title: Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.
abstract: Recent genomic sequencing of 10 additional Drosophila genomes provides a rich resource for comparative genomics analyses aimed at understanding the similarities and differences between species and between Drosophila and mammals. Using a phylogenetic approach, we identified 64 genomic elements that have been highly conserved over most of the Drosophila tree, but that have experienced a recent burst of evolution along the Drosophila melanogaster lineage. Compared to similarly defined elements in humans, these regions of rapid lineage-specific evolution in Drosophila differ dramatically in location, mechanism of evolution, and functional properties of associated genes. Notably, the majority reside in protein-coding regions and primarily result from rapid adaptive synonymous site evolution. In fact, adaptive evolution appears to be driving substitutions to unpreferred codons. Our analysis also highlights interesting noncoding genomic regions, such as regulatory regions in the gene gooseberry-neuro and a putative novel miRNA.
authors.affiliation: Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95691, USA. akholloway@ucdavis.edu
authors.forename: Alisha K
authors.initials: AK
authors.lastname: Holloway
authors.forename: David J
authors.initials: DJ
authors.lastname: Begun
authors.forename: Adam
authors.initials: A
authors.lastname: Siepel
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Pollard
mesh_terms: D000818:Animals; D003062:Codon; D017124:Conserved Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D049750:Genome, Insect; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D003062:Codon; D035683:MicroRNAs