The analysis of rRNA sequence-structure in phylogenetics: An application to the family Pectinidae (Mollusca: Bivalvia)

Molecular Phylogenetics and Evolution

Volumn 56, Issue 3, 2010, Pages 1059-1067

  Salvi, Daniele ^a   Bellavia, Gabriella ^a   Cervelli, Manuela ^a   Mariottini, Paolo ^a  

^a ROMA TRE UNIVERSITY   (Italy)

Author keywords

16S rDNA; Evolutionary history; ITS2 rDNA; Pectinidae; Phylogeny; Secondary structure

Indexed keywords

RIBOSOMAL SPACER DNA; RNA 16S;

ANIMAL; ARTICLE; BAYES THEOREM; CLASSIFICATION; CONFORMATION; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; SCALLOP; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; NUCLEIC ACID CONFORMATION; PECTINIDAE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

BIVALVIA; MOLLUSCA; PECTINIDAE;

EID: 77954426349     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.04.025     Document Type: Article

References (54)

1. Adamkewicz S.L., Harasewych M.G., Blake J., Saudek D., Bult C.J. A molecular phylogeny of the bivalve mollusks. Mol. Biol. Evol. 1997, 14:619-629.
2. Barucca M., Olmo E., Schiaparelli S., Canapa A. Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA. Mol. Phylogenet. Evol. 2004, 31:89-95.
3. Bauer M., Klau G.W., Reinert K. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics 2007, 8:271.
4. Beaumont A.R. Genetic distances between some scallop species. An international Compendium of Scallop Biology and Culture 1991, 151-155. The World Aquaculture Society, Baton Rouge, LA. S.E. Shumway, P.A. Sandifer (Eds.).
5. Bologna M.A., D'Inzillo B., Cervelli M., Oliverio M., Mariottini P. Molecular phylogenetics of the Mylabrini blister beetles (Coleoptera, Meloidae). Mol. Phylogenet. Evol. 2005, 37:306-311.
6. Bologna M.A., Oliverio M., Pitzalis M., Mariottini P. Phylogeny and evolutionary history of the blister beetles (Coleoptera, Meloidae). Mol. Phylogenet. Evol. 2008, 48:679-693.
7. Canapa A., Barucca M., Marinelli A., Olmo E. A molecular approach to the systematics of Antarctic scallop Adamussium colbecki. Ital. J. Zool. 1999, 66:379-382.
8. Canapa A., Barucca M., Marinelli A., Olmo E. Molecular data from the 16S rRNA gene for the phylogeny of Pectinidae (Mollusca: Bivalvia). J. Mol. Evol. 2000, 50:93-97.
9. Canapa A., Barucca M., Caputo V., Marinelli A., Cerioni P.N., Olmo E., Capriglione T., Odierna G. A molecular analysis of the systematics of three Antarctic bivalves. Ital. J. Zool. 2000, 1:127-132.
10. Coleman A.W. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet. 2003, 19:370-375.
11. Coleman A.W. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 2007, 35:3322-3329.
12. Coleman A.W., Vacquier V.D. Phylogenetic reconstruction of the Abalone (genus Haliotis) using ITS sequences. J. Mol. Evol. 2002, 54:246-257.
13. Frischer M.E., Williams J., Kenchington E. A molecular phylogeny of some major groups of Pectinidae inferred from 18S rRNA gene sequences. Bivalves: an Eon of Evolution. Paleobiological Studies Honoring Norman D. Newell 1998, 213-221. University of Calgary Press, Calgary. P.A. Jonston, J.W. Haggart (Eds.).
14. Gutell R.R., Fox G.E. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 1988, 16:175-313.
15. Gutell R.R., Gray M.W., Schnare M.N. Compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 1993, 21:3055-3074.
16. Hadjiolova K.V., Nicoloso M., Mazan S., Hadjiolov A.A., Bachellerie J.P. Alternative pre-rRNA processing pathways in human cells and their alteration by cycloheximide inhibition of protein synthesis. Eur. J. Biochem. 1993, 212:211-215.
17. Horovitz I., Meyer A. Systematics of new world monkeys (Platyrrhini, Primates) based on 16S mitochondrial DNA sequences: a comparative analysis of different weighting methods in cladistic analysis. Mol. Phylogenet. Evol. 1995, 4:448-456.
18. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
19. Insua A., López-Piñón M.J., Freire R., Méndez J. Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae). Genome 2003, 46:595-604.
20. Joseph N., Krauskopf E., Vera M.I., Michot B. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 1999, 27:4533-4540.
21. Jow H., Hudelot C., Rattray M., Higgs P.G. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 2002, 19:1591-1601.
22. Keller A., Schleicher T., Forster F., Ruderisch B., Dandekar T., Muller T., Wolf M. ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evol. Biol. 2008, 8:218.
23. Liu B., Dong B., Xiang J., Wang Z. The phylogeny of native and exotic scallops cultured in China based on 16S rDNA sequences. Chin. J. Oceanol. Limnol. 2007, 25:85-90.
24. Lydeard C., Holznagel W.E., Schnare M.N., Gutell R.R. Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequenze and secondary structures. Mol. Phylogenet. Evol. 2000, 15:83-102.
25. Mahidol C., Na-Nakorn U., Sukmanomon S., Taniguchi N., Nguyen T.T. Mitochondrial DNA diversity of the Asian moon scallop, Amusium pleuronectes (Pectinidae), in Thailand. Mar. Biotechnol. 2007, 9:352-359.
26. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 1999, 288:911-940.
27. Matsumoto M., Hayami I. Phylogenetic analysis of the family Pectinidae (Bivalvia) based on mitochondrial cytochrome c oxidase subunit I. J. Mollusc. Stud. 2000, 66:477-488.
28. Michot B., Joseph N., Mazan S., Bachellerie J.P. Evolutionary conserved structural features in the ITS2 of mammalian pre-rRNA and potential interactions with the snoRNA U8 detected by comparative analysis of new mouse sequences. Nucleic Acids Res. 1999, 27:2271-2282.
29. Müller T., Rahmann S., Dandekar T., Wolf M. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol. Biol. 2004, 4:20.
30. Oliverio M., Mariottini P. A molecular framework for the phylogeny of Coralliophila and related muricoids. J. Moll. Stud. 2001, 67:215-224.
31. Oliverio M., Mariottini P. Contrasting morphological and molecular variation in Coralliophila meyendorffii (Muricidae, Coralliophilinae). J. Moll. Stud. 2001, 67:243-246.
32. Oliverio M., Cervelli M., Mariottini P. ITS2 rRNA evolution and its use in the phylogeny of muricid neogastropods (Caenogastropoda, Muricoidea). Mol. Phylogenet. Evol. 2002, 25:63-69.
33. Oliverio M., Barco A., Modica M.V., Richter A., Mariottini P. Ecological barcoding of corallivory by ITS2 sequences: hosts of coralliophiline gastropods detected by the cnidarian DNA in their stomach. Mol. Ecol. Res. 2009, 9:94-103.
34. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
35. Puslednik L., Serb J.M. Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology. Mol. Phylogenet. Evol. 2008, 48:1178-1188.
36. Saavedra C., Peña J.B. Nucleotide diversity and Pleistocene population expansion in Atlantic and Mediterranean scallops (Pecten maximus and P. jacobaeus) as revealed by the mitochondrial 16S ribosomal RNA gene. J. Exp. Mar. Biol. Ecol. 2005, 323:138-150.
37. Saavedra C., Peña J.B. Phylogenetics of American scallops (Bivalvia: Pectinidae) based on partial 16S and 12S ribosomal RNA gene sequences. Mar. Biol. 2006, 150:111-119.
38. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
39. Schlötterer C., Hauser M.-T., van Haesler A., Tautz D. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol. Biol. Evol. 1994, 11:513-522.
40. Schultz J., Wolf M. ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol. Phylogenet. Evol. 2009, 52:520-523.
41. Schultz J., Müller T., Achtziger M., Seibel P.N., Dandekar T., Wolf M. The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res. 2006, 34:W704-W707.
42. Seibel P.N., Müller T., Dandekar T., Schultz J., Wolf M. 4SALE-a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 2006, 7:498.
43. Selig C., Wolf M., Müller T., Dandekar T., Schultz J. The ITS2 database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res. 2008, 36:D377-D380.
44. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
45. Skaloud P., Peksa O. Evolutionary inference based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta). Mol. Phylogenet. Evol. 2010, 54:36-46.
46. Smith A.D., Lui T.W.H., Tillier E.R.M. Empirical models for substitution in ribosomal RNA. Mol. Biol. Evol. 2004, 21:419-427.
47. Swofford D.L. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0b10 win 32 2002, Sinauer Associates, Sunderland.
48. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 24:4876-4882.
49. van Nues R.W., Rientjes M.J., Morré S.A., Mollee E., Planta R.J., Venema J., Raué H.A. Evolutionarily conserved structural elements are critical for processing of Internal Transcribed Spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA. J. Mol. Biol. 1995, 250:24-36.
50. Waller T.R. Evolutionary relationships among commercial scallops (Mollusca: Bivalvia: Pectinidae). Scallops: Biology, Ecology and Aquaculture 1991, 1-73. Elsevier, New York. S.E. Shumway (Ed.).
51. Waller T.R. The evolution of ''Chlamys" (Mollusc: Bivalvia: Pectinidae) in the tropical western Atlantic and eastern Pacific. Am. Malacol. Bull. 1993, 10:195-249.
52. Waller T.R. New phylogenies of the Pectinidae (Mollusca: Bivalvia): reconciling morphological and molecular approaches. Scallops: Biology, Ecology and Aquaculture 2006, 1-43. Elsevier B.V, Amsterdam, The Netherlands. S.E. Shumway, G.J. Parsons (Eds.).
53. Weekers P.H.H., De Jonckheere J.F., Dumont H.J. Phylogenetic relationships inferred from ribosomal ITS sequences and biogeographic patterns in representatives of the genus Calopteryx (Insecta: Odonata) of the West Mediterranean and adjacent West European zone. Mol. Phylogenet. Evol. 2001, 20:89-99.
54. Wolf M., Ruderisch B., Dandekar T., Schultz J., Müller T. ProfDistS: (profile-) distance based phylogeny on sequence-structure alignments. Bioinformatics 2008, 24:2401-2402.