Summary of all known and novel miRNAs recovered within 12 Drosophila genomes. (A) Counts of known and novel miRNAs recovered or identified, respectively, at our two highest confidence classes—“confident” and “candidate-rescued.” MiRNAs from a third confidence class—“candidate” miRNAs—are shown in Supplemental Figure S5. (B) The proportion of miRNAs recovered within three classes defined by biogenesis pathway, and testes-restricted, clustered status. Pie charts are provided for all novel or known annotations and for the merged collection. (C) The distribution of alignment sizes upon assignment of all miRNAs into 1004 alignments. Paralogous miRNAs were assigned to single-species alignment. The majority of miRNAs identified are singletons (species-specific) or doubletons (clade-specific). (D,E) Empirical cumulative distribution function (ECDF) of alignment expression. Alignments are segregated based on age (D) and miRNA class (E). Empirical CDFs are plotted using the maximum expression values computed across all constitutive members of each alignment. (RPMM) Reads per Million mapped miRNA reads.