Taxonomic and Molecular Phylogenetic Studies of Stomiiforms from Taiwan

巨口魚為棲息於中層洋帶 (水深200-1000 m)及漸深洋帶的魚類，本研究針對台灣附近海域之巨口魚目進行廣泛採集與形態分類，並利用粒線體之序列特徵來探討該目內之類緣關係。根據Nelson (1994)之分類系統，本研究共紀錄台灣有4科34屬56種巨口魚目之魚類，其中包括一新種及25種台灣之新記錄種，它們分別是新種台灣星衫魚(Astronesthes formosana n. sp.)、黑圓罩魚 (Cyclothone atraria)、蒼圓罩魚 (C. pallida)、東方雙光魚(Diplophos orientalis)、西鑽光魚 (Gonostoma atlanticum)、長體頜光魚(Ichthyococcus elongatus)、莫氏軸光魚 (Pollichthys mauli)、長刀光魚(Polymetme elongata)、串光魚 (Vinciguerria nimbaria)、印太星衫魚 (Astronesthes. indopacifica)、絲球星衫魚 (A. splendida)、四絲深巨口魚 (Bathophilus kingi)、絲鬚深巨口魚 (B. nigerrimus)、掠食巨口魚 (Borostomias elucens) 、馬康氏蝰魚 (Chauliodus macouni)、單鬚刺巨口魚 (Echiostoma barbatum)、真芒巨口魚 (Eupogonesthes xenicus)、歧鬚真巨口魚 (Eustomias bifilis)、蛇口異星杉魚 (Heterophotus ophistoma)、多紋纖巨口魚 (Leptostomias multifilis)、黑柔骨魚 (Malacosteus niger)、瓦氏黑巨口魚 (Melanostomias valdiviae)、厚巨口魚 (Pachystomias microdon)、格氏光巨口魚（Photostomias guernei）、細杉魚 (Rhadinesthes decimus)及纓光魚(Thysanactis dentex)等。但仍有下列3屬5種巨口魚過去雖有紀錄，卻查無標本包括：雙光魚(Diplophos pacificus)、大棘燭光魚 (Polyipnus spinosus)、三齒燭光魚 (P. tridentifer)、單棘燭光魚 (P. unispinus)及長鬚真巨口魚 (Eustomias longibaba)，這5種目前暫不列入紀錄之中。本論文除提供各種類之同種異名、標本資訊、形態描述及鑑定特徵、體色、標本照、線繪圖、分布、棲息深度等資料外，並製作台灣產巨口魚之檢索表，供未來相關研究之參考依據。 有關巨口魚目的科與科之間以及科內各屬之間的類緣關係目前仍不清楚。此外，鑽光魚科 (Gonostomatidae)的雙鑽光魚 (Diplophos)、參鉆光魚 (Triplophos)兩個屬在該科及巨口魚目內的類緣關係亦有待釐清；光魚科 (Phosichthyidae)是否為單一係群仍須待檢視。因此本論文乃利用粒線體之Cyt b及CO1基因序列等分子特徵來探討巨口魚目內之類緣關係。採用最大檢約法 (Maximum Parsimony)、最大概似法 (Maximum Likelihood)及貝氏 (Bayesian)方法等，來建立巨口魚目之分子類緣關係。結果顯示，所有巨口魚目為一單系群，巨口魚科 (Stomiidae)也是一單系群。不同方法所建構之分子類緣關係樹狀圖皆顯示，利用分子特徵所建構之類緣關係與依據形態特徵所推論的結果並不完全一致。例如鑽光魚科、褶胸魚科(Sternoptychidae)及光魚科並不形成單系群，且各科之間的類緣關係仍無法有效釐清。此外，雙鑽光魚屬為巨口魚目內原始的一支。又參鉆光魚與其他鑽光魚科種類之類緣關係較近，應不屬於光魚科之類群。 由於巨口魚的分子演化樹上顯示有分支較長、結間較短、序列變異位點比例偏高及鹽基置換呈現飽和等現象，這些特性是造成bootstrapping時得到較低支持度的原因，並且可能會影響推論結果。但由於巨口魚之化石證據及其深海環境較穩定之特性，故上述分子演化樹的特性也可能是來自於巨口魚在出現後，又已經過較長時間 (約56-15百萬年前) 的演化歷史有關。Stomiiforms are mesopelagic and bathypelagic fishes. The purposes of this study include expading taxonomic studies of Stomiiformes around Taiwanese waters and inferring phylogenetic relationships among this group of fishes based on mitochondrial Cyt b and CO1 gene sequences.A total of 56 species in 34 genera and 5 families have been recorded based on the classification system of Nelson (2006). Among them, there is one new species and 25 newly recorded species. They are: Astronesthes formosana n. sp. ; Cyclothone atraria, C. pallida, Diplophos orientalis, Gonostoma atlanticum, Ichthyococcus elongatus, Pollichthys mauli, Polymetme elongate, Vinciguerria nimbaria, Astronesthes indica, A. indopacifica, A. splendida, Bathophilus kingi, B. nigerrimus, Borostomias elucens, Chauliodus macouni, Echiostoma barbatum, Eupogonesthes xenicus, Eustomias bifilis, Heterophotus ophistoma, Leptostomias multifilis, Malacosteus niger, Melanostomias valdiviae, Pachystomias microdon, Photostomias guernei, Rhadinesthes decimus, and Thysanactis dentex. Five species in 3 genera i.e. Diplophos pacificus, Polyipnus spinosus, P. tridentifer, P. unispinus, and Eustomias longibarba, that have been reported in early literatures were not included herein due to lack of specimens. Synonyms, specimen, diagnostic characters, color photographs or line-drawings, distributions, depth, and a key to species of Taiwan are given. The phylogenetic relationships within Stomiiformes were studied using the mitochondrial Cyt b and CO1 genes, and the Phylogenetic inference method including naximum parsimony, maximum likelihoos, and Bayesian methods. The results indicate that Stomiiformes is a monophyletic group, and Stomiidae could also be monophyly. The phylogenetic relationships constructed by different methods were incongruent with those by morphological characters. For example, the monophyly of families Diplophidae, Gonostomatidae, Sternoptychidae, and Phosichthyidae were not supported. Besides, Diplophos is a basal taxa to other Stomiiformes and Triplophos are clustered with Gonostomatidae rather than with Phosichthyidae. The special molecular characteristics such as longer branch length and short interior branch length from tree topologies, high proportion of variable sites, and saturation for base substitutions may obscure the phylogenetic relationships of Stomiiformes and result in lower bootstrap supporting value. The evidences from fossil records and the molecular tree of Stomiformes suggest that these deep-sea fishes had a very long evolutionary history (56-15 million years ago) and they might pass through species radiation shortly in stable deep-sea environment.口試委員會審定書.......................................I 謝誌..................................................II 中文摘要.............................................III ABSTRACT..............................................VI 目錄................................................VIII 第一節 前言............................................1 1.1 形態分類...........................................1 1.2 形態類緣關係.......................................8 1.3 分子類緣關係.......................................9 第二節 研究目的.......................................11 第三節 材料與方法.....................................13 3.1 形態分類..........................................13 3.1.1 標本採集........................................13 3.1.2 標本處理........................................13 3.1.3 標本檢視........................................14 3.1.4 文獻整理........................................14 3.1.5 標本典藏........................................14 3.1.6 物種描述及製作檢索表............................15 3.2 分子類緣關係......................................15 3.2.1 材料............................................15 3.2.2 方法............................................15 第四節 結果...........................................20 4.1 形態分類..........................................20 4.1.1 台灣產巨口魚之種類描述..........................21 4.1.2 檢索表..........................................56 4.2 分子類緣關係......................................63 第五節 討論...........................................72 5.1 形態分類..........................................72 5.1.1 台灣產巨口魚目之魚類相..........................72 5.1.2 Astronesthes ijimai之有效性.....................72 5.2 分子類緣關係......................................73 5.2.1 不同基因片段序列比較之一致性....................73 5.2.2 與目前形態分類結果之比較........................74 第六節 結論...........................................86 6.1 形態分類..........................................86 6.2 分子類緣關係......................................86 第七節 未來研究方向...................................88 參考文獻..............................................89 附錄.................................................10