Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura

G3: Genes, Genomes, Genetics

Volumn 3, Issue 7, 2013, Pages 1151-1163

  Wallace, Andre G ^a   Detweiler, Don ^a   Schaeffer, Stephen W ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Breakpoints; Chromosomal inversion; Drosophila pseudoobscura; Linkage disequilibrium

Indexed keywords

NUCLEOTIDE;

ANIMAL; ARTICLE; BREAKPOINTS; CHROMOSOME; CHROMOSOME BREAKAGE; CHROMOSOME INVERSION; DNA POLYMORPHISM; DNA SEQUENCE; DROSOPHILA; DROSOPHILA PSEUDOOBSCURA; GENE CONVERSION; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC VARIABILITY; GENETICS; HETEROZYGOSITY; KARYOTYPE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NONHUMAN; PERSONAL EXPERIENCE; POPULATION GENETICS;

DROSOPHILA PSEUDOOBSCURA;

EID: 84883231599     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.006122     Document Type: Article

References (53)

1. Babcock, C. S., and W. W. Anderson, 1996 Molecular evolution of the sexratio inversion complex in Drosophila pseudoobscura: Analysis of the Esterase-5 gene region. Mol. Biol. Evol. 13: 297-308.
2. Begun, D. J., and C. F. Aquadro, 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
3. Betran, E., J. Rozas, A. Navarro, and A. Barbadilla, 1997 The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data. Genetics 146: 89-99.
4. Chovnick, A., 1973 Gene conversion and transfer of genetic information within the inverted region of inversion heterozygotes. Genetics 75: 123-131.
5. Dobzhansky, T., 1943 Genetics of natural populations. IX. Temporal changes in the composition of populations of Drosophila pseudoobscura. Genetics 28: 162-186.
6. Dobzhansky, T., 1944 Chromosomal races in Drosophila pseudoobscura and Drosophila persimilis. Carnegie Inst. Washington Publ. 554: 47-144.
7. Dobzhansky, T., 1949 Observations and experiments on natural selection in Drosophila, pp. 210-224 in Proceedings of the International Congress of Genetics, edited by G. Bonnier, and R. Larsson. Berlingska Boktryckeriet, Lund, Sweden.
8. Dobzhansky, T., 1950 The genetics of natural populations. XIX. Origin of heterosis through natural selection in populations of Drosophila pseudoobscura. Genetics 35: 288-302.
9. Dobzhansky, T., and C. Epling, 1944 Taxonomy, geographic distribution, and ecology of Drosophila pseudoobscura and its relatives, pp. 1-46 in Contributions to the Genetics, Taxonomy, and Ecology of Drosophila pseudoobscura and its Relatives, edited by T. Dobzhansky, and C. Epling. The Lord Baltimore Press, Baltimore, MD.
10. Dobzhansky, T., and A. H. Sturtevant, 1938 Inversions in the chromosomes of Drosophila pseudoobscura. Genetics 23: 28-64.
11. Dobzhansky, T., and M. L. Queal, 1938 Genetics of natural populations. II. Genic variation in populations of Drosophila pseudoobscura inhabiting isolated mountain ranges. Genetics 23: 463-484.
12. Gloor, G., and W. Engels, 1992 Single-fly DNA preps for PCR. Drosoph. Inf. Serv. 71: 148-149.
13. Hamblin, M. T., and C. F. Aquadro, 1999 DNA sequence variation and the recombinational landscape in Drosophila pseudoobscura: a study of the second chromosome. Genetics 153: 859-869.
14. Hilliker, A. J., G. Harauz, A. G. Reaume, M. Gray, S. H. Clark et al., 1994 Meiotic gene conversion tract length distribution within the rosy locus of Drosophila melanogaster. Genetics 137: 1019-1026.
15. Hudson, R. R., 1990 Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-44.
16. Hudson, R. R., and N. L. Kaplan, 1986 On the divergence of alleles in nested subsamples from finite populations. Genetics 113: 1057-1076.
17. Hudson, R. R., M. Kreitman, and M. Aguadé, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
18. Innan, H., and W. Stephan, 2000 The coalescent in an exponentially growing metapopulation and its application to Arabidopsis thaliana. Genetics 155: 2015-2019.
19. Jukes, T. H., and C. R. Cantor, 1969 Evolution of protein molecules, pp. 21- 132 in Mammalian Protein Metabolism, edited by H. N. Munro. Academic Press, New York.
20. Kimura, M., 1986 DNA and the neutral theory. Philos. Trans. R. Soc. Lond., B 312 343-354
21. Kirkpatrick, M., 2010 How and why chromosome inversions evolve. PLoS Biol. 8: e1000501.
22. Kirkpatrick, M., and N. Barton, 2006 Chromosome inversions, local adaptation and speciation. Genetics 173: 419-434.
23. Lewontin, R. C., 1995 The detection of linkage disequilibrium in molecular sequence data. Genetics 140: 377-388.
24. Librado, P., and J. Rozas, 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
25. Muller, H. J., 1940 Bearings of the 'Drosophila' work on systematics, pp. 185- 268 in The New Systematics, edited by J. Huxley. Clarendon Press, Oxford.
26. Navarro, A., A. Barbadilla, and A. Ruiz, 2000 Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila. Genetics 155: 685-698.
27. Navarro, A., E. Betrán, A. Barbadilla, and A. Ruiz, 1997 Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes. Genetics 146: 695-709.
28. Noor, M. A.,D.A.Garfield, S. W. Schaeffer, and C. A.Machado, 2007 Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics 177: 1417-1428.
29. Painter, T. S., 1934 A new method for the study of chromosomal aberrations and the plotting of chromosomal maps in Drosophila melanogaster. Genetics 19: 175-188.
30. Powell, J. R., 1992 Inversion polymorphisms in Drosophila pseudoobscura and Drosophila persimilis, pp. 73-126 in Drosophila Inversion Polymorphism, edited by C. B. Krimbas, and J. R. Powell. CRC Press, Ann Arbor, MI.
31. Richards, S., Y. Liu, B. R. Bettencourt, P. Hradecky, S. Letovsky et al., 2005 Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene and cis-element evolution. Genome Res. 15: 1-18.
32. Roberts, P. A., 1976 The genetics of chromosome aberration, pp. 67-184 in The Genetics and Biology of Drosophila 1a, edited by M. Ashburner, and E. Novitski. Academic Press, New York, NY.
33. Rozas, J., and M. Aguadé, 1990 Evidence of extensive genetic exchange in the rp49 region among polymorphic chromosome inversions in Drosophila subobscura. Genetics 126: 417-426.
34. Rozas, J., and M. Aguadé, 1993 Transfer of genetic information in the rp49 region of Drosophila subobscura between different gene arrangements. Proc. Natl. Acad. Sci. USA 90: 8083-8087.
35. Rozas, J., and M. Aguadé, 1994 Gene conversion is involved in the transfer of genetic information between naturally occurring inversions of Drosophila. Proc. Natl. Acad. Sci. USA 91: 11517-11521.
36. Schaeffer, S. W., 2002 Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genet. Res. 80: 163-175.
37. Schaeffer, S. W., 2008 Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura. Evolution 62: 3082-3099.
38. Schaeffer, S. W., and W. W. Anderson, 2005 Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics 171: 1729-1739.
39. Schaeffer, S. W., P. Goetting-Minesky, M. Kovacevic, J. Peoples, J. L. Graybill et al., 2003 Evolutionary genomics of inversions in Drosophila pseudoobscura: Evidence for epistasis. Proc. Natl.Acad. Sci. USA100: 8319-8324.
40. Schaeffer, S. W., A. Bhutkar, B. F. McAllister, M. Matsuda, L. M. Matzkin et al., 2008 Polytene chromosomal maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics 179: 1601-1655.
41. Slatkin, M., and R. R. Hudson, 1991 Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
42. Sokal, R. R., and F. J. Rohlf, 1981 Biometry. W. H. Freeman and Co., New York.
43. Sperlich, D., and P. Pfriem, 1986 Chromosomal polymorphism in natural and experimental populations, pp. 257-309 in The Genetics and Biology of Drosophila 3e, edited by M. Ashburner, H. L. Carson, and J. N. Thomson. Academic Press, New York, NY.
44. Storey, J. D., 2002 A direct approach to false discovery rates. J. R. Stat. Soc., B 64: 479-498.
45. Sturtevant, A. H., 1917 Genetic factors affecting the strength of genetic linkage in Drosophila. Proc. Natl. Acad. Sci. USA 3: 555-558.
46. Sturtevant, A. H., and G. W. Beadle, 1936 The relations of inversions in the X chromosome of Drosophila melanogaster to crossing over and disjunction. Genetics 21: 544-604.
47. Tajima, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
48. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
49. Toomajian, C., R. S. Ajioka, L. B. Jorde, J. P. Kushner, and M. Kreitman, 2003 A method for detecting recent selection in the human genome from allele age estimates. Genetics 165: 287-297.
50. Wallace, A. G., D. Detweiler, and S. W. Schaeffer, 2011 Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints. Mol. Biol. Evol. 28: 2219-2229.
51. Wasserman, M., 1982 Evolution of the repleta group, pp. 61-139 in The Genetics and Biology of Drosophila 3b, edited by M. Ashburner, H. L. Carson, and J. N. Thompson. Academic Press, New York.
52. Watterson, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
53. Wright, S., and T. Dobzhansky, 1946 Genetics of natural populations. XII. Experimental reproduction of some of the changes caused by natural selection in certain populations of Drosophila pseudoobscura. Genetics 31: 125-156.