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

Biology Direct

Table 4 Log-likelihood values and parameter estimates under fixed-site models for flaA sequences

Model^a	np^a	ℓ	AIC	rs^b	κ^b	ω^b
A (homogeneous model)	44	-6830.350	13748.700	1	2.093	0.062
B (different rs)	46	-6645.595	13383.190	rs₂ = 4.473 rs₃ = 1.614	2.286	0.049
C (different rs and πs^c)	64	-6613.420	13354.840	rs₂ = 5.595 rs₃ = 1.608	2.262	0.046
D (different rs, κ, and ω)	50	-6613.537	13327.074	rs₂ = 3.372 rs₃ = 1.703	κ₁ = 2.089 κ₂ = 1.929 κ₃ = 2.958	ω₁ = 0.025 ω₂ = 0.084 ω₃ = 0.026
D2 (different rs and ω)^d	47	-6617.228	13328.456	rs₂ = 3.439 rs₃ = 1.650	2.286	ω₁ = 0.025 ω₂ = 0.084 ω₃ = 0.025
E (different rs, κ and ω, and different πs)	68	-6580.030	13296.060	rs₂ = 3.944 rs₃ = 1.688	κ₁ = 1.929 κ₂ = 1.929 κ₃ = 3.005	ω₁ = 0.023 ω₂ = 0.083 ω₃ = 0.025

The three partitions correspond to the 1: N-terminal extreme (104 codons), 2: the central region (101 codons) and 3: the C-terminal extreme (80 codons).
^a np, number of parameters including 33 branch lengths.
^b rs, nucleotide substitution rate. The subscript corresponds to the three partitions of flaA sequences (rs₁ is 1 in all models and it is not shown); κ: transition/transversion ratio; ω: d_N/d_S ratio.
^c πs, codon frequencies (data not shown).
^d Model D but with κ fixed to 2.286.

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