Table 1.

Distribution of syntenic block sizes (≥3 genes) at the root of the Drosophila tree under various relaxed criteria

	No. of blocks
Syntenic block size (no. of genes)	Criterion 1	Criterion 2	Criterion 3
3	283	279	162
4	119	113	57
5	137	136	67
6	86	82	52
7	73	71	55
8	54	59	53
9	34	30	29
10	39	35	33
11	36	33	27
12	26	28	19
13	22	23	28
14	22	24	27
15	16	15	18
16	11	13	14
17	9	12	10
18	9	10	9
19	6	5	7
20	7	7	9
21	6	5	7
22	5	5	7
23	1	3	6
24	4	4	6
25	2	2	4
26	4	4	5
27	2	2	6
28	2	2	2
29	4	3	5
30	1	2	4
31	0	1	5
32	3	2	5
33	2	3	2
35	0	0	2
36	1	1	2
38	0	0	1
39	1	1	1
40	1	1	2
41	0	1	1
43	0	0	1
44	0	0	1
46	0	0	1
47	0	0	2
48	1	1	1
51	0	0	1
54	0	0	1
61	0	0	1

Note that criterion 2 is weaker than criterion 1 and criterion 3 includes the weakest assumptions. Criterion 1: first-pass syntenic blocks. Criterion 2: result of bridging syntenic blocks with genes on block edges paired using outgroup species 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. See Additional data files 6 and 7 for gene composition of blocks.