Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees

Molecular Biology and Evolution

Volumn 19, Issue 5, 2002, Pages 736-747

  Kusumi, Junko ^a   Tsumura, Yoshihiko ^a   Yoshimaru, Hiroshi ^a   Tachida, Hidenori ^a  

^a KYUSHU UNIVERSITY   (Japan)

Author keywords

Cupressaceae; Dispersion index; Lineage effect; Substitution rate; The neutral theory

Indexed keywords

FERREDOXIN;

AMINO ACID SUBSTITUTION; ARTICLE; CONIFER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC LINE; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PHOTOSYNTHESIS; PHYLOGENY; PLASTID; SEQUENCE ANALYSIS;

CONIFEROPHYTA; CUPRESSACEAE;

EID: 0036094963     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004132     Document Type: Article

References (59)

1. Inferring weak selection from pattern of polymorphism and divergence at silent sites in Drosophila DNA
2. Synonymous and nonsynonymous substitution in genes from Gramineae: Intragenic correlations
3. Bottleneck effect on evulotionary rate in the nearly neutral mutation model
4. The compositional evolution of vertebrate genomes
5. The mosaic genome of warm-blooded vertebrates
6. Rates of nucleotide substitution and mammalian nuclear gene evolution: Approximate and maximum-likelihood methods leads to different conclusions
7. Phylogenetic relationships among the genera of Taxodiaceae and Cupressaceae: Evidence from rbcL sequences
8. Compositional properties of homologous coding sequence from plants
9. Understanding the overdispersed molecular clock
10. Substitution rates in Drosophila nuclear genes: Implications for translational selection
11. Correlated rates of synonymous site evolution among plant genomes
12. Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons
13. Isochores results from mutation not selection
14. Relationships within Cupressaceae sensu lato: A combined morphological and mplecular approach
15. Molecular clocks and nucleotide substitution rates in higher plants
16. Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL
17. A general model to account for enzyme variation in natural populations. V. The SAS-CFF model
18. Lineage effects and the index of dispersion of molecular evolution
19. Substitution processes in molecular evolution. III. Deleterious alleles
20. Covariation of GC content and the silent site substitution rate in rodents: Implications for methodology and for the evolution of isochores
21. Codon usage and tRNA content in unicellular and multicellular organisms
22. Overdispersed molecular evolution in constant environments
23. Cleaved amplified polymorpic sequence markers in Sugi, Cryptomeria japonica
24. Evolutionary rate at the molecular level
25. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
26. Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences
27. Codons: A microcomputer program for codon usage analysis
28. The isochores organization and compositional distribution of homologous coding sequences in nuclear genomes of plants
29. Chromosomal location effects on gene sequence evolution in mammals
30. Mesozoic conifers
31. The origin of modern conifer families
32. A linkage map for sugi (Cryptomeria japonica) based on RFLP RAPD, and isozyme loci
33. Variances of the average number of nucleotide substitutions within and between populations
34. Molecular phylogenetic and evolutionary studies of parasitic plants
35. Likelihood models for detecting positively selected amino-acid sites and applications to the HIV-1 envelope gene
36. Slightly deleterious mutant substitutions in evolution
37. The nearly neutral theory of molecular evolution
38. Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory
39. Variation in synonymous substitution rates among mammalian genes and the correlation between synonymous and nonsynonymous divergences
40. An immunological comparison of the Sciadopityaceae Taxodiaceae, and Cupressaceae
41. The neighbor-joining method: A new method for reconstructing phylogenetic trees
42. Compositional compartmentalization and compositional patterns in the nuclear genomes of plants
43. Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences
44. Simple methods for testing the molecular evolutionary clock hypothesis
45. The Clustal-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
46. Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes
47. Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers
48. Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes
49. Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica
50. Mutation rates differ among regions of the mammalian genome
51. The 'effective number of codons' used in a gene
52. Synonymous and nonsynonymous rate variation in nuclear genes of mammals
53. Codon-substitution models for heterogeneous selection pressure at amino acid sites
54. The molecular clock revisited: The rate of synonymous vs. replacement change in Drosophila