The objective of this research is to study evolutionary forces that govern unusual variation of the D. melanogaster fourth chromosome uncovered recently by us. For a long time, this chromosome has been viewed as a canonical textbook example of how natural selection can result in low within-species variation in a genome region of low recombination. Our preliminary work has indicated that the previous conclusion that the entire chromosome 4 harbors low variation is incorrect and should not be taken as a paradigm any more. We have found a high level of nucleotide variation in large blocks of this chromosome in D. melanogaster and simulans. The following objectives will be pursued. (1) Using Monte Carlo simulations based on the coalescent process with selection and recombination, we will investigate a theoretical population genetic process associated with a low average recombination rate in the whole chromosome but with sporadic recombination hot spots. We expect that this theoretical analysis will shed new light on the relationship between recombination and variation. (2) To determine the length of the high variation region in the chromosome, we will characterize the polymorphism distribution in natural populations in whole euchromatin regions of the D. melanogaster fourth chromosome. (3) To compare the high variation region of D. melanogaster with the corresponding region in other sibling species, we will investigate sequence variation in D. simulans and D. yakuba. Finally, using these theoretical results and variation data, we will test several hypotheses that might explain the variation and evolution of the chromosome: selective sweep, background selection, balancing selection, and neutrality. We will also characterize the variation and evolution of the sphinx gene, a gene that recently originated on the D. melanogaster fourth chromosome, with structural and expression analysis, and investigate its potential role in the evolution of the chromosome. These studies should add significantly to the understanding of the evolutionary genetics of the Drosophila fourth chromosome.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM065429-04
Application #
7081329
Study Section
Genetics Study Section (GEN)
Program Officer
Eckstrand, Irene A
Project Start
2003-07-01
Project End
2007-06-30
Budget Start
2006-07-01
Budget End
2007-06-30
Support Year
4
Fiscal Year
2006
Total Cost
$255,596
Indirect Cost
Name
University of Chicago
Department
Biology
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
Chen, Sidi; Ni, Xiaochun; Krinsky, Benjamin H et al. (2012) Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene. EMBO J 31:2798-809
Chen, Ying; Dai, Hongzheng; Chen, Sidi et al. (2011) Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster. PLoS One 6:e18853
Cardoso-Moreira, Margarida M; Long, Manyuan (2010) Mutational bias shaping fly copy number variation: implications for genome evolution. Trends Genet 26:243-7
Chen, Sidi; Zhang, Yong E; Long, Manyuan (2010) New genes in Drosophila quickly become essential. Science 330:1682-5
Arguello, J Roman; Zhang, Yue; Kado, Tomoyuki et al. (2010) Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome. Mol Biol Evol 27:848-61
Vibranovski, Maria D; Chalopin, Domitille S; Lopes, Hedibert F et al. (2010) Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis. Genetics 186:431-3
Vibranovski, Maria D; Zhang, Yong; Long, Manyuan (2009) General gene movement off the X chromosome in the Drosophila genus. Genome Res 19:897-903
Vibranovski, Maria D; Lopes, Hedibert F; Karr, Timothy L et al. (2009) Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. PLoS Genet 5:e1000731
Dai, Hongzheng; Chen, Ying; Chen, Sidi et al. (2008) The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci U S A 105:7478-83
Yang, Shuang; Arguello, J Roman; Li, Xin et al. (2008) Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS Genet 4:e3

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