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研究生:陳逸文
研究生(外文):Yi-Wen Chen
論文名稱:從分子資料檢視台灣地區鬼鼠之遺傳變異
論文名稱(外文):Genetic Variation of the Greater Bandicoot Rat (Bandicota indica) in Taiwan Based on Molecular Data
指導教授:林良恭林良恭引用關係
指導教授(外文):Liang-Kong Lin
學位類別:碩士
校院名稱:東海大學
系所名稱:生命科學系
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:74
中文關鍵詞:鬼鼠引進種親緣關係網狀關係
外文關鍵詞:Bandicota indicaintroduced speciesphylogenyhaplotypes network
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摘要
鬼鼠(Bandicota indica)為分布於東南亞最大型的鼠科動物,亦是台灣體型最大的鼠類動物,普遍分布於較低海拔地區,Swinhoe (1870)曾提出鬼鼠可能是1630年荷蘭人殖民時引進台灣的,但是缺乏歷史記載的證據。以遺傳學的角度來看,物種在拓殖到新環境時,應該會受到創立者效應或瓶頸效應的影響而呈現較低的遺傳多樣性。因此透過探討不同地理分布族群的遺傳結構,以及各族群間的分化程度與親緣關係,可追溯物種的演化歷史。本研究選用粒線體核苷酸之控制區域(d-loop)及細胞色素b基因(cytb)的序列建構親緣關係樹,以探討台灣地區鬼鼠的族群遺傳變異,並以基因單型的網狀關係圖以及不相合分布分析檢驗鬼鼠是否具有短期內引進物種的遺傳特性,並檢驗與福建、廣東和越南樣本的親緣關係。控制區域片段序列(700 bp)及細胞色素b基因完整序列(1140 bp)的親緣關係分析可將台灣的樣本分為台灣型與花蓮型兩大群,兩型間遺傳距離遠,族群分化指數高且基因交流指數低,AMOVA分析亦顯示大部分的變異是存在於兩型之間。台灣型在cytb的單型網狀關係圖呈現分支較多的結構,與短期內引進種的情形不太一致。不相合分佈分析中具有族群擴張的現象且未受瓶頸效應影響。此外台灣型與福建的單型具有高度相近的親緣關係,顯示台灣型的鬼鼠可能是從大陸地區拓殖而來。而花蓮型單型在cytb所呈現的高遺傳多樣性指數,可能與多次入侵有關,來源初步可以排除福建、廣東及越南南部等地區。未來應該針對越南北部以及其他東南亞地區進行更多樣本的分析以釐清與花蓮型單型的親緣關係。
Abstract
Bandicota indica is the largest muridae animal distributed in Southeast Asia, and also the biggest rodent generally habitat at lower elevation area in Taiwan. Swinhoe (1870) speculated that this rat had been introduced to Taiwan by the Dutch in the 17th century, but lacking the historical evidence. From the view of the genetics, species colonize a new environment should affect by the founder effect or the bottleneck effect, exhibiting a lower genetic diversity. The evolutionary history of the species could be traced by understand the genetic variations, population divergence and phylogenetic relationships of the populations in different geographical regions. In this study, I used the d-loop region and cytochrome b gene sequences of the mitochondrial DNA to reconstruct the phylogenetic trees in order to understand the population genetic structure of Bandicota indica in Taiwan, and examine the phylogenetic relationships of samples from Fujian, Guangdong, and Vietnam. I used the haplotypes network and mismatch distribution analysis to examine any genetic pattern of the recent introduced species in Bandicota indica. The phylogenetic analysis of the d-loop partial sequence (700 base pairs) and cytochrome b gene complete sequence (1140 base pairs) can separate the Taiwan samples into two groups, Taiwan type and Hualien type. The genetic distance and sequence divergence were high between two types. Most of the variance is between two types in AMOVA analysis and the gene flow was low. The large divergent star-like structure in cytochrome b gene haplotypes network of Taiwan types was not consist with the pattern of recent introduced species. The unimodal displays in mismatch distribution analysis revealed the population expansion of Taiwan types, and closely relationships between Taiwan types and Fujian haplotypes suggest that the rat might have been colonized from mainland. The high genetic diversity of cytochrome b sequences in Hualien types might be resulted from the multiple introduction events. In this study, however, I excluded the Fujian, Guangdong, and Southern Vietnam as the possible origin of the Hualien types. Futher investigation on relationships among populations of Hualien and Northern Vietnam and other regions of Southeast Asia should be conducted in detail with more samples.
目錄
中文摘要‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥Ⅰ
英文摘要‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥Ⅲ
一、前言‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥1
二、材料與方法‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥7
1. 樣本採集‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥7
2. 去氧核糖核苷酸(DNA)分析‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥7
3. 序列片段增幅反應(PCR)及定序‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥8
(1) 控制區域(d-loop) ‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥8
(2) 細胞色素b基因(cytochrome b gene, cytb gene) ‥‥‥‥‥‥‥‥9
4. 序列分析‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥10
(1) 排序(alignment)及定義單型(haplotype) ‥‥‥‥‥‥‥‥‥‥‥10
(2) 繪製親緣關係樹(phylogenetic tree) ‥‥‥‥‥‥‥‥‥‥‥‥10
(3) 核苷酸多樣性、單型多樣性與遺傳變異‥‥‥‥‥‥‥‥‥‥‥11
(4) 單型的網狀結構(haplotype network)‥‥‥‥‥‥‥‥‥‥‥‥12
(5) 不相合分佈分析(mismatch distribution analysis) ‥‥‥‥‥‥‥12
三、 結果‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
1. 序列資料‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
(1) 控制區域片段序列資料‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
(2) 細胞色素b基因序列資料‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
2. 分子親緣關係‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥14
(1) 控制區域片段序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥14
(2) 細胞色素b基因序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥15
3. 遺傳變異‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥17
(1) 控制區域片段序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥17
(2) 細胞色素b基因序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥19
4. 單型網狀關係‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥20
(1) 控制區域片段序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥20
(2) 細胞色素b基因序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥21
5. 不相合分佈(mismatch distribution) ‥‥‥‥‥‥‥‥‥‥‥‥‥‥22
四、討論‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥24
1. 鬼鼠的親緣地理‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥24
2. 台灣地區鬼鼠之引進的可能性‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥30
五、參考文獻‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥35
六、表目‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥42
七、圖目‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥43
八、表和圖‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥44
九、附錄一‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥62
十、附錄二‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥68
十一、附錄三‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥70
十二、作者資訊‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥74
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