Heterotachy and tree building: A case study with plastids and eubacteria

Molecular Biology and Evolution

Volumn 23, Issue 1, 2006, Pages 40-45

  Lockhart, Peter ^a   Novis, Phil ^b   Milligan, Brook G ^c   Riden, Jamie ^a   Rambaut, Andrew ^d   Larkum, Tony ^e  

^a MASSEY UNIVERSITY   (New Zealand)

^b LANDCARE RESEARCH   (New Zealand)

^c NEW MEXICO STATE UNIVERSITY   (United States)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Covarion evolution; Heterotachy; Long branch attraction; Plastid origins

Indexed keywords

RNA POLYMERASE;

ARTICLE; BACTERIUM; CONTROLLED STUDY; EMPIRICISM; LONG BRANCH ATTRACTION; NONHUMAN; PARSIMONY ANALYSIS; PLASTID; SIMULATION; TREE;

BACTERIA; CLASSIFICATION; COMPUTER SIMULATION; DNA-DIRECTED RNA POLYMERASES; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; PLASTIDS; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS);

EID: 28944440718     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj005     Document Type: Article

References (42)

1. Ané, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in the plastid genome evolution: a new statistical test. Mol. Biol. Evol. 22:914-924.
2. Brown, R. P. 2005. Large subunit mitochondrial rRNA secondary structures and site-specific rate variation in two lizard lineages. J. Mol. Evol. 60:45-56.
3. Bruno, W. J., and A. L. Halpern. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-566.
4. Felsenstein, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
5. _. 2004. PHYLIP (phylogeny inference package). Version 3.6. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle.
6. Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-593.
7. Galtier, N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18:866-873.
8. Guo, Z., and J. W. Stiller. 2005. Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain. Mol. Biol. Evol. 10.1093/molbev/msi215.
9. Hillis, D. M., J. P. Huelsenbeck, and D. L. Swofford. 1994. Hobglobin of phylogenetics? Nature 369:363-364.
10. Horner, D. S., and T. M. Embley. 2001. Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol. Biol. Evol. 18:1970-1975.
11. Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698-707.
12. Huson, D. 1998. SplitsTree: a program for analyzing and visualizing evolutionary data. Bioinformatics 14:68-73.
13. Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artefact that unites microsporidia and archaebacteria in EF-1{alpha} phylogenies. Mol. Biol. Evol. 21:1340-1349.
14. Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
15. Lockhart, P. J., A. W. D. Larkum, M. A. Steel, P. J. Waddell, and D. Penny. 1996. Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93:1930-1934.
16. Lockhart, P. J., M. A. Steel, A. C. Barbrook, D. H. Huson, and C. J. Howe. 1998. A covariotide model describes the evolution of oxygenic photosynthesis. Mol. Biol. Evol. 15:1183-1188.
17. Lockhart, P. J., D. Huson, U.-G. Maier, M. J. Fraunholz, Y. Van de Peer, A. C. Barbrook, C. J. Howe, and M. A. Steel. 2000. How molecules evolve in eubacteria. Mol. Biol. Evol. 17:835-838.
18. Lockhart, P. J., and M. A. Steel. 2005. A tale of two processes. Syst. Biol. (in press).
19. Lopez, P., D. Casane, and H. Philippe. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19:1-7.
20. Martin, W., B. Stoebe, V. Goremykin, S. Hansmann, M. Hasegawa, and K. V. Kowallik. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162-165.
21. Mathsoft. 1999. S-Plus 2000 user's guide. Data Analysis Products Division, Mathsoft Inc., Seattle, Wash.
22. McFadden, G. I., and G. G. van Dooren. 2004. Evolution: red algal genome confirms a common origin for all plastids. Curr. Biol. 14:R514-R516.
23. Mintseris, J., and Z. Weng. 2005. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci. USA 102:10930-10935.
24. Misof, B., C. L. Anderson, T. R. Buckley, D. Erpenbeck, A. Rickert, and K. Misof. 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.
25. Morgenstern, B. 1999. Dialign 2 improvement to the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15:211-218.
26. Palmer, J. D., and C. F. Delwiche. 1998. The origin and evolution of plastids and their genomes. Pp. 375-409 in D. E. Soltis, P. S. Soltis, and J. J. Doyle, eds. Molecular systematics of plants II. Kluwer, Boston.
27. Penny, D., B. J. McComish, M. A. Charleston, and M. D. Hendy. 2001. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53:711-723.
28. Philippe, H., and A. Germot. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:830-834.
29. Philippe, H., and P. Lopez. 2001. On the conservation of protein sequences in evolution. Trends Biochem. Sci. 26:414-416.
30. Rambaut, A., and N. C. Crassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
31. Siddall, M. E. 1998. Success of parsimony in the four taxon case: long-branch repulsion by likelihood in the Farris zone. Cladistics 14:209-220.
32. Simon, C., L. Nigro, J. Sullivan, K. Holsinger, A. Martin, A. Grapputo, A. Franke, and C. McIntosh. 1996. Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes. Mol. Biol. Evol. 13:923-932.
33. Spencer, M., E. Susko, and A. J. Roger. 2005. Likelihood, parsimony, and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164.
34. Steel, M. A. 2005. Should phylogenetic models be trying to fit an elephant. Trends Genet. 21:307-309.
35. Steel, M. A., D. Huson, and P. J. Lockhart. 2000. Invariable site models and their use in phylogeny reconstruction. Syst. Biol. 49:225-232.
36. Sullivan, J. A., and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-729.
37. Susko, E., Y. Inagaki, and A. J. Roger. 2004. On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modelled. Mol. Biol. Evol. 21:1629-1642.
38. Swofford, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
39. Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-539.
40. Thornton, J. W., and B. Kolaczowski. 2005. No magic pill for phylogenetic error. Trends Genet. 21:310-311.
41. Tuffley, C., and M. Steel. 1998. Modeling the covarion hypothesis of nucleotide substitution. Math. Biosci. 147:63-91.
42. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.