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研究生:趙淑貞
研究生(外文):Chao, Shu-Chen
論文名稱:印度太平洋甲尻魚Pygoplites diacanthus (Pomacanthidae)成對種之全粒線體基因組比較及親緣地理學分析
論文名稱(外文):Mitogenome comparison and phylogeography of the Pygoplites diacanthus(Pomacanthidae) geminate species in Indo-Pacific Ocean
指導教授:莊守正莊守正引用關係沈康寧沈康寧引用關係
指導教授(外文):Joung, Shoou-JengShen, Kang-Ning
口試委員:蕭仁傑張至維莊守正沈康寧
口試委員(外文):Hsiao, Jen-ChiehChang, Chih-WeiJoung, Shoou-JengShen, Kang-Ning
口試日期:2015-06-26
學位類別:碩士
校院名稱:國立臺灣海洋大學
系所名稱:環境生物與漁業科學學系
學門:農業科學學門
學類:漁業學類
論文種類:學術論文
論文出版年:2015
畢業學年度:103
語文別:中文
論文頁數:50
中文關鍵詞:蓋刺科親緣地理次世代測序粒線體基因組成對種冰河期
外文關鍵詞:PomacanthidaePhylogeographyNext Generation sequencing (NGS)MitogenomeGeminate speciesGlaciation period
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全世界蓋刺科魚類 (Pomacanthidae)約8屬90種。研究對象甲尻魚(Pygoplites diacanthus)是屬於甲尻魚屬,全世界僅1屬1種。此種甲尻魚的分布範圍非常廣,涵蓋整個印度西太平洋地區,東從東非及紅海,西至法屬玻里尼西亞、土木土群島,北達日本,南到澳洲。甲尻魚色彩鮮豔,是觀賞魚中非常受歡迎的種類。此魚種的臉部在印度洋及太平洋區的顏色並不相同,在印度洋區是呈現橘色;而在太平洋區是呈現灰色。不同洋區的甲尻魚是否為不同族群?或是不同種?尚不清楚。全粒線體DNA序列及生命條碼(DNA barcoding)分析將有助於了解印度洋及太平洋區甲尻魚族群、親緣關係及演化等課題。
本研究首先以次世代定序(Next Generation Sequencing),透過短片段DNA組裝進行,太平洋(印尼)及印度洋(馬爾地夫)甲尻魚全粒線體序列解碼。太平洋甲尻魚的mitogenome總長為16,784 bp,包括13個蛋白質編碼基因(protein coding genes), 22個轉移RNAs,2個核醣體ribosomal RNAs及一個控制區(control region);印度洋甲尻魚的mitogenome則為16,767 bp。整體核酸的組成兩者大致相同,包括28.5% 為A,28.9%為C,16.3%為G,26.3%為T。印度洋及太平洋甲尻魚全粒線體基因組差異達1.55%。其中的控制區差異最大達10%,其次為ND6達1.73%。生命條碼COI分析顯示甲尻魚可分為印度洋及太平洋兩群,分子時鐘推算演化時間約在0.44-1.15百萬年,推測是在更新世冰河期海平面下降,印度馬來半島露出水面形成了印度及太平洋間的地理障礙,使甲尻魚在印度太平洋海域間產生分化。此分化時間可能也造成其他印度太平洋成對魚種的形成。

There are 8 genus and around 90 species of Pomacanthidae in the world. The Royal angelfish or regal angelfish, Pygoplites diacanthus, is a species of marine angelfish of the family Pomacanthidae, and the monotypic genus Pygoplites. It was found in tropical Indo-Pacific oceans, ranged from East Africa, Red Sea, east to French Polynesia Tuamotu Archipelago, north to Japan and south to Australia. This species is popular in aquarium trade because of its colorful body patterns. The Royal angelfish in Indian and Pacific Oceans have has different color morph, The Indian Royal angelfish has an orange face; while Pacific one has a grey face. Whether the Royal angelfish in different Ocean represent different populations or different species is still unclear. The establishment of mitogenome and the analysis of DNA barcode may help to resolve the questions of population genetics, molecular phylogenetics, and evolution for Royal angelfishes. Firstly, we used Next Generation Sequencing (NGS) for the short reads sequencing to decode the mitogenome of Royal angelfish from Pacific (Indonesia) and Indian Ocean (Maldives). The mitogenome of Pacific Royal angelfish was totally 16,784 bp, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs and one control region; while the mitogenome of Indian Ocean Royal angelfish was 16,767 bp.The nucleotides composition is similar between two geminate species, including 28.5% A, 28.9%C, 16.3%G and 26.3%T. The mitogenome difference between these two morph types is about 1.55%. The most different region was 10% for control region, then 1.73% for ND6. The analyses of life barcode COI suggested that Royal angelfishes can be divided was into two groups. The estimated divergence time based on the molecular clock concept was about 0.5 My, it could because of the low sea level during Pleistocene ice ages, the emerge of the Indo-Australian Archipelago may form vicariance which direct to the divergence of Royal angelfish in different Oceans and led to the formation of many geminated species in Indo-Pacific.
摘要 I
Abstract II
目次 III
圖目次 IV
表目次 V
第一章 前言 1
1.成對種 (Geminate species) 之親緣地理學 1
2.以分子生物技應用於分子親緣 1
3.次世代測序 Next Generation Sequencing (NGS) 3
4.蓋刺科魚類的研究回顧 4
5.研究動機與目的 5
第二章 材料方法 6
1.樣本收集及DNA萃取 6
2. PCR (Polymerase Chain Reaction) 6
3.基因體DNA及粒線體DNA電泳 7
4. NGS測序 (Next Generation Sequencing) 7
5.序列排序及親緣關係分析 7
6.分子時鐘 8
第三章 結果 9
1.太平洋甲尻魚的全粒線體定序 9
2.印度洋及太平洋甲尻魚親緣地理分析 10
3.印度洋及太平洋甲尻魚分子時鐘 10
第四章 討 論 11
1.太平洋皇帝神仙魚的全粒線體定序 11
2.印度洋及太平洋甲尻魚親緣地理分析及生物條碼之應用 11
3.印度洋及太平洋甲尻魚分子時鐘 12
4.結論 14
參考文獻 15


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