利用粒線體DNA與形態分析發現新種沼蝦（Macrobrachium）

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研究生：	詹姆斯 James David Khoo
論文名稱：	利用粒線體DNA與形態分析發現新種沼蝦（Macrobrachium） The discovery of a new species of Macrobrachium using mitochondrial DNA and morphological analysis
指導教授：	曾晴賢 Professor Chyng-Shyan Tzeng
口試委員:
學位類別：	碩士 Master
系所名稱：	生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology
論文出版年：	2007
畢業學年度：	95
語文別：	英文
論文頁數：	58
中文關鍵詞：	mtDNA
外文關鍵詞：	mitochondrial tDNA, DNA barcoding, taxonomy
相關次數：	點閱：1 下載：0
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A cryptic species complex containing two members of the genus Macrobrachium Bate, 1868 (Crustacea: Decapoda: Palaemonidae) has been resolved using a combination of morphology and DNA-based taxonomy.
While the character set used in morphological analysis yielded limited differentiating data, by using mtDNA sequence distances from part of the cytochrome oxidase sub unit I (COI) gene, commonly known as the “DNA barcode”, it was possible to support the inference of a new species of Macrobrachium. Based on the COI sequence data, several species groups of Macrobrachium from Taiwan could be recognised including a distinct cluster of 16 individuals of the new species. Analysis of the COI sequence showed that the majority of species groups displayed high interspecific and low intraspecific variation with all forming clusters that concur with known taxonomic boundaries.
The morphological similarity of this new species to M. latidactylus is presented here with only the shape and proportions of the terminal part of the major periopod functioning to distinguish it from the new species.
This work highlights the importance of combining traditional morphology-based taxonomy with DNA sequence data to assist in the identification of cryptic species and delineation of the genus Macrobrachium, particularly in instances of morphologically similar or damaged material.

Contents

Acknowledgements--------------------------------------------------------------------------------- I
Abstract ----------------------------------------------------------------------------------------------II
Introduction ---------------------------------------------------------------------------------------- 1
    (1) Classification challenges ------------------------------------------------------------ 2
    (2) Mitochondrial DNA (mtDNA) as a marker--------------------------------------- 4
    (3) COI as a DNA barcode -------------------------------------------------------------- 5
    (4) Building on previous research ------------------------------------------------------ 7
Material and methods
    (1) Collection of material ---------------------------------------------------------------- 9
    (2) Morphological analysis -------------------------------------------------------------- 9
    (3) DNA extraction ---------------------------------------------------------------------- 10
    (4) Primer design ------------------------------------------------------------------------- 11
    (5) PCR amplification and sequencing ------------------------------------------------ 12
    (6) Post sequence editing ---------------------------------------------------------------- 13
    (7) Sequence alignment and analysis--------------------------------------------------- 13
Results
    (1) General morphology----------------------------------------------------------------- 14
    (2) Morphological diagnosis – M. latidactylus --------------------------------------- 15
    (3) Morphological diagnosis – Macrobrachium sp. nov. --------------------------- 16
    (4) COI sequence data ------------------------------------------------------------------- 17


Discussion
    (1) Challenges of morphology based taxonomy-------------------------------------- 20
    (2) Morphological differences ----------------------------------------------------------21
    (3) COI inference- ----------------------------------------------------------------------- 21
    (4) Intraspecific boundaries ------------------------------------------------------------ 22
(5) A note on the comparison of Macrobrachium sp. nov. with Macrobrachium
grandimanus (Randall, 1840)----------------------------------------------------------- 24
(6) A note on the comparison of Macrobrachium sp. nov. with Palaemon (Macrobrachium) lampropus (De Man, 1892) ---------------------------------------25
    (7) Further research ---------------------------------------------------------------------- 26
Conclusion ------------------------------------------------------------------------------------------28
References ------------------------------------------------------------------------------------------ 29
Tables ----------------------------------------------------------------------------------------------- 37
Figures ---------------------------------------------------------------------------------------------- 47









Table contents

Table 1.    Additional sources of COI sequences from GenBank-----------------------37
Table 2.    Specimen ID, sex, total length and locality recordings----------------------38
Table 3.    Morphological measurements – rostrum--------------------------------------39
Table 4.    Morphological measurements -carapace length,  rostral length, major second periopod and telson -----------------------------------------------------40
Table 5.    Morphological measurements - second periopod----------------------------41
Table 6.    Total length and ratios of segments of the major second periopod--------42
Table 7.    Pollex measurements and no. of teeth-----------------------------------------43
Table 8.    Pairwise divergence among species complex from 1120bp COI sequences---------------------------------------------------------------------------------------------------------44
Table 9.    Pairwise divergence among individuals of the genus Macrobrachium based on 535bp COI sequence--------------------------------------------------------------------45
Table 10.    Variable sites of 7 haplotypes of the Macrobrachium species complex---46








Figure contents

Fig. 1.        General schematic of Macrobrachium showing main appendages--------47
Fig. 2.        Primer binding sites to positions on COI gene-------------------------------48
Fig. 3.        Photographs of M. latidactylus and Macrobrachium sp. nov. – Full body and cephalothorax----------------------------------------------------------------------------------49
Fig. 4.        Photographs of M. latidactylus and Macrobrachium sp. nov. – Major periopod and rostrum------------------------------------------------------------------------------50
Fig. 5.        Measurements taken from major periopod------------------------------------51
Fig. 6.        Measurements taken from pollex-----------------------------------------------52
Fig. 7.        Bar graphs to show mean pollex width and length--------------------------53
Fig. 8.        Bar graph showing mean total no. of teeth in chela-------------------------54
Fig. 9.         Neighbor-joining (NJ) tree based on 1120bp COI sequences-------------55
Fig. 10.    Neighbor-joining (NJ) tree based on 608bp COI sequences – GenBank--
--------------------------------------------------------------------------------------------------------56
Fig. 11.    Neighbor-joining (NJ) tree based on 535bp COI sequences – GenBank-- only--------------------------------------------------------------------------------------------------57
Fig. 12.    Neighbor-joining (NJ) tree based on 535bp COI sequences – GenBank and experimental samples-----------------------------------------------------------------------------58
Fig. 13.    Chela of Palaemon lampropus and Macrobrachium sp. nov. ------------59

                                

Armand, M. K., Ra’anan, Z., Sagi, A., & Cohen, D. 1987. Morphotypic differentiation of male Malaysian giant prawns, Macrobrachium rosenbergii. Journal of Crustacean Biology, 7 (2): 219-237.
Avise, J. C., Arnold, J., Ball, M. R., Bermingham, E., Lamb, T., Neigel, J. E., Reeb, C. A., & Saunders, N. C. 1987. The mitochondrial bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18: 489-522.
Avise, J. C., & Walker, D. 1999. Species realities and numbers in sexual vertebrates: Perspectives from an asexually transmitted genome. Proc. Natl. Acad. Sci. USA, 96: 992-995.
Bensasson, D., Zhang, D. X., Hartl, D. L., & Godfrey, M. H. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends in Ecology & Evolution, 16 (6): 314-321.
Blaxter, M. L. 2004. The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society. 359: 367-379.
Brown, W. M., George, M., & Wilson, A. C. 1979. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA, 76 (4): 1967-1971.
Cai, Y., & Dai, A. Y. 1999. Freshwater shrimps (Crustacea: Decapoda: Caridea), from the Xishuangbanna region of Yunnan Province, Southern China. Hydrobiologia, 400: 211-241.
Cai, Y., & Jeng, M. S. 2001. On a new species of Macrobrachium Bate, 1868 (Decapoda, Palaemonidae) from Northern Taiwan. Crustaceana, 74 (3): 275-283.
Clare, E. L., Burton, L. M., Engstrom, M. D., Eger, J. L., & Hebert, P. D. N. 2006. DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes, 7 (2): 184-190.
Cobb, J. S., Tamm, G. R., & Wang, D. 1982. Behavioural mechanisms influencing moult frequency in the American Lobster Homarus americanus. Journal of Experimental and Marine Biology and Ecology, 62: 185-200.
Cox, A. J., & Hebert, P. D. N. 2001. Colonization, extinction, and phylogeographic patterning in a freshwater crustacean. Molecular Ecology, 10: 371-386.
Dimmock, A., Williamson, I., & Mather, P. B. 2004. The influence of environment on the morphology of Macrobrachium australiense (Decapoda: Palamonidae). Aquaculture International, 12: 435-456.
Doyle, J. J., & Gaut, B. S. 2000. Evolution of genes and taxa : a primer. Plant Mol. Biol., 42: 1-6.
Fincham, A. A. 1987. A New Species of Macrobrachium (Decapoda, Caridea, Palaemonidae) from Northern Territory, Australia and a key to Australian species of the Genus. Zoological Scripta, 16 (4): 351-354.
Elizabeth, L. C., Burton K. L., Engstrom, M. D., Eger J. L., & Herbert, P. D. N. 2007 DNA barcoding of Neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes, 7 (2): 184–190.
Excoffier, L., Laval G., & Schneider.S. 2005 Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47-50.
Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W., & Herbert, P. D. N. 2005. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. USA, 103: 968-971.
Hajibabaei, M., Smith, M. A., Janzen, Rodriguez, J. J., Whitfield, J. B., & Herbert, P. D. N. 2005. A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6: 959-964.
Hebert, P. D. N., Cywinska, A., Ball, S. B., & DeWaard, J. R. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B., 270: 313-321.
Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., & Hallwachs, W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. USA, 101(41): 14812-14817.
Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. 2004. Identification of birds through DNA barcodes. Public Library of Science Biology, 2(10): 1657-1663.
Holthuis, L. B. 1950. The Decapoda of the Siboga Expedition. Part X. The Palaemonidae collected by the Siboga and Snellius expeditions, with remarks on other species, Part I: Subfamily Palaemoninae. Siboga-Exped. Leiden 39a: 1-268.
Jayachandran, K. V. 2001. Palaemonid Prawns: Biodiversity, Taxonomy, Biology and Management. USA: Science Publishers Inc. Press.
Jayachandran, K. V., & Raji, A.V. 2005. Three new species of Macrobrachium BATE, 1868 (Decapoda: Palaemonidae), from the Western Ghats of Kerala State, India. Crustaceana, 77 (10): 1179-1192.
Karplus I., Hulata, G., & Zafrir S. 1992. Social control of growth in Macrobrachium rosenbergii. IV. The mechanism of growth suppression in runts. Aquaculture, 106: 275–283.
Karplus I., Barki, A., Manor, R., Parnes, S., Aflalo, E. D., & Amir, S. 2005. Growth of redclaw crayfish (Cherax quadricarinatus) in a three-dimensional compartments system: Does a neighbor matter? Aquaculture, 252: 348-355
Knowlton, N. 2000. Molecular genetic analysis of species boundaries in the sea. Hydrobiologia, 420: 73-90.
Knowlton, N., & Weigt, L. A. 1998. New dates and new rates for divergence across the Isthmus of Panama. Proc. R. Soc. Lond. B., 265: 2257-2263.
Keenan, C. P., Davie, P. J. F., & Mann, D. L. 1998. A revision of the genus Scylla de Haan, 1833 (Crustacea: Decapoda: Brachyura: Portunidae). Raffles Bulletin of Zoology, 46 (1): 217-245.
Kumar, S., Tamura, K., & Nei, M. 2004. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence. Alignment Briefings in Bioinformatics, 5: 150-163.
Kuris, K. M., Raanan, N., Sagi, A., & Cohen, D. 1987. Morphotypic differentiation of male Malaysian giant prawns, Macrobrachium rosbergii. Journal of Custacean Biology, 7 (2): 219-237.
Lambert, D. M., Baker, A., Huynen, L., Haddrath, O., Hebert, P. D. N., & Millar, C. D. 2005. Is a large-scale DNA-based inventory of ancient life possible? Jounral of Heridity, 96 (3): 279-284.
Lee, C. L. 1979. A mass migration of the freshwater prawn, Macrobrachium australiense Holthuis 1950 (Decapoda: Palaemonidae). Crustaceana, 37: 219-222.
Li, J., Cai, C., & Clarke, A. 2006. A new species of troglobitic freshwater prawn of the genus Macrobrachium from Southern China (Crustacea: Decapoda: Palaemonidae). The Raffles Bulletin of Zoology, 54 (2): 277-282.
Lin, C. J., 2007. A field guide to freshwater fish and shrimps in Taiwan. Tian xia yuan jianchu ban Press (in Chinese).
Liu, M. Y. 2006. Molecular systematics of the genus Macrobrachium with notes on the phylogeography and population genetics of M. asperulum in Taiwan. [Ph.D. thesis]: National Tsing Hua University, Taiwan, 73p.
Liu, M. Y., Cai, Y. X., & Tzeng, C. S. 2007. Molecular systematics of the freshwater prawn genus Macrobrachium Bate, 1868 (Crustacea: Decapoda: Palaemonidae) inferred from mtDNA sequences, with emphasis on East Asian species. Zoological Studies, 46 (3): 272-289.
Ng, P. K. L. 1992. On a new species of blackwater prawn, Macrobrachium oxyphilus (Crustacea: Decapoda: Caridea: Palaemonidae), from peat swamps in Peninsular Malaysia. Zoologische Mededelingen, 66: 441-445.
Ou, A. C. T., & Yeo, D. C. J. 1995. A new species of freshwater prawn, Macrobrachium platycheles (Decapoda: Caridea: Palaemonidae) from Singapore and Peninsular Malaysia. The Raffles Bulletin of Zoology, 43 (2): 299-308.
Pereira, S. L., & Baker, A. J. 2004. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evolutionary Biology, 4:17.
Ra’anan, Z., Sagi, A., Wax, Y., Karplus, I., Hulata, G., & Kuris, A. 1991. Growth, size rank, and maturation of the freshwater prawn, Macrobrachium rosenbergii: analysis of marked prawns in an experimental population. The Biological Bulletin, 181: 379-386.
Rice, N. H. 2005. Further evidence for paraphyly of the Formicariidae (Passeriformes). The Condor, 107: 910-915.
Riek, E. F. 1951. The Australian Freshwater Prawns of the Family Palaemonidae. Records of the Australian Museum, 22(4): 358-367.
Saitou, N., & Nei, M. 1987. The neighbour-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4 (4): 406-425.
Salman, D. S., Page, P. J., Naser, D. N., & A. G. Yasser. 2006. The invasion of Macrobrachium nipponense (De Hann, 1849) (Caridea: Palaemonidae) into the Southern Iraqi Marshes. Aquatic Invasions, 1 (3): 109-115.
Segal, E., & Roe, A. 1975. Growth and behaviour of post-juvenile Macrobrachium rosenbergii in close confinement. Proceedings of the World Mariculture Society, 6: 67-88.
Short, J. W., 2000. Systematics and Biogeography of Australian Macrobrachium (Crustacea: Decapoda: Palaemonidae) [Ph.D. thesis]: University of Southern Queensland, 395p.
Short, J. W. 2004. A revision of Australian river prawns, Macrobrachium (Crustacea: Decapoda: Palaemonidae). Hydrobiologia, 525: 1-100.
Shy, J. Y., & Yu, H. P. 1998. Freshwater shrimps of Taiwan. National Museum of Marine Biology and Aquarium Press, Kaohsiung, Taiwan, (in Chinese).
Simison, B. W., & Lindberg, D. R. 1999. Morphological and molecular resolution of a putative cryptic species complex : A case study of Notoacmea fascicularis (Menke, 1851) (Gastropoda: Patellogastropoda). Journal of Molluscan Studies, 65: 99-109.
Smith, A. M., Woodley, N. E., Janzen, D. H., Hallwachs, W., & Hebert, P. D. N. 2005. DNA barcodes reveal cryptic host-specificity within the presumed polyphagousi members of a genus of parasitoid flies (Diptera: Tachinidae). Proc. Natl. Acad. Sci. USA, 103 (10): 3657-3662.
Sorenson, M. D., & Quinn, T. W. 1998. Numts : A challenge for avian systematics and population biology, The Auk. 115(1): 214-221.
Stoeckle M. 2003. Taxonomy, DNA, and the barcode of life. BioScience, 53: 796–797.
Thalmann, O., Hebler, J., Poinar, H. N., Paabo, S., & Vigilant, L. 2004. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Molecular Ecology, 13: 321-335.
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. 2005. DNA Barcoding Australia’s fish species. Philosophical Transactions of the Royal Society, 360: 1847-1857.
Wares, J. P., & Cunningham, C. W. 2001. Phylogeography and historical ecology of the North Atlantic Intertidal. Evolution, 55 (12): 2455-2469.
Winker, K., & Pruett, C. L. 2006. Seasonal migration, speciation, and morphological convergence in the genus Catharus (Turdidae). The Auk, 123 (4): 1052-1068.
Witt, J. D. S., Threloff, D. L., Hebert, P. D. N. 2006. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology, 15: 3073-3082
Woese, C. R., & Fox, G. E. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA, 74 (11): 5088-90.
Wowor, D. 1999. Description of a new species of blackwater prawn, Macrobrachium purpureamanus (Crustecea: Decapoda: Caridea: Palaemonidae), from Kundur Island, Indonesia. The Raffles Bulletin of Zoology, 47 (1): 33-43.
Xuan, N. V. 2003. Two new freshwater prawns of the genus Macrobrachium (Decapoda, Caridea, Palaemonidae) from the highlands of South Vietnam. Crustaceana, 76 (4):453-467.

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