Large subunit mitochondrial rRNA secondary structures and site-specific rate variation in two lizard lineages

Journal of Molecular Evolution

Volumn 60, Issue 1, 2005, Pages 45-56

  Brown, Richard P ^a  

^a LIVERPOOL JOHN MOORES UNIVERSITY   (United Kingdom)

Author keywords

16S rRNA; Bayesian inference; Covarion; Helix; Lizard; Phylogeny; Secondary structure; Skink

Indexed keywords

MITOCHONDRIAL RNA;

ARTICLE; BAYES THEOREM; COMPARATIVE STUDY; CONTROLLED STUDY; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC LINE; GENETIC VARIABILITY; LIZARD; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE;

ANIMALS; BASE SEQUENCE; DATABASES, NUCLEIC ACID; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; LIZARDS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL; VARIATION (GENETICS);

EID: 14644417169     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0119-3     Document Type: Article

References (32)

1. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:878-879
2. Buckley TR, Simon C, Flook PK, Misof B (2000) Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect large subunit rRNA gene. Insect Mol Biol 9:565-580
3. Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: Compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256-267
4. Espinosa de los Monteros A (2003) Models of the primary and secondary structure for the 12S rRNA of birds: A guideline for sequence alignment. DNA Sequence 14:241-256
5. Fu J (1998) Toward the phylogeny of the family Lacertidae: Implications from mitochondrial DNA 12S and 16S gene sequences (Reptilia: Squamata). Mol Phylogenet Evol 9:118-130
6. Fu J (2000) Toward the phylogeny of the family Lacertidae - Why 4708 base pairs of mtDNA sequences cannot draw the picture. Biol J Linn Soc 71:203-217
7. Galtier N (2001) Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol 18:866-873
8. Gutell RR, Fox GE (1988) A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res 6:R175-R269
9. Gutell RR, Weiser B, Woese CR, Noller HF (1985) Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res 32:155-216
10. Harris DJ, Arnold EN, Thomas RH (1998a) Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondria DNA sequences and morphology. Proc Roy Soc Lond B 265:1939-1948
11. Harris DJ, Arnold EN, Thomas RH (1998b) Rapid speciation, morphological evolution, and adaptation to extreme Environments in South African sand lizards (Meroles) as revealed by mitochondrial gene sequences. Mol Phylogenet Evol 10:37-48
12. Hickson RE, Simon C, Perrey SW (2000) The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol Biol Evol 17:530-539
13. Honda M, Ota H, Kobayashi M, Nabhitabhata J, Yong H-S, Hikida T (2000) Phylogenetic relationships, character evolution and biogeography of the subfamily (Reptilia: Scincidae) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 15:452-461
14. Honda M, Ota H, Köhler G, Ineich I, Chirio L, Chen S-L, Hikida T (2003) Phylogeny of the lizard subfamily Lygosominae (Reptilia: Scincidae), with special reference to the origin of the New World taxa. Genes Genet Syst 78:71-80
15. Huelsenbeck JP, Ronquist F (2001) Mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:154-755
16. Juan V, Wilson C (1999) RNA secondary structure prediction based on free energy and phylogenetic analysis. J Mol Biol 289:935-947
17. Lin SM, Chen CA, Lue KY (2002) Molecular phylogeny and biogeography of the grass lizards genus Takydromus (Reptilia: Lacertidae) of east Asia. Mol Phylogenet Evol 22:276-288
18. Kjer KM (1995) Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from frogs. Mol Phylogenet Evol 4:314-330
19. Mausfeld P, Vences M, Schmitz A, Veith M (2000) First data on the molecular phylogeography of Scincid lizards of the genus Mabuya. Mol Phylogenet Evol 17:11-14
20. Mausfeld P, Schmitz A, Bohme W, Misof B, Vrcibradic D, Rocha CFD (2002) Phylogenetic affinities of Mabuya atlantica Schmidt 1945, endemic to the Atlantic ocean archipelago of Fernando de Noronha (Brazil): necessity of partitioning the genus Mabuya Fitzinger, 1826 (Scincidae, Lygosominae). Zool Anzeiger 241:281-293
21. Misof B, Anderson CL, Buckley TR, Erpenbeck D, Rickert A, Misof K (2002) An empirical analysis of mt 16S rRNA covarion-like evolution in insects: Site specific rate variation is clustered and frequently detected. J Mol Evol 55:460-469
22. Parsch J, Braverman JM, Stephan W (2000) Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154:909-921
23. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818
24. Rodriguez F, Oliver JF, Marin A, Medina JR (1990) The general stochastic model of nucleotide substitutions. J Theor Biol 142:485-501
25. Savill NJ, Hoyle DC, Higgs PG (2001) RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum-likelihood methods. Genetics 157:399-411
26. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
27. Whiting AS, Bauer AM, Sites JW Jr (2003) Phylogenetic relationships and limb loss in Saharan African scincine lizards (Squamata: Scincidae). Mol. Phylogenet Evol 29:582-598
28. Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R (2001a) The European large subunit ribosomal RNA database. Nucleic Acids Res 29:175-177
29. Wuyts J, Van de Peer Y, De Wachter R (2001b) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 29:5017-5028
30. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 39:306-314
31. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
32. Zuker M (1989) On finding all suboptimal foldings of an RNA molecule. Science 244:48-52