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博碩士論文 etd-0112114-144609 詳細資訊
Title page for etd-0112114-144609
論文名稱
Title
以多基因分析油杉屬之遺傳分化
Genetic divergence between Keteleeria species (Pinaceae) using multilocus analysis
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
134
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
2014-01-17
繳交日期
Date of Submission
2014-02-12
關鍵字
Keywords
多基因座、油杉屬、遺傳歧異度、族群動態歷史、避難所、分歧時間、更新世冰河時期
divergent times, Pleistocene glaciation, genetic divergence, Keteleeria
統計
Statistics
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中文摘要
松科 (Pinaceae) 油杉屬 (Keteleeria) 為溫帶常綠喬木,化石證據推測曾廣泛分布於北半球,現今僅分布族群孤立分散於台灣、中國南部以及越南、寮國北部。在分類上各研究學者依據形態特徵難以訂出一致的物種定義。本研究取得台灣油杉之功能性表現基因組,並以此成功篩選出27個細胞核基因座,另取得4個葉綠體基因座,以12個分類群共91個樣本進行油杉屬親緣演化研究。
遺傳歧異度分析顯示分布於雲南省、福建省、海南省與台灣之物種遺傳歧異度較低,貴州省與廣西省之物種歧異度高,STRUCTURE分析支持K=2將油杉屬分為DE group (鐵堅油杉、雲南油杉與旱地油杉) 及FP group (油杉、柔毛油杉、江南油杉、黃枝油杉、青岩油杉、矩鱗油杉、海南油杉、台灣油杉及短果油杉),DE group分布在雲南省,FP group則廣泛分布,重疊區域約在貴州省、廣西省北部,本研究分析結果與地理分布相符。兩分群以RASP推估因地理隔離分歧,以IMa推估分歧時間約為327 ~42萬年前,推論兩分群因340萬年前青藏高原隆升,間接影響橫斷山脈形成而成為屏障,因而使基因交流低 (2.7~8.7 ∗ 10-8),分歧後進入更新世冰河時期,相對溫暖多雨的橫斷山脈成為DE group的避難所而後族群擴張 (Fu's Fs=-7.018, P=0.013, SSD=0.0011, P=0.97),呈現單一的遺傳組成,擴張時間為305~189萬年前;推論北美物種殘存於中國東南部之族群為FP group之共祖,以RASP推估物種播遷路徑,推論由物種歧異度高的貴州與廣西省之避難所往東擴張至福建與台灣,往南擴張至海南形成現今的族群分布。
位於台灣的台灣油杉以及海南的海南油杉在STRUCTURE分析中皆有獨立基因型,兩物種皆顯示現生有效族群小 (7.0萬~27.0萬,1.2萬~6.0萬),並且與FP group之間的基因交流低 (1.55~9.3 ∗ 10-10, 26~1.6 ∗ 10-10),分別為7.0萬與1.8萬年前與FP group分歧,以RASP推估因地理隔離分歧,推測冰河時期族群在大陸棚裸露時抵達台灣及海南島避難所,間冰期海平面上升使島嶼隔離而分化。
Abstract
Speciation is an important issue in evolutionary biology and species complex is a good model to test the pattern of speciation. Keteleeria (Pinaceae) is an Asian gymnosperm genus and restricted to subtropical to north tropical hill regions of South China, Taiwan, and Hainan. Fossil records have been wild distributed in Northern Hemisphere. Current distribution indicates that apparently affected by Quaternary climate shifts and almost extinction. The definition of species is difficult to consensus because taxonomists had different opinions based on morphological similarities. In this study, we build a transcriptome based on high-throughput Illumina RNA-seq sequencing technique using K. davidiana var. formosana as target taxa. We surveyed sequence variation for 4 chloroplast (cp) DNA fragments, and 27 nuclear genes among 91 individuals sampled from 12 taxa of Keteleeria.
The assignment test based on STRUCTURE show the best clustering was assumed at K=2, DE group in Yunnan and other species include in FP group. The RASP based on S-DIVA indicates the divergence because vicariance events and IMa suggesting low level of gene flow (2.7-8.7 ∗ 10-8) among group. The divergence time estimates c. 3.3-0.5 mya, a timescale with recent uplift of Qinghai-Tibet Plateau and the formation Hengduan Mountains. Pleistocene glaciation in Hengduan Mountains is relatively warm and rainy, became a refuge of DE group. FP group associated with the extinctive species of North America, and the refugia of glaciation located in Guizhou and Guangxi that have high genetic diversity of species. The RASP analysis inferred species expansion from west to east and north to south in southeast China.
Keteleeria davidiana var. formosana in Taiwan and K. hainanensis in Hainan have unique genotype in assignment test respectively. Two species suggesting low level of gene flow (1.55-9.3 ∗ 10-10, 26-1.6 ∗ 10-10), small effective population size (70-270 k, 12-6 k), diverged c. 70 and 18 ka with FP group by IMa and the vicariance events inferred by RASP. The period of continental shelf was almost free of marine influence, these islands provided refugia for northern species that migrated south during glacial periods. Keteleeria revealed species evolving through glacial cycles and caused separation, migration, and extinction as well as accelerating speciation.
目次 Table of Contents
論文審定書 i
謝誌 ii
中文摘要 iii
Abstract iv
目錄 v
圖次 vii
表次 viii
第一章 前言 1
1.1 中國與台灣地區油杉屬分類與分布 1
1.2 中國溫帶常綠樹種的族群動態歷史 4
1.3 物種的定義與種化機制 5
1.4 中性假說與天擇作用 9
1.5 油杉屬細胞學與分子演化證據 10
1.6 利用多個核基因座研究物種的種化機制 11
1.7 研究動機與目的 14
第二章 材料與方法 16
2.1 研究材料採集與製備 16
2.2 利用次世代定序取得油杉之功能性表現基因組 17
2.2.1 次世代定序 17
2.2.2 資料分析 18
2.3 核基因分子標記實驗方法 19
2.3.1 引子設計 19
2.3.2 聚合酵素連鎖反應 (Polymerase Chain Reaction, PCR) 19
2.3.3 DNA的純化 (DNA Purification) 及定序 20
2.3.4 TA clone 20
2.4 多基因序列資料分析 21
2.4.1 序列比對與排列 (Alignment) 21
2.4.2 遺傳變異分析 21
2.4.3 親緣演化樹分析 22
2.4.4 中性假說測試 22
2.4.5 Isolation-With-Migration 24
2.4.6 分歧時間的推論 25
2.4.7 Assignment test 26
2.4.8 Dispersal-Vicariance model 27
2.4.9 Mismatch distribution 28
第三章 結果 30
3.1 台灣油杉之功能性表現基因組 30
3.2 油杉屬多基因分析 31
3.2.1 樣本採集及跨物種之核基因分子標記開發 31
3.2.2 遺傳歧異度分析 33
3.2.3 中性假說與天擇檢測 37
3.2.4 Assignment test 分群結果 38
3.2.5 親緣演化樹之譜系關係推論 41
3.2.6 分歧時間與基因交流估計 43
3.2.7 Dispersal-Vicariance model推測 45
3.2.8 分群計算遺傳歧異度、中性假說及族群動態檢測 46
第四章 討論 48
4.1 台灣油杉之功能性表現基因組 48
4.2 油杉屬物種遺傳多樣性與親緣關係 49
4.3 油杉屬第四紀冰河時期之族群歷史動態 54
4.4 油杉屬之親緣地理與避難所推論 58
4.5 島嶼物種的親緣地理與族群動態歷史 60
4.6 油杉屬之威脅與保育方向 63
第五章 結論 65
第六章 參考文獻 68
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