Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications

Table 3 Best fit of codon-based models of evolution to ring-tailed lemur MHC-DRB variation

MHC-DRB	LnL	AIC	ΔAIC	Parameters	PSS
M0 - one ratio [ω]	−1464.19	3184.38	378.64	ω = 0.60	Not applicable
M1a - neutral	−1302.65	2863.3	57.56	p0 = 0.65, ω0 = 0.0	Not applicable
M2a - selection	−1271.87	2805.74	0	p0 = 0.64, ω0 = 0.01, p1 = 0.25, ω1 = 1.0, p2 = 0.11, ω2 = 3.94	5, 16, 36, 56, 57
M7 - nearly neutral with β	−1298.41	2854.82	49.08	p = 0.05, q = 0.15	Not applicable
M8 - positive selection with β	−1273.31	2808.62	2.88	p0 = 0.87, p1 = 0.13, p = 0.02, q = 0.05, ω = 3.84	5, 16, 36, 56, 57

Note. Fit of data compared between models of strict neutral evolution [M0, M1a, & M7] and models including positive selection (M2a & M8; [91]). Fit assessed by log likelihood score [LnL], and Akaike information criteria [AIC] values; the model with the lowest AIC value, or a ΔAIC of zero, indicates the model that best fits the data. Estimated proportions of sites [p_X] evolving at corresponding estimated rates [ω_X = dN/dS] are given in the parameters column, as well as positively selected sites [PSS], or AA sites under positive selection in each model

ISSN: 1471-2164