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博碩士論文 etd-0731112-181244 詳細資訊
Title page for etd-0731112-181244
論文名稱
Title
穗花杉複合群之族群遺傳與保育研究
The study of population genetics and conservation in Amentotaxus argotaenia complex
系所名稱
Department
畢業學年期
Year, semester
語文別
Language
學位類別
Degree
頁數
Number of pages
155
研究生
Author
指導教授
Advisor
召集委員
Convenor
口試委員
Advisory Committee
口試日期
Date of Exam
2012-07-20
繳交日期
Date of Submission
2012-07-31
關鍵字
Keywords
微衛星體基因座、穗花杉、分派分析、台灣穗花杉、族群遺傳、遺傳單位、遺傳保育
assignment test, A. formosana, Amentotaxus argotaenia, genetic unit, population genetic, conservation genetic
統計
Statistics
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中文摘要
穗花杉 [Amentotaxus argotaenia (Hance) Pilger] 複合群 (complex) 為一古老裸子植物的支系,根據第三紀化石證據顯示,曾廣泛分布於北半球,並於更新世 (Pleistocene) 與全新世 (Holocene) 期間分布縮減,現今侷限分布於中國南部、越南及台灣。本研究利用台灣穗花杉為測試物種,篩選出15組具多型性之微衛星體基因座,分別進行物種與族群階層兩部份之研究,於物種階層,針對台灣穗花杉、穗花杉、雲南穗花杉及越南穗花杉進行跨物種測試,於族群階層,針對台灣穗花杉之&#63998;&#63998;牙賴山 (簡寫:Cha) 與浸水營 (簡寫:Jin) 兩生育地族群進行遺傳多樣性及遺傳結構探討,界定不同遺傳單位,提出可行之遺傳保育策略。物種階層分析結果顯示,本次使用之微衛星體基因座於穗花杉複合群間具高度適用性 (100%) 及多型性 (PIC=0.25-0.61)。族群階層分析結果顯示,台灣穗花杉兩生育地族群之異基因合子的期望值與觀測值分別介於0.52-0.60與0.28-0.36之間,所有基因座經由檢測顯示皆有偏離哈溫平衡的現象 (P<0.001),族群呈現近親交配情況 (FIS=0.48368; P <0.05),推測台灣穗花杉族群由於長期近親繁殖,導致遺傳僵化現象。分子變異分析 (AMOVA) 顯示族群遺傳變異多存在族群內 (83.85%及52.39%),族群間遺傳分化顯著 (FST =0.10972-0.16155; P<0.05),IMa分析顯示兩族群之基因交流程度低 (1.13×10-6-1.15×10-4),現生族群有效族群大小 (Cha: 77.36-1830.67; Jin: 21.41-506.67) 遠小於祖先族群有效族群大小 (10496.8-248424.17),顯示台灣穗花杉處於族群驟縮的情況。利用以貝氏定律和MCMC分析法為基礎的SAMOVA、STRUCTURE及INSTRUCT分析進行分派分析,顯示 K=2時為最佳之分群結果。利用GENELAND進行分群,顯示Cha及Jin族群可被分成11分群及9分群。並根據所界分之遺傳單位結合年齡結構,挑選出需要加強維護之母樹,以維持族群之遺傳多樣性。
Abstract
Amentotaxus is an ancient lineage of gymnosperm genus. Based on the Tertiary fossil evidence, the ancient lineage was once widespread in the Northern Hemisphere but range contraction in Pleistocene and Holocene. Currently, the distributional range is restricted to southwestern China, Vietnam and Taiwan. In this study, the 15 polymorphic microsatellite primers were designed from A. formosana H. L. Li, and were used these primers for genetic research of species level and population level. In species level, we tested the transferability and polymorphism in four species, A. argotaenia (Hance) Pilger, A. formosana H. L. Li, A. poilanei (Ferr&eacute; & Rouane) D.K. Ferguson and A. yunnanensis H. L. Li were evaluated. In population level, we evaluate the genetic variation and genetic structure on two habitats including Mt. Chachayalaisham and Jinshueiying for the delimited of relevant genetic units and to establish useful conservation strategies. In species level, the 15 microsatellite primers had 100% successfully amplified fragments in these three species, also showing high polymorphisms (PIC=0.25-0.61). In population level, the genetic diversity analysis in the two population of A. formosana show that expected and observed heterozygosities were ranged from 0.52 to 0.60 and 0.28 to 0.36, respectively. In addition, 15 loci were deviated from Hardy-Weinberg equilibrium (P<0.001) and the inbreeding coefficient were displayed positive (FIS=0.48368; P <0.05), revealing the genetic fixation causing by inbreeding. The analysis of molecular variance (AMOVA) revealed that high genetic variation with population (83.85% and 52.39%), and also showed high levels of population differentiation (FST =0.10972-0.16155; P <0.05). IMa revealed low migration rate (1.13×10-6-1.15×10-4), also showed small effective population size (Cha: 77.36-1830.67; Jin: 21.41-506.67) and large ancestral population size (10496.8-248424.17), inferring the A. formosana undergo significant population declined. Using Bayesian clustering algorithms and Markov chain Monte Carlo (MCMC) iterations to distinct genetic units and make assignments in the programs SAMOVA、STRUCTURE and INSTRUCT, the best clustering was occurred at K=2, and found 11 and 9 distinct genetic groups in Mt. Chachayalaisham and Jinshueiying based on GENELAND analysis, respectively. We correlated the distinct genetic units and the age structures to evaluate the individuals with unique genotype for seed source to maintain the maximum genetic diversity of A. formosana.
目次 Table of Contents
論文審定書………………………………………………………………………………I
謝誌……………………………………………………………………………………...II
中文摘要……………………………………………………………………………….III
Abstract …...………………………………………………..………………………….IV
目次………………………………………………………………………………….…VI
附圖目次…………………………………………………………………………….…IX
附表目次……………………………………………………………………….XI
第一章 前言 .................................................................................................................... 1
1.1 族群遺傳學 ....................................................................................................... 1
1.2 親緣地理學 ....................................................................................................... 3
1.3 台灣冰河時期避難所 ....................................................................................... 4
1.4 保育與遺傳多樣性 ........................................................................................... 6
1.5 穗花杉複合群之簡介、應用價值及瀕危程度評估 ....................................... 9
1.6 穗花杉複合群族群結構及文獻回顧 ............................................................. 12
1.7 分子標記技術 ................................................................................................. 14
1.8 微衛星體分子標記技術及跨物種適用性 ..................................................... 17
1.9 亞族群結構劃分與MCMC演算法 ............................................................... 20
1.10 研究動機與目的 ........................................................................................... 23
第二章 材料與方法 ...................................................................................................... 24
2.1 材料 ................................................................................................................. 24
2.1.1 野外採集 ............................................................................................... 24
2.1.2 DNA萃取 .............................................................................................. 24
2.2 基因選殖 ......................................................................................................... 25
2.2.1 DNA&#37238;切作用 ...................................................................................... 25
2.2.2 雜合反應及磁珠富集法 ....................................................................... 25
2.2.3 微衛星序列之選殖 ............................................................................... 26
2.2.4 質體DNA之萃取 ................................................................................ 27
2.2.5 DNA定序 .............................................................................................. 28
2.2.6 設計微衛星序列基因座之引子 ........................................................... 28
2.2.7 檢測微衛星體基因座之多形性 ........................................................... 28
2.3 資料分析 ......................................................................................................... 29
2.3.1基因型判讀 ............................................................................................ 29
2.3.2 基因座中性檢測 ................................................................................... 30
2.3.3 遺傳多樣性分析 ................................................................................... 30
2.3.4 遺傳結構分析 ....................................................................................... 31
2.3.5 族群變動分析 ....................................................................................... 32
2.3.6 族群結構分析 ....................................................................................... 34
2.3.7 Mantel test ........................................................................................... 38
2.3.8 評估族群分歧時間 ............................................................................... 39
2.3.9 遺傳保育個體之挑選 ........................................................................... 40
第三章 結果 .................................................................................................................. 41
3.1 穗花杉複合群之跨物種測試 ......................................................................... 41
3.1.1微衛星體基因座之穗花杉複合群跨物種適用性 ................................ 41
3.1.2微衛星體基因座於穗花杉複合群間之多型性分析 ............................ 41
3.1.3微衛星體基因座於穗花杉複合群之遺傳多樣性 ................................ 42
3.2 台灣穗花杉之族群遺傳多樣性、遺傳結構及保育遺傳單位之探討 ......... 43
3.2.1基因座中性檢測 .................................................................................... 43
3.2.2台灣穗花杉族群間遺傳多樣性分析 .................................................... 44
3.2.3台灣穗花杉族群遺傳結構分析 ............................................................ 44
3.2.4台灣穗花杉族群變動分析 .................................................................... 45
3.2.5台灣穗花杉族群結構分析 .................................................................... 46
3.2.6隱蔽性基因型家族 (遺傳單位) 之鑑定與遺傳保育個體之挑選 ..... 49
3.2.7 Mantel test ........................................................................................... 59
3.2.8台灣穗花杉族群分歧時間 .................................................................... 60
第四章 討論 .................................................................................................................. 61
4.1 穗花杉複合群之跨物種測試 ......................................................................... 61
4.1.1微衛星體基因座之穗花杉複合群跨物種適用性 ................................ 61
4.1.2微衛星體基因座於穗花杉複合群之多型性及遺傳多樣性 ................ 62
4.2 台灣穗花杉族群遺傳多樣性、遺傳結構及保育遺傳單位之探討 ............. 64
4.2.1台灣穗花杉族群遺傳多樣性及遺傳結構 ............................................ 64
4.2.2台灣穗花杉族群變動、族群結構分析及隱蔽性遺傳單位之鑑定 .... 69
4.2.3遺傳保育單位之挑選及保育遺傳策略 ................................................ 78
第五章 結論 .................................................................................................................. 81
第六章 參考文獻 .......................................................................................................... 83
作者簡介.......................................................................................................................143
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