Comparison between number of syntenic blocks and total number of genes in syntenic blocks of various sizes at the Drosophila root. Values are normalized between 0 and 1 with the maximum value set to 1. The x-axis shows various criteria based on the different relaxed assumptions discussed in the text. Criterion 1: first-pass syntenic blocks. Criterion 2: results of further merging based on outgroup evidence. Criterion 3: further merging of syntenic blocks based on relaxed assumption of bridging blocks using genes on block edges paired in at least one fly species. As additional evidence is incorporated using relaxed assumptions, blocks are merged into longer chains, which results in a lowering of the total number of syntenic blocks (1: 1,029 blocks, 2: 1,018 blocks, 3: 758 blocks). Correspondingly, the number of genes in larger blocks increases (for blocks >5 genes in size: 1: 5,532 genes, 2: 5,656 genes, 3: 6,576 genes; for blocks ≥20 genes in size: 1: 1,230 genes, 2: 1,329 genes, 2,638 genes).