利用粒腺體DNA控制區序列來探討西北太平洋烏魚之親緣地理及演化史

PHYLOGEOGRAPHY AND EVOLUTIONARY HISTORY OF FLATHEAD MULLET MUGIL CEPHALUS IN THE NORTHWEST PACIFIC DERIVED FROM MITOCHONDRIAL DNA CONTROL REGION

賈曼德(Brian Wade Delizo Jamandre)

指導教授 ： 曾萬年

國立臺灣大學/生命科學院/漁業科學研究所/博士(2010年)

https://doi.org/10.6342/NTU.2010.02818

摘要

烏魚Mugil cephalus是一種全球分布、經濟價值高的沿岸性魚類。其生活史特徵和族群動態在過去有很多相關的研究，但是族群遺傳結構及親緣地理則不甚清楚。本研究的目的是以粒腺體DNA中的控制區 (Control region) 序列來分析西北太平洋烏魚的親緣地理結構、遺傳多樣性及其演化史。
粒腺體DNA控制區序列的親緣關係分析顯示西北太平洋地區的烏魚有兩個演化支序，分別為：大陸東海支序及大陸南海支序。 東海支序的標本來自台灣及大陸青島。南海支序的標本則來自於菲律賓、大陸珠江以及日本的橫須賀和沖繩。橫須賀及沖繩的烏魚混合不同比例的兩個演化支序個體。兩演化支序在歷史族群數量分析的變異顯示更新世的冰河期曾經影響西北太平洋烏魚的地理分布，並導致過去大陸東海支序烏魚族群數量的下降。而大陸南海支序烏魚族群的數量則維持穩定。親緣地理分析也顯示此衝擊在高緯度地區更為明顯，暗示西北太平洋的兩烏魚演化支序在更新世曾經被隔離。
西北太平洋區兩烏魚演化支序的粒腺體DNA控制區序列的變異已超過一般脊椎動物種內的遺傳多型性範圍，因此本研究將不同演化支序烏魚的控制區DNA結構和序列變異結合非洲、太平洋及大西洋區其他烏魚族群的粒腺體DNA控制區序列做進一步的親緣地理之分析。另外，為了證明西北太平洋區兩烏魚演化支序粒腺體DNA控制區序列的高突變率及歧異度並非偏差所致，我們也另外分析了Cytochrome b (Cyt b) 基因的演化速率並和控制區序列進行比較。烏魚控制區序列長度的變異是因為在3’端的高度變異區出現了核苷酸的嵌入和刪除以及不同數目的重複序列。這些變異可能導致烏魚控制區序列的高演化速率。雖然烏魚粒腺體DNA的控制區序列和Cytb序列比較起來有較高的序列變異，但在核苷酸的取代率上並無明顯的飽和現象。由親緣關係樹所顯示的全球樣本粒腺體DNA控制區序列的高歧異度也暗示過去烏魚族群快速的幅射演化，這也許是全球廣布的河口域魚類的一項特徵。
綜合本研究及其他相關的研究證據顯示，全球性分布的烏魚歷經快速的演化以及地理的隔離效應和地質事件的影響而形成不同的譜系。而且從DNA序列的變異程度來看，應該已經不是同一種而是複合種。

關鍵字

類緣地理學 ； 烏魚 ； 粒腺體DNA ； 控制區 ； 遺傳歧異度 ； 更新世 ； 西北太平洋

並列摘要

The flathead mullet Mugil cephalus is a coastal bound and circumglobally distributed fish, and the fishery is one of the most important commercial fisheries in many parts of the world. Its life history and population dynamics have been intensively studied but its genetic structure and phylogeography remained unresolved. This study investigated the phylogeographic structure, genetic diversity, and evolutionary history of M. cephalus in the Northwest Pacific region based on the analysis of the mitochondrial control region (mtDNA CR) sequences.
Phylogenetic analysis of the CR sequences indicated that M. cephalus in the Northwest Pacific was composed of two highly divergent lineages: Lineage 1 from the East China Sea and Lineage 2 from the South China Sea. The specimens of the former were collected from Taiwan and Qingdao of North China, while those of the latter from the Philippines, Pearl River of South China, and Japan. The specimens from Okinawa and Yokosuka of Japan were a mixing between lineages 1 and 2. Historical demographic variables of both lineages indicated that Pleistocene glaciations might have strong impacts on the distribution and division of the population of M. cephalus in the northwest Pacific, resulting in a recent demographic decline for the East China Sea population but in demographic equilibrium for the South China Sea population. The results of the Phylogeographic analysis also indicated that such impacts were more drastic at high latitudes than at low latitudes, suggesting that Lineage 1 and Lineage 2 were isolated during the Pleistocene era.
The mtDNA CR sequence variations between two M. cephalus lineages largely exceeded intraspecific polymorphisms that are generally observed in other vertebrates. Therefore, the structure and sequence variations of the CR gene between M. cephalus lineages from northwest Pacific were further analyzed by comparing them with those from African, other Pacific, and Atlantic regions to assess their usefulness for the phylogeographic study. In order to prove the high mutation rate or divergence rate found in M. cephalus is not due to the mutational bias of the CR gene, mitochondrial cytochrome b (mtDNA cyt b) of a few northwest Pacific mullets were also sequenced and analyzed to determine their evolutionary rate and compared to that of the CR gene. The length of CR sequence varied among M. cephalus populations due to the presence of indels and variable number of tandem repeats at the 3’ hypervariable domain. The high evolutionary rate of the CR gene was probably originated from these mutations. The CR showed higher sequence variation as compared with the cyt b. However, there was no clear indication of the saturation on the nucleotide substitutions in these two mitochondrial genes. The high CR divergence among worldwide populaions of M. cephalus inferred from the phylogenetic tree indicated the occurrence of a rapid radiation in its evolutionary history, a peculiar case for an estuarine species with global distribution.
The results of this study showed that the high divergence of M. cephalus lineages might be due to its rapid radiation of the species in evolution and to the geographic isolation caused by geological events. Therefore, in congruence to the growing number of evidences, results obtained from this study, and its worldwide scale distribution, M. cephalus is recognizable as a complex species.

並列關鍵字

Phylogeography ； Mugil cephalus ； mitochondrial DNA control region ； genetic divergence ； Pleistocene period ； Northwest Pacific

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