臺灣博碩士論文加值系統

頭足類生物包括鸚鵡螺，烏賊，魷魚，章魚，鎖管…等。在過去幾十年中，頭足類漁獲量有明顯增加的趨勢，頭足類漁獲量的上升反映出世界人口的增加以及對動物性蛋白質的需求，了解頭足類系群之族群結構為建構有效漁業管理策略之重要基礎。
目前多數研究皆以商業目標物種(尤其管魷類)為主要對象，對烏賊類之研究則相對較少。虎斑烏賊 (Sepia pharaonis Ehrenberg，1831) 在印度太平洋地區是經濟價值非常高的漁業生物，在先前的形態及遺傳研究顯示虎斑烏賊是一個複合種(species complex)，但複合種間的親緣關係仍不明朗。
為了釐清複合種間的親緣關係，本研究基因庫下載了印度太平洋區所有虎斑烏賊的粒線體 COI (cytochrome oxidase subunit I) 序列共65筆，另外也下載3筆唇瓣烏賊 (Sepia lycidas) 及2筆目烏賊 (Sepia aculeata) COI序列作為親緣關係分析時之外群。
分子親緣分析顯示在整個印度太平洋的虎斑烏賊為一單系群 (monophyly)的複合種 (species complex)，其下又可分為七個演化支序分別為 1.紅海支序 (Red Sea clade)：包括亞丁灣（Gulf of Aden）及紅海 (Red Sea)；2.北澳洲支序 (North Australia clade)；
3.波斯灣支序(Persian Gulf clade)：包括伊朗 (Iran) 及阿曼灣(Gulf of Oman)；4.東印度洋支序 (West Indian clade)：包括印度東西側 (India ) 及泰國之安達曼海側 (Andaman Sea coast of Thailand)；5.西太平洋支序 (West Pacific clade)：包括臺灣、中國大陸及泰國暹羅灣側 (Gulf of Thailand coast)；另外也包括新發現的菲律賓支序 (Philippines clade) 及莫三比克 (Mozambique) 支序。
支序間關係可以看出莫三比克支序最原始；紅海和澳洲支序的關係較近，與紅海較接近的波斯灣卻是與東印度洋及西太平洋群關係較接近，具有96-100% bootstraps值的支持。
本研究從紅海及波斯灣支序中各發現一個來自中國的樣本(HQ846149, HQ846150)，推測並非是中國本地的樣本，也並不可能是從西太平洋洄游至西印度洋，可能和遠洋漁業或水產品進口有關。資料中有一筆Sepia gibba的COI序列來自以色列，經分析亦屬於紅海的虎斑烏賊支序，可能是種類鑑定錯誤。
本研究推測印度太平洋的虎斑烏賊可能包含了數個隱蔽種，透過DNA條碼分析可大致區分出不同的來源區域，但複合種在形態上的差異仍需進一步釐清。
族群歷史動態解析顯示，除了澳洲及西太平洋兩個支序外，大部分支序普遍具有高單倍型及高核甘酸歧異度，顯示太平洋支序在演化歷史中可能經歷族群擴增。但不匹配分布及中性檢測卻顯示澳洲支序及東印度洋支序可能經歷族群擴增。這些分析的不一致性可能和樣本數較小有關，因此在歷史族群動態分析部分僅供參考。

Cephalopoda can be divid into four orders: Nautilida, Sepiida, Teuthida and Octopoda. The creatures in Cephalopoda including nautilus, squids, cuttlefishes, octopus etc. In the past decedes, the fishery landing of cephalopods is getting increase which reflecting the increase of human population and the needed for animal proteins. Therefore, it is important to understand the population genetic structure in order to establish an effcieint stategy for fishery resources management. Most researchs were focus on the commercial important squids while the research for cuttlefishes is limitted. The pharaoh cuttlefish, Sepia pharaonis Ehrenberg, 1831, is a commercially species found from East Africa to Japan. Previous morphological and genetic works suggested that S. pharaonis is a species complex, but phylogenetic relationships within the complex remained unresolved. To clarify these relationships, this study have download the COI (cytochrome oxidase subunit I) sequences over 60 specimens from NCBI from throughout the range of S. pharaonis. We have also added three Sepia lycidas and two Sepia aculeata sequences data as outgroup. Molecular Phylogenetic analyses of the dataset revealed a monophyletic S. pharaonis complex consisting of at least seven clades, including a Red Sea clade, a north Australia clade, a Persian Gulf clade, a west Pacific clade, a east Indian Ocean clade a Philippines Clade and a Mozambique clade. Phylogenetic relationships suggested that Mozambique clade is the most ancestral clade for S. pharaonis species complex, Red Sea Clade is genetically closer to the Australia clade; Persian Gulf, west Pacific and east Indian Ocean clades are also closer with the support of 94-100% bootstraps value. Two S. pharaonis specimens, which were collected from China (HQ846149, HQ846150), were found to be a member of the Red Sea clade and Persian Gulf clade, respectively, suggesting the possibility of fishery product importation or came from distant fishery. One specimen of Sepia gibba from Israel is also the member of S. pharaonis complex, suggesting the possibility of species misidentification. We suggest that ‘S. pharaonis’ may consist of several cryptic species, but morphological work is needed to clarify species-level taxonomy within this complex. Most clades have high haplotype diversity and high nucleotide diversity except Australia and West Pacific clades, which have low nucleotide diversity, suggesting the possibility of population expansion of S. pharaonis in Pacific. However, the mismatch distribution and neutrality test suggested that Australia and East Indian Ocean clades might have experienced historical population expansion during the recent evolutionary history. These discordance in different historical demographic tests may reflex the small sample size and therefore only for reference.

摘 要………… VII
ABSTRACT III
目次………………………………………………………………...………………………....V
圖次………………………………………………………………...………………………..VI
表次…………………………………………………………………………………….…...VII
壹、前言 1
1. 頭足類之分類及重要性 1
2. 虎斑烏賊之漁業及生物學 3
3. 隱蔽種對頭足類漁業的影響 6
4. 虎斑烏賊型態及親緣分析回顧 6
5. 研究動機及目的 8
貳、材料與方法 9
1. COI序列來源 9
2. DNA序列分析 10
參、結果 13
1. 親緣分析 13
2. 遺傳距離 14
3. 族群遺傳多樣性及歷史族群動態 14
肆、討論 15
1. 生物地理分布 16
2. 型態與分子分類 17
3. 分子親緣關係 18
4. 不同虎斑烏賊支序的遺傳多樣性及歷史族群動態 20
伍、結論 21
陸、參考文獻 22

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