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Title: | 海鰱總目之系統分類及其視紫質基因的演化 Systematics and rhodopsin gene evolution in the Elopomorpha (Teleostei) |
Authors: | Jhen-Nien Chen 陳貞年 |
Advisor: | 陳韋仁 |
Keyword: | 海鰱總目,康吉鰻亞目,分子系統分類,分類,視紫質基因,基因演化,模式魚群, Elopomorpha,Congroidei,Molecular systematics,Classification,Rhodopsin gene,Gene evolution,Model fish group, |
Publication Year : | 2017 |
Degree: | 博士 |
Abstract: | 海鰱總目(鰻魚及其近親)為一群形態多樣性高、主要生活在海水的魚類類群,包含至少一千個物種,25個科,四或五個目(海鰱目,北梭魚目,背棘鰻目,鰻鱺目及囊鰓鰻目)。其類群擁有高度的棲地多樣性,分佈在沙岸,珊瑚礁,遠洋及深海等棲地。海鰱總目為現生硬骨魚三大分群之一(其他二者為骨舌魚總目及鯡型總目)。過去數篇研究利用外部形態或分子證據欲重建海鰱總目之親緣關係及系統分類,並無一致結果,這限制了海鰱總目相關的演化研究。為提倡海鰱總目作為一模式魚群以應用於魚類演化及其基因體研究範疇,在此論文中將全面性地探討海鰱總目的親緣關係假說。第一,利用多基因分子資料建構一完整海鰱總目之親緣關係,藉以釐清海鰱總目在硬骨魚中的分類地位及其中目之間的親緣關係與分類。結果顯示,海鰱總目為所有其他硬骨魚的姊妹群並包含四個主要單系群或目,而其中鰻鱺目可進一步被分成四個亞目。第二,接續前部份研究結果,利用相似的研究方法針對鰻鱺目中最大的亞目類群(康吉鰻亞目)建構親緣關係樹,結果發現在康吉鰻亞目中廣泛存在多個多系群科。本論文基於此重建之親緣關係樹,進一步討論康吉鰻亞目的分類修訂。第三,以本論文所建構的親緣關係及海鰱總目為研究重心,深入探討視紫質基因在脊椎動物中的演化。本研究分析了227條來自179種脊椎動物的視紫質基因及其類似基因序列,並針對在脊椎動物演化過程中,數個關於基因演化的假說進行分析(包含基因複製和基因遺失事件),並討論其結果。本研究發現在大部分鰻鱺目物種(除鯙科外)的基因體中,均可發現兩對視紫質基因。根據分析結果推測,在過去早期硬骨魚的演化歷史中,共發生兩次基因複製事件。一次發生在所有硬骨魚的共同祖先,與演化史上“魚類特定基因體複製“事件相符;另一次則發生於鯡型總目的共同祖先。而在此兩次基因複製事件之後,其中一複製的視紫質基因在某些特定魚類類群的基因體中因未被保留而遺失。最後,本論文期許海鰱總目能成為研究魚類演化及其基因體研究的模式魚群,而此篇論文即能作為之後旨在更了解海鰱總目或其他硬骨魚的演化歷史及其生物多樣性研究的重要參考。 Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine teleost fishes which comprising more than 1000 species classified in 25 families and four or five orders (i.e. Elopiformes, Albuliformes, Notacanthiformes, Anguilliformes and Saccopharyngiformes). The elopomorph fishes are also ecologically diversified as their habitats include sandy shore, coral reef, pelagic ocean, and deep-sea benthos. Elopomorpha is one of the three major living teleost lineages along with the Osteoglossomorpha and Clupeocephala. Several studies aiming at reconstructing the elopomorph phylogeny using morphological and/or molecular characters led to inconsistent results, precluding us from further investigation of their evolution. To promote the Elopomorpha as a model fish group in the evolutionary and genomic studies, new phylogenetic hypotheses (at different taxonomic levels) are presented in this dissertation. First, the phylogenetic position of the Elopomorpha related to other teleosts and the inter-ordinal phylogeny within the Elopomorpha were investigated using a large multi-gene dataset with an extensive taxonomic sampling. The results show that Elopomorpha is the sister group of the rest of the Teleostei and the Elopomorpha comprises four main monophyletic groups or orders. Within the Anguilliformes, four main lineages (suborders) were presented. Second, the phylogeny of the most speciose suborder, the Congroidei, was examined using similar multi-gene approaches but with different taxon samplings focusing on congroids. The result demonstrates an extensive polyphyly at the familial level within the Congroidei. According to the reconstructed phylogeny, a revised classification of the Congroidei is presented and discussed. Third, with the new phylogenetic framework established in this dissertation and the Elopomorpha as the focus, a thorough perspective of the rhodopsin gene (rh1) evolution within the vertebrates was presented. 227 sequences of rh1 and rh1-like from 179 vertebrate species were included in the analysis. Several hypotheses concerning the rh1 evolutionary events like gene duplication/lost event during the evolution of the vertebrates were evaluated. In this study, two paralogous copies of rh1 were found in the genomes of the most of anguilliforms (except the Muraenidae). According to the analyses, rh1 was likely duplicated two times during the early evolutionary of the Teleostei, one occurred close to the origin of teleosts corresponding to the Fish-Specific Genome Duplication and the other in the common ancestor of the Clupeocephala. After those gene duplication events, one copy was secondarily lost in some specific teleost lineages. Eventually, I expect that the Elopomoprha as a potential model fish group for evolutionary and genomic studies in fishes and hopefully this study could provide a guide for researches which intend to better understanding of the evolution and of biodiversity of the Elopomorpha and other early teleost fishes. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59670 |
DOI: | 10.6342/NTU201700464 |
Fulltext Rights: | 有償授權 |
Appears in Collections: | 海洋研究所 |
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ntu-106-1.pdf Restricted Access | 12.6 MB | Adobe PDF |
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