biostudies-literatureParsch JNIGMS NIH HHS1226-34https://www.ebi.ac.uk/biostudies/studies/S-EPMC2877998biostudies-literatureUnknown27(6)The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding regions highlight the difficulties in choosing such a reference sequence. Here, we investigate the utility of short intron sequences as a reference for the detection of selection. For a set of 119 Drosophila melanogaster genes containing 195 short introns (<or=120 bp), we analyzed polymorphism and divergence at 1) 4-fold synonymous sites, 2) all sites of introns <or=120 bp, 3) all sites of introns <or=65 bp, 4) bases 8-30 of introns <or=120 bp, and 5) bases 8-30 of introns <or=65Molecular biology and evolutionOn the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.PMC2877998GM083228-01A2R01 GM083228Saminadin-Peter SSWong KMAndolfatto PParsch JNovozhilov SfalseOn the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding regions highlight the difficulties in choosing such a reference sequence. Here, we investigate the utility of short intron sequences as a reference for the detection of selection. For a set of 119 Drosophila melanogaster genes containing 195 short introns (<or=120 bp), we analyzed polymorphism and divergence at 1) 4-fold synonymous sites, 2) all sites of introns <or=120 bp, 3) all sites of introns <or=65 bp, 4) bases 8-30 of introns <or=120 bp, and 5) bases 8-30 of introns <or=652010-01-01T00:00:00Z2010 Jun2025-04-04T11:31:45.21Z2019-03-27T00:31:10ZS-EPMC28779982015034010.1093/molbev/msq046