Our long-term goal is to understand the biological significance and evolutionary implications of contrasting levels of DNA sequence polymorphism within and between species. Of particular interest are the frequency and nature of variants with functional consequences that are the targets of adaptive evolution. We are interested in the evolutionary forces shaping specific genes, and in the determinants of genome-wide patterns of variation and molecular evolution as they are influenced by variation in rates of recombination. We propose completing single and multi-gene analyses aimed at inferring the distribution of selective effects acting on synonymous, non-synonymous, and intron sequence variants within and between Drosophila melanogaster and D. simulans. Sequence polymorphism data will be generated in order to test hypotheses concerning the efficacy and direction of selection acting on different classes of sequence variants. Our primary focus will also shift to an extension of our microsatellite-based genome scan for adaptive fixations, focusing on a 2 Mb high-recombination region on the X chromosome of D. melanogaster and D. simulans. Evidence for selective sweeps will be verified and the targets of these selective sweeps localized within the genome using a finer resolution, DNA sequence polymorphism scan. These data will allow estimation of the timing, strength, and target of selection. Finally, we will carry out a molecular characterization of the genes and associated variation at identified targets of selection. Our proposed research will make significant contributions to our understanding of the processes by which genomes evolve and organisms adapt to their environments. It will also contribute to gene annotation efforts, continue to serve as empirical motivation for new theoretical studies and statistical tests, and will provide a conceptual framework in which to interpret DNA polymorphism data increasingly available from other organisms including humans.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM036431-20
Application #
7082033
Study Section
Genetics Study Section (GEN)
Program Officer
Eckstrand, Irene A
Project Start
1986-04-01
Project End
2008-12-31
Budget Start
2006-07-01
Budget End
2008-12-31
Support Year
20
Fiscal Year
2006
Total Cost
$301,724
Indirect Cost
Name
Cornell University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Singh, Nadia D; Stone, Eric A; Aquadro, Charles F et al. (2013) Fine-scale heterogeneity in crossover rate in the garnet-scalloped region of the Drosophila melanogaster X chromosome. Genetics 194:375-87
Clark, Nathan L; Alani, Eric; Aquadro, Charles F (2013) Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals. Genetics 193:529-38
Singh, Nadia D; Jensen, Jeffrey D; Clark, Andrew G et al. (2013) Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 193:215-28
Clark, Nathan L; Alani, Eric; Aquadro, Charles F (2012) Evolutionary rate covariation reveals shared functionality and coexpression of genes. Genome Res 22:714-20
Wong, Alex; Turchin, Michael; Wolfner, Mariana F et al. (2012) Temporally variable selection on proteolysis-related reproductive tract proteins in Drosophila. Mol Biol Evol 29:229-38
Clark, Nathaniel L; Aquadro, Charles F (2010) A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins. Mol Biol Evol 27:1152-61
Singh, Nadia D; Arndt, Peter F; Clark, Andrew G et al. (2009) Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila. Mol Biol Evol 26:1591-605
Zamora, Alejandro; Sun, Qi; Hamblin, Martha T et al. (2009) Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics. Mol Biol Evol 26:2015-30
Clark, Nathaniel L; Gasper, Joe; Sekino, Masashi et al. (2009) Coevolution of interacting fertilization proteins. PLoS Genet 5:e1000570
Rebeiz, Mark; Pool, John E; Kassner, Victoria A et al. (2009) Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science 326:1663-7

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