Eukaryotes contain short (∼80-200 bp) regions that have few or no substitutions 
among species that represent hundreds of millions of years of evolutionary 
divergence. These ultraconserved elements (UCEs) are candidates for containing 
essential functions, but their biological roles remain largely unknown. Here, we 
report the discovery and characterization of UCEs from 12 sequenced Drosophila 
species. We identified 98 elements ≥80 bp long with very high conservation 
across the Drosophila phylogeny. Population genetic analyses reveal that these 
UCEs are not present in mutational cold spots. Instead we infer that they 
experience a level of selective constraint almost 10-fold higher compared with 
missense mutations in protein-coding sequences, which is substantially higher 
than that observed previously for human UCEs. About one-half of these Drosophila 
UCEs overlap the transcribed portion of genes, with many of those that are 
within coding sequences likely to correspond to sites of ADAR-dependent RNA 
editing. For the remaining UCEs that are in nongenic regions, we find that many 
are potentially capable of forming RNA secondary structures. Among ten chosen 
for further analysis, we discovered that the majority are transcribed in 
multiple tissues of Drosophila melanogaster. We conclude that Drosophila species 
are rich with UCEs and that many of them may correspond to novel noncoding RNAs.