Gene duplications are a ubiquitous feature of eukaryotic genomes. However, we know relatively little about the evolutionary forces responsible for their preservation in, or loss from, the genome. The proposed research involves a resequencing survey of duplicated loci in three Drosophila species, D. melanogaster, D. simulans, and D. yakuba. We will also obtain mate pair sequencing data using the Illumina Genome Analyzer platform to survey D. simulans and D. yakuba species for segregating duplications. The resequencing data set will be used to quantify the extent of selective constraint within, and adaptive divergence between duplicated loci. Additionally, these data will provide valuable insight on the extent of ectopic gene conversion in the genus. The mate pair data will be used to infer the frequency spectrum of coding and non-coding duplications in all three species, and to quantify the extent to which such segregating variation may be deleterious or adaptive. We will also use these data to look for regions of the genome where polymorphism and divergence for duplication may be uncoupled, indicating a role for natural selection on the evolution of gene families.

Public Health Relevance

The gain and loss of genes over time is a major contributor to the evolution of genome structure, and variation in the number of genes is a contributor to phenotypic variation and disease within human populations. This study will use the fruit fly Drosophila melanogaster as a model system to elucidate the various evolutionary forces acting on recently duplicated genes, including those that are fixed within species as well as those segregating as polymorphisms. The design of the proposed research is intended to complement the Drosophila Population Genomics Project (DPGP,, which is focusing its near-term effort on D. melanogaster, by providing comparative data on duplicate loci and structural polymorphism in two other species from the genus, D. simulans and D. yakuba. 1

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Genetic Variation and Evolution Study Section (GVE)
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Eckstrand, Irene A
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University of California Irvine
Schools of Arts and Sciences
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Cridland, Julie M; Thornton, Kevin R; Long, Anthony D (2015) Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect. Genetics 199:85-93
Rogers, Rebekah L; Cridland, Julie M; Shao, Ling et al. (2015) Tandem Duplications and the Limits of Natural Selection in Drosophila yakuba and Drosophila simulans. PLoS One 10:e0132184
Baldwin-Brown, James G; Long, Anthony D; Thornton, Kevin R (2014) The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol 31:1040-55
Garrigan, Daniel; Kingan, Sarah B; Geneva, Anthony J et al. (2014) Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution. Genome Biol Evol 6:2444-58
Rogers, Rebekah L; Cridland, Julie M; Shao, Ling et al. (2014) Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans. Mol Biol Evol 31:1750-66
Thornton, Kevin R (2014) A C++ template library for efficient forward-time population genetic simulation of large populations. Genetics 198:157-66
Rogers, Rebekah L; Shao, Ling; Sanjak, Jaleal S et al. (2014) Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3 (Bethesda) 4:2345-51
Thornton, Kevin R; Foran, Andrew J; Long, Anthony D (2013) Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genet 9:e1003258
Hu, Tina T; Eisen, Michael B; Thornton, Kevin R et al. (2013) A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 23:89-98
Cridland, Julie M; Macdonald, Stuart J; Long, Anthony D et al. (2013) Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Mol Biol Evol 30:2311-27

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