Surprising differences in the variability of y chromosomes in african and cosmopolitan populations of drosophila melanogaster

Genetics

Volumn 193, Issue 1, 2013, Pages 201-214

  Larracuente, Amanda M ^a,b   Clark, Andrew G ^a  

^a Cornell University ^*  (United States)

^b UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; AUSTRALIA; CHINA; CHROMOSOME VARIANT; CONFERENCE PAPER; CONTROLLED STUDY; DEMOGRAPHY; DNA POLYMORPHISM; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION; GENETIC VARIABILITY; HETEROCHROMATIN; INHERITANCE; MALE FERTILITY; NATURAL SELECTION; NETHERLANDS; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION GENETICS; PRIORITY JOURNAL; UGANDA; UNITED STATES; Y CHROMOSOME; Y CHROMOSOME LINKAGE; ZIMBABWE;

ANIMALS; CLUSTER ANALYSIS; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; MALE; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SELECTION, GENETIC; X CHROMOSOME; Y CHROMOSOME;

DROSOPHILA MELANOGASTER;

EID: 84871751953     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.146167     Document Type: Conference Paper

References (58)

1. Andolfatto, P., 2001 Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 279-290.
2. Baudry, E., B. Viginier, and M. Veuille, 2004 Non-African populations of Drosophila melanogaster have a unique origin. Mol. Biol. Evol. 21: 1482-1491.
3. Begun, D. J., and C. F. Aquadro, 1995 Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics 140: 1019-1032.
4. Benjamini, Y., and Y. Hochberg, 1995 Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57: 289-300.
5. Bochdanovits, Z., and A. W. de Jong, 2003 Experimental evolution in Drosophila melanogaster: interaction of temperature and food quality selection regimes. Evolution 57: 1829-1836.
6. Caballero, A., 1995 On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139: 1007-1011.
7. Capy, P., M. Veuille, M. Paillette, J. M. Jallon, J. Vouidibio et al., 2000 Sexual isolation of genetically differentiated sympatric populations of Drosophila melanogaster in Brazzaville, Congo: The first step towards speciation? Heredity 84(4): 468-475.
8. Caracristi, G., and C. Schlötterer, 2003 Genetic differentiation between American and European Drosophila melanogaster populations could be attributed to admixture of African alleles. Mol. Biol. Evol. 20: 792-799.
9. Carvalho, A. B., B. P. Lazzaro, and A. G. Clark, 2000 Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides. Proc. Natl. Acad. Sci. USA 97: 13239-13244.
10. Carvalho, A. B., B. A. Dobo, M. D. Vibranovski, and A. G. Clark, 2001 Identification of five new genes on the Y chromosome of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 98: 13225-13230.
11. Charlesworth, B., 2001 The effect of life-history and mode of inheritance on neutral genetic variability. Genet. Res. 77: 153-166.
12. Chippindale, A. K., and W. R. Rice, 2001 Y chromosome polymorphism is a strong determinant of male fitness in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 98: 5677-5682.
13. Clark, A. G., 1987 Variation in Y chromosome segregation in natural populations of Drosophila melanogaster. Genetics 115: 143-151.
14. David, J. R., and P. Capy, 1988 Genetic variation of Drosophila melanogaster natural populations. Trends in genetics. TIG 4: 106-111.
15. Gershenson, S., 1928 A new sex-ratio abnormality in Drosophila obscura. Genetics 13: 488-507.
16. Goldstein, L. S., R. W. Hardy, and D. L. Lindsley, 1982 Structural genes on the Y chromosome of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 79: 7405-7409.
17. Haddrill, P. R., K. R. Thornton, B. Charlesworth, and P. Andolfatto, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15: 790-799.
18. Hale, L. R., and R. S. Singh, 1991 A comprehensive study of genic variation in natural populations of Drosophila melanogaster. IV. Mitochondrial DNA variation and the role of history vs. selection in the genetic structure of geographic populations. Genetics 129: 103-117.
19. Hanks, G. D., 1968 RD (Recovery Disrupter) activity associated with various wild type X chromosomes. Drosoph. Inf. Serv. 43: 98.
20. Hardy, R. W., K. T. Tokuyasu, and D. L. Lindsley, 1981 Analysis of spermatogenesis in Drosophila melanogaster bearing deletions for Y-chromosome fertility genes. Chromosoma 83: 593-617.
21. Hoskins, R. A., C. D. Smith, J. W. Carlson, A. B. Carvalho, A. Halpern et al., 2002 Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 3: research0085-0085.
22. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
23. Hudson, R. R., and N. L. Kaplan, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
24. Hurst, L. D., 1996 Further evidence consistent with Stellate's involvement in meiotic drive. Genetics 142: 641-643.
25. Hutter, S., H. Li, S. Beisswanger, D. DeLorenzo, and W. Stephan, 2007 Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data. Genetics 177: 469-480.
26. Hutter, S., S. S. Saminadin-Peter, W. Stephan, and J. Parsch, 2008 Gene expression variation in African and European populations of Drosophila melanogaster. Genome Biol. 9: R12.
27. James, A. C., and J. Jaenike, 1990 "Sex ratio" meiotic drive in Drosophila testacea. Genetics 126: 651-656.
28. Jiang, P. P., D. L. Hartl, and B. Lemos, 2010 Y not a dead end: epistatic interactions between Y-linked regulatory polymorphisms and genetic background affect global gene expression in Drosophila melanogaster. Genetics 186: 109-118.
29. Kaiser, V. B., and B. Charlesworth, 2009 The effects of deleterious mutations on evolution in non-recombining genomes. Trends Genet. 25: 9-12.
30. Kauer, M., D. Dieringer, and C. Schlötterer, 2003 Nonneutral admixture of immigrant genotypes in African Drosophila melanogaster populations from Zimbabwe. Mol. Biol. Evol. 20: 1329-1337.
31. Kennison, J. A., 1981 The genetic and cytological organization of the Y chromosome of Drosophila melanogaster. Genetics 98: 529-548.
32. Kolaczkowski, B., A. D. Kern, A. K. Holloway, and D. J. Begun, 2011 Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics 187: 245-260.
33. Kopp, A., A. K. Frank, and O. Barmina, 2006 Interspecific divergence, intrachromosomal recombination, and phylogenetic utility of Y-chromosomal genes in Drosophila. Mol. Phylogenet. Evol. 38: 731-741.
34. Krsticevic, F. J., H. L. Santos, S. Januario, C. G. Schrago, and A. B. Carvalho, 2010 Functional copies of the Mst77F gene on the Y chromosome of Drosophila melanogaster. Genetics 184: 295-307.
35. Laurent, S. J., A. Werzner, L. Excoffier, and W. Stephan, 2011 Approximate Bayesian analysis of Drosophila melanogaster polymorphism data reveals a recent colonization of Southeast Asia. Mol. Biol. Evol. 24: 2041-2051.
36. Lemos, B., L. O. Araripe, and D. L. Hartl, 2008 Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences. Science 319: 91-93.
37. Lemos, B., A. T. Branco, and D. L. Hartl, 2010 Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict. Proc. Natl. Acad. Sci. USA 107: 15826-15831.
38. Li, H., andW. Stephan, 2006 Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2: e166.
39. Lyckegaard, E. M., and A. G. Clark, 1989 Ribosomal DNA and Stellate gene copy number variation on the Y chromosome of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 86: 1944-1948.
40. Meiklejohn, C. D., J. Parsch, J. M. Ranz, and D. L. Hartl, 2003 Rapid evolution of male-biased gene expression in Drosophila. Proc. Natl. Acad. Sci. USA 100: 9894-9899.
41. Montchamp-Moreau, C., D. Ogereau, N. Chaminade, A. Colard, and S. Aulard, 2006 Organization of the sex-ratio meiotic drive region in Drosophila simulans. Genetics 174: 1365-1371.
42. Myers, S. R., and R. C. Griffiths, 2003 Bounds on the minimum number of recombination events in a sample history. Genetics 163: 375-394.
43. Nunney, L., 1993 The influence of mating system and overlapping generations on effective population size. Evolution 47: 1329-1341.
44. Orr, H. A., and S. Irving, 2005 Segregation distortion in hybrids between the Bogota and USA subspecies of Drosophila pseudoobscura. Genetics 169: 671-682.
45. Paredes, S., A. T. Branco, D. L. Hartl, K. A. Maggert, and B. Lemos, 2011 Ribosomal DNA deletions modulate genome-wide gene expression: "rDNA-sensitive" genes and natural variation. PLoS Genet. 7: e1001376.
46. Pool, J. E., and C. F. Aquadro, 2006 History and structure of sub-Saharan populations of Drosophila melanogaster. Genetics 174: 915-929.
47. Pool, J. E., and R. Nielsen, 2007 Population size changes reshape genomic patterns of diversity. Evolution 61: 3001-3006.
48. Przeworski, M., 2003 Estimating the time since the fixation of a beneficial allele. Genetics 164: 1667-1676.
49. Reed, F. A., R. G. Reeves, and C. F. Aquadro, 2005 Evidence of susceptibility and resistance to cryptic X-linked meiotic drive in natural populations of Drosophila melanogaster. Evolution 59: 1280-1291.
50. Rohmer, C., J. R. David, B. Moreteau, and D. Joly, 2004 Heat induced male sterility in Drosophila melanogaster: adaptive genetic variations among geographic populations and role of the Y chromosome. J. Exp. Biol. 207: 2735-2743.
51. Schlötterer, C, H. Neumeier, C. Sousa, and V. Nolte, 2006 Highly structured Asian Drosophila melanogaster populations: A new tool for hitchhiking mapping? Genetics 172: 287-292.
52. Singh, N. D., J. D. Jensen, A. G. Clark, and C. F. Aquadro, 2013 Inferences of demography and selection in an African population of D. melanogaster. Genetics 193: 215-228.
53. Tao, Y., L. Araripe, S. B. Kingan, Y. Ke, H. Xiao et al., 2007 A sexratio meiotic drive system in Drosophila simulans. II: an X-linked distorter. PLoS Biol. 5: e293.
54. Thornton, K., 2003 Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
55. Thornton, K., and P. Andolfatto, 2006 Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
56. Vibranovski, M. D., L. B. Koerich, and A. B. Carvalho, 2008 Two new Y-linked genes in Drosophila melanogaster. Genetics 179: 2325-2327.
57. Zhang, P., 2000 A trans-activator on the Drosophila Y chromosome regulates gene expression in the male germ line. Genetica 109: 141-150.
58. Zurovcova, M., and W. F. Eanes, 1999 Lack of nucleotide polymorphism in the Y-linked sperm flagellar dynein gene Dhc-Yh3 of Drosophila melanogaster and D. simulans. Genetics 153: 1709-1715.