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作者:賴建宏
作者(英文):Chien-Hung Lai
論文名稱:台灣及沖繩大和沼蝦(Macrobrachium japonicum)族群遺傳結構之研究
論文名稱(英文):Populations genetic structure of Macrobrachium japonicum de Haan, 1849 (Decapoda, Palaemonidae) in Taiwan and Okinawa.
指導教授:韓僑權
指導教授(英文):Chiao-Chuan Han
口試委員:林弘都
朱育民
口試委員(英文):Hung-Du Lin
Yu-Min Ju
學位類別:碩士
校院名稱:國立東華大學
系所名稱:海洋生物研究所
學號:610363103
出版年(民國):106
畢業學年度:106
語文別:中文
論文頁數:73
關鍵詞:大和沼蝦兩側迴游型COI 基因沖繩遺傳結構差異
關鍵詞(英文):Macrobrachium japonicumamphidromous migrationcytochrome oxidase subunit I geneOkinawagenetic structure
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本篇研究利用粒線體DNA的COI基因檢視了在台灣及日本沖繩大和沼蝦族群的遺傳結構,共取樣234個樣本,包含12個台灣族群和1個沖繩族群,依地理位置分群為西北、西南、東部和北部分群。本篇採用了COI gene 644 base pairs的長度分析,分析結果總共有142個單倍型,Haplotype diversity = 0.988,Nucleotide diversity = 0.00896,Fu’s Fs = -234.352*,Tajima’s D = -2.14489*,高Hd、低Nd以及中性測試為顯著負值,表示族群有擴張的情況,Mismatch distribution analysis也支持此結果,並且透過在MIGRATE v3.6上的M值分析顯示:基因流的方向主要是從台灣往沖繩的單一方向。Pairwise FST estimates顯示在沖繩與大部分台灣族群以及大安溪與部分族群呈現中度分化的現象。在AMOVA以及SAMOVA分析中四個分群間以及族群之間並沒有明顯的遺傳差異,差異主要出現在族群內。從NJ tree可以看出台灣族群並沒有形成依地理位置區分的分支,Minimum spanning network也顯示大部分單倍型間沒有明顯的分群,但在沖繩族群中有特化的單倍型及分支存在。在Bayesian skyline plot中顯示,族群擴張約在距今1.25萬年前緩慢上升,在2500年前快速擴張,約1500年前達到穩定的族群。
In this study, we used the COI gene of mitochondrial DNA to examine the genetic structure of populations of Macrobrachium japonicum in Taiwan and Okinawa of Japan. A total of 234 individuals were sampled, including 12 Taiwanese populations and 1 Okinawa population. They were grouped by geography site (Northwest, Southwest, east and North).We used the length of 644 base pairs COI gene to analysis. There are 142 haplotypes, Haplotype diversity = 0.988, Nucleotide diversity = 0.00896, Fu's Fs = -234.352*, Tajima's D = -2.14489*. High level of Hd, Low level of Nd and neutral tests were significantly negative, which means that populations had expanded, this result also be supported by Mismatch distribution analysis, in addition, the M falue analysed by MIGRATE v3.6 shows the direction of gene flow is mainly from Taiwan to Okinawa in a single direction. Pairwise FST estimates shows there are a median degree of differentiation between most of Taiwanese and Okinawa population as well as the Da-an River and parts of other populations. The proportion of genetic difference among four groups and among populations within group are very low in AMOVA analysis, the genetic difference is mainly within populations. From the NJ tree we can see that all populations do not form the geographically distinct branches. Minimum spanning network also shows that there is no obvious grouping among haplotypes, except of Okinawa haplotypes, some of them form a special branch. In the Bayesian skyline plot, population expansion rose slowly about 1.25 ten thousand years ago, rapidly expanded in 2500 years ago, and reached a stable population about 1500 years ago.
謝辭----------------------------------------------------------------I
中文摘要-----------------------------------------------------------III
英文摘要-------------------------------------------------------------V
目錄--------------------------------------------------------------VII
表目錄-------------------------------------------------------------IX
圖目錄-------------------------------------------------------------XI
附件目錄----------------------------------------------------------XIII
第一章、 前言-----------------------------------------------------1
一、 大和沼蝦-----------------------------------------------------1
二、 沼蝦屬(Macrobrachium)--------------------------------------1
三、 不同的遺傳結構-----------------------------------------------3
四、 台灣地理環境-------------------------------------------------5
五、 粒線體DNA---------------------------------------------------6
六、 族群遺傳學---------------------------------------------------7
七、 親緣地理學---------------------------------------------------7
八、 研究目的-----------------------------------------------------9
第二章、 研究方法與材料-------------------------------------------11
一、 樣本採集----------------------------------------------------11
二、 DNA萃取和PCR擴增--------------------------------------------12
三、 DNA序列分析-------------------------------------------------14
第三章、 結果----------------------------------------------------19
一、 遺傳變異分析(Genetic diversity)---------------------------19
二、 親緣關係重建(Phylogeny reconstruction)--------------------20
三、 親緣網狀圖之建立和網狀支序分析(Minimum spanning comparison and nested clade analysis)--------------------------------------------21
四、 族群結構(Population structure)----------------------------21
五、 族群歷史動態分析(Historical demographic analysis)----------22
第四章、 討論----------------------------------------------------25
一、 遺傳多樣性(Genetic diversity)-----------------------------25
二、 族群差異(population differentiation)----------------------26
三、 歷史動態(Demography history)------------------------------28
第五章、 結論----------------------------------------------------29
參考文獻------------------------------------------------------------31
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