The objective of this research is to systematically study new genes in the Drosophila melanogaster subgroup and to investigate the tempo and mode of new gene originations. We will focus on the new chimerical genes created by RNA-involved retroposition that often evolve novel functions associated with the mosaic gene structures. To meet these objectives, the following four-prong integrated approaches will be pursued using the D. melanogaster subgroup as our model taxa. (1) Detection of New Genes by Genomic Analyses: Taking advantage of the known divergence times within the subgroup (0.5-12 million years (mys)), new gene detection will be based upon an interdisciplinary approach that integrates computational and experimental genomic analyses. Our computational analyses will utilize available genome sequences and work in conjunction with Fluorescence In Situ Hybridization with multiple species genomes (MFISH) and Comparative Genomic Hybridization (CGH) using DMA microarrays. These analyses will detect and provide new gene candidates on the genome-wide scale. (2) Inference of the Functionality of the New Genes: To infer functionality for these new genes we will examine the molecular evolutionary and transcriptional constraints of each new gene and their temporal-spatial expression patterns. Molecular evolution and population genetic analyses will be also conducted to detect adaptive evolution of new functional genes. (3) Analysis of phylogenetic Distribution of New Gene Originations: We will map all detected origination events of new genes on the phylogenetic tree of the melanogaster subgroup species. We will estimate the rate of new gene origination and its variation along branches of the phylogeny, using related statistical analyses including maximum likelihood approach. (4) Sex Chromosome-dependence of the Origination of New Genes: Taking advantage of the young ages of the identified new genes (between 0.5 and 12 mys), we will investigate whether or not the male gene traffic that we observed in ancient retrogene samples is an on- going process by analyzing the chromosomal location distribution of new genes and their parental genes. The results from these four categories of studies will generate the first phylogenetic distribution of new genes and provide the fresh-insight into the rates and patterns of new gene originations in genomes. ? ? ?
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