TABLE 4.

d_N/d_S ratios in pairwise comparisons between members of gene clusters with two to three sequences

			NG			MLE
Cluster	N	bp	dN/dS	dN	dS	ω	dN	dS
1	2	609 (417)	0.61	0.45	0.73	0.61	0.38	0.62
2	2	546	1.96	0.18	0.09	2.14	0.19	0.09
3	2	336 (177)	1.55	0.08	0.05	1.14	0.07	0.06
4	2	190 (129)	2.82	0.10	0.04	3.39	0.11	0.03
5	2	549 (432)	0.71	0.14	0.20	1.01	0.16	0.16
7	2	213 (210)	1.25	0.19	0.15	1.93	0.21	0.11
8	3	270	3.06, 2.97, ∞	0.03–0.27	0.00–0.09	6.21, 5.98, ∞	0.30–0.03	0.05–0.00
9	3	225 (147)	0.82	0.16	0.19	1.04	0.21	0.21
10	3	264	0.30, 0.61, 0.90	0.04–0.29	0.13–0.38	0.39, 0.75, 1.21	0.04–0.33	0.11–0.34
Acp16a/b	2	276 (150)	1.29	0.33	0.25	2.20	0.61	0.28
Acp27a/b	2	351 (303)	2.25	0.11	0.05	3.60	0.12	0.03

Cluster numbers correspond to D. mayaguana clusters in Table 3. Acp16a/b and Acp27a/b are D. mojavensis gene clusters. bp, number of sites in the alignment before and after gap deletion (in parentheses). N, number of sequences in the cluster; NG, Nei–Gojobori method; MLE, maximum-likelihood estimate. For cluster 9, the analysis included only the two most similar sequences because the third sequence was too divergent and alignment of ORFs did not seem reliable.The symbol ∞ means that d_S = 0 and therefore it is not possible to calculate d_N/d_S.