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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 蕭仁傑(Jen-Chieh Shiao) | |
| dc.contributor.author | Chih-Ting Yeh | en |
| dc.contributor.author | 葉治廷 | zh_TW |
| dc.date.accessioned | 2021-06-16T04:13:33Z | - |
| dc.date.available | 2021-02-20 | |
| dc.date.copyright | 2021-02-20 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-02-09 | |
| dc.identifier.citation | Arai T, Tsukamoto K (1998). Application of otolith Sr:Ca ratios to estimate the migratory history of masu salmon, Oncorhynchus masou. Ichthyological Research 45, 309–313. Avise JC, Arnold J, Ball RM, Bermingham E, et al. (1987). Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology, Evolution, and Systematics 18, 489–522. Bandelt HJ, Forster P, Skyes BC, et al. (1995) Mitochondrial portraits of human populations using median networks. Genetics, vol. 141, no. 2, 743–753. Beerli P (2009). How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use. Population genetics for animal conservation, 17, 42–79. Benoît HP, Pepin P (1999). Interaction of rearing temperature and maternal influence on egg development rates and larval size at hatch in yellowtail flounder (Pleuronectes ferrugineus). Canadian Journal of Fisheries and Aquatic Sciences, 56(5), 785–794. Bermingham E, McCafferty SS, Martin AP, et al. (1997). Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. Molecular systematics of fishes (Kocher TD and Stepien CA, eds). San Diego: Academic Press, 113–128 Bowen BW, Bass AL, Muss A, et al. (2006). Phylogeography of two Atlantic squirrelfishes (Family Holocentridae): exploring links between pelagic larval duration and population connectivity. Marine Biology 149: 899–913. Brooks DR, McLennan DA (1991). Phylogeny, Ecology, and Behavior, A Research Program in Comparative Biology. University of Chicago Press, Chicago, Illinois, USA. Brown RJ, Severin KP (2009). Otolith chemistry analyses indicate that water Sr:Ca is the primary factor influencing otolith Sr:Ca for freshwater and diadromous fish but not for marine fish. Canadian Journal of Fisheries and Aquatic Sciences 66, 1790–808. Campana SE (1999). Chemistry and composition of fish otoliths: pathways, mechanisms and applications. Marine Ecology Progress Series 188, 263−297. Chang MY, Tzeng WN, Wang CH, et al. (2008). Differences in otolith elemental composition of the larval Rhinogobius giurinus (Perciformes, Gobiidae) among estuaries of Taiwan: implications for larval dispersal and connectance among metapopulation. Zoological Studies 47, 676-684. Chen IS, Fang LS (1999). The freshwater and estuaries fishes of Taiwan. National Museum of Marine Biology and Aquarium, Pingtung, 287 pp. [in Chinese] Chen IS, Kottelat M (2003). Three new freshwater gobies of the genus Rhinogobius (Teleostei : Gobiidae) from northeastern Laos. The Raffles Bulletin of Zoology 51, 87–95. Closs GP, Hicks AS, Jellyman PG (2013). Life histories of closely related amphidromous and non‐migratory fish species: A trade‐off between egg size and fecundity. Freshwater Biology 58(6), 1162–1177. Covich A (2006). Dispersal - Limited biodiversity of tropical insular streams. Polish Journal of Ecology 54(4), 523–547. Cowie RH, Holland BS (2006). Dispersal is fundamental to biogeography and the evolution of biodiversity on oceanic islands. Journal of Biogeography 33, 193–198. Crisci JV, Katinas L (2009). Darwin, historical biogeography, and the importance of overcoming binary opposites. Journal of Biogeography 36, 1027–1032. Drummond AJ, Rambaut A (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC evolutionary biology, 7(1), 1-8. Felsenstein J (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17, 368–376. Froese R, Pauly D (2008). Fishbase. World Wide Web electronic publication. www.fishbase.org, version 12/2008. Fu YX (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147, 915–925. Fu YX Li, WH (1993). Statistical tests of neutrality of mutations. Genetics 133, 693–709. Hartl DL, Clark AG (1997). Principles of population genetics (fourth edition). Sinauer Associates, Inc. Publishers. Sunderland, Massachusetts Haubold B (2013). Alignment-free phylogenetics and population genetics. Briefings in Bioinformatics 15, 407–418. He LJ, Mukai T, Chu KH, et al. (2015). Biogeographical role of the Kuroshio Current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data. Scientific Reports 5(1), 1–12. Hoareau T, Lecomte-Finiger R, Grondin HP, et al. (2007). Oceanic larval life of La Reunion ‘bichiques’, amphidromous gobiid post-larvae. Marine Ecology Progress Series 333, 303–308. Huang ZG, Zhang WQ, Zhong XJ, et al. (1995). Plate tectonics of Taiwan and its environmental evolution. Ocean publishing company, Beijing, China. [in Chinese] Hudson RR, Slatkin M, Maddison WP (1992). Estimation of levels of gene flow from DNA-sequence data. Genetics 132, 583–589. Hüssy K, Limburg KE, de Pontual H, et al. (2020). Trace element patterns in otoliths: the role of biomineralization. Reviews in Fisheries Science Aquaculture, 1–33. Jang-Liaw NH, Tominaga K, Zhang C, et al. (2019). Phylogeography of the Chinese false gudgeon, Abbottina rivularis, in East Asia, with special reference to the origin and artificial disturbance of Japanese populations. Ichthyological Research, 66(4), 460–478. Jones GP, Planes S, Thorrold SR (2005) Coral reef fish larvae settleclose to home. Current Biology 15, 1314–1318. Ju YM, Hsu CH, Fang LS, et al. (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. Kano Y, Iida M, Tetsuka K, et al. (2014). Effect of waterfalls on fluvial fish distribution and landlocked Rhinogobius brunneus populations on Yakushima Island, Japan. Ichthyological Research 61, 305–316. Katayama S (2018). A description of four types of otolith opaque zone. Fisheries Science 84, 735–745. Kawanabe H. Mizuno N (1989). Freshwater Fishes of Japan. Tokyo: Yama-to-Keikoku-sha. Keith P (2003). Biology and ecology of amphidromous Gobiidae of the Indo‐Pacific and the Caribbean regions. Journal of Fish Biology 63, 831–847. Kimura M (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press. King JL, Jukes TH (1969). Non-darwinian evolution. Science, 164(3881), 788-798. Kumar S, Stecher G, Li M, et al. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35, 1547–1549. Leigh JW, Bryant D (2015). POPART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6, 1110–1116. Leis JM (2002). Pacific coral-reef fishes: the implications of behaviour and ecology of larvae for biodiversity and conservation, and a reassessment of the open population paradigm. Environmental Biology of Fishes 65, 199–208. Liao TY, Huang WC, Iizuka Y, et al. (2020). Facultative amphidromy and pelagic larval duration plasticity of Rhinogobius formosanus (Teleostei, Gobioidei). ZooKeys 951, 91–107. Limburg KE, Walther BD, Lu Z, et al. (2015). In search of the dead zone: use of otoliths for tracking fish exposure to hypoxia. Journal of Marine Systems 141, 167–178. Ložys L, Shiao JC, Iizuka Y, et al. (2017). Habitat use and migratory behaviour of pikeperch Sander lucioperca in Lithuanian and Latvian waters as inferred from otolith Sr:Ca ratios. Estuarine, Coastal and Shelf Science 198, Part A, 43–52. McDowall RM (2007). On amphidromy, a distinct form of diadromy in aquatic organisms. Fish and Fisheries 8, 1–13 Morales-Nin (2000). Review of the growth regulation processes of otolith daily increment formation. Fisheries Research 46, 53–67. Ohara K, Hotta M, Takahashi D, et al. (2009). Use of microsatellite DNA and otolith Sr:Ca ratios to infer genetic relationships and migration history of four morphotypes of Rhinogobius sp. OR. Ichthyol Res 56, 373–379. Okasha S (2006). Evolution and the Levels of Selection. Oxford, UK: Oxford University Press. Pannella G (1971). Fish otoliths: daily growth layers and periodical patterns. Science 173: 1124–1127. Popper AN, Lu Z (2000). Structure–function relationships in fish otolith organs. Fisheries Research 46, 15–25. Radtke RL, Kinzie RA, Folsom RA (1988). Age at recruitment of Hawaiian freshwater gobies. Environmental Biology of Fishes 23, 3, 205–213. Rambaut A, Drummond AJ, Xie D, et al. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic biology, 67(5), 901. Robertson DR (2001). Population maintenance among tropical reef fishes: Inferences from small-island endemics. Proceedings of the National Academy of Sciences of the United States of America, 98(10), 5667–5670. Robertson DR, Grove JS, McCosker JE (2004). Tropical Transpacific Shore Fishes. Pacific Science 58, 4, 507–565. Rocha L, Bass AL, Robertson DR, et al. (2002). Adult habitat preferences, larval dispersal, and the comparative phylogeography of three Atlantic surgeonfishes (Teleostei: Acanthuridae). Molecular Ecology 11, 243–252. Rogers AR, Harpending H (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9, 552–569. Rojo JH, Fernández DA, Figueroa DE, et al. (2020). Phenotypic and genetic differentiation between diadromous and landlocked puyen Galaxias maculatus. Journal of Fish Biology 96, 956–967. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, et al. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34, 12, 3299–3302. Rudnick DL, Jan S, Centurioni L, et al. (2011). Seasonal and mesoscale variability of the Kuroshio near its origin. Oceanography 24(4), 52–63. Saitou N, Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, Volume 4, Issue 4, 406–425. Shen KN, Jamandre BW, Hsu CC, et al. (2011). Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus. BMC Evolutionary Biology 11, 83. Shen KN, Tzeng WN (2008). Reproductive strategy and recruitment dynamics of amphidromous goby Sicyopterus japonicus as revealed by otolith microstructure. Journal of Fish Biology 73, 2497–2512. Shiao JC, Chen CY, Zhang J, et al. (2016). Habitat use and migratory life history of salangid icefish (Salangidae) revealed by otolith Sr/Ca ratios. Zoological Studies 55, 1–3. Shiao JC, Tzeng CS, Li PC, et al. (2015). Upstream migration and marine early life history of amphidromous gobies inferred from otolith increments and microchemistry. Environmental Biology of Fishes 98, 933–950. Shih HT, Fang SH, Ng PKL (2007) Phylogeny of the freshwater crab genus Somanniathelphusa Bott (Decapoda: Parathelphusidae) from Taiwan and the coastal regions of China, with notes on their biogeography. Invertebrate Systematics 21, 29–37. Slarkin M (1985). Gene flow in natural populations. Annual Review of Ecology and Systematics, vol. 16, 393–430. Sorensen PW, Hobson KA (2005). Stable isotope analysis of amphidromous Hawaiian gobies suggests their larvae spend a substantial period of time in freshwater river plumes. Environmental Biology of Fishes 74, 31–42. Su B, Xiao J, Underhill P, et al. (1999). Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age. The American Journal of Human Genetics, 65(6), 1718–1724. Taillebois L, Castelin M, Ovenden JR, et al. (2013). Contrasting genetic structure among populations of two amphidromous fish species (Sicydiinae) in the Central West Pacific. PLOS ONE 8, 10, e75465. Tsunagawa T, Arai T (2008). Flexible migration of Japanese freshwater gobies Rhinogobius spp. as revealed by otolith Sr:Ca ratios. Journal of Fish Biology 73, 2421–2433. Tzeng CS (1986). Distribution of the freshwater fishes of Taiwan. Journal of the Taiwan Museum 39(2), 127–146. [in Chinese with English abstract] Tzeng WN, Shiao JC, Iizuka Y (2002). Use of otolith Sr:Ca ratios to study the riverine migratory behaviors of Japanese eel Anguilla japonica. Marine Ecology Progress Series 245: 213–221. Victor BC, Wellington GM (2000). Endemism and the pelagic larval duration of reef fishes in the eastern Pacific Ocean. Marine Ecology Progress Series 205, 241–248. Ward RD, Zemlak TS, Innes BH, et al. (2005). DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360, 1847–1857. Watanabe S, Iida M, Kimura Y, et al. (2006). Genetic diversity of Sicyopterus japonicus as revealed by mitochondrial DNA sequencing. Coastal Marine Science 30(2), 473–479. Watson RE (1992). A review of the gobiid fish genus Awaous from insular streams of the Pacific Plate. Ichthyological Exploration of Freshwaters 3, 161–176. Yamasaki YY, Nishida M, Suzuki T, et al. (2015). Phylogeny, hybridization, and life history evolution of Rhinogobius gobies in Japan, inferred from multiple nuclear gene sequences. Molecular Phylogenetics and Evolution 90, 20–33. Yang Y, Liu CT, Lee TN, et al. (2001). Sea surface slope as an estimator of the Kuroshio volume transport east of Taiwan. Geophysical Research Letters, 28(12), 2461–2464. Yuan LY, Zhou ZC, Zhou JJ, et al. (2012). Preliminary investigation of fish resources in the Tongshan River. Sichuan Journal of Zoology 31, 961–964. [in Chinese with English abstract] | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/55627 | - |
| dc.description.abstract | 台灣吻鰕虎 (Rhinogobius formosanus) 長期被認為是台灣北部的特有洄游性物種，然而在2012年，於中國福建發現亦有其族群的存在。近期，兩個台灣的族群被研究且發現位於台北翡翠水庫上游的族群為陸封型族群。不過，對於中國的族群仍研究不足並且對該物種的生物地理模式的了解仍然有限。本研究主要為了探討兩個目的。首先，透過耳石的鍶鈣比分析探討中國的台灣吻鰕虎族群是否也存在陸封型族群。再來，透過台灣以及中國共五個族群的遺傳結構分析來探討造成族群分離的機制。本研究中所採樣的樣本供來自五個地區，其中兩個來自中國、三個包括一個陸封型族群來自北台灣。本研究所使用的分子標記為粒腺體DNA，用於分析五個台灣吻鰕虎族群的族群遺傳，而耳石的鍶鈣比分析則用於重建鰕虎的生活史。耳石的分析實驗結果顯示中國福清鰕虎的鍶鈣比為持續不間斷低走向的現象，判斷其為陸封型族群。另一方面，中國福鼎鰕虎的鍶鈣比則顯示出由高往低的走向，因此判斷其為洄游型族群。至於分子分析的結果，由分子變異分析 (AMOVA) 的結果來看，中國以及台灣兩邊的族群顯示出顯著性的遺傳差異。另外，中性檢定的結果顯示出台灣的兩個洄游型族群發生近期族群擴張的現象，而中國的族群則無，並且此現象由貝氏天際線來推測可能發生於冰河期結束後。雖然台灣吻鰕虎能在浮游階段進入到海洋，但是牠可能傾向於不活動至太遠處，進而避免了中國以及台灣族群間的基因交流。族群遷移分析的結果呈現台灣往中國的方向性，不過，從分子變異分析(AMOVA)以及遺傳分化程度(ФST) 的結果推測，地理隔離的效應較播遷的影響來得強。台灣洄游型的族群擴張現象可能因於時間尺度及環境的差別。總結來說，中國方面發現了一個陸封型族群，而中國及台灣的族群分離式由台灣海峽作為物理障蔽形成地理隔離所造成。 | zh_TW |
| dc.description.abstract | Rhinogobius formosanus is an amphidromous species of goby, which had been long considered endemic to northern Taiwan. However, a population was reported from Fujian, China in 2012. Recently, two populations in Taiwan were identified and a landlocked population at the upstream of the Feitsui Reservoir in Taipei was confirmed. Nevertheless, the populations in China were still being understudied and the knowledge of the biogeographic pattern of this species is still limited. There are two objectives in this study. First, to investigate as to whether there is a landlocked population of the R. formosanus in China by analyzing the otolith Sr:Ca ratios. Second, to examine the mechanism that causes the disjunction of R. formosanus in Taiwan and China by comparing the genetic structure among the five populations. In this study, the samples were collected from five locations, two from Fujian, China and three from northern Taiwan, including one landlocked habitat. Mitochondrial DNA was used as the molecular marker to study the population genetics of the five R. formosanus populations, while the otolith Sr:Ca ratios were used to reconstruct the life history of the gobies. The results showed a consistently low Sr:Ca ratios in the gobies from Fuqing in China, suggesting the Fuqing population being a landlocked goby. On the other hand, the gobies from Fuding, China showed a high to low Sr:Ca ratios, suggesting the Fuding population being amphidromous gobies. As for the molecular analysis results, the populations between Taiwan and China showed a significant genetic differentiation based on the AMOVA analysis result. Besides, the two amphidromous populations in Taiwan showed a recent population expansion based on the neutrality test result, but not the China populations and the Bayesian skyline result suggested it happened at the end of glaciation. Although R. formosanus can enter the ocean during the larval stage, it might not travel for a long distance, which can prevent the gene flow between the Taiwan and China populations. The population migration result showed a direction of Taiwan to China, however, the AMOVA and ФST results suggested the vicariance effect stronger than dispersal. The results of population expansion happened in Taiwan’s amphidromous populations might be due to the time scale and environmental differences. In conclusion, a landlocked population is found in China and the disjunction of the China and Taiwan populations is caused by a vicariance in which the Taiwan Strait formed a barrier that separated the populations. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T04:13:33Z (GMT). No. of bitstreams: 1 U0001-0402202120120100.pdf: 3450729 bytes, checksum: 6f800dfbe757c1b26746e62ace049048 (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | 口試委員會審定書 i Acknowledgement ii 摘要 iii Abstract iv List of Tables viii List of Figures ix Appendix x Introduction 1 The life cycle of amphidromous gobies 1 Factors affecting population structure 1 Rhinogobius species 2 Rhinogobius formosanus 2 Fish otoliths 2 Population genetics and otolith analysis of Gobioidei 3 Research purposes and hypothesis 4 Materials and Methods 5 Sampling 5 Otolith preparation and otolith X-ray microprobe analysis 5 Otolith extraction and preparation 5 Otolith grinding 5 Otolith Sr:Ca ratio analysis 5 Molecular biology experiments 6 DNA extraction 6 Polymerase chain reaction (PCR) 6 Gel analysis 7 DNA purification and sequencing 7 Sequenced data analysis 7 Sequence alignment arrangement 7 Neighbor-joining tree (NJ Tree) 7 Maximum likelihood tree (ML tree) 8 Median joining network 8 Population genetics analysis 8 Genetic differentiation 8 Analysis of molecular variance (AMOVA) 9 Population variation analysis 9 Neutrality test 9 Mismatch distribution 10 Isolation by distance 10 T-test 10 The most recent common ancestor (TMRCA) Bayesian skyline 10 Population migration 10 Results 11 Sample collection 11 Otolith Sr:Ca ratios analysis pelagic larval durations of R. formosanus samples in China 11 Molecular analysis 11 Genetic diversities 11 Phylogenetic Trees 11 Haplotype network 12 AMOVA and pairwaise ФST values 12 Neutrality test 13 Mismatch distribution 13 Isolation by distance 13 T-test 13 The most recent common ancestor (TMRCA) Bayesian skyline 13 Population migration 13 Discussion 14 Life cycle of R. formosanus populations in China 14 Population differentiation of R. formosanus 15 Population expansion in Taiwan 16 Conclusion 18 References 19 | |
| dc.language.iso | en | |
| dc.subject | 耳石 | zh_TW |
| dc.subject | 地理隔離 | zh_TW |
| dc.subject | 播遷 | zh_TW |
| dc.subject | 貝氏天際線 | zh_TW |
| dc.subject | 台灣吻鰕虎 | zh_TW |
| dc.subject | 陸封型物種 | zh_TW |
| dc.subject | 族群遺傳結構 | zh_TW |
| dc.subject | 粒線體DNA | zh_TW |
| dc.subject | Bayesian skyline | en |
| dc.subject | Rhinogobius formosanus | en |
| dc.subject | mtDNA | en |
| dc.subject | otolith | en |
| dc.subject | landlocked species | en |
| dc.subject | population genetic structure | en |
| dc.subject | vicariance | en |
| dc.subject | dispersal | en |
| dc.title | 東亞地區台灣吻鰕虎 (Rhinogobius formosanus) 之生活史及族群遺傳 | zh_TW |
| dc.title | Life history and population genetics of Rhinogobius formosanus in East Asia | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 109-1 | |
| dc.description.degree | 碩士 | |
| dc.contributor.coadvisor | 廖德裕(Te-Yu Liao) | |
| dc.contributor.oralexamcommittee | 戴昌鳳(Chang-Feng Dai),林秀瑾(Hsiu-Chin Lin) | |
| dc.subject.keyword | 台灣吻鰕虎,粒線體DNA,耳石,陸封型物種,族群遺傳結構,地理隔離,播遷,貝氏天際線, | zh_TW |
| dc.subject.keyword | Rhinogobius formosanus,mtDNA,otolith,landlocked species,population genetic structure,vicariance,dispersal,Bayesian skyline, | en |
| dc.relation.page | 46 | |
| dc.identifier.doi | 10.6342/NTU202100535 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2021-02-14 | |
| dc.contributor.author-college | 理學院 | zh_TW |
| dc.contributor.author-dept | 海洋研究所 | zh_TW |
| 顯示於系所單位： | 海洋研究所 | |
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