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博碩士論文 etd-0724115-101740 詳細資訊
Title page for etd-0724115-101740
論文名稱
Title
以微衛星體分析肖楠屬遺傳多樣性、遺傳分歧、 地理親緣
Genetic diversity, genetic divergence and phylogeographical patterns in Calocedrus based on microsatellites
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
86
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
2015-07-23
繳交日期
Date of Submission
2015-08-24
關鍵字
Keywords
遺傳分化、遺傳多樣性、微衛星體基因座、地理親緣、肖楠屬
genetic diversity, genetic differentiation, microsatellite, phylogeographical, Calocedrus
統計
Statistics
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中文摘要
肖楠屬為東亞-北美間斷分布,肖楠屬有四個物種分別為台灣肖楠、翠柏、岩生翠柏以及美國肖楠;分布於台灣、中國西南地區以及中南半島北部和北美西部地區。在化石記錄中肖楠屬曾經廣泛分布在北半球地區。本研究使用20組微衛星體引子分析肖楠屬四個物種的地理親緣、遺傳多樣性和遺傳分歧,檢測27個族群共627個樣本,其中包含台灣肖楠10個族群265個樣本,14個翠柏族群314個樣本、2個岩生翠柏族群33個樣本以及15個美國肖楠個體。在遺傳多樣性的研究顯示四個物種的遺傳多樣性指數包含等位基因數(Na)、有效等位基因數(Ne)、異型合子觀察值(Ho)、異型合子期望值(He)。在四個物種的平均值範圍分別在Na: 3.65-8.05;Ne:2.04-2.66;Ho:0.14-0.26;He:0.48-0.54。台灣肖楠10個族群的遺傳多樣性指數的平均值範圍分別為:Na: 2.35-4.4;Ne:1.76-2.17;Ho:0.13-0.19;He:0.36-0.49。翠柏14個族群的遺傳多樣性指數的平均值範圍分別為Na:2.45-4.25;Ne:1.83-2.39;Ho:0.18-0.35;He:0.36-0.53。在AMOVA分析中物種之間的有高度遺傳分化(FST=0.22)物種的遺傳變異累積在族群內(78.12%),另外在台灣肖楠以及翠柏與岩生翠柏的遺傳變異分別來自於族群內的個體(61%)以及個體之間(48.72%),族群間均有低度的遺傳分化(FST:0.07&0.094)。在主座標分析中,物種之間除了翠柏和岩生翠柏無基因分歧之外其他有顯著的基因分歧,另外在肖楠和翠柏族群的主座標分析顯示族群之間有顯著的遺傳分化。在STRUCTURE的K=2 和 K=3中肖楠屬四個物種的分析結果顯示,物種的分化與古近紀、新近紀以及更新世的冰期造成的地理隔離有關,另外台灣肖楠與翠柏在IMa的分析中,祖先族群(21萬)遠大於台灣肖楠和翠柏現生族群(385和7,048);顯示兩物種因為氣候動盪使族群收縮所導致。台灣肖楠遷移到翠柏遷移率(M12)以及翠柏遷移到台灣肖楠遷移率(M21)分別為: 1.08×10-3和M21=2.55×10-5,顯示東亞地區的肖楠屬遷移方向是島嶼遷移至大陸。在台灣肖楠族群的STRUCTURE的結果顯示,台灣肖楠族群因為族群之間有基因交流因此在遺傳結構上顯示沒有地理上的隔離。在翠柏與岩生翠柏的族群遺傳結構顯示有地理分化,造成的原因是距離隔離或物種收縮在不同避難所而導致,在台灣肖楠保育方面建議,除了現有的母樹林繼續維持之外,需要將人為可以到達的野外族群設立母樹林並進行種子收集。另外也需要建立跨物種的分子鑑定技術,避免在造林時與翠柏混淆。
Abstract
The genus Calocedrus is Eastern Asian – North American disjunctive distribution. Calocedrus formosana (Florin) Florin is restricted to Taiwan, Calocedrus macrolepis Kurz, and C. rupestris Aver., T.H. Nguyên & K.L. Phan are scattered throughout southwestern of China to northern of Indochina and Hainan Island, and Calocedrus decurrens Florin is native to western North America. According to fossil records, Calocedrus had been widespread in the Northern Hemisphere. In this study, we examined phylogeographical patterns, genetic diversity and genetic divergence in this genus based on 20 microsatellite markers. These 20 polymorphic microsatellite loci were used to evaluate genetic diversity among 627 samples from 27 populations of four taxa in Calocedrus, including 10 populations from C. formosana 265 individuals, 14 populations from C. macrolepis 314 individuals, 2 populations from C. rupestris 33 individuals, and 15 individuals from C. decurrens. Genetic diversity indices for 4 species based on 20 polymorphic loci, including the number of alleles (Na), the number of effective alleles (Ne) and the observed and expected heterozygosity (Ho and He), were estimated. The 4 species genetic diversity indices mean value range are: Na: from 3.65 to 8.05, Ne: from 2.04 to 2.66, Ho: from 0.14 to 0.26, He: from 0.48 to 0.54. In 10 C. formosana populations, genetic diversity indices mean value range are: Na: from 3.65 to 8.05, Na: from 2.35 to 4.4, Ne: from 1.76 to2.17, Ho: from 0.13 to 0.19, He: from 0.36 to 0.49. In 14 C. macrolepis populations, genetic diversity indices mean value range are: Na: from 4.25 to 2.45, Ne: from 1.83 to 2.39, Ho: from 0.18 to 0.35, He: from 0.36 to 0.53. AMOVA showed 78.12% genetic variation accumulated within population and high levels of genetic differentiation (FST =0.22). In C. formosana, C. macrolepis and C. rupestris AMOVA showed 61% and 48.72% genetic variation accumulated in among individuals within populations and with individuals and low levele of genetic differentiation (FST=0.07&0.094). The results of PCoA showed high genetic divergence among species except between C. macrolepis and C. rupestris, also significant genetic divergence among populations in C. formosana and C. macrolepis. In STRUCTURE analysis at K=2 and K=3 significant genetic clustering for four Calocedrus species might caused by Neogene, Paleogene and Quaternary climatic oscillations. In IMa result, the ancestral effective population size (21 million) is greater than C. formosana and C. macrolepis (385 and 7048). This result indicated these two species retreated to refugia caused by Quaternary climatic oscillations. The migration rate from C. formosana to C. macrolepis (M12)was 1.08×10-3and migration rate from C. macrolepis to C. formosana (M21) was 2.55×10-5. This result indicated species migration path from island to mainland at Eastern Asian. In STRUCTURE result no significant geographical barrier caused by gene flow in C. formosana populations. In C. macrolepis populations, the population geographical differentiation and caused by long distance dispersal or species retreat to multipule refuges. For C. formosana conservation suggestions was the seed production stand should be maintained and established. In addition, the species molecular identification system was needed to avoid confusion between the seedeing of C. formosana and C. macrolepis during reforestation.
目次 Table of Contents
壹、 前言..........................................................................1
一、 物種形態描述介紹以及形態差異比較........................1
二、 台灣肖楠生殖週期與種子保存...................................3
三、 物種分布與化石記錄以及相關的分子研究.................4
四、 地理親緣學介紹.........................................................5
五、 地質歷史與冰河歷史..................................................7
六、 白令陸橋的物種交流、大陸與台灣地區物種交流.......9
七、 微衛星體序列............................................................11
八、 研究目的...................................................................14
貳、材料方法....................................................................15
一、 研究材料採集............................................................15
二、 DNA萃取...................................................................15
三、 微衛星體引子測試.....................................................16
四、 電泳...........................................................................18
五、 資料處理....................................................................18
六、 資料分析....................................................................19
參、結果............................................................................22
一、 樣本採集以及跨物種引子測試....................................22
二、 基因多樣性指數..........................................................23
三、 遺傳變異分析.............................................................26
四、 主座標分析................................................................28
五、 STRUCTURE分群結果.............................................30
六、 IMa............................................................................31
肆、 討論...........................................................................33
一、 肖楠屬四個物種的遺傳分化.......................................33
二、 台灣肖楠族群遺傳分析..............................................35
三、 翠柏族群遺傳分析.....................................................38
伍、 結論...........................................................................41
陸、 引用文獻...................................................................43
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