Population Genetics and Geographic Variation of Alcohol Dehydrogenase (Adh) Paralogs and Glucose-6-Phosphate Dehydrogenase (G6pd) in Drosophila mojavensis

Molecular Biology and Evolution

Volumn 21, Issue 2, 2004, Pages 276-285

  Matzkin, Luciano M ^a,b  

^a STONY BROOK UNIVERSITY   (United States)

^b University of Arizona   (United States)

Author keywords

Adh; Cactophilic Drosophila; Duplication; Geographic variation; Sequence variation; Subfunctionalization

Indexed keywords

ALCOHOL; ALCOHOL DEHYDROGENASE; AMINO ACID; DNA; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; MESSENGER RNA PRECURSOR;

ADAPTATION; ALLELE; ARTICLE; DROSOPHILA; FEMALE; GENE; GENE LINKAGE DISEQUILIBRIUM; GENETIC POLYMORPHISM; GEOGRAPHICAL VARIATION (SPECIES); HAPLOTYPE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; POLYMERASE CHAIN REACTION; POPULATION GENETICS; UNINDEXED SEQUENCE;

ALCOHOL DEHYDROGENASE; ALLELES; ANIMALS; BASE SEQUENCE; CALIFORNIA; DROSOPHILA; DROSOPHILA PROTEINS; GENES, INSECT; GENETICS, POPULATION; GLUCOSEPHOSPHATE DEHYDROGENASE; MEXICO; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; SEQUENCE ALIGNMENT; VARIATION (GENETICS);

CACTACEAE; DROSOPHILA ARIZONAE; DROSOPHILA MOJAVENSIS;

EID: 1542286768     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh019     Document Type: Article

References (59)

1. Antezana, M. A. and M. Kreitman. 1999. The nonrandom location of synonymous codons suggests that reading frame-independent forces have patterned codon preferences. J. Mol. Evol. 49:36-43.
2. Atkinson, P. W., L. E. Mills, W. T. Starmer, and D. L. Sullivan. 1988. Structure and evolution of the Adh genes of Drosophila mojavensis. Genetics 120:713-723.
3. Au, S. W., N., S. Gover, V. M. S. Lam, and M. J. Adams. 2000. Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency. Struct. Fold Des. 8:293-303.
4. Batterham, P., J. A. Lovett, W. T. Starmer, and D. T. Sullivan. 1983. Differential regulation of duplicate alcohol dehydrogenase genes in Drosophila mojavensis. Develop. Biol. 96: 346-354.
5. Benach, J., S. Atrian, R. Gonzalez-Duarte, and R. Ladenstein. 1998. The refined crystal structure of Drosophila lebanonensis alcohol dehydrogenase at 1.9 Å resolution. J. Mol. Biol. 282:383-399.
6. -. 1999. The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 Å resolution by X-ray crystallography. J. Mol. Biol. 289:335-355.
7. Carlini, D. B., Y. Chen, and W. Stephan. 2001. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr. Genetics. 159:623-633.
8. Chambers, G. K. 1988. The Drosophila alcohol dehydrogenase gene enzyme system. Adv Genet. 25:39-107.
9. Clark, A. G. 1997. Neutral behavior of shared polymorphism. Proc. Natl. Acad. Sci. USA 94:7730-7734.
10. Eanes, W. F., M. Kirchner, and J. Yoon. 1993. Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages. Proc. Natl. Acad. Sci. USA 90:7475-7479.
11. Eanes, W. F., M. Kirchner, J. Yoon, C. H. Biermann, I.-N. Wang, M. A. McCartney, and B. C. Verrelli. 1996. Historical selection, amino acid polymorphism and lineage-specific divergence at the G6pd locus in Drosophila melanogaster and D. simulans. Genetics 144:1027-1041.
12. Etges, W. J. 1989. Evolution of developmental homeostasis in Drosophila mojavensis. Evol. Ecol. 3:189-201.
13. -. 1990. Direction of life history evolution in Drosophila mojavensis. Pp. 37-56 in J. S. F. Barker, W. T. Starmer and R. J. MacIntyre, eds. Ecological and evolutionary genetics of Drosophila. Plenum Press, New York.
14. -. 1993. Genetics of host-cactus response and life-history evolution among ancestral and derived populations of cactophilic Drosophila mojavensis. Evolution 47:750-767.
15. Fellows, D. F. and W. B. Heed. 1972. Factors affecting host plant selection in desert-adapted cactiphilic Drosophila. Ecology 53:850-858.
16. Filatov, D. A. 2002. PROSEQ: A software for preparation and evolutionary analysis of DNA sequence data sets. Mole. Ecol. Notes 2:621-624.
17. Fogleman, J. C. 1982. The role of volatiles in the ecology of cactophilic Drosophila. Pp. 191-208 in J. S. F. Barker and W. T. Starmer, eds. Ecological genetics and evolution: the cactus-yeast-Drosophila model system. Academic Press, New York.
18. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
19. Fu, Y. X., and W. H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
20. Heed, W. B. 1978. Ecology and genetics of Sonoran desert Drosophila. Pp. 109-126 in P. F. Brussard, ed. Ecological genetics: the interface. Springer-Verlag, New York.
21. Heinstra, P. W. H. 1993. Evolutionary genetics of the Drosophila alcohol dehydrogenase gene enzyme system. Genetica 92:1-22.
22. Hey, J., and J. Wakeley. 1997. A coalescent estimator of the population recombination rate. Genetics 145:833-846.
23. Hudson, R. R. 1987. Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50:245-250.
24. Hudson, R. R., K. Bailey, D. Skarecky, J. Kwiatowski, and F. J. Ayala. 1994. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136:1329-1340.
25. Hudson, R. R., D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9:138-151.
26. Hudson, R. R., M. Kreitman, and M. Aguade. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
27. Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
28. Hughes, A. L. 1994. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci. 256:119-124.
29. Jeffery, J., B. Persson, I. Wood, T. Bergman, R. Jeffery, and H. Jornvall. 1993. Glucose-6-phosphate dehydrogenase: structure-function relationships and the Pichia jadinii enzyme structure. Eur. J. Biochem. 212:41-49.
30. Kimura, M. 1981. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK.
31. Kirby, D. A., S. V. Muse, and W. Stephan. 1995. Maintenance of pre-mRNA secondary structure by epistatic selection. Proc. Natl. Acad. Sci. USA 92:9047-9051.
32. Kircher, H. W. 1982. Chemical composition of cacti and its relationship to Sonoran Desert Drosophila. Pp. 143-158 in J. S. F. Barker and W. T. Starmer, eds. Ecological genetics and evolution: the cactus-yeast-Drosophila model system. Academic Press, New York.
33. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
34. Mangan, R. L. 1982. Adaptations to competition in cactus breeding Drosophila. Pp. 257-272 in J. S. F. Barker and W. T. Starmer, eds. Ecological genetics and evolution: the cactus-yeast-Drosophila model system. Academic Press, New York.
35. Markow, T. A. 1981. Courtship behavior and control of reproductive isolation between Drosophila mojavensis and Drosophila arizonensis. Evolution 35:1022-1026.
36. -. 1991. Sexual isolation among populations of Drosophila mojavensis. Evolution 45:1525-1529.
37. Markow, T. A., J. C. Fogleman, and W. B. Heed. 1983. Reproductive Isolation in Sonoran Desert Drosophila. Evolution 37:649-652.
38. Matzkin, L. M., and W. F. Eanes. 2003. Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila. Genetics 163:181-194.
39. McDonald, J. H. 1996. Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 13:253-260.
40. McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
41. Moriyama, E. N., and T. Gojobori. 1992. Rates of synonymous substitution and base composition of nuclear genes in Drosophila. Genetics 130:855-864.
42. Notaro, R., A. Afolayan, and L. Luzzatto. 2000. Human mutations in glucose 6-phosphate dehydrogenase reflect evolutionary history. FASEB J. 14:485-494.
43. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Heidelberg, Germany.
44. Ohta, T. 1974. Mutational pressure as main cause of molecular evolution and polymorphism. Nature 252:351-354.
45. -. 1987. Simulating evolution by gene duplication. Genetics 115:207-213.
46. -. 1988a. Evolution by gene duplication and compensatory advantageous mutations. Genetics 120:841-847.
47. -. 1988b. Time for acquiring a new gene by duplication. Proc. Natl. Acad. Sci. USA 85:3509-3512.
48. -. 1992. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23:263-286.
49. -. 1993. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc. Natl. Acad. Sci. USA 90:4548-4551.
50. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
51. Ruiz, A., and W. B. Heed. 1988. Host-plant specificity in the cactophilic Drosophila mulleri species complex. J. Anim. Ecol. 57:237-249.
52. Ruiz, A., W. B. Heed, and M. Wasserman. 1990. Evolution of the Mojavensis cluster of cactophilic Drosophila with descriptions of two new species. J. Hered. 81:30-42.
53. Stephan, W., and D. A. Kirby. 1993. RNA folding in Drosophila shows a distance effect for compensatory fitness interactions. Genetics 135:97-103.
54. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
55. Triglia, T., M. G. Peterson, and D. J. Kemp. 1988. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16:8186.
56. Vacek, D. C. 1979. The microbial ecology of the host plants of Drosophila mojavensis. Ph.D. Thesis, University of Arizona, Tucson.
57. Winnepenninckx, B., T. Backeljau, and R. Dewachter. 1993. Extraction of high molecular weight DNA from mollusks. Trends Genet. 9:407-407.
58. Zouros, E. 1973. Genic differentiation associated with the early stages of speciation in the mulleri subgroup of Drosophila. Evolution. 27:601-621.
59. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.