Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals

Journal of Molecular Evolution

Volumn 45, Issue 4, 1997, Pages 397-411

  Romano, Sandra L ^a,b   Palumbi, Stephen R ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b UNIVERSITY OF GUAM   (Guam)

Author keywords

Mitochondrial 16S ribosomal RNA; Phylogenetic analysis; Scleractinia; Secondary structure models

Indexed keywords

DNA; RNA 16S;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORAL; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEIN SECONDARY STRUCTURE; TAXONOMY;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; CNIDARIA; DNA PRIMERS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; TIME FACTORS;

ANIMALIA; ANTHOZOA; METAZOA; SCLERACTINIA;

EID: 0030875715     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006245     Document Type: Article

References (71)

1. Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schrier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457-465
2. Attardi G (1985) Animal mitochondrial DNA: an extreme example of genetic economy. Int Rev Cyt 93:93-145
3. Avise JC (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Phil Trans R Soc London, (B) 312:325-342
4. Beckman KB, Smith MF, Orrego C (1993) Purification of mitochondrial DNA with Wizard™ Minipreps DNA purification system. Promega Notes 43:10-13
5. Best BA, Thomas WK (1993) Anthozoa mitochondrial DNA: a fundamentally different rate of evolution. Amer Zool 43:99A (abstract 459)
6. Bibb MJ, VanEtten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167-180
7. Bridge D (1994) PhD Dissertation, Yale University
8. Bridge D, Cunningham CW, deSalle R, Buss LW (1995) Class-level relationships in the phylum Cnidaria: Molecular and morphological evidence. Mol Biol Evol 12:679-689
9. Bridge D, Cunningham CW, Schierwater B, DeSalle R, Buss LW (1992) Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. PNAS 89:8750-8753
10. Cantatore P, Roberti M, Rainaldi G, Gadaleta MN, Saccone C (1989) The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J Biol Chem 264:10965-10975
11. Cedergren R, Gray MW, Abel Y, Sankoff D (1988) The evolutionary relationships among known life forms. J Mol Evol 28:98-112
12. Chen CA, Odorico DM, Lohuis Mt, Veron JEN, Miller DJ (1995) Systematic relationships within the Anthozoa (Cnidaria: Anthozoa) using the 5′-end of the 28S rDNA. Molec Phylog Evol 4:175-183
13. Christen R, Ratto A, Baroin A, Perasso R, Grell KG, Adoutte A (1991) An analysis of the origin of metazoans, using comparisons of partial sequences of the 28s RNA, reveals an early emergence of triploblasts. EMBO 10:499-503
14. Clary DO, Wolstenholme DR (1985) The ribosomal RNA genes of Drosophila mitochondrial DNA. Nucleic Acids Res 13:4029-4045
15. Cunningham CW, Buss LW (1993) Molecular evidence for multiple episodes of paedomorphosis in the family Hydractiniidae. Biochem Syst Ecol 21:57-69
16. Derr JN, Davis SK, Woolley JB, Wharton RA (1992) Variation and the phylogenetic utility of the large ribosomal subunit of mitochondrial DNA from the insect order Hymenoptera. Molec Phylog Evol 1: 136-147
17. DeSalle R, Freedman T, Prager EM, Wilson AC (1987) Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J Mol Evol 26:157-164
18. Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256-267
19. Fang Q, IV WCB, Blocker HD, Whitcomb RF (1993) A phylogeny of new world Deltocephalus-like leafhopper genera based on mitochondrial 16S ribosomal DNA sequences. Molec Phylog Evol 2: 119-131
20. Felsenstein J (1993) Phylogeny inference package (PHYLIP) 5.3c. Dept. of Genetics, University of Washington, Seattle
21. France SC, Rosel PE, Agenbroad JE, Mullineaux LS, Kocher TD (1996) DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two subclass organization of the Anthozoa (Cnidaria). Mol Mar Bio Biotechnol 5:15-28
22. Fukuda M, Wakasugi S, Tsuzuki T, Homiyama H, Shimada K, Miyata T (1985) Mitochondrial DNA-like sequences in the human nuclear genome. J Mol Biol 186:257-266
23. Gatesy J, Yelon D, DeSalle R, Vrha ES (1992) Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences. Mol Biol Evol 9:433-446
24. GCG (1993) The GCG Package 7.3. The Genetics Computer Group, Madison
25. Gellissen G, Michaelis G (1987) Gene transfer: mitochondria to nucleus. In: Lee JJ, Frederick JF (eds) Endocytobiology III. Annals of the New York Academy of Sciences, NY, pp 391-401
26. Gerbi SA (1985) Evolution of ribosomal DNA. In: MacIntyre RJ (ed) Molecular evolutionary genetics. Plenum Press, New York, pp 419-517
27. Glotz C, Zwieb C, Brimacombe R, Edwards K, Kossel H (1981) Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes. Nucleic Acids Res 9:3287-3306
28. Gravel M, Leclerc D, Melançon P, Brakier-Gingras L (1989) The conserved 900 stem/loop region in Escherichia coli 16S ribosomal RNA is not required for protein synthesis. Nucleic Acids Res 17: 2723-2732
29. Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Micro Rev 58:10-26
30. Harrison PL, Babcock RC, Bull GD, Oliver JK, Wallace CC, Willis BL (1984) Mass spawning in tropical reef corals. Science 223:1184-1189
31. Harrison PL, Wallace CC (1990) Reproduction, dispersal and recruitment of scleractinian corals. In: Dubinsky Z (ed) Coral reefs. Elsevier, New York, pp 133-207
32. Hori H, Satow Y (1991) Dead-end evolution of the Cnidaria as deduced from 5S ribosomal RNA sequences. Hydrobiol 216/217:505-508
33. Jacobs HT, Elliott DJ, Math VB, Farquaharson A (1988) Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol 202:185-217
34. Jacobs HT, Posakony JW, Grula JW, Roberts JW, Xin J-H, Britten RJ, Davidson EH (1983) Mitochondrial DNA sequences in the nuclear genome of Strongylocentrotus purpuratus. J Mol Biol 165:609-632
35. Li W-H, Graur D (1991) Fundamentals of molecular evolution. Sinauer Associates, Inc., Sunderland
36. Li W-H, Luo C-C, Wu CI (1985) Evolution of DNA sequences. In: MacIntyre RJ (ed) Molecular Evolutionary Genetics. Plenum Press, New York, pp 1-94
37. Lopez, JV, Yuhki N, Masuda R, Modi W, O'Brien SJ (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39:174-190
38. Maly P, Brimacombe R (1983) Refined secondary structure models for the 16S and 23S ribosomal RNA of Escherichia coli. Nucleic Acids Res 11:7263-7286
39. Marchuk D, Drumm M, Saulino A, Collins FS (1991) Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res 19:1154
40. McMillan J, Mahony T, Veron JEN, Miller DJ (1991) Nucleotide sequencing of highly repetitive DNA from seven species in the coral genus Acropora (Cnidaria: Scleractinia) implies a division contrary to morphological criteria. Mar Biol 110:323-327
41. Miyamoto MM, Tanhauser SM, Laipis PJ (1989) Systematic relationships in the artiodactyl tribe Bovini (family Bovidae), as determined from mitochondrial DNA sequences. Syst Zool 38:342-349
42. Moazed D, Noller HF (1989) Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57:585-597
43. Moritz C, Brown WM (1986) Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425-1427
44. Moritz C, Brown WM (1987) Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. PNAS 84:7183-7187
45. Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR (1992) The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130:471-498
46. Okimoto R, Macfarlane JL, Wolstenholme DR (1994) The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis. J Mol Evol 39:598-613
47. Palumbi SR (1996) Nucleic acids II: The polymerase chain reaction. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer Associates, Inc, pp. 205-247
48. Palumbi SR, Baker CS (1994) Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Mol Biol Evol 11:426-135
49. Palumbi SR, Martin AP, Romano SL, McMillan WO, Stice L, Grabowski G (1991) The Simple Fool's Guide to PCR. Dept. of Zoology, University of Hawaii, Honolulu
50. Pashley DP, Ke LD (1992) Sequence evolution in mitochondrial ribosomal and ND-1 genes in Lepidoptera: implications for phylogenetic analyses. Mol Biol Evol 9:1061-1075
51. Pont-Kingdon GA, Okada NA, Macfarlane JL, Beagley CT, Wolstenholme DR, Cavalier-Smith T, Clark-Walker GD (1995) A coral mitochondrial mutS gene. Nature 375:109-111
52. Richmond RH, Hunter CL (1990) Reproduction and recruitment of corals: Comparisons among the Caribbean, the Tropical Pacific, and the Red Sea. Mar Ecol Prog Ser 60:185-203
53. Roe BA, Ma D-P, Wilson RK, Wong JF-H (1985) The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem 260:9759-9774
54. Romano SL (1995) A molecular phylogenetic analysis of reef-building corals. PhD Dissertation, University of Hawaii, Manoa
55. Romano SL, Palumbi SR (1996) Evolution of scleractinian corals inferred from molecular systematics. Science 271:640-642
56. Seilhamer JJ, Gutell RR, Cummings DJ (1984) Paramecium mitochondrial genes. 2 Large subunit rRNA gene sequence and microevolution. J Biol Chem 259:5173-5181
57. Smith AB, Lafay B, Christen R (1992a) Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids. Phil Trans R Soc London, (B) 338:365-382
58. Smith MF, Thomas WK, Patton JL (1992b) Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent. Mol Biol Evol 9:204-215
59. Sor F, Fukuhara H (1983) Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria. Nucleic Acids Res 11:339-348
60. Stanley GDJ (1981) Early history of scleractinian corals and its geological consequences. Geology 9:507-511
61. Swofford DL (1993) Phylogenetic Analysis Using Parsimony (PAUP) 3.1.1. Illinois Natural History Survey, Champaign
62. Tsuzuki T, Nomiyama H, Setoyama C, Maeda S, Shimada K (1983) Presence of mitochondrial-DNA-like sequences in the human nuclear DNA. Gene 25:223-229
63. Uhlenhusch I, McCracken A, Gellissen G (1987) The gene for the large (16S) ribosomal RNA from the Locusta migratoria mitochondrial genome. Curr Genet 11:631-638
64. Veron JEN (1995) Corals in space and time: the biogeography and evolution of the Scleractinia. University of New South Wales Press, Sydney
65. Wainright PO, Hinkle G, Sogin ML, Stickel SK (1993) Monophyletic origins of the Metazoa: an evolutionary link with Fungi. Science 260:340-342
66. Warrior R, Gall J (1985) The mitochondrial DNA of Hydra attenuata and Hydra littoralis consists of two linear molecules. Archives des Sciences Genève 38:439-445
67. Willis BL, Babcock RC, Harrison PL, Wallace CC (1992) Experimental evidence of hybridization in reef corals involved in mass spawning events (Abstract). In: Richmond RH (ed) Proceedings of the 7th International Coral Reef Symposium, Guam, University of Guam Press, 1:504
68. Wilson AC, Cann RL, Carr SM, George M, Gyllensten UB, Helm-Bychowski KM, Higuchi RG, Palumbi SR, Prager EM, Sage RD, Stoneking M (1985) Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linn Soc 26:375-400
69. Wolstenholme DR (1992) Animal mitochondrial DNA: structure and evolution. Int Rev Cyt 141:173-216
70. Zouros E, Ball AO, Saavedra C, Freeman KR (1994) An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus. PNAS 91:7463-7467
71. Zullo S, Sieu LC, Slightom JL, Hadler HI, Eisenstadt JM (1991) Mitochondrial D-loop sequences are integrated in the rat nuclear genome. J Mol Biol 221:1223-1235