飛魚科(Exocoetidae)分佈在熱帶及溫暖的水域，在西北太平的飛魚有四亞科六屬35種。然而，擁有四屬及最多物種的唇鬚飛魚亞科(Cypselurinae)的親緣關係中仍有不同的推論。並且在西北太平洋針對飛魚的族群遺傳研究仍相當缺乏。本論文的目的，第一是用形態及兩段粒線體DNA序列建構西北太平洋飛魚的親緣關係；第二是使用全部粒線體序列來建構唇鬚飛魚亞科的親緣關係；第三是利用一段粒線體DNA序列研究西北太平洋尖頭細身飛魚(Hirundichthys oxycephalus)的族群遺傳結構。目前為止，研究共蒐集到六屬32種的飛魚。使用22個形態特徵建構的親緣關係樹顯示飛魚科及三個亞科都是單系群。在唇鬚飛魚亞科中，細身飛魚屬(Hirundichthys)是位於最基部的支系，而另外唇鬚飛魚屬(Cheilopogon)、斑鰭飛魚屬(Cypselurus) 及原飛魚屬(Prognichthys)則呈現多分岔的支系，並不能解決三屬的關係。分子部份共定序了67個樣本使用了1637 bp包含COI (615 bp)及Cytb (1022 bp)序列。分子親緣關係支持飛魚科及三個亞科也都是單系群。而細身飛魚屬與唇鬚飛魚屬、斑鰭飛魚屬及原飛魚屬可區分開來。唇鬚飛魚屬是旁系群且切分成三個支系。原飛魚屬及斑鰭飛魚屬則形成姊妹群並靠近唇鬚飛魚屬的第三支系。根據分子的結果，唇鬚飛魚屬的三個支系對應到五個亞屬，而新的分類可能需要被提出。本論文使用次世代定序成功完整地定序出白鰭飛魚(Cheilopogon unicolor)、弓頭飛魚(Ch. arcticeps)及紅斑鰭飛魚(Ch. atrisignis)的全部粒線體序列。而透過Primer walkimg方法部份定序出阿戈飛魚(Ch. agoo)、黑鰭飛魚(Ch. cyanopterus)、短鰭原飛魚(Pr. brevipinnis)及尖頭細身飛魚(Hi. oxycephalus)的粒線體序列。唇鬚飛魚亞科的親緣關係指出細身飛魚屬較唇鬚飛魚屬、斑鰭飛魚屬及原飛魚屬原始，而斑鰭飛魚屬及原飛魚屬成為一姊妹群。而結果也指出唇鬚飛魚屬是旁系群且切分成三個支系。將來的研究需要在唇鬚飛魚屬的不同亞屬分類上再繼續探討。在尖頭細身飛魚的族群遺傳結構中，共定序了156個樣本，長度為615 bp的COI 序列。結果指出不同地點的遺傳分化程度很低，並且有很高的基因交流。親緣關係樹顯示在西北太平洋的尖頭細身飛魚是分成兩群，但是在地理上並沒有明顯區隔開來，加上高度的基因交流，這兩群被認為是一個族群來探討。因此，對於尖頭細身飛魚的漁業資源管理，需要在其族群的邊界上邀請不同國家共同參與使其能永續發展。

The flyingfish family Exocoetidae is widespread in tropical and temperate waters with about 35 species in six genera, four subfamilies in the northwestern Pacific. The phylogeny of the subfamily Cypselurinae including four genera and most species had controvsersy. In addition, research on population genetics of flyingfish in the northwestern Pacific is rare. The aims of this study were 1. to reconstruct phylogeny of flyingfishes from the northwestern Pacific Ocean based on morphology and two mitochondrial sequences; 2. to reconstruct the phylogeny of Cypselurinae using complete mitochondrial genome; 3. to investigate the population genetic structure of Hirundichthys oxycephalus in the northwestern Pacific Ocean. Six genera and 32 species were included in this study. Morphological phyologeny used 22 characters showed that the family Exocoetidae and three subfamilies were found to be monophyly. In Cypselurinae clade, Hirundichthys was at the basal place, but Cheilopogon + Cypselurus + Prognichthys formed a trichotomy which could not resolve the relationship of these genera. A total of 1637 bp of the partial COI gene (615 bp) and Cytb gene (1022 bp) was sequenced from 66 samples. Molecular phyologeny showed that the family Exocoetidae and three subfamilies were found to be monophyletic. Genus Hirundichthys was separated from Prognichthys + Cheilopogon + Cypselurus. Genus Cheilopogon was paraphyletic and divided into three clades. Genera Cypselurus + Prognichthys formed a sister group which was close to Cheilopogon clade III. According to molecular phylogeny, three clades of Cheilopogon corresponded with the five subgenera and new classification might need to be proposed. The complete mitogenomes of Cheilopogon unicolor, Ch. arcticeps and Ch. atrisignis were successfully determined by next-generation sequencing method. Partial mitogenomes of Ch. agoo, Ch. cyanopterus, Pr. brevipinnis and Hi.oxycephalus were determined by primer walking method. Phylogeny of Cypselurinae indicated that the Hirundichthys was ancestral genus than Cheilopogon + Cypselurus + Prognichthys, and Cypselurus + Prognichthys formed a sister group. Our results indicated that Cheilopogon was paraphyletic and can be divided into three clades. Future work should be designed to explore and classify the relationships of the subgenera within Cheilopogon. For the population genetic structure of H. oxycephalus, 156 specimens were collected and 616 bp of mtDNA COI gene were sequenced. Results indicated that the genetic differentiations among different localities were small and a high gene flow in the region with undergoing population expansion. Although phylogenetic trees showed two groups of H. oxycephalus in the northwestern Pacific Ocean, the separation was not geologically evident. However, due to high gene flow, an association of either group to a spatial distribution was not observed, and so the two groups may be considered as one population. Therefore, effective fishery management of H. oxycephalus requires joint efforts from countries within its population boundary in order to maintain sustainable exploitation.

Acknowledgment…i
Abstract……ii
List of Figures………vii
List of Tables……ix
Chapter 1: Introduction 1
Appendix .……17
Chapter 2: Systematics of Flyingfishes (Teleostei Exocoetidae) in the Northwestern Pacific Ocean
Introduction………21
Materials and methods………………23
Results……………25
Discussion…………27
Conclusion…………30
Chapter 3: Phylogeny of the Cypselurinae based on mitochondrial DNA sequences
Introduction……………43
Materials and methods…………………45
Results……………48
Discussion…………50
Chapter 4: Population structure of Hirundichthys oxycephalus in the northwestern Pacific inferred from mitochondrial cytochrome oxidase I genes
Introduction………………63
Materials and methods………………………65
Results…………………68
Discussion………………69
Conclusion………………74
Chapter 5: Conclusion……………86
References ……………………………88

Abdul-Muneer, P.M. 2014. Application of microsatellite markers in conservation
genetics and fisheries management: recent advances in population structure
analysis and conservation strategies. Genetics Research International 2014:11.
Asgharian, H., H.H. Sahafi, A.A. Ardalan, S. Shekarriz and E. Elahi. 2011. Cytochrome coxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species. Molecular Ecology Resources 11: 461–472.
Avise, J.C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge, Massachusetts, USA.
Bentzen, P. 1998. Seeking evidence of local stock structure using molecular genetic methods. In: Herbing, I.H., I. Kornfield, M. Tupper and J. Wilson (eds) The implications of localized fisheries stocks. Regional Agricultural Engineering Service, New York, pp 20–30.
Bermingham, E. and S.S. McCafferty and P.P. Martin. 1997. Fish biogeography and molecular clocks: perspectives from the Panamian Isthmus. In: Stepien, C.A. and T.D. Kocher (eds). Molecular Systematics of Fishes, San Diego, pp 113–228.
Bohonak, A.J. 1999. Dispersal, gene flow, and population structure. Quarterly Review of Biology 74:21–45.
Breder, C.M. 1938. A Contribution to the Life Histories of Atlantic Ocean Flyingfishes. Bingham Oceanographic Foundation, New Haven. 126 pp.
Bruun, A.F. 1935a. Flying-fishes (Exocoetidae) of the Atlantic: systematic and biological studies. Dana Reports 2:1-106.
Bruun, A.F. 1935b. Parexocoetus, a red sea flying fish in the Mediterranean. Nature 136:553.
Campana, S. E., H. A. Oxenford and J.N. Smith. 1993. Radiochemical determination of longevity in flyingfish Hirundichthys affinis using Th-228/Ra-228. Marine Ecology-Progress Series 100:211-211.
Chang, C.W., C.H. Lin, Y.S. Chen, M.H. Chen and S.K. Chang. 2012. Age validation, growth estimation and cohort dynamics of the bony flying fish Hirundichthys oxycephalus off eastern Taiwan. Aquatic Biology 15:251-260.
Chang, S.K., C.W. Chang and E. Ame. 2012. Species composition and distribution of the dominant flyingfishes (Exocoetidae) associated with the Kuroshio Current, South China Sea. Raffles Bulletin of Zoology 60:539-550.
Chen, C.H. 1978. Taxonomical studies on the flying fishes (Oxyporhamphidae and Exocoetidae) from the waters around Taiwan. Bulletin of Taiwan Fisheries Research Institute 30:291-300.
Chen, C.H. 1987. Studies of the early life history of flying fishes (Family Exocoetidae) in the northwestern Pacific. Taiwan Museum Special Publication Series 7:1-203 (in Chinese).
Chiang, H.C., C.C. Hsu, G.C.C. Wu, S.K. Chang and H.Y. Yang. 2008. Population structure of bigeye tuna (Thunnus obesus) in the Indian Ocean inferred from mitochondrial DNA. Fisheries Research 90:305–312.
Chiou, W.D. and L.K. Lee. 2004. Migration of kawakawa Euthynnus affinis in the waters near Taiwan. Fisheries Science 70:746–757.
Chou, C.E., T.Y. Liao, H.W. Chang and S.K. Chang. 2015. Population structure of Hirundichthys oxycephalus in the northwestern Pacific inferred from mitochondrial cytochrome oxidase I gene. Zoological Studies 54:19.
Chu, T.J., D. Wang, H.L. Huang, F.J. Lin and T.D. Tzeng. 2012. Population structure and historical demography of the whiskered velvet shrimp (Metapenaeopsis barbata) off China and Taiwan inferred from the mitochondrial control region. Zoological Studies 51:99–107.
Collette, B., G. McGowen, N. Parin and S. Mito. 1984. Beloniformes: development and relationships. In: Moser, H.G., W.J. Richards, D.M. Cohen, M.P. Fahay, A.W. Kendall, and S.L. Richardson, (eds). Ontogeny and Systematics of Fishes. Special Publication No. 1. American Society of Ichthyologists and Herpetologists, Pp. 335-354.
Cumberbatch, J.A. and C.J. Hinds. 2013. Barbadian bio-cultural heritage: an analysis of the flyingfish. International Journal of Intangible Heritage 8:118–134.
Dalzell, P. 1993. The fisheries biology of flying fishes (Families: Exocoetidae and Hemiramphidae) from the Camotes Sea, Central Philippines. Journal of Fish Biology 43:19-32.
Dammannagoda, S.T., D.A. Hurwood and P.B. Mather. 2008. Evidence for fine geographical scale heterogeneity in gene frequencies in yellowfin tuna (Thunnus albacares) from the north Indian Ocean around Sri Lanka. Fisheries Research 90:147–157.
Dasilao, J.C., K. Sasaki and O. Okamura. 1997. The hemiramphid, Oxyporhamphus, is a flyingfish (Exocoetidae). Ichthyological Research 44:101-107.
Dasilao, J.C. and K. Sasaki. 1998. Phylogeny of the flyingfish family Exocoetidae (Teleostei, Beloniformes). Ichthyological Research 45:347-353.
Davenport, J. 1994. How and why do flying fish fly? Reviews in Fish Biology and Fisheries 4:184-214.
De Croos, M. 2009. Status of the fishery of flying fish off northwestern coast of Sri Lanka and the effect of lunar pattern on catchability. Sri Lanka Journal of Aquatic Sciences 14:1-13.
Díaz-Jaimes, P., M. Uribe-Alcocer, S. Ortega-García and J.D. Durand 2006. Spatial and temporal mitochondrial DNA genetic homogeneity of dolphinfish populations (Coryphaena hippurus) in the eastern central Pacific. Fisheries Research 80:333–338.
Dirhansyah. 2009. The Urgent need of development of fisheries management plan of flyingfish in Macassar Strait and Flores Sea. Oseanologi dan Limnologi di Indonesia 35:291-310.
Drummond, A.J. and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214.
Ekblom, R. and J. Galindo. 2011. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1-15.
Excoffier, L. and H.E.L. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10:564–567.
Excoffier, L., P.E. Smouse and J.M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491.
FAO. 2010. Report of the Third Meeting of the WECAFC Ad Hoc Flyingfish Working Group of the Eastern Caribbean. Mount Irvine, Tobago, 21-25 July 2008. FAO Fisheries and Aquaculture Report No. 929, Rome. 88 pp.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
Fisheries Agency. 2010. Fisheries statistical yearbook - Taiwan, Kinmen and Matsu Area, 2009. Fisheries Agency, Council of Agriculture, Taipei.
Froese, R. and D. Pauly. 2016. FishBase: World Wide Web electronic publication. Available via http://www.fishbase.org.
Fu, Y.X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–925.
Funk, D.J. and K.E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics 34: 397–423.
Garcia, S. M. 1994. World review of Highly Migratory Species and Straddling Stocks.
United Nations Food and Agriculture Organization. FAO Fisheries Technical
Paper 337, Rome. 70 pp.
Garcia, S.M. 2005. Fisheries and aquaculture topics. Defining fishery stocks. Topics Fact Sheets. FAO Fisheries and Aquaculture Department [online].
http://www.fao.org/fishery/topic/14787/en. Accessed 23 April 2014
Gillett, R. and J. Ianelli. 1991. Aspects of the Biology and Fisheries of Flyingfish in the Pacific Islands. FAO/UNDP Regional Fishery Suppot Programme, Document 91/7. Rome: FAO, 35 pp.
Goloboff, P.A., J.S. Farris and K.C. Nixon. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24:774–786.
Gomes, C., R. B. Dales and H. A. Oxenford. 1998. The application of RAPD markers in stock discrimination of the four‐wing flyingfish, Hirundichthys affinis in the central western Atlantic. Molecular Ecology 7:1029-1039.
Gomes, C., H. Oxenford and R. Dales. 1999. Mitochondrial DNA D-loop variation and implications for stock structure of the four-wing flyingfish, Hirundichthys affinis, in the central western Atlantic. Bulletin of Marine Science 64:485-500.
Gomes, C., H.A. Oxenford and R.B.G. Dales. 2000. Restriction site mapping of the mitochondrial DNA of the four-wing flyingfish, Hirundichthys affinis. DNA Sequence 11:277–280.
Grant, W. and B. Bowen. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89:415–426.
Graves, J.E. and J.R. McDowell. 1995. Inter-ocean genetic divergence of istiophorid billfishes. Marine Biology 122:193–203.
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
Halliburton, R. 2004. Introduction to population genetics. Pearson Education, Upper Saddle River, NJ.
Han, Z.Q., T.X. Gao, T. Yanagimoto and Y. Sakurai. 2008a. Deep phylogeographic break among white croaker Pennahia argentata (Sciaenidae, Perciformes) populations in North-western Pacific. Fisheries Science 74:770–780.
Han, Z.Q., T.X. Gao, T. Yanagimoto and Y. Sakurai. 2008b. Genetic population structure of Nibea albiflora in Yellow Sea and East China Sea. Fisheries Science 74:544–552.
Han, Y.S., C.L. Hung, Y.F. Liao and W.N. Tzeng. 2010. Population genetic structure of the Japanese eel Anguilla japonica: panmixia at spatial and temporal scales. Marine Ecology Progress Series 401:221–232.
Harpending, H.C. 1994. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology 66:591–600.
Hebert, P. D. N., A. Cywinska, S. L. Ball and J. R. de Waard. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences 270: 313–322.
Hohenlohe, P.A. 2004. Limits to gene flow in marine animals with planktonic larvae: models of Littorina species around Point Conception, California. Biological Journal of the Linnean Society 82:169–187.
Huang, M.H. and C.H. Ou. 2012. A discussion of management disputes arising from the multiple utilization of flying fish resources in Taiwan and suggested countermeasures. Marine Policy 36:512-519.
Hubbs, C.L. and E.M. Kampa. 1946. Hubbs the the early stages (egg, prolarva and juvenile) and the classification of the California flyingfish. Copeia 4:188-218.
Ichimaru, T. 2005. The life cycle of three species of flying fish in the north western waters of Kyushu and the recruitment of young flying fish to the fishing ground. Bulletin of Nagasaki Prefectural Institute of Fisheries 33:7-110.
Iida, M., K. Zenimoto, S. Watanabe, S. Kimura and K. Tsukamoto. 2010. Larval transport of the amphidromous goby Sicyopterus japonicus by the Kuroshio Current. Coastal marine science 34:42–46.
Iwasaki, W., T. Fukunaga, R. Isagozawa, K. Yamada, Y. Maeda, T. P. Satoh, T. Sado, K. Mabuchi, H. Takeshima and M. Miya. 2013. MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular Biology and Evolution 30:2531-2540.
Ju, Y.M., C.H. Hsu, L.S. Fang, H.D. Lin, J.H. Wu, C.C. Han, I.S. Chen and T.Y. Chiang. 2013. Population structure and demographic history of Sicyopterus japonicus (Perciformes; Gobiidae) in Taiwan inferred from mitochondrial control region sequences. Genetics and Molecular Research 12:4046–4059.
Kenchington, E., M. Heino and E.E. Nielsen. 2003. Managing marine genetic diversity: time for action? ICES Journal of Marine Science 60:1172–1176.
Khokiattiwong, S., R. Mahon and W. Hunte. 2000. Seasonal abundance and reproduction of the fourwing flyingfish, Hirundichthys affinis, off Barbados. Environmental Biology of Fishes 59:43-60.
Kokita, T. and K. Nohara. 2011. Phylogeography and historical demography of the anadromous fish Leucopsarion petersii in relation to geological history and oceanography around the Japanese Archipelago. Molecular Ecology 20:143–164.
Kuo, T.H. 2013. Population Genetic Structure of Cypselurus poecilopterus in the Waters off Taiwan Based on Cytochrome b Sequences. Master’s thesis, National Sun Yat-Sen University, Kaohsiung.
Kutschera, U. 2005. Predator-driven macroevolution in flyingfishes inferred from behavioural studies: historical controversies and a hypothesis. Annals of the History and Philosophy of Biology 10:59–77.
Lavoué, S., M. Miya, J. G. Inoue, K. Saitoh, N. B. Ishiguro and M. Nishida. 2005. Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala. Molecular Phylogenetics and Evolution 37:165-177.
Lewallen, E. A., R. L. Pitman, S. L. Kjartanson and N.R. Lovejoy. 2011. Molecular systematics of flyingfishes (Teleostei: Exocoetidae): evolution in the epipelagic zone. Biological Journal of the Linnean Society 102:161-174.
Lin, T.W. 2011. Phylogenetic relationship of Hirundichthys oxycephalus of Northwestern Pacific inferred from mitochondrial cytochrome oxidase I gene. Master’s thesis, National Sun Yat-Sen University, Kaohsiung.
Liu, J.X., T.X. Gao, Z.M. Zhuang, X.S. Jin, K. Yokogawa and Y.P. Zhang. 2006. Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis). Molecular Phylogenetic Evolution 40:712–723.
Liu, J.X., T.X. Gao, S.F. Wu and Y.P. Zhang. 2007. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular Ecology 16:275–288.
Liu, J.Y., C.L. Brown and T.B. Yang. 2009. Population genetic structure and historical demography of grey mullet, Mugil cephalus, along the coast of China, inferred by analysis of the mitochondrial control region. Biochemical Systematics and Ecology 37:556–566.
Lourie, S.A. and A.C.J. Vincent. 2004. A marine fish follows Wallace’s Line: the
phylogeography of the three-spot seahorse (Hippocampus trimaculatus,
Syngnathidae, Teleostei) in Southeast Asia. Journal of Biogeography
31:1975–1985.
Lovejoy, N.R. 2000. Reinterpreting recapitulation: systematics of needlefishes and their allies (Teleostei: Beloniformes). Evolution 54:1349-1362.
Lovejoy, N.R., M. Iranpour and B.B. Collette. 2004. Phylogeny and jaw ontogeny of beloniform fishes. Integrative and Comparative Biology 44:366-377.
Lowe, R.T. 1840. On new species of fishes from Madeira. Proceedings of the Zoological Society of London 8:36-39.
Masuda, H., K. Amaoka, C. Araga, T. Uyeno and T. Yoshino. 1984. The fishes of the Japanese archipelago. Tokai University Press, Tokyo.
McCormack, J.E., S.M. Hird, A.J. Zellmer, B.C. Carstens and R.T. Brumfield. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution 66:526-538.
Minegishi, Y., J. Aoyama, J.G. Inoue, M. Miya, M. Nishida and K. Tsukamoto. 2005. Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Molecular Phylogenetics and Evolution 34:134-146.
Miya, M. and M. Nishida. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Marine Biotechnology 1:416-426.
Miya, M., A. Kawaguchi and M. Nishida. 2001. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Molecular Biology and Evolution 18:1993-2009.
Miya, M., H. Takeshima, H. Endo, N.B. Ishiguro, J.G. Inoue, T. Mukai, T. P. Satoh, M. Yamaguchi, A. Kawaguchi and K. Mabuchi. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 26:121-138.
Miya, M., T.P. Satoh and M. Nishida. 2005. The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray‐finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences. Biological Journal of the Linnean Society 85:289-306.
Nagase, M., T. Aimi, K. Suginaka, Y. Kitamoto and T. Morinaga. 2005. Complete mitochondrial DNA sequence of the Japanese flying fish Cypselurus hiraii. Fisheries Science 71:914-923.
Nakabo, T. 2002. Fishes of Japan: with Pictorial Keys to the Species. Tokai University Press, Tokyo. 1749 pp.
Nelson, J.S. 2006. Fishes of the World, Forth edition. Wiley and Sons, New York, USA. 601 pp.
Nesbø, C.L., E.K. Rueness, S.A. Iversen, D.W. Skagen and K.S. Jakobsen. 2000. Phylogeography and population history of Atlantic mackerel (Scomber scombrus L.): a genealogical approach reveals genetic structuring among the eastern Atlantic stocks. Proceedings of the Royal Society of London B: Biological Sciences 267:281-292.
Nichols, J.T. and C.M. Breder. 1928. An annotated list of the Synentognathi with remarks on their development and relationship. Zoologica (New York) 8:423-448.
Nylander, J. 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
Oxenford, H. 1994. Movements of flyingfish (Hirundichthys affinis) in the eastern Caribbean. Bulletin of Marine Science 54:49-62.
Oxenford, H., R. Mahon and W. Hunte. 1995a. Distribution and relative abundance of flyingfish (Exocoetidae) in the eastern Caribbean. I. Adults. Marine Ecology Progress Series 117:11-23.
Oxenford, H., R. Mahon and W. Hunte. 1995b. Distribution and relative abundance of flying fish (Exocoetidae) in the eastern Caribbean. III. Juveniles. Marine Ecology Progress Series 117:39-47.
Oxenford, H.A. and W. Hunte. 1999. Feeding habits of the dolphinfish (Coryphaena hippurus) in the eastern Caribbean. Scientia Marina 63:303–315.
Oxenford, H.A., R. Mahon and W. Hunte. 2007. Biology and Management of Eastern Caribbean Flyingfish. UWI, Centre for Resource Management and Environmental Studies, Barbados.
Pajot, G. 1991. Capture of flying fish: Findings of BOBP trials and studies. Bay of Bengal News 41:1-19.
Palumbi, S.R. 1994. Genetic divergence, reproductive isolation, and marine speciation. Annual Review of Ecology and Systematics 25:547–572.
Palumbi, S.R. 2003. Population genetics, demographic connectivity, and the design of marine reserves. Ecological Applications 13:146–158.
Parin, N.V. 1960. The flying fishes (Exocoetidae) of the Northwest Pacific. Trudy Instituta Okeanologi 31:205-285.
Parin, N. V. 1961. Principles of classification of flyingfishes (Oxyporhamphidae and Exocoetidae). Trudy Instituta Fiziologii, Akademiia Nauk Gruzinskoi SSR 43: 92–183. [In Russian, Systematics Lab. Translation No. 67].
Parin, N. 1970. Ichthyofauna of the Epipelagic Zone. Akademiya Nauk SSSR, Moscow. Translated by Israel Program for Scientific Translations:1-206.
Parin, N.V. 1999. Exocoetidae. Flyingfishes. Carpenter, K.E. and V.H. Niem. (eds.), The Living Marine Resources of the Western Central Pacific. FAO, Rome. Pp. 2162-2179.
Píndaro, D.J., U.A. Manuel, O.G. Sofía and J.D. Durand. 2006. Spatial and temporal mitochondrial DNA genetic homogeneity of dolphinfish populations (Coryphaena hippurus) in the eastern central Pacific. Fisheries Research 80:333-338.
Planes, S., P.J. Doherty and G. Bernardi. 2001. Strong genetic divergence among populations of a marine fish with limited dispersal, Acanthochromis polyacanthus, within the Great Barrier Reef and the Coral Sea. Evolution 55:2263–2273.
Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25:1253-1256.
Potts, A.C., A.D. Thomas and E. Nichols. 2003. An Economic and Social Assessment of the Flying Fish (Pelagic) Fishery of Tobago, Trinidad and Tobago. Proceedings of the Fifty Fourth Annual Gulf and Caribbean Fisheries Institute, Pp 635-649.
Purcell, J.F.H., R.K. Cowen, C.R. Hughes and D.A. Williams. 2006. Weak genetic structure indicates strong dispersal limits: a tale of two coral reef fish. Proceedings of the Royal Society B Biological Sciences 273:1483–1490.
Purcell, J.F.H., R.K. Cowen, C.R. Hughes and D.A. Williams. 2009. Population structure in a common Caribbean coral-reef fish: implications for larval dispersal and early life-history traits. Journal of Fish Biology 74:403–417.
Rambaut, A. and A. Drummond. 2003. Tracer: a program for analysing results from Bayesian MCMC programs such as BEAST & MrBayes. Available at
http://tree.bio.ed.ac.uk/software/tracer.
Ravago-Gotanco, R.G. and M.A. Juinio-Meñez. 2010. Phylogeography of the mottled spinefoot Siganus fuscescens: Pleistocene divergence and limited genetic connectivity across the Philippine archipelago. Molecular Ecology 19:4520–4534.
Reiss, H., G. Hoarau, M. Dickey-Collas and W.J. Wolff. 2009. Genetic population structure of marine fish: mismatch between biological and fisheries
management units. Fish and Fisheries 10:361–395.
Rennie, J. 2002. Review of the social and economic status of the flyingfish fishery in Grenada. In: FAO/WECAFC (ed) Report on the second meeting of the
WECAFC Ad Hoc Flyingfish Working Group of the Eastern Caribbean.
Bridgetown, Barbados, 8–12 January 2001. FAO Fisheries Report No. 670, 156
pp., FAO, Rome, pp 103–157.
Resosudarmo, B.P. 1995. The construction of a bioeconomic model of the
Indonesian flying fish fishery. Marine Resource Economics 10:257-372.
Riginos, C. and M.W. Nachman. 2001. Population subdivision in marine
environments: the contributions of biogeography, geographical distance and
discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus
nigricaudus. Molecular Ecology 10:1439–1453.
Ronquist, F., M. Teslenko, P. van der Mark, D.L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M.A. Suchard and J.P. Huelsenbeck. 2012. MrBayes 3.2:
efficient Bayesian phylogenetic inference and model choice across a large
model space. Systematic Biology 61:539-542.
Saitoh, K., M. Miya, J.G. Inoue, N.B. Ishiguro and M. Nishida. 2003. Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and
biogeography. Journal of Molecular Evolution 56:464-472.
Saitoh, K., T. Sado, R. Mayden, N. Hanzawa, K. Nakamura, M. Nishida and M. Miya. 2006. Mitogenomic evolution and interrelationships of the Cypriniformes
(Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-
level relationships of the world’s largest freshwater fish clade based on 59
whole mitogenome sequences. Journal of Molecular Evolution 63:826-841.
Scheffler, I.E. 1999. Mitochondria. John Wiley & Sons, New York .
Setiamarga, D.H., M. Miya, Y. Yamanoue, K. Mabuchi, T.P. Satoh, J.G. Inoue and M. Nishida. 2008. Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): the first evidence based on whole mitogenome sequences. Molecular Phylogenetics and Evolution 49:598-605.
Shao, K. 2012. Taiwan fish database. World Wide Web electronic publication. version 2014/05. Available at http://fishdb.sinica.edu.tw.
Shen, K.N., B.W. Jamandre, C.C. Hsu, W.N. Tzeng and J.D. Durand. 2011. Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globallydistributed flathead mullet Mugil cephalus. BMC Evolutionary Biology 11:83–83.
Shulman, M.J. 1998. What can population genetics tell us about dispersal and biogeographic history of coral-reef fishes? Australian Journal of Ecology 23:216–225.
Staiger, J.C. 1965. Atlantic flyingfishes of the genus Cypselurus, with descriptions of the juveniles. Bulletin of Marine Science 15:672-725.
Stott, L., C. Poulsen, S. Lund and R. Thunell. 2002. Super ENSO and global climate oscillations at millennial time scales. Science 297:222–226.
Swainson, W. 1839. The Natural History of Fishes, Amphibians and Reptiles or Monocardian Animals, vol. II. Longman, London. 368 pp.
Swofford, D.L. 2002. PAUP＊: Phylogenetic Analysis Using Parsimony (＊and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. 140 pp.
Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595.
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28:2731-2739.
Van Noord, J., E. Lewallen and R. Pitman. 2013. Flyingfish feeding ecology in the eastern Pacific: prey partitioning within a speciose epipelagic community. Journal of Fish Biology 83:326-342.
Waples, R.S. and O. Gaggiotti. 2006. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15:1419–1439.
Ward, R.D. 2000. Genetics in fisheries management. Hydrobiologia 420:191–201.
Ward, R. D., T.S. Zemlak, B.H. Innes, P.R. Last and P.D.N. Hebert. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360:1847-1857.
Worm, B., E.B. Barbier, N. Beaumont, J.E. Duffy, C. Folke, B.S. Halpern, J.B.C. Jackson, H.K. Lotze, F. Micheli, S.R. Palumbi, E. Sala, K.A. Selkoe, J.J. Stachowicz and R. Watson. 2006. Impacts of biodiversity loss on ocean
ecosystem services. Science 314:787–790.
Wu, G.C.C., H.C. Chiang, K.S. Chen, C.C. Hsu and H.Y. Yang. 2009. Population structure of albacore (Thunnus alalunga) in the Northwestern Pacific Ocean inferred from mitochondrial DNA. Fisheries Research 95:125-131.
Wu, G.C.C, H.C. Chiang, Y.W. Chou, Z.R. Wong, C.C. Hsu, C.Y. Chen and H.Y. Yang. 2010. Phylogeography of yellowfin tuna (Thunnus albacares) in the
Western Pacific and the Western Indian Oceans inferred from mitochondrial
DNA. Fisheries Research 105:248–253.
Wu, C.C., J.C. Lin and W.C. Su. 2006. Diet and feeding habits of dolphin fish
(Coryphaena hippurus) in the waters off eastern Taiwan. Journal of Taiwan
Fisheries Research 14:13–27.
Xu, J., T. Chan, L.M. Tsang and K.H. Chu. 2009. Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia: Pleistocene isolation, population
expansion and secondary contact. Molecular Phylogenetic Evolution
52:45– 56.
Xu, G.H., L.J. Zhao, K.Q. Gao and F.X. Wu. 2013. A new stem-neopterygian fish from the Middle Triassic of China shows the earliest over-water gliding
strategy of the vertebrates. Proceedings of the Royal Society B Biological
Sciences 280:20122261.
Yacapin, N. 1991. Growth, mortality and recruitment of short-wing flying fish
Oxyporhampus micropterus in Bohol Sea, Philippines. Fishbyte 9:10-12.
Yu, H.T., Y.J. Lee, S.W. Huang and T.S. Chiu. 2002. Genetic analysis of the
populations of Japanese anchovy (Engraulidae, Engraulis japonicus) using
microsatellite DNA. Marine Biotechnology 4:471–479.
Yuan, Y.C. 2014. Migratory patterns and trophic niche of flying fish Hirundichthys oxycephalus inferred by stable isotope composition. Master’s thesis, National Taiwan University, Taipei.
Zhang, J.B. and R. Hanner. 2011. DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochemical Systematics and Ecology 39: 31–42.