Analysis of the MIR319a locus. (A) Close-up of MIR319a and flanking region in Arabidopsis thaliana. Thick arrows indicate genes. The transcription start is labeled “+1,” and the 2 splice variants are shown below. (B) VISTA comparison of MIR319a region between A. thaliana with Arabidopsis halleri and Capsella rubella. Conserved coding and noncoding regions are indicated in purple and pink, respectively (90% identity over a 100-bp window). (C) Sliding window analysis of H (Fay and Wu 2000), assessing the frequency of derived alleles in 19 A. thaliana accessions with the sister species Arabidopsis lyrata as outgroup (window size 100 bp and step size 25 bp). Most high-frequency derived changes are upstream of MIR319a. (D) Sliding window representation of segregating sites (S) in pairwise comparisons of MIR319a and surrounding sequences in A. thaliana to orthologs from other species. The positions are based on the respective alignment; lengths differences are due to indel polymorphisms. The miRNA is marked in red, and the foldback is highlighted in yellow.