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16S and 28S rDNA Sequences in Phylogenetic Analyses of Freshwater Prawns (Macrobrachium Bate, 1868) from Taiwan

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Abstract Using 15 species of freshwater prawns (Macrobrachium Bate, 1868) from Taiwan as the study material, characters of mitochondrial 16S rDNA sequences (16S) and nuclear 28S rDNA sequences (28S) were examined. Their phylogenetic analyses were conducted with Bayesian (BI), maximum likelihood (ML), maximum parsimony (MP), and minimum evolution and neighbor-joining (MENJ) methods. The 16S extracted was smaller in sequence length, rich in adenine, poor in cyctosine, and biased strongly to transitions in the nucleotide substitutions, whereas the 28S extracted was larger, rich in guanine, and biased to transversions. In the separate analyses of the two genes, the phylogenetic trees derived from the 28S had appreciably higher topological resolution with deeper branching (less polytomies) and higher topological confidence with stronger phylogenetic signals than the 16S trees. The poor resolution and confidence of the 16S trees were attributable primarily to its poor sequence divergences associated with high transition/transversion (ts/tv) ratios and low α-values of the gamma distributions. The result was a severe convergence of taxa within a narrow range of small genetic distances, so that their bifurcation could not be determined unambiguously. The 28S was highly diverged and had larger genetic distances with low ts/tv ratios and high α-values, resulting in much less convergence of the taxa. The 28S tree reconstructed with BI produced the best topological resolution and confidence in the separate analyses. The partition homogeneity test indicated that the 16S and 28S data sets were congruent. Their combined analyses with ML, MP, and MENJ showed no improvement in both topological resolution and confidence from the separate analyses of the 28S. With BI the combined analysis produced mixed results; improved the estimates of phylogenies for some of the taxa but confused or even obscured for the others.

Affiliations: 1: b Taiwan Endemic Species Research Institute, Chichi, Nantou, Taiwan (RTC, CFT, ; 2: a Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan (RTC, correspondence,; WNT, correspondence,


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1. Bate C. S. 1868 "On a new genus, with four new species of freshwater prawns." Proceedings of the Zoological Society of London Vol 1868 363 368
2. Belshaw R. , Fitton M. , Herniou E. , Gimeno C. , Quicke D. J. 1998 "A phylogenetic reconstruction of the Ichneumonoidea (Hymenoptera) based on the D2 variable region of 28S ribosomal RNA." Systematic Entomology Vol 23 109 123 [Crossref]
3. Bloomberg S. P. , Garland T. J. , Ives A. R. 2003 "Testing for phylogenetic signal in comparative data: behavioral traits are more labile." Evolution Vol 57 717 745 [Crossref]
4. Bouchon D. , Souty-Grosset C. , Raimond R. 1994 "Mitochondrial DNA variation and markers of species identity in two penaeid shrimp species." Aquaculture Vol 127 131 144 [Crossref]
5. Brower A. V. Z. , Desalle R. , Vogler A. 1996 "Gene trees, species trees, and systematics: a cladistic perspective." Annual Review of Ecology and Systemstics Vol 27 423 450 [Crossref]
6. Brown W. M. , George M. Jr , Wilson A. C. 1979 "Rapid evolution of animal mitochondrial DNA." Proceedings of the National Academy of Sciences of the United States of America Vol 76 1967 1971 [Crossref]
7. Burggraf S. G. , Stetter K. O. , Woese C. R. 1992 "A phylogenetic analysis of Aquifex pyrophilus." Systematic and Applied Microbiology Vol 15 352 356 [Crossref]
8. Cai Y. , Jeng M. S. 2001 "On a new species of Macrobrachium Bate, 1868 (Decapoda, Palaemonidae) from northern Taiwan." Crustaceana Vol 74 275 283 [Crossref]
9. Chang C. H. , Chuang S. C. , Chen Y. R. , Chen J. H. 2005 "NADH Dehydrogenase Subunit 1 gene of the earthworm Amynthas gracilis (Kinberg, 1867) (Oligochaeta: Megascolecidae), with the discussion on inferring the megascolecid phylogeny using DNA sequences." Taiwania Vol 50 (2) 71 79
10. Chavarria G. , Carpenter J. M. 1995 "“Total evidence” and the evolution of highly social bees." Cladistics Vol 10 229 258 [Crossref]
11. Chen R. T. , Tsai C. F. , Tzeng W. N. 2009 "Freshwater prawns (Macrobrachium Bate, 1868) of Taiwan with special references to their biogeographic origins." Journal of Crustacean Biology Vol 29 232 244 [Crossref]
12. Conant G. C. , Lewis P. O. 2001 "Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference." Molecular Biology and Evolution Vol 18 1024 1033 [Crossref]
13. Cowles R. P. 1914 "Palaemons of the Philippine Islands." Philippine Journal of Science Vol 9 319 403
14. Crandall K. A. , Fetzner J. W. Jr , Lawler S. H. , Kinnersley M. , Austin C. M. 1999 "Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes." Australian Journal of Zoology Vol 47 199 214 [Crossref]
15. Crandall K. A. , Harris D. J. , Fetzner J. W. Jr 2000 "The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proceedings of the Royal Society of London." Series B. Biological Sciences Vol 267 1679 1686 [Crossref]
16. Dana J. D. 1852 "Conspectus Crustaceorum quae in Orbis Terrarum circumnavigatione, Carolo Wilkes e Classe Reipublicae Foederatae Duce, lexit et descripsit." Proceeding of the Academy of natural Sciences of Philadelphia Vol 1852 10 28
17. Daniels S. R. , Hamer M. , Rogers C. 2004 "Molecular evidence suggests an ancient radiation for the fairy shrimp genus Streptocephalus (Branchiopoda: Anostraca)." Biological Journal of the Linnean Society Vol 82 313 327 [Crossref]
18. David I. B. , Blackler A. W. 1972 "Maternal and cytoplasmic inheritance of mitochondrial DNA in Xenopus." Developmental Biology Vol 29 152 161 [Crossref]
19. De Haan W. 1833–1850 "Crustacea." In, von Siebold P. F. Fauna japonica sive descripto animalium, quae in itinere per japoniam, jussu et aus piciis superiorum, qui summum in India Batava Imperium Tenent, Suscepto, Annis 1823–1830 Collegit, Norts, Obervationibus et Adumbrationibus Illustravit, i-xxxi, ix-xvi, 1-243, plates A-J, L-Q, 1-55, circ. tab. 2 Lugduni-Batavorum
20. De Man J. G. 1892 "Decapoda des indischen Archipels." 265 527 In, Weber M. Zoologische Ergebnisse einer Reise in Niederländisch Ost-Indien
21. Farris J. S. , Källersjo M. , Kluge A. G. , Bult C. 1995 "Constructing a significance test for incongruence." Systematic Biology Vol 44 570 572 [Crossref]
22. Felsenstein J. 1978 "Cases in which parsimony or compatibility methods will be positively misleading." Systematic Zoology Vol 27 401 410 [Crossref]
23. Fetzner J. W. Jr , Crandall K. A. 2001 "Genetic Variation." 291 326 In, Holdich D. M. Biology of Freshwater Crayfish Blackwell Science Oxford
24. Galtier N. , Gouy M. 1995 "Inferring phylogenies from DNA sequences of unequal base compositions." Proceedings of the National Academy of Sciences of the United States of America Vol 92 11317 11321 [Crossref]
25. Galtier N. , Gouy M. 1998 "Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis." Molecular Biology and Evolution Vol 15 871 879 [Crossref]
26. Goldman N. , Yang Z. 1994 "A codon-based model of nucleotide substitution for protein-coding DNA sequences." Molecular Biology and Evolution Vol 11 725 736
27. Gonzalez I. L. , Sylvester J. E. , Smith T. F. , Stambolian D. , Schmickel R. D. 1990 "Ribosomal RNA gene sequences and hominoid phylogeny." Molecular Biology and Evolution Vol 7 203 219
28. Grandjean F. , Gouin N. , Frelon M. , Souty-Grosset C. 1998 "Genetic and morphological systematic studies on the crayfish Austropotamobius pallipes." Journal of Crustacean Biology Vol 18 549 555 [Crossref]
29. Graur D. , Li W. H. 2000 "Molecular Phylogenetics." 165 247 In, Graur D. , Li W. H. Fundamentals of Molecular Evolution Sinauer Sunderland, MA
30. Hall T. A. 1999 "BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT." Nucleic Acids Symposium Series Vol 41 95 98
31. Harding G. C. , Kenchington E. L. , Bird C. J. , Pezzack C. S. , Landry D. C. 1997 "Genetic relationships among subpopulations of the American lobster (Homarus americanus) as revealed by random amplified polymorphic DNA." Canadian Journal of Fisheries and Aquatic Science Vol 54 1762 1771 [Crossref]
32. Hasegawa M. , Kisino H. , Yano T. 1985 "Dating of the human-ape splitting by a molecular clock of mitochondrial DNA." Journal of Molecular Evolution Vol 21 160 174 [Crossref]
33. Hasegawa E. , Kasuya E. 2006 "Phylogenetic analysis of the insect order Odanata using 28S and 16S rDNA sequences: a comparison between data sets with different evolutionary rates." Entomological Science Vol 9 55 66 [Crossref]
34. Hasegawa M. , Hashimoto T. 1993 "Ribosomal RNA trees misleading?" Nature Vol 361 23 [Crossref]
35. Hassouna N. , Michot B. , Bachellerie J. P. 1984 "The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes." Nucleic Acids Research Vol 12 3563 3583 [Crossref]
36. Huelsenbeck J. P. , Ronquist F. 2001 "MR-BAYES: Bayesian inference of phylogeny." Bioinformatics Vol 17 754 755 [Crossref]
37. Hwang J. J. , Yu H. P. 1982 "Studies on the freshwater shrimps of the genus Macrobrachium (Crustacea: Decapoda: Palaemonidae) from Taiwan." Quarterly Journal of the Taiwan Museum Vol 25 157 180
38. Jarman S. N. , Nicol S. , Elliott N. G. , McMinn A. 2000 "28S rDNA evolution in the Eumalacostraca and the phylogenetic position of krill." Molecular Phylogenetics and Evolution Vol 17 26 36 [Crossref]
39. Jesus J. , Harris D. J. , Brehm A. 2007 "Relationships of Afroablepharus Greer, 1974 skinks from the Gulf of Guinea islands based on mitochondrial and nuclear DNA: Patterns of colonization and comments on taxonomy." Molecular Phylogenetics and Evolution Vol 45 904 914 [Crossref]
40. Jin L. , Nei M. 1990 "Limitations of the evolutionary parsimony of phylogenetic analysis." Molecular Biology and Evolution Vol 7 82 102
41. Keller I. , Bensasson D. , Nichols R. A. 2007 "Transition-Transversion bias is not universal: a counter example from grasshopper pseudogenes." PLoS Genetics Vol 3 (2) 0185 0191
42. Kemp S. 1917 "Leander styliferus, Milne Edwards, and related forms. Notes on Crustacea Decapoda in the Indian Museum. IX." Record of the Indian Museum Vol 13 203 231
43. Kimura M. 1980 "A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences." Journal of Molecular Biology Vol 16 111 120
44. Kumar S. K. , Tamura K. , Nei M. 2004 "MEGA3: Intergrated software for molecular evolutionary genetics analysis and sequence alignment." Briefings in Bioinformatics Vol 5 150 163 [Crossref]
45. Lecointre W. P. , Deleporte P. 2005 "Total evidence requires exclusion of phylogenetically misleading data." Zoologica Scripta Vol 34 101 117 [Crossref]
46. Li W. H. , Gouy M. , Sharp P. M. , O'hUigin C. , Yang Y. W. 1990 "Molecular phylogeny of Rodentia, Lagomorpha, Primates, Artidactyla and Carnivore and molecular clocks." Proceedings of the National Academy of Sciences of the United States of America Vol 87 6703 6707 [Crossref]
47. Liu M. Y. , Cai Y. X. , Tzeng C. S. 2007 "Molecular systematics of the freshwater prawn genus Macrobrachium Bate, 1868 (Crustacea: Decapoda: Palaemondiae) inferred from mtDNA sequences, with emphasis on East Asian species." Zoological Studies Vol 46 272 289
48. Lockhart P. J. , Steel M. A. , Hendy M. D. , Penny D. 1994 "Recovering evolutionary trees under a more realistic model of sequence evolution." Molecular Biology and Evolution Vol 11 605 612
49. Loomis W. F. , Smith D. W. 1990 "Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison." Proceedings of the National Academy of Sciences of the United States of America Vol 87 9093 9097 [Crossref]
50. Machordom A. , Macpherson E. 2004 "Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence." Molecular Phylogenetics and Evolution Vol 33 259 279 [Crossref]
51. Miers E. J. 1875 "On some new or undescribed species of Crustacea from the Samoa Islands." Annals and Magazine of Natural History Vol 16 (4) 341 344 [Crossref]
52. Misof B. , Rickert A. M. , Buckely T. R. , Freck G. , Sauer K. P. 2001 "Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of Anisoptera." Molecular Biology and Evolution Vol 18 27 37 [Crossref]
53. Miyamoto M. M. , Kraus F. , Ryder O. A. 1990 "Phylogeny and evolution of antlered deer determined from mitochondrial DNA sequences." Proceedings of the National Academy of Sciences of the United States of America Vol 87 6127 6131 [Crossref]
54. Moritz C. , Dowling T. E. , Brown W. M. 1987 "Evolution of animal mitochondrial DNA: Relevance for population biology and systematics." Annual Review of Ecology and Systematics Vol 18 269 292 [Crossref]
55. Morrison C. L. , Rios R. , Duffy J. E. 2004 "Phylogenetic evidence for an ancient rapid radiation of Caribbean sponge dwelling snapping shrimps (Synalpheus)." Molecular Phylogenetics and Evolution Vol 30 563 581 [Crossref]
56. Muraji M. , Tachikawa S. 2000 "Phylogenetic analysis of water striders (Hemiptera: Gerroidea) based on partial sequences of mitochondrial and nuclear ribosomal RNA genes." Entomological Science Vol 3 (4) 615 626
57. Murphy N. P. , Austin C. M. 2002 "A preliminary study of 16S rRNA sequence variation in Australian Macrobrachium shrimps (Palaemonidae: Decapoda) reveals inconsistencies in their current classification." Invertebrate Systematics Vol 16 697 701 [Crossref]
58. Murphy N. P. , Austin C. M. 2003 "Molecular taxonomy and phylogenetics of some species of Australian palaemonid shrimps." Journal of Crustacean Biology Vol 23 169 177 [Crossref]
59. Murphy N. P. , Austin C. M. 2004 "Multiple origins of the endemic Australia Macrobrachium (Decapoda: Palaemonidae) based on 16S rRNA mitochondrial sequences." Australian Journal of Zoology Vol 52 549 559 [Crossref]
60. Murphy N. P. , Austin C. M. 2005 "Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy and the convergent evolution of abbreviated larval development." Zoologica Scripta Vol 34 (2) 187 197 [Crossref]
61. Muse S. V. 1995 "Evolutionary analyses of DNA sequences subject to constraints on secondary structure." Genetics Vol 139 1429 1439
62. Muse S. V. 1996 "Estimating synonymous and nonsynonymous substitution rates." Molecular Biology and Evolution Vol 13 105 114 [Crossref]
63. Navidi W. C. , Churchill G. A. , Von Haeseler A. 1991 "Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants." Molecular Biology and Evolution Vol 8 128 143
64. Nichols R. 2001 "Gene trees and species trees are not the same." Trends in Ecology and Evolution Vol 16 358 364 [Crossref]
65. Ovendon J. R. , Booth J. D. , Smolenski A. J. 1997 "Mitochondrial DNA phylogeny of red and green rock lobsters." Marine and Freshwater Research Vol 48 1131 1136 [Crossref]
66. Page R. D. M. , Holmes E. C. 1998 "Measuring genetic change." 135 171 In, Page R. D. M. , Holmes E. C. Molecular evolution: a phylogenetic approach Blackwell Science Malden, MA
67. Palumbi S. R. , Benzie J. 1991 "Large mitochondrial DNA differences between morphologically similar penaeid shrimp." Molecular Marine Biology and Biotechnology Vol 1 27 34
68. Posada D. , Crandall K. A. 1998 "Modeltest: testing the model of DNA substitution." Bioinformatics Vol 14 817 818 [Crossref]
69. Purvis A. , Bromham L. 1997 "Estimating the Transition/Transversion ratio from independent pairwise comparisons with an assumed phylogeny." Journal of Molecular Evolution Vol 44 112 119 [Crossref]
70. Reeder T. W. 2003 "A phylogeny of the Australian Sphenomorphus group (Scincidae: Squamata) and the phylogenetic placement of the crocodile skinks (Tribolonotus): Bayesian approaches to assessing congruence and obtaining confidence in maximum likelihood inferred relationships." Molecular Phylogenetics and Evolution Vol 27 384 397 [Crossref]
71. Reeves J. H. 1992 "Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA." Journal of Molecular Evolution Vol 35 17 31 [Crossref]
72. Rodriguez F. J. , Oliver J. L. , Marin A. , Medina J. R. 1990 "The general stochastic model of nucleotide substitution." Journal of Theoretical Biology Vol 142 485 501 [Crossref]
73. Rozas J. , Sanchez-DelBarrio J. C. , Messeguer X. , Rozas R. 2003 "DnaSP, DNA polymorphism analyses by the coalescent and other methods." Bioinformatics Vol 19 2496 2497 [Crossref]
74. Sarver S. K. , Silberman J. D. , Walsh P. J. 1998 "Mitochondrial DNA sequence evidence supporting the recognition of two subspecies or species of the Florida Spiny Lobster." Journal of Crustacean Biology Vol 18 177 186 [Crossref]
75. Schoniger M. , Von Haeseler A. 1995 "Performance of the maximum likelihood, neighbor joining, and maximum parsimony methods when sequence sites are not independent." Systematic Biology Vol 44 533 547 [Crossref]
76. Shull H. C. , Perez-Losada M. , Blair D. , Sewell K. , Sinclair E. A. , Lawler S. , Ponniah M. , Crandall K. A. 2005 "Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA." Molecular Phylogenetics and Evolution Vol 37 249 263 [Crossref]
77. Shy J. Y. , Yu H. P. 1998 Freshwater Shrimps of Taiwan National Museum of Marine Biology and Aquarium Pingdong, Taiwan 103
78. Sidow A. , Steel T. P. 1992 "Estimating the fraction of invariable codons with a capture-recapture method." Journal of Molecular Evolution Vol 35 253 260 [Crossref]
79. Sullivan J. , Holsinger K. E. , Simon C. 1995 "Among-site rate variation and phylogenetic analysis of the 12S rRNA in Sigmodontine rodents." Molecular Biology and Evolution Vol 12 988 1001
80. Swofford D. L. , Olsen G. L. , Waddell P. J. , Hillis D. M. 1996 "Phylogenetic inference." 407 514 In, Hillis D. M. , Moritz C. , Mable B. K. Molecular Systematics Sinauer Sunderland, MA
81. Swofford D. L. 2002 PAUP *: Phylogenetic analysis using parsimony (and other methods) 4.0.b10 Sinauer Associates Sunderland Massachusetts, USA
82. Tamura K. , Nei M. 1993 "Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees." Molecular Biology and Evolution Vol 10 512 526
83. Tateno Y. , Takezaki N. , Nei M. 1994 "Relative efficiencies of the maximum likelihood, neighbor joining, and maximum parsimony methods when substitution rate varies with site." Molecular Biology and Evolution Vol 11 261 277
84. Thallwitz J. 1891 "Ueber einige neue Indo-Pacifische Crustaceen (vorläufige mittheilung)." Zoologische Anzeiger Vol 14 96 103
85. Thallwitz J. 1892 "Decapoden-Studien, inbesondere basirt auf A. B. Meyer's Sammlungen im Ostindischen Archipel, nebst einer Aufzähulung der Decapoden und Stomatopoden des Dresdener Museums." Abhandlungen und Berichte des Königlichen Zoologischen und Anthropologisch-Ethnographischen Museums zu Dresden Vol 1890–1891 (3) 1 55
86. Thompson J. D. , Higgins D. G. , Gibson T. J. 1994 "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." Nucleic Acids Research Vol 22 4673 4680 [Crossref]
87. Von Martens E. 1868 "Über einige ostasiatische Süsswasserthiere." Archiv für Naturgeschichte Vol 34 1 64
88. Wakeley J. 1993 "Substitution-rate variation among sites and the estimation of transition bias." Molecular Biology and Evolution Vol 11 426 442
89. Wakeley J. 1996 "The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance." Trends in Ecology & Evolution Vol 11 (4) 158 162 [Crossref]
90. Wiens J. J. 1998 "Combining data sets with different phylogenetic histories." Systematic Biology Vol 47 568 581 [Crossref]
91. Xia X. , Xie Z. 2001 "DAMBE: Data analysis in molecular biology and evolution." Journal of Heredity Vol 92 371 373 [Crossref]
92. Yang Z. 1993 "Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites." Molecular Biology and Evolution Vol 10 1396 1401
93. Yang Z. 1996 "Among-site rate variation and its impact on phylogenetic analyses." Trends in Ecology and Evolution Vol 11 (9) 367 372 [Crossref]

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