國立臺灣師範大學博碩士論文全文系統

簡易檢索 / 詳目顯示

回結果列表

研究生：	林雨昕 Lin, Yu-Hsin
論文名稱：	麗紋石龍子（Plestiodon elegans）在臺灣的族群遺傳分化與隱蔽種 Population genetic divergence and cryptic species of Plestiodon elegans in Taiwan
指導教授：	林思民 Lin, Si-Min
口試委員：	徐堉峰 Hsu, Yu-Feng 張智涵 Chang, Chih-Han 林思民 Lin, Si-Min
口試日期：	2022/01/14
學位類別：	碩士 Master
系所名稱：	生命科學系 Department of Life Science
論文出版年：	2022
畢業學年度：	110
語文別：	英文
論文頁數：	48
中文關鍵詞：	親緣關係樹、遺傳結構、隱蔽種、麗紋石龍子
英文關鍵詞：	cryptic species, genetic structure, phylogenetic tree, Plestiodon elegans
研究方法:	調查研究
DOI URL：	http://doi.org/10.6345/NTNU202200405
論文種類：	學術論文
相關次數：	點閱：127 下載：16
分享至:	分享至facebook 分享至twitter

查詢本校圖書館目錄查詢臺灣博碩士論文知識加值系統勘誤回報

廣泛分布的物種在現今空間上的遺傳結構分布，往往是由過去的地質事件或氣候事件所造成。受惠於分子技術的進步，某些在遺傳上有分化，但在形態上卻非常相似的隱藏譜系得以被發現，顯示兩棲爬行動物在台灣的物種多樣性是被低估的。隱蔽種的發現對於演化理論、生物地理和保育政策的制定有著深遠的影響，也能進而探究其種化機制或是種化歷史。麗紋石龍子（ Plestiodon elegans）廣泛分布於中國大陸、釣魚台列嶼、澎湖以及台灣本島，是台灣唯一分布海拔跨越 0到 3000公尺左右的蜥蜴，然而對此物種的族群遺傳結構研究甚少。為了瞭解麗紋石龍子在台灣的遺傳分化，我們在全島包含 1700公尺以上高海拔地區、澎湖和龜山島，以及代表中國族群的馬祖進行採集，利用定序取得遺傳資料，包括粒線體的cytochrome b和 ND1以及核基因的 RAG-1和 PRLR片段，重建親緣關係，比較各地族群的遺傳差異和分化時間，並進行形態分析。分子遺傳結果顯示在粒線體片段中，台灣東西部的麗紋石龍子並不呈現單系群。台東附近由低到高海拔的族群為一獨立的單系群，且與台灣其餘族群的遺傳距離高於其他在琉球群島的幾個近緣種。而核基因由於序列相對保守，較無可供辨識的序列特徵。形態分析結果顯示，台東族群的頭部鱗片包括眶前鱗、眶後鱗、上睫鱗、下唇鱗、頸鱗）、前肢第二指指墊數和後肢第二、第四趾趾墊數 (RFII、RTII、 RTIV)、吻肛長（ SVL）以及頭深（HD）皆顯著不同於台灣其餘族群。綜合以上，麗紋石龍子在台東的族群應為一獨立的新種，其分類地位必須進行重新的描述。

The elegant five-lined skink (Plestiodon elegans) is widely distributed in Mainland China, Senkaku island, Penghu, and Taiwan and is the only lizard in Taiwan with an altitude range from 0 to 3000 meters. However, the genetic structure of this species within the island has never been well addressed. In order to investigate the genetic divergence of populations in Taiwan, we sampled a wide range around the island including high elevation areas (above 1700 meters), two offshore islets (Penghu and Gueishan island), and Matsu Archipelago which represents population from Mainland China. Genetic data was applied to reconstruct the phylogenetic relationship and divergence time among the clades and their closely related species, while morphology of the samples were analyzed. Molecular genetic structure demonstrated that the western and eastern populations do not represent a monophyletic group in mitochondrial DNA. The populations near Taitung are a distinct lineage, with its genetic distances from other populations in Taiwan higher than that among other species distributed in Japan and Ryukyu islands. Nuclear genes are relatively conserved and have no identifiable sequence features. Morphological analyses showed that head scales (PrO, PoO, SuC, IL, Nu), subdigital lamellae on Finger-II, Toe-II, and Toe-IV (RFII, RTII, RTIV), snout-vent length (SVL), and head depth (HD) of Taitung population showed significantly differences from the other populations in Taiwan. This population should be regarded as an independent species.

摘要 .............................................................................................................................................I
Abstract ...................................................................................................................................... II
1. Introduction .......................................................................................................................... 1
2. Materials and Methods .......................................................................................................... 5
2.1 Sample collection ............................................................................................................ 5
2.2 DNA extraction, PCR, and sequencing................................................................................ 5
2.3 Phylogenetic analyses of DNA .......................................................................................... 6
2.4 Haplotype network of nuclear genes ................................................................................... 8
2.5 Morphological analysis..................................................................................................... 8
2.6 Divergence time estimation ............................................................................................. 10
3. Results ................................................................................................................................ 12
3.1. Phylogenetic relationships of mitochondrial DNA .............................................................. 12
3.2. Haplotype network of nuclear genes ................................................................................. 13
3.3. Morphological comparison.............................................................................................. 14
3.4. Divergence time ............................................................................................................ 15
4. Discussion .......................................................................................................................... 16
5. References .......................................................................................................................... 19
Tables ........................................................................................................................................ 25
Table 1. ................................................................................................................................... 25
Table 2. ................................................................................................................................... 26
Table 3. ................................................................................................................................... 27
Table 4. ................................................................................................................................... 29
Table 5. ................................................................................................................................... 31
Figures....................................................................................................................................... 32
Figure 1. .................................................................................................................................. 32
Figure 2. .................................................................................................................................. 37
Figure 3. .................................................................................................................................. 39
Figure 4. .................................................................................................................................. 40
Figure 5. .................................................................................................................................. 41
Figure 6. .................................................................................................................................. 42
Figure 7. .................................................................................................................................. 43
Appendixes ................................................................................................................................ 45
Appendix 1. ............................................................................................................................. 45
Appendix 2. ............................................................................................................................. 47
Appendix 3. ............................................................................................................................. 48
                                

Andreone, F., & Greer, A. E. (2002). Malagasy scincid lizards: descriptions of nine new species, with notes on the morphology, reproduction and taxonomy of some previously described species (Reptilia, Squamata: Scincidae). Journal of Zoology, 258(2), 139-181.
Bandelt, H. J., Forster, P., & Röhl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular biology and evolution, 16(1), 37-48.
Bauret, L., Rouhan, G., Hirai, R. Y., Perrie, L., Prado, J., Salino, A., ... & Gaudeul, M. (2017). Molecular data, based on an exhaustive species sampling of the fern genus Rumohra (Dryopteridaceae), reveal a biogeographical history mostly shaped by dispersal and several cryptic species in the widely distributed Rumohra adiantiformis. Botanical Journal of the Linnean Society, 185(4), 463-481.
Beck, J., Liedtke, H. C., Widler, S., Altermatt, F., Loader, S. P., Hagmann, R., ... & Fiedler, K. (2016). Patterns or mechanisms? Bergmann’s and Rapoport’s rule in moths along an elevational gradient. Community Ecology, 17(2), 137-148.
Bickford, D., Lohman, D. J., Sodhi, N. S., Ng, P. K., Meier, R., Winker, K., ... & Das, I. (2007). Cryptic species as a window on diversity and conservation. Trends in ecology & evolution, 22(3), 148-155.
Bocourt, M. F. (1879). Etudes sur les reptiles, p. i-xiv, 1-1012. In Recherches Zoologiques pour servir a l'Histoire de Ia Faune de l'Amérique Centrale et du Mexique. Mission Scientifique au Mexique et dans l'Amérique Centrale, Recherches zoologiques. Part 2, sect. 1; In A Imprimerie Impériale, Paris [3, Pt. 6], pp. 360–440.
Bouckaert, R., Vaughan, T. G., Barido-Sottani, J., Duchêne, S., Fourment, M., Gavryushkina, A., ... & Drummond, A. J. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology, 15(4), e1006650.
Boulenger, G. A. (1887). Catalogue of the lizards in the British Museum (Nat. Hist.) III. Lacertidae, Gerrhosauridae, Scincidae, Anelytropsidae, Dibamidae, Chamaeleontidae. London: 575 pp.
Brandley, M. C., OTA, H., Hikida, T., Nieto Montes De Oca, A., Feria-Ortiz, M., Guo, X., & Wang, Y. (2012). The phylogenetic systematics of blue-tailed skinks (Plestiodon) and the family Scincidae. Zoological Journal of the Linnean Society, 165(1), 163-189.
Brandley, M. C., Wang, Y., Guo, X., Montes de Oca, A. N., Fería-Ortíz, M., Hikida, T., & Ota, H. (2011). Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards. Systematic Biology, 60(1), 3-15.
Burbrink, F. T., Yao, H., Ingrasci, M., Bryson Jr, R. W., Guiher, T. J., & Ruane, S. (2011). Speciation at the Mogollon Rim in the Arizona mountain kingsnake (Lampropeltis pyromelana). Molecular Phylogenetics and Evolution, 60(3), 445-454.
Cruz, F. B., Fitzgerald, L. A., Espinoza, R. E., & Schulte Ii, J. A. (2005). The importance of phylogenetic scale in tests of Bergmann's and Rapoport's rules: lessons from a clade of South American lizards. Journal of evolutionary biology, 18(6), 1559-1574.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature methods, 9(8), 772-772.
Evans, S. E. (2003). At the feet of the dinosaurs: the early history and radiation of lizards. Biological Reviews, 78(4), 513-551.
Glossip, D., & Losos, J. B. (1997). Ecological correlates of number of subdigital lamellae in anoles. Herpetologica, 192-199.
Gray, J. E. (1838). Catalogue of the slender-tongued saurians, with descriptions of many new genera and species. Part 2. Ann. Mag. Nat. Hist. (1) 1: 287-293.
Guarnizo, C. E., Amézquita, A., & Bermingham, E. (2009). The relative roles of vicariance versus elevational gradients in the genetic differentiation of the high Andean tree frog, Dendropsophus labialis. Molecular Phylogenetics and Evolution, 50(1), 84-92.
Günther, A. (1864). The Reptiles of British India. London (Taylor & Francis), xxvii + 452 pp.
Hallowell, E. (1861). Report upon the Reptilia of the North Pacific Exploring Expedition, under
command of Capt. John Rogers, U. S. N. Proc. Acad. Nat. Sci. Philadelphia 12 [1860]: 480 – 510.
Hillis, D. M., & Bull, J. J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic biology, 42(2), 182-192.
Huelsenbeck, J. P., & Rannala, B. (2004). Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic biology, 53(6), 904-913.
Kurita, K., & Hikida, T. (2014). A New Species of Plestiodon (Squamata: Scincidae) from Kuchinoshima Island in the Tokara Group of the Northern Ryukyus, Japan. Zoological science, 31(7), 464-474.
Kurita, K., & Hikida, T. (2014). Divergence and long-distance overseas dispersals of island populations of the Ryukyu five-lined skink, Plestiodon marginatus (Scincidae: Squamata), in the Ryukyu Archipelago, Japan, as revealed by mitochondrial DNA phylogeography. Zoological science, 31(4), 187-194.
Kurita, K., Ota, H., & Hikida, T. (2017). A new species of Plestiodon (Squamata: Scincidae) from the Senkaku Group, Ryukyu Archipelago, Japan. Zootaxa, 4254(5), 520-536.
Lamb, T., & Bauer, A. M. (2006). Footprints in the sand: independent reduction of subdigital lamellae in the Namib–Kalahari burrowing geckos. Proceedings of the Royal Society B: Biological Sciences, 273(1588), 855-864.
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2017). PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular biology and evolution, 34(3), 772-773.
Leaché, A. D., & Reeder, T. W. (2002). Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Systematic biology, 51(1), 44-68.
Leigh, J. W., & Bryant, D. (2015). popart: full℃feature software for haplotype network construction. Methods in Ecology and Evolution, 6(9), 1110-1116.
Lin, H. C., Li, S. H., Fong, J., & Lin, S. M. (2008). Ventral coloration differentiation and mitochondrial sequences of the Chinese Cobra (Naja atra) in Taiwan. Conservation Genetics, 9(5), 1089-1097.
Lin, H. D., Chen, Y. R., & Lin, S. M. (2012). Strict consistency between genetic and topographic landscapes of the brown tree frog (Buergeria robusta) in Taiwan. Molecular Phylogenetics and Evolution, 62(1), 251-262.
Lue, K. Y., & Lin, S. M. (2008). Two new cryptic species of Takydromus (Squamata: Lacertidae) from Taiwan. Herpetologica, 64(3), 379-395.
Martin, A. P., & Bermingham, E. (2000). Regional endemism and cryptic species revealed by molecular and morphological analysis of a widespread species of Neotropical catfish. Proceedings of the Royal Society of London. Series B: Biological Sciences, 267(1448), 1135-1141.
Miralles, A., Koehler, J., Glaw, F., & Vences, M. (2011). A molecular phylogeny of the “Madascincus polleni species complex”, with description of a new species of scincid lizard from the coastal dune area of northern Madagascar. Zootaxa, 2876(1), 1-16.
Okamoto, T., & Hikida, T. (2009). Three genetic lineages of the Japanese skink Plestiodon japonicus (Scincidae, Squamata) and the genetic composition of their contact zones. Journal of Zoological Systematics and Evolutionary Research, 47(2), 181-188.
Peters, W. C. H. (1864). Die Eidechsenfamilie der Scincoiden, insbesondere über die Schneider'schen, Wiegmann'schen und neue Arten des zoologischen Museums. Monatsber. K. Akad. Wiss. Berlin, 1864: 44-58.
Pfenninger, M., & Schwenk, K. (2007). Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC evolutionary biology, 7(1), 1-6.
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic biology, 67(5), 901.
Richman, A.D. & Price, T. (1992). Evolution of ecological differences in the Old World leaf
warblers. Nature, 355(6363), 817-821.
Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., ... & Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic biology, 61(3), 539-542.
Rouhan, G., & Gaudeul, M. (2021). Plant Taxonomy: a historical perspective, current challenges, and perspectives. Molecular Plant Taxonomy, 1-38.
Sibuet, J. C., & Hsu, S. K. (2004). How was Taiwan created ?. Tectonophysics, 379(1-4), 159-181.
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313.
Steinbauer, M. J., Field, R., Grytnes, J. A., Trigas, P., Ah℃Peng, C., Attorre, F., ... & Beierkuhnlein, C. (2016). Topography℃driven isolation, speciation and a global increase of endemism with elevation. Global Ecology and Biogeography, 25(9), 1097-1107.
Stejneger, LEONHARD H. (1907). Herpetology of Japan and adjacent territory. Bull. US Natl. Mus. 58: xx, 1-577.
Stejneger, LEONHARD H. (1924). A new Chinese lizard of the genus Eumeces. J. Washington Acad. Sci. 14 (16): 383-384.
Stephens, M., & Scheet, P. (2005). Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. The American Journal of Human Genetics, 76(3), 449-462.
Stephens, M., Smith, N. J., & Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. The American Journal of Human Genetics, 68(4), 978-989.
Stuart, B. L., Inger, R. F., & Voris, H. K. (2006). High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs. Biology letters, 2(3), 470-474.
Swinhoe,R. (1863). A list of the Formosan reptiles; with notes on a few of the species, and some remarks on a fish (Orthagoriscus, sp.). Ann. Mag. nat. Hist. (3) 12: 219-226.
Taylor, E. H. (1936). A taxonomic study of the cosmopolitan lizards of the genus Eumeces with an account of the distribution and relationship of its species. Univ. Kansas Sci. Bull. 23 (14): 1-643 [1935].
Teng, L. S. (1990). Geotectonic evolution of late Cenozoic arc-continent collision in Taiwan. Tectonophysics, 183(1-4), 57-76.
Thompson, J.C. (1912). Herpetological notices, No. 2. Prodrome of descriptions of new species of Reptilia and Batrachia from the Far East. Privately published, San Francisco.
Townsend, T. M., Alegre, R. E., Kelley, S. T., Wiens, J. J., & Reeder, T. W. (2008). Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Molecular phylogenetics and evolution, 47(1), 129-142.
Van Denburgh, J., (1912). Concerning certain species of reptiles and amphibians from China, Japan, the Loo Choo Islands, and Formosa. Proc. Cal. Ac. Sci. (Series 4) 3 (10): 187-258.
Van Rossum, F., Martin, H., Le Cadre, S., Brachi, B., Christenhusz, M. J., & Touzet, P. (2018). Phylogeography of a widely distributed species reveals a cryptic assemblage of distinct genetic lineages needing separate conservation strategies. Perspectives in Plant Ecology, Evolution and Systematics, 35, 44-51.
You, C. W., Poyarkov Jr, N. A., & Lin, S. M. (2015). Diversity of the snail℃eating snakes Pareas (S erpentes, P areatidae) from T aiwan. Zoologica Scripta, 44(4), 349-361.
Zamora℃Camacho, F. J., Reguera, S., & Moreno℃Rueda, G. (2014). Bergmann's Rule rules body size in an ectotherm: heat conservation in a lizard along a 2200℃metre elevational gradient. Journal of Evolutionary Biology, 27(12), 2820-2828.

簡易檢索 / 詳目顯示

相關論文