Table 1. .

Maximum-Likelihood Estimates of Selection^[Note]

Model and Parameters	l	Positively Selected Sites
M0 (one ratio):	−14831.677	None
dN/dS=.3914
M1 (neutral):	−14743.041	Not allowed
p0=.632 and ω0=.071
p1=.368 and ω1=1.000
M2 (selection):	−14739.552	314, 351, 1129, 1147, 1367, 1480, 1522, 345, 351, 387, 436, 528, and 547
p0=.656 and ω0=.092
p1=.326 and ω1=1.000
p2=.018 and ω2=3.170
M3 (discrete):	−14738.992	286, 312, 314, 345, 351, 387, 436, 528, 547, 629, 797, 870, 891, 953, 972, 1010, 1052, 1074, 1120, 1129, 1136, 1147, 1305, 1367, 1422, 1480, 1492, 1497, 1522, 1534, 1553, 1564, 1610, 1663, 1666, 1673, 1731, 2034, 2106, and 2209
p0=.448 and ω0=.000
p1=.497 and ω1=.623
p2=.054 and ω2=2.398
M7 (β):	−14744.192	Not allowed
p=.103 and q=.145
M8 (β and ω):	−14739.187	286, 312, 314, 345, 351, 547, 797, 870, 972, 1129, 1147, 1305, 1367, 1422, 1480, 1497, 1522, 1553, and 1666
p0=.967, p=.229, and q=.402
p1=.033 and ω=2.703
M8a (β and fixed ω):	−14743.051	Not allowed
p0=.646, p=7.695, and q=99.0
p1=.355 and ω=1.000

Note.— p is the proportion of sites in each class, ω is the d_N/d_S ratio, and l is the log likelihood.