Molecular Systematics of Threadfin Breams and Relatives (Teleostei: Nemipteridae)

金線魚科 (Nemipteridae) 包含五個屬六十九個有效種，分別為金線魚屬 (Nemipterus)、錐齒鯛屬 (Pentapodus)、眶棘鱸屬 (Scolopsis)、副眶棘鱸 (Parascolopsis)、裸顳鯛屬 (Scaevius)，皆分布在熱帶至副熱帶的印度西太平洋 (Indo-West Pacific)地區。 各屬間之種類在形態上非常相似，尤其是金線魚屬之種類，目前用來鑑定種類之方法多依賴新鮮標本之顏色，但這些特徵往往於標本保存過程中褪去，因此經常造成種類鑑定上的困難與錯誤。 近年來分子技術日漸發達，利用去氧核醣核酸(DNA)序列的種間差異，能有效提高種類鑑定的精準度並為物種間的演化歷史提供新觀點。本研究利用分子系統分類 (molecular systematics) 的方法，針對金線魚科種類探討以下的問題: (1)利用多基因分子標記來建構較完整的金線魚科內親緣關係 (2)檢驗目前各種類的種名有效性，並尋找是否含有隱蔽種與新種 (3)檢驗前人對於金線魚科各屬間與屬內所提出的親緣關係假說。本研究中建構了兩個資料矩陣，一為包含兩個核基因(RAG1和RH)與一個粒線體基因(COI)，用以建構金線魚科屬間之親緣關係樹；另一個包含了657條COI基因序列 (329條為本研究提供，328條由資料庫取得)，搭配種類界定軟體(ABGC與GMYC)以探索金線魚科物種多樣性。結果顯示金線魚科內的五個屬皆為單系群，其中裸顳鯛屬 (Scaevius) 是錐齒鯛屬 (Pentapodus) 的姊妹群，金線魚屬 (Nemipterus)為前兩者的姊妹群；而眶棘鱸屬 (Scolopsis) 與副眶棘鱸屬 (Parascolopsis) 為姊妹屬。 於本研究中分析的53個形態種(morphospecies)中，大部分種名皆是有效的，除了以下幾個種: Parascolopsis inermis, Scolopsis affinis, Scolopsis vosmeri, Scolopsis torquata, Nemipterus balinensoides, Nemipterus balinensis, Nemipterus mesoprion and Nemipterus randalli，並沒有在種間形成單系群。 此外，透過種類界定軟體的協助，本研究定義約30個演化系群(Evolutionarily Significant Units), 它們可能是新種或是隱蔽種。 最後，本研究指出資料庫(GenBank/BOLD)中有些序列之種類可能有誤鑑的情形。The family Nemipteridae (threadfin breams and relatives) contains five genera including Nemipterus, Pentapodus, Scolopsis, Parascolopsis and Scaevius with 69 currently recognized species that are all confined to the tropical and subtropical Indo-West Pacific. The congeneric species of the family are similar to each other in morphology, especially in the genus Nemipterus. While the precise identification with these species relies notably on coloration of fresh specimens, the results of identification based on the preserved specimens may be problematic. Recently developed molecule-based approaches exploiting DNA sequence variation among species are useful to improve the accuracy of species identification in such the circumstance and to study the evolutionary relationships of taxa. By taking this approach, in this study, multiple-gene analyses for the Nemipteridae were conducted to (1) reconstruct a comprehensive phylogeny of the Nemipteridae; (2) examine the validity of species and explore the cryptic diversity of the family; (3) to test the previous phylogenetic hypotheses, especially those ones infering to intra-generic relationships based on morphology. Two datasets were herein built, for the above objectives: the combined dataset with two nuclear genes (RAG1 and RH) and one mitochondrial gene (COI) that was used for the analyses to infer the higher-level phylogeny; and the dataset with only COI gene sequences (329 newly obtained and 328 from Genebank/BOLD databases) that was primarily used to test species validity by using the species delimitation programs, ABGD and GMYC. The results show that all the genera were monophyletic. The genus Scaevius is the sister-group of Pentapodus and they are sister to Nemipterus. The former three genera together appear to be the sister-group of the clade comprising Parascolopsis and Scolopsis. The validity of most of the examined species is confirmed except some cases. Parascolopsis inermis, Scolopsis affinis, Scolopsis vosmeri and Scolopsis torquata, Nemipterus balinensoides, Nemipterus balinensis, Nemipterus mesoprion and Nemipterus randalli, are non-monophyletic. In addition, several species are found to contain cryptic Evolutionarily Significant Units (or delaminated species); some cannot be unambiguously assigned to any known nemipterid species based on morphology should be considered as new species for further description. Finally, problematic sequences deposited in public databases (Genbank and BOLD) (probably due to misidentification) are also revised in this study