Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

Biology Direct

Table 2 Log-likelihood, AIC and parameter estimates under random-site models for flaA sequences

Model	p ^a	ω^b	ℓ^c	AIC^d	κ^e	Estimates of parameters	Positively selected sites
M0: one ratio	1	0.062 ± 0.000	-6830.350	13662.700	2.093	ω = 0.062	None
M1a: nearly neutral	2	0.114 ± 0.015	-6689.544	13383.089	2.192	p₀ = 0.92 (p₁ = 0.08) ω = 0.034, ω = 1	Not allowed
M2a: positive selection	4	0.114 ± 0.015	-6689.544	13387.092	2.192	p₀ = 0.918, p₁ = 0.082, (p₂ = 0.000), ω₀ = 0.034, ω₁ = 1; ω₂ = 58.267	179 I (at P = 0.747)
M3: discrete (K = 3)	5	0.071 ± 0.008	-6601.883	13213.766	2.085	p₀ = 0.675, p₁ = 0.254 (p₂ = 0.071), ω₀ = 0.003 ω₁ = 0.122, ω₂ = 0.546	None
M7: beta	2	0.071 ± 0.009	-6603.940	13211.879	2.087	p = 0.152, q = 1.683	Not allowed
M8: beta & ω > 1	4	0.072 ± 0.008	-6600.818	13209.635	2.082	p₀ = 0.996, (p₁ = 0.004) p = 0.160, q = 1.976 ω = 1.92	179 I (at P = 0.967)
M8a: beta & ω_s = 1	4	0.072 ± 0.008	-6601.490	13210.978	2.086	p₀ = 0.991, (p₁ = 0.009) p = 0.165, q = 2.190 ω = 1.0	Not allowed

^a p, number of free parameters for each model
^b ω, averaged ω ± standard error of d_N/d_S ratio over all sites in the flaA gene alignment
^c ℓ, log-likelihood value for each model
^d AIC, Akaike's Information Criterion value
^e κ, transition/transversion rate [27]
Values of ω > 1 and sites inferred to be under positive selection are in bold

ISSN: 1745-6150