Cynomys gunnisoni
Model†	ln L §	ΔAIC	Parametersφ
M0 – one ω	−675.361	37.50	0.290
M1a – nearly neutral (ω 0  < 1, ω 1  = 1)	−655.611	best *	p 0  = 0.733, ω 0  = 0.034
M2a – positive selection (ω 0 < 1, ω 1 = 1, ω 2 > 1)	−653.777	0.331	p0 = 0.805, p2 = 0.195,ω 0 = 0.073, ω 2 = 2.145
M7 – beta (p, q)	−656.058	0.892	p = 0.017; q = 0.034
M8 – beta and ω (p, q, ωs > 1)	−653.782	0.341	p0 = 0.806, (p1 = 0.194), p = 8.015, q = 99.0, ω = 2.155
Cynomys ludovicianus
Model†	ln L §	ΔAIC	Parametersφ
M0 – one ω	−552.710	26.682	0.325
M1a – nearly neutral (ω 0 < 1, ω 1 = 1)	−542.278	5.818	p0 = 0.654, ω 0 = 0.059
M2a – positive selection (ω 0  < 1, ω 1  = 1, ω 2  > 1)	−539.369	best *	p 0  = 0.631, p 2  = 0.091, ω 0  = 0.089, ω 2  = 13.813
M7 – beta (p, q)	−542.612	6.487	p = 0.111; q = 0.171
M8 – beta and ω (p, q, ωs > 1)	−539.275	−0.187	p0 = 0.905, (p1 = 0.095), p = 0.253, q = 0.502, ω = 12.803

Estimated proportions of sites (p _x) evolving at corresponding estimated rates (ω _x = d _N/d _S) are given in the parameters column.

^†Alternative models of codon evolution from PAML (Yang 1997, 2007).

^§Log likelihood score.

^φProportion of sites (p) evolving at corresponding rate (ω).

^*Model of best fit.