Table 1.

Number and (percent) of genes falling under accelerated, clock-like, and slow-rate categories in recently diverged species when compared to older species pairs. (a) Analysis using the published divergence boundaries according to Kliman et al. [33] for D. simulans and D. sechellia, and Tamura et al. [34] for D. melanogaster-D. simulans and D. yakuba-D. erecta. (b) Analysis using the revised divergence time estimates for D. simulans and D. sechellia. (c) Analysis applying the 95% confidence interval boundaries on revised divergence estimates.

	Rate Categories
	Slow	Clock-like	Accelerated
(a)
mel-sim versus yak-ere
d N	1096 (22.63)	2251 (46.48)	1496 (30.89)
d S	348 (7.19)	3628 (74.91)	867 (17.90)
sim-sec versus yak-ere
d N	173 (3.99)	314 (7.26)	3840 (88.75)
d S	37 (0.86)	184 (4.25)	4106 (94.89)
(b)
sim-sec versus yak-ere
d N	594 (13.73)	2275 (52.58)	1458 (33.69)
d S	311 (7.19)	3241 (74.90)	775 (17.91)
(c)
mel-sim versus yak-ere
d N	963 (19.89)	2996 (61.86)	884 (18.25)
d S	242 (5.00)	4359 (90.00)	242 (5.00)
sim-sec versus yak-ere
d N	469 (10.84)	3007 (69.49)	851 (19.67)
d S	216 (5.00)	3895 (90.00)	216 (5.00)
pse-per versus sim-sec
d N	327 (8.20)	2962 (74.27)	699 (17.53)
d S	199 (5)	3590 (90)	199 (5)