors such as environment heterogeneity may lead local adaptation which can block gene flow in parts of the genome, and the hitchhiking effect may expand the isolation area of genome until the speciation complete. These processes are not mutually exclusive and may accelerate diversification rate of colonized species. Genus with high endemism in an island is therefore suitable for accessing the relative importance of both neutral and adaptive process on diversification of island species. The genus Scutellaria L. comprised eight species with six of them are endemic species, which is suitable for ecological speciation study. The endemism is almost the highest in East Asia. Previous studies revealed very recent divergence of these species (within 500 kilo years ago, kya) and at least three times colonization with subsequently radiation may invoke the high endemism of Taiwanese Scutellaria. Amongst them, S. indica, S. tashiroi, S. playfairii and S. austrotaiwanensis (hereafter: indica group) are the most monophyletic group in which relatively short divergent time (less than 200 kya). We aimed to ask whether the ecological species can be associated with rapid species diversification in Taiwanense Scutellaria.
    Methods
    We adopt microsatellite as our molecular marker due to its high mutation rate and variation. We also used coalescence analyses and evolutionary model choice to evaluate the magnitude of historical gene flow, so that we can check whether species divergence was accomplished with gene flow as expectation of ecological speciation.
    Results
    According to results of coalescence simulation using IMa3, highly historical gene flow can be found among members of indica group during divergence, but Bayesian clustering analysis revealed very few interspecific admixture, implying clear species divergence. Homogenizing genetic components between species can be often accived by historical gene flow. Therefore it is hard to believe that geographic factors along can lead to complete speciation in these rapid divergent Scutellaria. The historical gene flow often correlated to ecological speciation. Hence the ecological factors may also involve in these rapid divergent Scutelliara. We focus whether ecological factors can be associated with the divergence of the endemic Scutellaria in Taiwan. We adopt two sympatric or parapatric and morphological similar pair species as case, S. tashiroi/S. playfairii and S. barbata/S. taipeiensis, respectively, for understanding whether differentiation can be associated with neutral geographic distance or climatic driven local adaptation. We found that the clear divergence, local adaptation and niche differentiation can be found in former group even with consideration of geographic factors. Though gene flow can be detected with approximate Bayesian computation coalescence simulation analysis but differentiation in multidimensional hypervolume niches blocks the gene flow nowadays, indicating heterogeneity in environment drive divergence of S. tashiroi and S. playfairii. On the other hand, coalescence simulation, clustering analysis and tree/network analysis do not found the divergence between widespread species, S. barbata, and endemic S. taipeiensis. The distinct characters such as nutlet coat and leaf shape merely reflect different developmental stage or phenotypic plasticity. However, population level differentiation can be found to be associated with climatic factors such as Summer-Fall precipitation.
    Conclusions
    These two paired studies revealed that local adaptation driven by environmental factors may lead population differentiation and may subsequently lead to rapid speciation.

    致謝 I 摘要 1 Abstract 3 第一章 概論 5 1.1 物種分化的力量 5 1.2 高特有種比例的島嶼例子 6 1.3 研究材料介紹 6 1.4 本論文研究議題 9 第二章 台灣產近緣黃芩屬植物的分歧及種間基因交流測定 10 2.1 前言 10 2.2 材料與方法 12 2.2.1材料收集 12 2.2.2 基因多樣性整理 13 2.2.3 遺傳組成及基因交流檢測 13 2.3 結果 14 2.3.1 遺傳多樣性 14 2.3.2 物種遺傳結構分析 15 2.3.3 基因交流計算 17 2.4討論 18 2.4.1更新世末期的台灣產黃芩具有旺盛的種間基因交流 18 2.4.2族群間具有明顯結構 19 第三章 島嶼上的空間環境異質性趨使島嶼物種持續分化以致生態種化 22 3.1前言 22 3.2材料與方法 25 3.2.1採樣地點與遺傳分析 25 3.2.2遺傳分析 25 3.2.3利用ABC評估物種種化模型 26 3.2.4以降維的環境因子計算物種間的生態區位差異 27 3.2.5利用生態區位模擬來預測物種分佈趨勢 28 3.2.6利用冗餘分析(redundancy analysis)評估環境變量對遺傳變異的影響 29 3.3結果 29 3.3.1遺傳多樣性與族群結構 29 3.3.2種化模型 34 3.3.3布烈氏黃芩與田代氏黃芩的棲位分化 35 3.3.4生態棲位模擬 38 3.3.5環境變量能否解釋兩種黃芩的遺傳變異 40 3.4討論 41 3.4.1非異域種化的遺傳證據 41 3.4.2生態因子趨使物種持續維持生殖隔離 43 3.5結論 45 第四章 區域性環境異質性形塑兩種未分化完全的島嶼物種的遺傳組成 46 4.1前言 46 4.2材料與方法 50 4.2.1分佈現況與採集 50 4.2.2定序與基因型讀取 51 4.2.3中性檢測與遺傳多樣性 52 4.2.4利用貝氏群聚分析來檢視族群的遺傳組成 54 4.2.5利用Discriminant analysis of principal components法區分物種及族群 54 4.2.6利用approximate Bayesian computation評估種化情境 54 4.2.7藉生態棲位模擬預測物種潛在分佈地點 55 4.2.8利用Mantel test檢測isolation-by-distance及isolation-by-environment 56 4.2.9檢測氣候對族群遺傳組成的影響 56 4.3結果 57 4.3.1成熟種子的小堅果外衣紋路形態差異 57 4.3.2中性檢測及遺傳多樣性 57 4.3.3向天盞與台北黃芩的族群結果 60 4.3.4台北黃芩的多次起源與近期族群分化可用以解釋為何兩種間無明顯遺傳分化 62 4.3.5台北黃芩與向天盞的Grinnellian niche明顯交疊 65 4.3.6藉生態棲位模擬預測物種的分佈 66 4.3.7Isolation-by-distance及isolation-by-environment的模型比較 67 4.3.8以環境因子解釋族群遺傳結構 68 4.4討論 68 4.4.1向天盞與台北黃芩的形態特徵難以區別 68 4.4.2遺傳及棲地分化不明顯暗示種化不完全 69 4.4.3氣候因子並不與物種區別有關 71 4.4.4氣候異質性致使區域性適應 71 4.4.5夏末初秋的降雨是主要解釋遺傳分佈的環境因子 72 4.5結論 75 第五章 結語 76 附表 78 參考文獻 83

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