Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors

Table 2 Estimates of the proportion of adaptive substitutions

α model	Par	log(L)	2Δlog(L)	χ² p-value	AIC	Akaike weight	α_a	α_b
An. gambiae vs. An. melas
α = 0	29	-336.49			730.98	0.424	[0]	[0]
α ~ (all loci)	30	-335.76	1.46	0.23	731.52	0.323	0.23	[0.23]
α ~ (control, serpin)	31	-335.66	0.19	0.91	733.33	0.131	0.18	0.25
α ~ (other, immune)	31	-335.73	0.06	0.97	733.46	0.123	0.24	0.07
An. arabiensis vs. An. melas
α = 0	29	-329.36			716.73	0.495	[0]	[0]
α ~ (all loci)	30	-329.31	0.10	0.75	718.63	0.191	-0.05	[-0.05]
α ~ (control, serpin)	31	-328.07	2.48	0.29	718.15	0.243	-0.54	0.10
α ~ (other, immune)	31	-329.30	0.02	0.99	720.61	0.071	-0.03	-0.15
An. gambiae vs. An. merus
α = 0	34	-333.36			734.72	0.349	[0]	[0]
α ~ (all loci)	35	-332.60	1.52	0.22	735.21	0.274	0.15	[0.15]
α ~ (control, serpin)	36	-331.59	2.02	0.36	735.18	0.277	0.34	0.03
α ~ (other, immune)	36	-332.60	0.00	1.00	737.21	0.101	0.15	0.17
An. arabiensis vs. An. merus
α = 0	34	-311.04			690.07	0.053	[0]	[0]
α ~ (all loci)	35	-307.96	6.15	0.01	685.92	0.422	0.34	[0.34]
α ~ (control, serpin)	36	-307.22	1.48	0.48	686.44	0.325	0.47	0.25
α ~ (other, immune)	36	-307.71	0.50	0.78	687.42	0.200	0.36	0.10

α_a and α_b are estimates of the proportion of adaptive substitutions in each of the two classes of gene (control/serpin or non-immune/immune, respectively), Par is the number of parameters in the model. Where the value of α is constrained by the model it is marked in square brackets. Negative values arise from an 'excess' of non-synonymous polymorphism, and could represent sampling error, or mildly deleterious polymorphisms [7]. AIC is the Akaike Information Criterion. The Akaike weighting can be interpreted as the weight of evidence in favour of the corresponding model, given the relative support for all the available models [52].

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