(3.235.191.87) 您好!臺灣時間:2021/05/13 04:59
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果

詳目顯示:::

我願授權國圖
: 
twitterline
研究生:張朝欽
研究生(外文):Chao-Ching Chang
論文名稱:以多組分子遺傳標誌探討表孔珊瑚屬的分子親緣關係
論文名稱(外文):Multi-loci approached to the molecular phylogeny of reef-building coral, Montipora (Cnidaria; Scleractinia)
指導教授:陳昭倫陳昭倫引用關係
指導教授(外文):Chaolun Allen Chen
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:海洋研究所
學門:自然科學學門
學類:海洋科學學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:英文
論文頁數:51
中文關鍵詞:表孔珊瑚分子親緣關係造礁珊瑚
外文關鍵詞:Scleractiniamolecular phylogenyMontipora
相關次數:
  • 被引用被引用:1
  • 點閱點閱:136
  • 評分評分:系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔系統版面圖檔
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
表孔珊瑚屬為造礁珊瑚中的第二大屬,包含了七十五種。由於種類數多,過去的學者在進行表孔珊瑚分類時,通常先將形態相似的物種分成不同的種群,而這些種群基本上不具有分類上的意義。表孔珊瑚種群的特徵是依據珊瑚共骨的細微骨骼構造或是以珊瑚群體的生長型來分群。珊瑚共骨結構包含平凹狀、針狀、管狀以及疣狀共四類,珊瑚群體的生長型包含葉片狀、匍匐或團塊狀以及分枝狀共三類。然而,依據共骨結構或是生長型所分出的種群,在過去的文獻結果具有很大的差異。另外,同一株珊瑚群體常同時具有不同生長型,常造成分類鑑定上的困擾。本研究採集產於台灣海域的三十二種表孔珊瑚,利用三組獨立的分子遺傳標誌,包括粒線體第三基因區間、調鈣蛋白基因第二介入子以及核糖體轉錄區間,建構表孔珊瑚屬的巢狀系群分析及分子親緣關係樹,驗證以珊瑚共骨結構以及生長型為依據的分類群假說。分析結果顯示,粒線體第三基因區間的巢狀系群分析可將疣狀共骨與其他共骨結構區分出不同系群,而其親緣關係樹則可分出平凹狀、疣狀,以及針狀與管狀混合的三系群。調鈣蛋白基因第二介入子的巢狀系群分析與親緣關係樹區分出三個共骨形態系群,疣狀與平凹各自獨立成一個系群,而針狀與管狀則混合於另外的系群。但是在核糖體轉錄區間的親緣關係樹只能區分出平凹狀的系群。這些分群現象的差異可能肇因於此三組標誌具有不同的分子演化特性。然而,三組分子遺傳標誌得到共同的分子親緣分析無法支持以生長型為依據的種群假說。相反的,除了少數的例外,分子親緣研究結果傾向支持以共骨結構為依據的種群假說,進一步證明共骨結構不僅在分類上具有明顯的貢獻,同時也具有親緣上的意義。重整過去的文獻與本研究的結果,未來表孔珊瑚屬可以依據平凹狀、針管狀及疣狀三群主要共骨結構進行種群的分類。
Montipora is the second speciose genus of scleractinians with 75 species currently described. In order to accommodate this speciose genus, species groups were adopted to cluster morphologically similar species based on either the final skeleton structure of coenosteums or the colony growth forms. These conventional groupings, however, do not imply any taxonomic affinity. Four major coenosteums and three growth forms including, glabrous-foveolate, papillae, tuberculae, verrucae, and laminar, encrusting-massive, and branches were used, either respectively or jointly, to define the species groups and species in the literatures. However, the results were usually conflict. In addition, more than one growth form was often observed within a single colony that confused identification of Montipora. In this study, we examined two taxonomical grouping hypotheses: (1) coenosteum hypothesis, groups based on glabrous-foveolate, papillae, tuberculae and verrucae, and (2) growth form hypothesis, groups based on laminar, encrusting-massive, and branches. Molecular phylogenies of 32 Montipora species were constructed using three independent loci, including mitochondrial intergenic region 3 (mtigr3, 472bp) spanning between cytochrome b (Cytb) and NADH dehydrogenase subunit 2 (ND2) genes, nuclear ribosomal internal transcribed spacer (ITS; ITS1+ITS2, 393bp), and an intron spanning between exon 2 and 3 of the calmodulin gene (CaM-II, 270bp). Species phylogeny analysis of the three independent loci using nested clade analysis (NCA) and phylogenetic trees with neighbour-joining, maximum-parsimony, maximum-likelihood, and Bayesian-likelihood approaches were largely corresponded with coenosteum structures groups, but not with growth forms. The NCA and phylogenetic trees based on mtigr3 and CaM-II loci could distinguish three coenosteum monophyletic groups consisted of “glabrous-foveolate”, “papillae-tuberculae” and “verrucae”, but the ITS can only divided glabrous-foveolate coenosteum from the others. Combining the three molecular markers suggested that growth forms did not contribute to resolve the taxonomic complexity of species groups for genus Montipora. Instead, with a few exceptions, the phylogenetic analyses tended to support the grouping based on coenosteum structures, which divided the genus into three major groups, included glabrous-foveolate, papillae-tuberculae and verrucae. This result highlighted not only the phylogenetic significance but also the utility of coenosteum structures in the future revision of species group and species taxonomy in genus Montipora.
Table of Contents

Abstract in Chinese……………………...………………………………..………………….II
Abstract………………………...…………...………...……...………………………………III
Table of contents……………………………..…………….……………….………………..V
Contents of tables………………………………..……………..……………………….….VII
Contents of figure……………………………….….…………..……..………………..….VIII
Contents of appendix…..…………………………...……………….………………..……..IX

Introduction……………………………………………………………..…………………….1
Materials and methods…………………….…………………………………………………5
Samples collection…………………………………………………………………………….5
Identification and grouping…………………………………………………………..………...5
DNA extraction……………………………………………………………………………….5
PCR amplification, cloning, and sequencing ………………………………………………….5
Sequences alignment, molecular evolution analysis and phylogenetic inferences………..…...7
Morphological grouping hypotheses test………………………………………………………7
Results…………………………………………………………………………………………9
Morphological information…………………………………………………………..………...9
Molecular characters of molecular markers…………………………………………..………..9
Nested clade analysis………………………………………………………………………....10
Phylogenetic analysis……………………………………..…………………………………..11
Monophyly tests with morphology hypothesis……………………………………….………13
Discussion………………………………………………………………...…………………..14
Evolutionary patterns and utilities of three independent loci…………………………..…….14
Taxonomic Implications based on molecular phylogenetic analyses…..…………………….16
Conclusions and Further Study…….…………………………………………………………18
Reference……………………………………………………………………………………19
Tables………………………………………………………………………………………...24
Figures……………………………..………………………………………………………..37
Appendix……………………..……………………………………………………………48

Contents of Tables

Table 1. Morphological grouping in Montipora……………….……………………………..24
Table 2. A revision of molecular approaches for coral species phylogeny…………….…….25
Table 3. A list of Species names, sample and location codes, molecular sequences obtained
and morphological characters…………………………..…………………………...27
Table 4. Base composition, sequence lengths and best-fit nucleotide substitution models of
three molecular markers……………………..….…………………………………...29
Table 5. The mtigr3 haplotypes defined by nested clade analysis…………..………………..30
Table 6. Nested exact contingency analyses based on two morphological hypotheses with
nested clade analyses of mtigr3…………………………….………...……………..31
Table 7. The CaM-II haplotypes defined by nested clade analysis…………..…………...….32
Table 8. Nested exact contingency analyses based on two morphological hypotheses with
nested clade analyses of CaM-II…………………………………………………….34
Table 9. Results of Shimodaira-Hasegawa tests enforcing monophyly based on growth form
hypothesis with three molecular markers and combined data……………………..35
Table 10. Results of Shimodaira-Hasegawa tests enforcing monophyly based on coenosteum
hypothesis with three molecular markers and combined data……..…………….….36

Contents of Figures

Fig. 1. Variable colony growth forms of Montipora peltiformis….………….……………..37
Fig. 2. Coenosteums of Montipora……..…………….……………………………………....38
Fig. 3. Map showing the sampling location of Montipora species in Taiwan……..………....39
Fig. 4. Saturation pattern of three markers……..…………….……………………………….40
Fig. 5. Haplotypes network and nested clades for mtigr3……..…………….………………..41
Fig. 6. Haplotypes network and nested clades for CaM-II……..…………….………………42
Fig. 7. Maximum-likelihood tree of mtigr3, ……..…………….…………………………….43
Fig. 8. Maximum-likelihood tree of CaM-II……..…………….……………………………..44
Fig. 9. Maximum-likelihood tree of ITS……..…………….………………………………..45
Fig. 10. Maximum-likelihood tree of combined three molecular markers……..…………….46
Fig. 11. The distribution of frequencies against to K81 corrected pairwise distances in three
levels of ITS sequences……………………………………….…..…………….….47



Appendix

Appendix 1. Two definitions of coenosteum characters……..…………….…………………48
Appendix 2. Growth forms of Montipora.. ……..…………….……………………………...49
Appendix 3. Coenosteums of Montipora……..…………….………………………………...50
Appendix 4. Secondary structure of nuclear ribosomal internal transcribed spacer ITS of Montipora taiwanensis…………………………...……………………………51
Ayre DJ, Veron JEN, Dufty SL (1991) The Acropora palifera and Acropora cuneata are genetically and reproductive variation. Coral Reefs 10: 13-18
Barnes DJ (1973) Growth in colonial scleractinians. Bull of Mar Sci 23: 280-298
Bernard HM (1897) The genus Montipora. The genus Anacropora. Cat. Madreporarian corals Br. Mus. (Natural History) 3: 1-192, pl. 191-134
Bruno JF, Edmunds PJ (1997) Clonal variation for phenotypic plasticity in the coral Madracis mirabilis. Ecology 78: 2177-2190
Chen CA, Chang CC, Wei NV, Chen CH, Lein YT, Lin HE, Dai CF, Wallace CC (2004) Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals. Zoological Studies submitted
Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657-1659
Dana JD (1848) Zoophytes. U.S. Exploring Exped. 1838-1842 7: 1-740, pl. 741-761
de Blainville HM (1830) Zoophytes. In ''Dictionnaire des Sciences naturelles'', Paris 60: 295-364
Diekmann OE, Bak RPM, Stam WT, Olsen JL (2001) Molecular genetic evidence for probable reticulate speciation in the coral genus Madracis from a Caribbean fringing reef slope. Mar Biol 139: 221-233
Felsentstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376
Forsman ZH (2003) The phylogeny and population genetics of the scleractinian coral genus Porites in the western hemisphere revealed by ribosomal spacers and morphometrics. PhD thesis, University of Houston, Houston, TX
Fukami H, Budd AF, Levitan DR, Jara J, Kersanach R, Knowlton N (2004) Geographic differences in species boundaries among members of the Montastraea annularis complex based on molecular and morphological markers. Evolution 58: 324-337
Fukami H, Omori M, Hatta M (2000) Phylogenetic relationships in the coral family Acroporidae, reassessed by inference from mitochondrial genes. Zool Sci 17: 689-696
Gilbert DC (1994) SeqApp 1.9 A biological sequence editor and analysis program for Macintosh computers. Available via anonymous ftp to ftp.bio.indiana.edu.
Graur D, Li WH (2000) Fundamentals of molecular evolution. Sunderland, Mass.: Sinauer Associates
Hasegawa M, Kishino K, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondial DNA of the great apes and human: sequence, structure, evolution and phylogenetic implications. Mol Biol Evol 3: 1-18
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755
Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78: 454-458
Knowlton N (2000) Molecular genetic analyses of species boundaries in the sea. Hydrobiologia 420: 73-90
Lam K, Morton B (2004) Morphological and ITS1, 5.8S, and partial ITS2 ribosomal DNA sequence distinctions between two species Playtygyra (Cnidaria : Scleractinia) from Hong Kong (vol 5, pg 555, 2003). Mar Biotechnol 6: 104-104
Lang JC (1984) Whatever works: the variable importance of skeletal and of non-skeletal characters in scleractinian taxonomy. Palaeontogr Am 54: 18-44
Lin HE, Lein YT, Lam K, Fukami H, Knowlton N, Jarayabhand P, Chen CA (2004) Phylogeography and connectivity of zebra coral, Oulastrea crispata (Scleractinia; Faviidae) in the West Pacific. Proc 10th Int. Coral Reef Symp. (abstracts, p. 101)
Marquez LM, Miller DJ, MacKenzie JB, van Oppen MJH (2003) Pseudogenes contribute to the extreme diversity of nuclear ribosomal DNA in the hard coral Acropora. Mol Biol Evol 20: 1077-1086
Medina M, Weil E, Szmant AM (1999) Examination of the Montastraea annularis species complex (Cnidaria : Scleractinia) using ITS and COI sequences. Mar Biotechnol 1: 89-97
Muko S, Kawasaki K, Sakai K, Takasu F, Shigesada N (2000) Morphological plasticity in the coral Porites sillimaniani and its adaptive significance. Bull Mar Sci 66: 225-239
Odorico DM, Miller DJ (1997) Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): Patterns of variation consistent with reticulate evolution. Mol Biol Evol 14: 465-473
Philippe H, Forterre P (1999) The rooting of the universal tree of life is not reliable. J Mol Evol 49: 509-523
Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818
Quoy JRC, Gaimard JP (1833) Zoophytes. In Dumont d''Urville, J. S. C. ''Voyage de decourvertes de l''Astrolabe, execute pae ordre du Roi, Pendant les annees 1826-29, sous le commandement de M. J. Dumont d''Urville''. zoologie 4: 175-254, pl. 114-120
Roff DA, Bentzen P (1989) The statistical analysis of mitochondrial DNA polymorphism: X2 and the problem of small samples. Mol Biol Evol 6: 539-545
Shearer TL, Van Oppen MJH, Romano SL, Worheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 11: 2475-2487
Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116
Stobart B, Benzie JAH (1994) Allozyme electrophoresis domonstrates that the scleractinian coral Montipora digitata is two species. Mar Biol 118: 183-190
Swofford DL (2002) PUAP*. Phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Massachusetts
Templeton AR, Crandall KA, F. SC (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. III. Cladogram estimation. Genetics 134: 659-669
Thompson J, Higgins D, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids. Res. 22: 4673-4680
van Oppen MJH, Catmull J, McDonald BJ, Hislop NR, Hagerman PJ, Miller DJ (2002a) The mitochondrial genome of Acropora tenuis (Cnidaria : Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol 55: 1-13
van Oppen MJH, Koolmees EM, Veron JEN (2004) Patterns of evolution in the scleractinian coral genus Montipora (Acroporidae). Mar Biol 144: 9-18
van Oppen MJH, McDonald BJ, Willis B, Miller DJ (2001) The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: Reticulation, incomplete lineage sorting, or morphological convergence? Mol Biol Evol 18: 1315-1329
van Oppen MJH, Willis BL, Miller DJ (1999) Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proc Royal Soc London Ser B-Biol Sci 266: 179-183
van Oppen MJH, Willis BL, Van Rheede T, Miller DJ (2002b) Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals. Mol Ecol 11: 1363-1376
van Oppen MJH, Willis BL, Van Vugt H, Miller DJ (2000) Examination of species boundaries in the Acropora cervicornis group (Scleractinia, Cnidaria) using nuclear DNA sequence analyses. Mol Ecol 9: 1363-1373
Veron JEN (1995) Corals in space and time. The biogeography and evolution of the Scleractinia. UNSW Press, Sydney
Veron JEN (2000) Coral of the world. Australian Institute of Marine Science, Townsville
Veron JEN, Wallace CC (1984) Scleractinia of eastern Australia. Part V. Family Acroporidae., Aust Inst Mar Sci Monogr Ser 6.
Warner RR (1997) Evolutionary ecology: how to reconcile pelagic dispersal with local adaptation. Coral Reefs 16: S115-S120
Xia X, Xie Z (2001) DAMBE: Software package for data analysis in molecular biology and evolution. J Hered 92: 371-373
Yuasa HJ, Suzuki T, Yazawa M (2001) Structural organization of lower marine nonvertebrate calmodulin genes. Gene 279: 205-212
Zuker M (1989) On Finding All Suboptimal Foldings of an RNA Molecule. Science 244: 48-52
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top
系統版面圖檔 系統版面圖檔