Selection on rapidly evolving proteins in the arabidopsis genome

Genetics

Volumn 163, Issue 2, 2003, Pages 723-733

  Barrier, Marianne ^a   Bustamante, Carlos D ^a   Yu, Jiaye ^b   Purugganan, Michael D ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CODE; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; POLYMORPHIC LOCUS; PRIORITY JOURNAL; SPECIES COMPARISON; UNINDEXED SEQUENCE;

ARABIDOPSIS; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; MOLECULAR SEQUENCE DATA; PROTEINS; SELECTION (GENETICS);

ARABIDOPSIS; ARABIDOPSIS LYRATA; ARABIDOPSIS THALIANA; BRASSICACEAE; EMBRYOPHYTA;

EID: 0037296452     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (39)

1. AGUADE, M., 2001 Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana. Mol. Biol. Evol. 18: 1-9.
2. ANISIMOVA, M., J. P. BIELAWSI and Z. H. YANG, 2001 Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18: 1585-1591.
3. ARABIDOPSIS GENOME. INITIATIVE, 2000 Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
4. BOLDIN, M. P., I. L. METT and D. WALLACH, 1995 A protein related to a proteasomal subunit binds to the intracellular domain of the p55 TNF receptor upstream to its 'death domain'. FEBS Lett. 367: 39-44.
5. BUSTAMANTE, C. D., R. NIELSEN and D. L. HARTL, 2002a A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Mol. Biol. Evol. 19: 110-117.
6. BUSTAMANTE, C. D., R. NIELSEN, S. SAWYER, K. M. OLSEN, M. D. PURUGGANAN et al., 2002b The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
7. DOEBLEY, J., and L. LUKENS, 1998 Transcriptional regulators and the evolution of plant form. Plant Cell 10: 1075-1082.
8. ENDO, T., K. IKEO and T. GOJOBORI, 1996 Large-scale selection for genes on which positive selection may operate. Mol. Biol. Evol. 13: 685-690.
9. EWING, B., L. HILLIER, M. C. WENDL and P. GREEN, 1998 Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
10. GELMAN, A., J. S. CARLIN, H. S. STERN and D. B. RUBIN, 1997 Bayesian Data Analysis. Chapman & Hall, Boca Raton, FL.
11. HAAG, E. S., and J. R. TRUE, 2001 Perspective: From mutants to mechanisms? Assessing the candidate gene paradigm in evolutionary biology. Evolution 55: 1077-1084.
12. HUGHES, A. L., 1991 Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions. Genetics 127: 345-353.
13. HUGHES, A. L., and M. YEAGER, 1998 Natural selection at major histocompatibility complex loci of vertebrates. Annu. Rev. Genet. 32: 415-435.
14. KOCH, M., B. HAUBOLD and T. MITCHELL-OLDS, 2000 Comparative evolutionary analysis of the chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis and related genera. Mol. Biol. Evol. 17: 1483-1498.
15. KUMAR, S., K. TAMURA and M. NEI, 1993 MEGA: Molecular Evolutionary Genetics Analysis, Version 1.0. Pennsylvania State University, University Park, PA.
16. LAWTON-RAUH, A., E. S. BUCKLER and M. D. PURUGGANAN, 1999 Patterns of molecular evolution among paralogous floral homeotic genes. Mol. Biol. Evol. 16: 1037-1045.
17. LI, W.-H., T. GOJOBORI and M. NEI, 1981 Pseudogenes as a paradigm of neutral evolution. Nature 292: 237-239.
18. LI, W.-H., C.-I Wu and C. C. LUO, 1985 A new method for estimating synonymous and nonsynonymous rates on nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
19. MCDONALD, J., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
20. MESSIER, W., and C. B. STEWART, 1997 Episodic adaptive evolution of primate lysozymes. Nature 385: 151-154.
21. METROPOLIS, N., A. ROSENBLUTH, M. ROSENBLUTH, A. TELLER and E. TELLER, 1953 Equation of state calculations by fast computing machines. J. Chem. Phys. 21: 1087-1092.
22. MIYASHITA, N. T., A. KAWABE, H. INNAN and R. TERAUCHI, 1998 Intra- and interspecific DNA variation and codon bias of the Alcohol Dehydrogenase (Adh) locus in Arabis and Arabidopsis species. Mol. Biol. Evol. 15: 1420-1429.
23. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
24. NEI, M., and T. GOJOBORI, 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
25. NIELSEN, R., 2001 Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
26. OLSEN, K. M., A. WOMACK, A. R. GARRETT, J. I. SUDDITH and M. D. PURUGGANAN, 2002 Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway. Genetics 160: 1641-1650.
27. ORR, H. A., and J. A. COYNE, 1992 The genetics of adaptation: a reassessment. Am. Nat. 140: 725-742.
28. PURUGGANAN, M. D., and J. I. SUDDITH, 1998 Molecular population genetics of floral homeotic loci: departures from the equilibriumneutral model at the AP3 and PI genes of Arabidopsis thaliana. Genetics 151: 839-848.
29. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
30. SAWYER, S. A., and D. L. HARTL, 1992 Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
31. SCHMID, K. J., and C. F. AQUADRO, 2001 The evolutionary analysis of "orphans" from the Drosophila genome identifies rapidly diverging and incorrectly annotated genes. Genetics 159: 589-598.
32. SUCENA, E., and D. L. STERN, 2000 Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cisregulatory evolution of ovo/shaven-baby. Proc. Natl. Acad. Sci. USA 97: 4530-4534.
33. SWANSON, W. J., and V. D. VACQUIER, 1995 Extraordinary divergence and positive Darwinian selection in a fusagenic protein coating the acrosomal process of abalone spermatozoa. Proc. Natl. Acad. Sci. USA 92: 4957-4961.
34. SWANSON, W. J., A. G. CLARK, H. M. WALDRIP-DAIL, M. F. WOLFNER and C. F. AQUADRO, 2001 Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc. Natl. Acad. Sci. USA 98: 7375-7379.
35. TIFFIN, P., and M. HAHN, 2002 Coding sequence divergence between two closely-related plant species - Arabidopsis thaliana and Brassica rapa ssp. pekinensis. J. Mol. Evol. 54: 746-753.
36. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
37. WU, C.-I, 2001 The genic view of the process of speciation. J. Evol. Biol. 14: 851-865.
38. XIE, Q., G. FRUGIS, D. COLGAN and N. H. CHUA, 2000 Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev. 14: 3024-3036.
39. ZHANG, J., H. F. ROSENBERG and M. NEI, 1998 Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95: 3708-3713.