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姓名	普來都(Bagus Priambodo)  查詢紙本館藏	畢業系所	生命科學系
論文名稱	利用粒腺體基因(16S rRNA & ND4) 和細胞核基因(7IβFIB & 3ITBP) 研究亞洲蝮蛇在印尼地區的地理親緣演化 (Phylogeography study of Asian pit vipers in Indonesia using mitochondrial genes (16S rRNA & ND4) and nuclear genes (7IβFIB & 3ITBP))
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摘要(中)	利用粒腺體基因(16S rRNA & ND4)和細胞核基因(7IβFIB & 3ITBP) 研究亞洲蝮蛇在印尼地區的地理親緣演化 摘要 印度尼西亞及其周邊地區的特殊地質歷史對其生物演化扮演重要的腳色，而亞洲蝮蛇的演化歷史也相對反映在這些地理變化上。亞洲蝮蛇廣泛的分佈在東南亞地區，包含印尼。在印尼地區，已確認有13種亞洲蝮蛇，但對其研究仍不完整，從保育的考量，其相關的基本資料是迫切需要的。因此本研究蒐集許多印尼的樣本，來評估牠們的地理親源演化關係，並預測牠們的族群大小。本研究在印尼採集了46個樣本，包含7種亞洲蝮蛇，利用16S rRNA、 ND4、 7IβFIB 和3ITBP基因序列，並蒐集genebank上公開的資料，共28種151筆亞洲蝮蛇的基因序列，用來進行地理親緣分析。親緣演化的推算主要使用maximum likelihood、maximum parsimony 和 bayesian inference；所得到的親緣關係能夠完整地區分物種，並有高度的可信度，5個屬均為單系群 (monophyletic group) (Trimeresurus、Parias、Popeia、Viridovipera和Cryptelytrops) 。在Trimeresurus屬形成了一個並系群(paraphyletic group)。本研究第一個提出T. andalasensis 與T. puniceus 為姊妹種。另一方面，我們發現認知的Cryptelytrops insularis 族群內可能有新種。亞洲蝮蛇最早的共同祖先大約在17.2百萬年前(中新世紀時代)，大部分的屬在中新世時代分歧開來，這也可能顯示亞洲蝮蛇受溫度氣候和熱帶雨林植被的影響，而分化出多樣性。使用Bayesian skyline plot(BSP)分析亞洲蝮蛇3個屬共5種物種的實際種群大小，發現其中3種亞洲蝮蛇(C. purpureomaculatus, P. sabahi, 和 T. puniceus) 的種群規模從新世紀時代到中新世時代期間逐漸增大(溫暖氣候)。然而，種群規模在更新世(寒冷氣候)後有逐漸減小的趨勢。另外2種亞洲蝮蛇(C. albolabris 和 C. insularis) 種群規模則在更新世(寒冷氣候)擴張，這代表此兩種亞洲蝮蛇能高度適應寒冷氣候。因此，我們推測不同種亞洲蝮蛇種群大小會對氣候改變的改變也不相同。 Keywords: 亞洲蝮蛇，粒腺體基因，細胞核基因，系統地理學，Bayesian skyline plot
摘要(英)	Phylogeography Study of Asian pit vipers in Indonesia using mitochondrial genes (16S rRNA & ND4) and nuclear genes (7IβFIB & 3ITBP) Abstract Unique geographical history of Indonesia and surrounding area played an important role in shaping of organism evolution. Evolutionary history of Asian pit vipers is relevant to those geography changes. Asian pit vipers widely distribute in Southern Asia, including Indonesia. There were total 13 known species of Asian pit vipers but not well studied in Indonesia. Their demographic information is required for conservational concerns. Hence, we collected more samples from Indonesia to evaluate the phylogeny and biogeography of Asian pit vipers, and to estimate their population size. This research involved 29 species of Asian pit vipers from Southeast Asia. We collected 46 samples consisting 7 species of Asian pit vipers from Indonesia. The DNA sequences of four genes, 16S rRNA, ND4, 7IβFIB & 3ITBP, were used to conduct the phylogeography analyses. Additional 151 sequences of the same four genes from 28 Asian pit vipers species were obtained from Genbank. The phylogenies are reconstructed using three different algorithms, maximum likelihood, maximum parsimony, and bayesian inference. Phylogenies based on these four genes were well-resolved with mostly high branch supports and formed 5 monophyletic groups, Trimeresurus clade, Parias clade, Popeia clade, Viridovipera clade, and Cryptelytrops clade. It was the first time to show in the phylogeny that T. andalasensis was a sister taxa to T. puniceus. On the other hand, we might recognize a new species within Cryptelytrops insularis. The most recent common ancestor of Asian pit viper diverged around 17.2 million years ago (Miocene). Most clades diversified during Miocene epoch, indicated that Asian pit vipers experienced the environment with predominantly warm climate and rainforest vegetation, thus this group had better chance to evolved. Bayesian skyline analyses (BSP) estimated the effective population size on 5 species which belonged to 3 genus of Asian pit vipers. 3 species, C. purpureomaculatus, P. sabahi, and T. puniceus showed slighlty increased and nearly constant during Miocene to Pliocene (warm climate), then at Pleistocene (cold climate) the population size were slightly decreased. The other 2 species, C. albolabris and C. insularis showed significant expansion, means they have strong adaptation at the cold period. Based on the BSP, we might suggested that the different species of Asian pit vipers might have different responses due to the climate changes. Keywords: Asian pit vipers, Mitochondrial genes, Nuclear genes, Phylogeography, Bayesian skyline plot
關鍵字(中)	★ 亞洲蝮蛇 ★ 粒腺體基因 ★ 細胞核基因 ★ 系統地理學 ★ Bayesian skyline plot	關鍵字(英)	★ Asian pit vipers ★ Mitochondrial genes ★ Nuclear genes ★ Phylogeography ★ Bayesian skyline plot
論文目次	Table of Contents 摘要 iii Abstract iv Aknowledments v Table of Contents vi List of Tables vii List of Figures viii Abbreviations ix 1. INTRODUCTION 1 1.1 Geographical history 1 1.2 Asian pit viper issues 2 1.3 Genes 3 2. MATERIALS AND METHODS 4 2.1 Sample collection 5 2.2 DNA extraction 5 2.3 PCR amplification 6 2.4 Gel electrophoresis and PCR Clean up 6 2.5 Sequence alignment 7 2.6 Phylogenetic tree reconstruction 7 2.7 Divergence time estimation 7 2.8 Population demography (Bayesian skyline plot) 8 3. RESULTS 9 3.1 DNA sequence characteristics 9 3.2 Genetic distances 9 3.3 Phylogeny of Asian pit vipers 9 3.4 Time divergence estimation 10 3.5 Bayesian skyline plot analysis 11 4. DISCUSSIONS 12 4.1 Phylogeny and Historical biogeography 13 4.2 Population demography 15 5. REFERENCES 16
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指導教授	劉阜果(Fu-Guo Robert Liu)	審核日期	2018-1-30
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