Table 3

Evidence of positive selection on Galápagos and Swainson's hawk MHC class II B exon 2 sequences

Sequence set

Model

ln L

Parameter estimates

Positively selected sites

LRT statistic


All sequences

M1a

-1151.58

p = 0.775 (p1 = 0.225), ω = 0.071, ω1 = 1

not allowed

M2a

-1106.64

p0 = 0.559, p1 = 0.379 (p2 = 0.062), ω0 = 0.078, ω1 = 1, ω2 = 9.80

3, 5, 29, 49, 62, 63, 78

89.9 (P < 0.001)

M7

-1157.11

p = 0.145, q = 0.334

not allowed

M8

-1106.97

p0 = 0.938 (p1 = 0.062) p = 0.104, q = 0.117, ω = 10.11

3, 5, 29, 49, 62, 63, 78, 82

100.3 (P < 0.001)

Group 1

M1a

-482.72

p = 0.770 (p1 = 0.230), ω = 0.0, ω1 = 1

not allowed

M2a

-465.93

p0 = 0.884, p1 = 0.00 (p2 = 0.116), ω0 = 0.00, ω1 = 1, ω2 = 48.82

49, 63, 78, 82

33.6 (P < 0.001)

M7

-482.79

p = 0.005, q = 0.020

not allowed

M8

-465.93

p0 = 0.884 (p1 = 0.116) p = 0.005, q = 16.87, ω = 48.82

3, 49, 63, 78, 82

33.7 (P < 0.001)

Group 2

M1a

-825.63

p = 0.683 (p1 = 0.317), ω = 0.054, ω1 = 1

not allowed

M2a

-793.03

p0 = 0.491, p1 = 0.432 (p2 = 0.077), ω0 = 0.00, ω1 = 1, ω2 = 16.66

5, 29, 63, 78

65.2 (P < 0.001)

M7

-828.09

p = 0.096, q = 0.149

not allowed

M8

-793.04

p0 = 0.922 (p1 = 0.078) p = 0.023, q = 0.028, ω = 16.13

5, 29, 49, 62, 63, 78

70.1 (P < 0.001)


Separate analyses were performed on all sequences (N = 23), Group 1 (N = 10), and Group 2 (N = 12). Log-likelihood values and parameter estimates calculated by CODEML are presented, as are the sites predicted by models M2a and M8 to be under positive selection with posterior probabilities >0.99 and likelihood ratio test (LRT) statistics. LRTs were used to compare M2a to M1a and M8 to M7. The test statistics were compared to a chi-square distribution with df = 2. The positively selected sites are numbered according to the alignment in Figure 2.

Bollmer et al. BMC Evolutionary Biology 2011 11:143   doi:10.1186/1471-2148-11-143

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