Genome-wide patterns of expression in Drosophila pure species and hybrid males. II. Examination of multiple-species hybridizations, platforms, and life cycle stages

Molecular Biology and Evolution

Volumn 24, Issue 1, 2007, Pages 137-145

  Moehring, Amanda J ^a   Teeter, Katherine C ^a   Noor, Mohamed A F ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Drosophila mauritiana; Drosophila sechellia; Drosophila simulans; Gene regulation; Hybrid male sterility; Speciation

Indexed keywords

ARTICLE; CHROMOSOME MAP; CONTROLLED STUDY; DNA HYBRIDIZATION; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE OVEREXPRESSION; GENETIC TRANSCRIPTION; GENOME; HYBRID; HYBRID GENE; LARVA; LIFE CYCLE; MICROARRAY ANALYSIS; NONHUMAN; REPRODUCTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SAMPLE; SEMEN ANALYSIS; SPERMATOGENESIS; X CHROMOSOME;

ANIMALS; CHIMERA; DROSOPHILA; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION; GENES, INSECT; GENOME, INSECT; HYBRIDIZATION, GENETIC; LARVA; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPERMATOGENESIS; X CHROMOSOME;

DROSOPHILA MAURITIANA; DROSOPHILA MELANOGASTER; DROSOPHILA SECHELLIA; DROSOPHILA SIMULANS;

EID: 33845889502     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl142     Document Type: Article

References (46)

1. Allison DB, Cui X, Page GP, Sabripour M. 2006. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet. 7:55-65.
2. Arbeitman MN, Furlong EEM, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. 2002. Gene expression during the life cycle of Drosophila melanogaster. Science. 297:2270-2275.
3. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI. 2002. Large clusters of co-expressed genes in the Drosophila genome. Nature. 420:666-669.
4. Clark AG. 2006. Genomics of the evolutionary process. Trends Ecol Evol. 21:316-321.
5. Coyne JA. 1984. Genetic basis of male sterility in hybrids between two closely related species of Drosophila. Proc Natl Acad Sci USA. 81:4444-4447.
6. Coyne JA, Orr HA. 2004. Speciation. Sunderland (MA): Sinauer Associates, Inc.
7. Cui X, Churchill GA. 2003. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4:210.
8. Fuller MT. 1998. Genetic control of cell proliferation and differentiation in Drosophila spermatogenesis. Semin Cell Dev Biol. 9:433-444.
9. Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. 2005. Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res. 15:674-680.
10. Goodisman MA, Isoe J, Wheeler DE, Wells MA. 2005. Evolution of insect metamorphosis: a microarray-based study of larval and adult gene expression in the ant Camponotus festinatus. Evolution. 59:858-870.
11. Grumbling G, Strelets V, Consortium TF. 2006. FlyBase: anatomical data, images and queries. Nucleic Acids Res. 34:D484-D488.
12. Haerty W, Singh RS. 2006. Gene regulation divergence is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila. Mol Biol Evol. 23:1707-1714.
13. Johnson NA, Porter AH. 2000. Rapid speciation via parallel, directional selection on regulatory genetic pathways. J Theor Biol. 205:527-542.
14. Kliman RM, Andolfatto P, Coyne JA, Depaulis F, Kreitman M, Berry AJ, McCarter J, Wakeley J, Hey J. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics. 156:1913-1931.
15. Lachaise D, David JR, Lemeunier F, Tsacas L, Ashburner M. 1986. The reproductive relationships of Drosophila sechellia with D. mauritiana, D. simulans, and D. melanogaster from the Afrotropical region. Evolution. 40:262-271.
16. Maside XR, Barral JP, Naveira HF. 1998. Hidden effects of X chromosome introgressions on spermatogenesis in Drosophila simulans X D. mauritiana hybrids unveiled by interactions among minor genetic factors. Genetics. 150:745-754.
17. H, Lazareva-Ulitsky B, Loo R, et al. (12 co-authors). 2005. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 33:D284-D288.
18. Michalak P, Noor MAF. 2003. Genome-wide patterns of expression in Drosophila pure-species and hybrid males. Mol Biol Evol. 20:1070-1076.
19. Michalak P, Noor MAF. 2004. Association of misexpression with sterility in hybrids of Drosophila simulans and D. mauritiana. J Mol Evol. 59:277-282.
20. Mukai M, Kitadate Y, Arita K, Shigenobu S, Kobayashi S. 2006. Expression of meiotic genes in the germline progenitors of Drosophila embryos. Gene Expr Patterns. 6:256-266.
21. Noor MA. 2005. Patterns of evolution of genes disrupted in expression in Drosophila species hybrids. Genet Res. 85:119-125.
22. Noor MAF, Feder JL. Forthcoming 2006. Speciation genetics: evolving approaches. Nat Rev Genet. 7:851-861.
23. Ortiz-Barrientos D, Counterman B, Noor MAF. Forthcoming 2006. Gene expression divergence and the origin of hybrid dysfunctions. Genetica.
24. Palopoli MF, Davis AW, Wu C-I. 1996. Discord between the phylogenies inferred from molecular versus functional data: uneven rates of functional evolution or low levels of gene flow? Genetics. 144:1321-1328.
25. Parisi M, Nuttall R, Edwards P, et al. (12 co-authors). 2004. A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol. 5:R40.
26. Pavlidis P, Li Q, Noble WS. 2003. The effect of replication on gene expression microarray experiments. Bioinformatics. 19:1620-1627.
27. Perezgasga L, Jiang J, Bolival B Jr, Hiller M, Benson E, Fuller MT, White-Cooper H. 2004. Regulation of transcription of meiotic cell cycle and terminal differentiation genes by the testis-specific Zn-finger protein matotopetli. Development. 131:1691-1702.
28. Porter AH, Johnson NA. 2002. Speciation despite gene flow when developmental pathways evolve. Evolution. 56:2103-2111.
29. Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL. 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science. 300:1742-1745.
30. Ranz JM, Machado CA. 2006. Uncovering evolutionary patterns of gene expression using microarrays. Trends Ecol Evol. 21:29-37.
31. Ranz JM, Namgyal K, Gibson G, Hartl DL. 2004. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and D. simulans. Genome Res. 14:373-379.
32. Rifkin SA, Kim J, White KP. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet. 33:138-144.
33. Sun S, Ting C-T, Wu C-I. 2004. The normal function of a speciation gene, Odysseus, and its hybrid sterility effect. Science. 305:81-83.
34. Thomas S, Singh RS. 1992. A comprehensive study of genic variation in natural populations of Drosophila melanogaster. VII. Varying rates of genic divergence as revealed by two-dimensional electrophoresis. Mol Biol Evol. 9:507-525.
35. Ting C-T, Tsaur S-C, Wu C-I. 2000. The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc Natl Acad Sci USA. 97:5313-5316.
36. Ting C-T, Tsaur S-C, Wu M-L, Wu C-I. 1998. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science. 282:1501-1504.
37. True JR, Haag ES. 2001. Developmental system drift and flexibility in evolutionary trajectories. Evol Dev. 3:109-119.
38. White KP. 2001. Functional genomics and the study of development, variation and evolution. Nat Rev Genet. 2:528-537.
39. White-Cooper H. 2004. Spermatogenesis: analysis of meiosis and morphogenesis. In: Henderson DS, editor. Drosophila cytogenetics protocols. Totowa (NJ): Humana Press. p. 45-75.
40. White-Cooper H, Leroy D, MacQueen A, Fuller MT. 2000. Transcription of meiotic cell cycle and terminal differentiation genes depends on a conserved chromatin associated protein, whose nuclear localisation is regulated. Development. 127:5463-5473.
41. White-Cooper H, Schäfer MA, Alphey LS, Fuller MT. 1998. Transcriptional and post-transcriptional control mechanisms coordinate the onset of spermatid differentiation with meiosis I in Drosophila. Development. 125:125-134.
42. Whitehead A, Crawford DL. 2006. Variation within and among species in gene expression: raw material for evolution. Mol Ecol. 15:1197-1211.
43. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol. 8:625-637.
44. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 20:1377-1419.
45. Wu C-I, Perez DE, Davis AW, Johnson NA, Cabot EL, Palopoli MF, Wu M-L. 1992. Molecular genetic studies of postmating reproductive isolation in Drosophila. In: Takahata N, Clark AG, editors. Molecular paleo-population biology. Berlin: Springer-Verlag. p. 191-212.
46. Zeng L-W, Singh RS. 1993. A combined classical genetic and high resolution two-dimensional electrophoretic approach to the assessment of the number of genes affecting hybrid male sterility in Drosophila simulans and Drosophila sechellia. Genetics. 135:135-147.