A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods

Molecular Biology and Evolution

Volumn 22, Issue 2, 2005, Pages 251-264

  Gibson, Andrew ^a   Gowri Shankar, Vivek ^a   Higgs, Paul G ^b   Rattray, Magnus ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b MCMASTER UNIVERSITY   (Canada)

Author keywords

Base composition; Mammals; Mitochondria; Nucleotide bias; Phylogenetics; Substitution model

Indexed keywords

DNA; HELICASE; PYRIMIDINE; RIBOSOME RNA;

AMINO ACID COMPOSITION; ARTICLE; CODON; DNA BASE COMPOSITION; GENE LOCATION; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOME; MITOCHONDRIAL GENETICS; PHYLOGENETIC TREE; PHYLOGENY; PROTEIN DOMAIN; RNA GENE;

ANIMALS; BASE COMPOSITION; DNA, MITOCHONDRIAL; GENOME; MAMMALS; MITOCHONDRIAL PROTEINS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 12344282043     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi012     Document Type: Article

References (48)

1. Alfaro, M.E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 20: 255-266.
2. Amrine-Madsen, H., K.-P. Koepfli, R. K. Wayne, and M. S. Springer. 2003. A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol. Phylogenet. Evol. 28:225-240.
3. Arnason, U., J. A. Adegoke, K. Bodin, E. W. Born, Y. B. Esa, A. Gullberg, M. Nilsson, R. V. Short, X. Xu, and A. Janke. 2002. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. USA 99:8151-8156.
4. Bielawski, J. P., and J. R. Gold. 2002. Mutation patterns of mitochondrial H- and L-strand DNA in closely related Cyprinid fishes. Genetics 161:1589-1597.
5. Bohr, V. A. 2002. Repair of oxidative DNA damage in nuclear and mitochondrial DNA, and some changes with aging in mammalian cells. Free Radical Biol. Med. 32:804-812.
6. Bowmaker, M., M. Y. Yang, T. Yasukawa, A. Reyes, H. T. Jacobs, J. A. Huberman, and I. J. Holt. 2003. Mammalian mitochondrial DNA replicates bidirectionally from an initiation zone. J. Biol. Chem. 278:50961-50969.
7. Buckley, T. R. 2002. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51:509-523.
8. Clayton, D. A. 1982. Replication of animal mitochondrial DNA. Cell 28:693-705.
9. Delsuc, F., M. J. Phillips, and D. Penny. 2003. Comment on "Hexapod origins: monophyletic or paraphyletic?". Science 301:1482.
10. Delsuc, F., M. Scally, O. Madsen, M. J. Stanhope, W. W. de Jong, F. M. Catzeflis, M. S. Springer, and E. J. Douzery. 2002. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol. Biol. Evol. 19:1656-1671.
11. Douady, C. J., F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. P. Douzery. 2003. Comparison of Bayesian and maximum likelihood measures of phylogenetic reliability. Mol. Biol. Evol. 20:248-254.
12. Faith, J. J., and D. D. Pollock. 2003. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics 165:735-745.
13. Felsenstein, J. P. 1989. PHYLIP (phylogeny inference package). Version 3.6. Available from http://evolution.gs.washington. edu/phylip.html.
14. Foster P. G., and D. A. Hickey. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:284-290.
15. Foster, P. G., L. S. Jermiin, and D. A. Hickey. 1997. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44:282-288.
16. Galtier, N., and M. Guoy. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-879.
17. Gutell, R. R., B. Weiser, C. Woese, and H. F. Noller. 1985. Comparative anatomy of 16S-like ribosomal RNA. Prog. Nucleic Acid Res. 32:155-215.
18. Higgs, P. G. 2000. RNA secondary structure: physical and computational aspects. Quart. Rev. Biophys. 33:99-253.
19. Holder, M., and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4:275-284.
20. Holt, I. J., H. E. Lorimer, H. T. Jacobs, M. Y. Yang, M. Bowmaker, A. Reyes, L. Vergani, P. Angeli, and E. Gringeri. 2000. Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA. Cell 100:515-524.
21. Hudelot, C., V. Gowri-Shankar, H. Jow, M. Rattray, and P. G. Higgs. 2003. RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol. Phylogenet. Evol. 28:241-252.
22. Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
23. Jameson, D., A. P. Gibson, C. Hudelot, and P. G. Higgs. 2003. OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucleic Acids Res. 31:202-206.
24. Jow, H., C. Hudelot, M. Rattray, and P. G. Higgs. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 19: 1591-1601.
25. Lake, J. A. 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. 91:1455-1459.
26. Lin, Y. H., P. A. McLenachan, A. R. Gore, M. J. Phillips, R. Ota, M. D. Hendy, D. Penny, and P. J. Waddell. 2002. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling.
27. Lin, Y. H., P. J. Waddell, and D. Penny. 2002. Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires. Gene 294:119-129.
28. Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605-612.
29. Madsen, O., M. Scally, C. J. Douady, D. J. Kao, R. W. DeBry, R. Adkins, H. M. Amrine, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001, Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
30. Murphy, W. J., E. Eizirik, W. E. Johnson, Y. P. Zhang, O. A. Ryder, and S. J. O'Brien. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409: 614-618.
31. Murphy, W. J., E. Eizirik, S. J. O'Brien, O. Madsen, M. Scally, C. J. Douady, E. Teeling, O. A. Ryder, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351.
32. Perna, N. T., and T. D. Kocher. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41:353-358.
33. Phillips, M. J., and D. Penny. 2003. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28:171-185.
34. Reyes, A., C. Gissi, F. Catzeflis, E. Nevo, G. Pesole, and C. Saccone. 2004. Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol. Biol. Evol. 21:397-403.
35. Reyes, A., C. Gissi, G. Pesole, and C. Saccone. 1998. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol. 15:957-966.
36. Schmitz, J., M. Ohme, and H. Zischler. 2002. The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA. Mol. Biol. Evol. 19:544-553.
37. Schmitz, J., and H. Zischler. 2003. A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates. Mol. Phylogenet. Evol. 28:341-349.
38. Shadel, G. S., and D. A. Clayton. 1997. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem. 66:409-435.
39. Singer, G. A. C., and D. A. Hickey. 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17:1581-1588.
40. Springer, M. S., and E. Douzery. 1996. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J. Mol. Evol. 43:357-373.
41. Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
42. Tanaka, M., and T. Ozawa. 1994. Strand asymmetry in human mitochondrial DNA mutations. Genomics 22:327-335.
43. Taylor, D. J., and W. H. Piel. 2004. An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Mol. Biol. Evol. 21:1534-1537.
44. Waddell, P. J., H. Kishino, and R. Ota. 2002. Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Genome Informat. Ser. 13:82-92.
45. Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylog. Evol. 25:361-371.
46. Yang, M. Y., M. Bowmaker, A. Reyes, L. Vergani, P. Angeli, E. Gringeri, H. T. Jacobs, and I. J. Holt. 2002. Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication. Cell 111:495-505.
47. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
48. -. 1996. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596.