The evolution of base composition and phylogenetic inference

Trends in Ecology and Evolution

Volumn 15, Issue 9, 2000, Pages 365-369

  Mooers, Arne Ø ^a   Holmes, Edward C ^b  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; BACTERIAL DNA; CYTOSINE; DNA; GUANINE; RNA; THYMINE;

EVOLUTION; NUCLEIC ACID; PHYLOGENETICS;

CODON USAGE; DNA BASE COMPOSITION; DNA REPLICATION; GENE MUTATION; GENOME; HUMAN; NATURAL SELECTION; NONHUMAN; PHYLOGENY; REVIEW;

BACTERIA (MICROORGANISMS); EMBRYOPHYTA;

EID: 0033844505     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-5347(00)01934-0     Document Type: Review

References (40)

1. Compositional variation and heterogeneity of nucleic acids and protein in bacteria
2. Evolutionary changes in CpG and methylation levels in the genome of vertebrates
3. The major compositional transitions in the vertebrate genome
4. Evolutionary genomics in Metazoa: The mitochondrial DNA as a model system
5. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
6. The human genome: Organization and evolutionary history
7. Warm-blooded isochore structure in Nile crocodile and turtle
8. Base composition and gene distribution: Critical patterns in mammalian genome organization
9. Compositional properties of homologous coding sequences from plants
10. Directional mutation pressure and neutral molecular evolution
11. Evidence of selection on silent site base composition in mammals: Potential implications for the evolution of isochores and junk DNA
12. Codon usage and tRNA content in unicellular and multicellular organisms
13. Mutation pressure, natural selection, and the evolution of base composition in Drosophila
14. Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex
15. Recombination and mammalian genome evolution
16. Sunlight ultraviolet and bacterial DNA base ratios
17. Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus
18. Relationships between genomic G+C content, RNA secondary structures, and optimal group temperature in prokaryotes
19. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group
20. Codon usage and genome evolution
21. Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila
22. Synonymous rates at the RpII215 gene of Drosophila: Variation among species and across the coding region
23. Adaptive evolution at the Adh locus in Drosophila
24. Sequence evolution in bacterial endosymbionts having extreme base compositions
25. A new method for calculating evolutionary substitution rates
26. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstruction
27. Recovering evolutionary trees under a more realistic model of sequence evolution
28. Reconstructing evolutionary trees from DNA and protein sequences-paralinear distances
29. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid invariant sites LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo and elephant
30. Inferring pattern and process: Maximum likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
31. Isochore evolution in mammals: A human-like ancestral structure
32. Impact of changes in GC content on the silent molecular clock in murids
33. A nonhyperthermophilic common ancestor to extant life forms
34. Inferring complex phylogenies
35. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
36. Compositional differences within and between eukaryotic genomes
37. A covariate model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
38. Invariable site models and their use in phylogeny reconstruction
39. Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences