1 |
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of procreative multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
DOI
|
2 |
White, T. J., T. Bruns, S. Lee, and J. Taylor. 1999. Amplification and direct sequencing of fungal ribosomal genes for phylogenetics, pp. 315-322, In Innis, M. A., D. H. Gelfand, J. J. Sninsky, and T. J. White (eds.), PCR Protocols: A Guide to Methods and Applications, New York Academic Press.
|
3 |
Wolfe, K. H., W. H. Li, and P. M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA. 84, 9054-9058.
DOI
|
4 |
Wright, F. 1990. The "effective number of codons" used in a gene. Gene 87, 23-29.
DOI
|
5 |
Zimmer, E. A., S. L. Martin, S. M. Beverly, W. Kan, and A. C. Wilson. 1980. Rapid duplication and loss of genes coding for the chains of hemoglobin. Proc. Natl. Acad. Sci. USA. 77, 2158-2162.
DOI
|
6 |
Kuzoff, R. K., J. A. Sweere, D. E. Soltis, and E. A. Zimmer. 1998. The phylogenetic potential of entire 26S rDNA sequences in plants. Mol. Biol. Evol. 15, 251-263.
DOI
ScienceOn
|
7 |
Lloyd, A. T. and P. M. Sharp. 1992. CODONS: a microcomputer program for codon usage analysis. J. Hered. 83, 239-240.
|
8 |
Alvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogen. Evol. 29, 417-434.
DOI
|
9 |
Moriyama, E. N. and J. R. Powell. 1997. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J. Mol. Evol. 45, 378-391.
DOI
|
10 |
Moore, M. J., A. Dhingra, P. S. Soltis, R. Shaw, W. G. Farmerie, K. M. Folta, and D. E. Soltis. 2006. Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol. 6, 17-30.
DOI
|
11 |
Palmer, J. D., K. L. Adams, Y. Cho, C. L. Parkinsonv, Y. L. Qiu, and K. Song. 2000. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc. Natl. Acad. Sci. USA. 97,
6960-6966.
DOI
|
12 |
Raspe, O., P. Saumitou-Laprade, J. Cuguen, and A. L. Jacquemart. 2000. Chloroplast DNA haplotype variation and population differentiation in Sorbus aucuparia L. (Rosaceae: Maloideae). Mol. Ecol. 9, 1113-1122.
DOI
|
13 |
Robertson, K. R., J. B. Phipps, J. R. Rohrer, and P. G. Smith. 1991. A synopsis of genera in Maloideae (Rosaceae). Syst. Bot. 16, 376-394.
DOI
ScienceOn
|
14 |
Sharp, P. M., D. C. Sields, K. H. Wolfe, and W. H. Li. 1989. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246, 808-810.
DOI
|
15 |
Shields, D. C., P. M. Sharp, D. G. Higgins, and F. Wright. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5, 704-716.
|
16 |
Small, R. L., R. C. Cronn, and J. F. Wendel. 2004. Use of nuclear genes for phylogeny reconstruction in plants. Aust. J. Bot. 17, 145-170.
DOI
|
17 |
Soltis, D. E., C. D. Bell, S. Kim, and P. S. Soltis. 2008. Origin and early evolution of angiosperms. Ann. N.Y. Acad. Sci. 1133, 3-25.
DOI
|
18 |
Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599.
DOI
|
19 |
Arnheim, N. 1983. Concerted evolution of multigene families, pp. 38-61, In Nei, M. and P. K. Koehn (eds.), Evolution and Proteins, Sinauer, Sunderland, MA.
|
20 |
Sorhannus, U. and M. Fox. 1999. Synonymous and nonsynonymous substitution rates in diatons: a comparison between chloroplast and nuclear genes. J. Mol. Evol. 48, 209-212.
DOI
|
21 |
Duret, L. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends in Genetics 16, 287-289.
DOI
|
22 |
Bailey, C. D., T. G. Carr, S. A. Harris, and C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and psudogenes. Mol. Phylogen. Evol. 29, 435-455.
DOI
|
23 |
Baldwin, B. G., M.J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell, and M. G. Donoghue. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard. 82, 247-277.
DOI
|
24 |
Campbell, C. S., M. J. Donoghue, B. G. Baldwin, and M. F. Wojciechowski. 1995. Phylogenetic relationships in Maloideae (Rosaceae): evidence from sequences of the internal transcribed spacers of nuclear ribosomal DNA and its congruence with morphology. Am. J. Bot. 82, 903-918.
DOI
|
25 |
Gaut, B. S. 1997. Molecular clocks and nucleotide substitution rates in higher plants, pp. 93-116, In Hecht, M. K., R. J. MacIntyre, and M. T. Clegg (eds.), Evolutionary Biology, Vol 30, Plenum Press, New York.
|
26 |
Huh, M. K., S. H. Kim, and S. H. Park. 2007. Phylogenetic study of genus Sorbus in Korea by internal transcribed spacer sequence (ITS). J. Life Sci. 17, 1610-1615.
DOI
|
27 |
Ino, Y. 1995. New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40, 190-226.
DOI
|
28 |
Li, W. H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99.
DOI
|
29 |
Li, W. H., C. I. Wu, and C. C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2, 150-174.
|