Mathematical elegance with biochemical realism: The covarion model of molecular evolution

Journal of Molecular Evolution

Volumn 53, Issue 6, 2001, Pages 711-723

  Penny, David ^a   McComish, Bennet J ^a   Charleston, Michael A ^a   Hendy, Michael D ^a  

^a MASSEY UNIVERSITY   (New Zealand)

Author keywords

Covarion model; Hidden Markov model; Rates across sites; Role of models in science

Indexed keywords

ARTICLE; BIOCHEMISTRY; GENE SEQUENCE; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; SIMULATION;

EVOLUTION, MOLECULAR; MODELS, BIOLOGICAL; MODELS, CHEMICAL;

EID: 0034777365     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002390010258     Document Type: Article

References (71)

1. Hidden Markov models of biological primary sequences information
2. Archaea sister-group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
3. Haemoglobin of the Antarctic fish Pagothenia bernacchii. Amino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative
4. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders
5. NADP-dependent enzymes II: Evolution of the mono- and dinucleotide binding domains
6. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
7. The effects of sequence length, tree topology and number of taxa on the performance of phylogenetic methods
8. The relation between the divergence of sequence and structure in proteins
9. The evolution of protein structures
10. Use of RNA secondary structure for evolutionary relationships: The case of RNase P and RNase MRP
11. The structure of cytochrome c and rates of molecular evolution
12. A hidden Markov model approach to variation among sites in rate of evolution
13. Functional correlation in amino acid residue mutations of yeast iso-2-cytochrome c that is consistent with the prediction of the concomitably variable codon theory in cytochrome c evolution
14. Rate of change of concomitantly variable codons
15. The estimate of total nucleotide substitutions from pairwise differences is biased
16. The superoxide dismutase molecular clock revisited
17. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
18. Maximum-likelihood phylogenetic analysis under a covarion-like model
19. More on the overdispersed molecular clock
20. A codon-based model of nucleotide substitution for protein-coding DNA sequences
21. Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates
22. Correlation of functional domains and rates of nucleotide substitution in cytochrome b
23. Hadamard conjugation: A versatile tool for modelling sequence evolution
24. A framework for the quantitative study of evolutionary trees
25. Discrete Fourier spectral analysis of evolution
26. The covarion model for the evolution of proteins: Parameter estimates and comparison with Holmquist, Cantor, and Jukes' stochastic model
27. Estimation of evolutionary distance between homologous nucleotide sequences
28. Evolution of RNA genomes: Does the high mutation rate necessitate high rate of evolution of viral proteins?
29. Hidden Markov models in computational biology: Applications to protein modeling
30. A unified statistical framework for sequences comparison and structural comparison
31. Using structural information in evolutionary inference: Transmembrane proteins
32. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis
33. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
34. How molecules evolve in bacteria
35. Evolutionarily conserved pathways of energetic connectivity in protein families
36. A method for extracting ancient phylogenetic signal: The rooting of the universal tree of life based on elongation factors
37. Dollo's law and the death and resurrection of genes
38. Testing the covarion hypothesis of molecular evolution
39. On the constancy of the evolutionary rate of cistrons
40. Rates of molecular evolution and the fraction of nucleotide positions free to vary
41. Analysis of insertions/deletions in protein structures
42. Mathematics yes, physics no
43. Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
44. Progress with evolutionary trees
45. The path from the RNA world
46. The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller
47. A stochastic model for the evolution of autocorrelated DNA sequences
48. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation conserved PCR primers
49. Instrumentalism revisited
50. A structural view of evolutionary divergence
51. Parsimony, likelihood and the role of models in molecular phylogenetics
52. Invariable site models and their use in phylogeny reconstruction
53. Reconstructing trees when sequence sites evolve at different rates
54. Inching toward reality: An improved likelihood of sequence evolution
55. Modeling the covarion hypothesis of nucleotide substitution
56. Fitting discrete probability distributions to evolutionary events
57. Substitution rate calibration of small subunit ribosomal subunit RNA identifies Chlorarachnida nucleomorphs as remnants of green algae
58. General time-reversible distances with unequal rates across sites: Mixing Γ and inverse Gaussian distributions with invariant sites
59. Variance-covariances matrices for evolutionary trees using Hadamard transforms
60. Hadamard conjugations and modeling sequence evolution with unequal rates across sites
61. Using novel phylogenetic methods to evaluate mammalian mtDNA
62. Hierarchical analysis of variation on the mitochondrial 16S rRNA gene among Hymenoptera
63. The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants
64. Among-site rate variation and its impact on phylogenetic analyses
65. Evolutionary processes and evolutionary noise at the molecular level