共生藻在貧營養鹽的珊瑚礁生態系具有相當重要的生態地位。在印度太平洋地區，珊瑚的歧異度相當高，但是共生藻相關的研究卻非常少。墾丁地區及澎湖群島是印度太平洋兩種不同典型的生態系，因此相當適合於探討印度太平洋共生藻的歧異度。本研究利用聚合脢連鎖反應（Polymerase chain reaction）增幅核糖體小次單元核甘酸（Small subunit ribosomal RNA gene）以及限制脢片段多型性（Restriction fragment length polymorphism）的方法，調查墾丁地區及澎湖群島32種石珊瑚、4種海葵、3種水螅珊瑚和1種藍珊瑚的共生藻。發現除了4種宿主：海葵Aiptasia puchella具有B系群、石珊瑚Oulastrea crispata具有E系群、Acropora palifera和Montipora cactus都同時具有C及E系群的共生藻；其他宿主所含之共生藻皆為C系群。所以，在印度太平洋地區C系群的共生藻是最優勢的系群，和之前的研究呈現一致的結果。根據分子親緣分析比較核糖體小次單元核甘酸序列的結果，支持共生藻的E系群是一個單系群，且目前僅出現在太平洋、淺水域的石珊瑚裡。進一步分析多型性共生組成的模式和分佈的生態區位，發現太平洋地區共生藻C和E系群組合的多型性共生分佈在淺水域，並不符合之前在加勒比海海域所提出之光適應假說。且整合分析目前已發表之共生藻的生物地理分佈資料，顯示不同系群共生藻的分佈及多型性共生的生態模式受到太平洋和加勒比海地理分隔的影響相當大。

Zooxanthellae are very important for the coral reef ecosystem. The diversity of coral hosts is high in the Indo-Pacific, but the diversity of zooxanthellae has not been broadly investigated. Southern Taiwan and Penghu Islands are coral reef and non-reefal communities, respectively. These localities were chosen as the sampling sites for this study to maximize the opportunity of surveying this region in the Indo-Pacific. Zooxanthellae diversity was investigated in 40 host species including 32 species of Scleractinia, 4 species of Actiniaria, 3 species of Milleporina and 1 species of Helioporacea using polymerase chain reaction (PCR) of the ssrRNA gene and restriction fragment length polymorphism (RFLP) patterns. The phylogenetic relationship of partial and complete sequences of the ssrRNA gene were also analysed. Aiptasia puchella harbors clade B; Oulastrea crispata only harbors clade E; while Acropora palifera and Montipora cactus harbor both clades C and E. Zooxanthellae isolated from all except the above 4 host species are identified as "clade C" sensu Rowan and Powers (1991a). Therefore, the clade C is the dominant type in the Indo-Pacific. Phylogenetic analyses based on partial and complete sequences obtained in this study and also from the GenBank data base demonstrate 4 clades (A, B, C and E) in the genus Symbiodinium. Clade E, classed as D3 RFLP type in previous studies, is a distinct clade differing from A, B and C by RFLP and sequencing data. Clade E has only been found in Scleractinia host species collected in shallow-water habitats in the Pacific. The composition of zooxanthellae clades and ecological pattern of polymorphic symbiosis is not consistent with the irradiance adaptation hypothesis in the Caribbean. A literature survey of zooxanthellae in Scleractinian hosts indicates a significant difference between the Caribbean and the Pacific. The documented biogeography of zooxanthellae clades and the ecological pattern of polymorphic symbiosis are also differ between the Caribbean and the Indo-Pacific.

1. Introduction………………1
2. Materials and Methods… 5
3. Results…………………… 9
4. Discussion…………………15
5. References…………………25
6. Tables………………………30
7. Figures…………………… 39

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