High variability and non-neutral evolution of the mammalian avpr1a gene

Fink, Sabine; Excoffier, Laurent; Heckel, Gerald

doi:10.1186/1471-2148-7-176

BMC Ecology and Evolution

Table 2 Results of avpr1a selection tests performed with the software PAML

From: High variability and non-neutral evolution of the mammalian avpr1a gene

model	parameters	likelihood l	positively selected sites
A: Microtus
M0, one ratio		-1970.4456	Not allowed
M1, neutral	p₀ = 0.9600, ω₀ = 0.0602	-1967.7956	Not allowed
	p₁ = 0.0400, ω₁ = 1
M2, selection	p₀ = 0.9600, ω₀ = 0.0602	-1967.7956	18,26
	p₁ = 0.0199, ω₁ = 1
	p₂ = 0.0200, ω₂ = 1
M3, discrete	p₀ = 0.1311, ω₀ = 0.0406	-1967.3614
	p₁ = 0.7474, ω₁ = 0.0407
	p₂ = 0.1215, ω₂ = 0.4609
M7, beta	p = 0.29056, q = 2.75313	-1967.4361	Not allowed
M8, beta and ω	p₀ = 1.0000, p = 0.29056, q = 2.75313	-1967.4361	18,26,30
	p₁ = 0.0000, ω = 1.0000
B: Mammals
M0, one ratio		-3628.0022	Not allowed
M1, neutral	p₀ = 0.8433, ω₀ = 0.0452	-3567.8186	Not allowed
	p₁ = 0.1568, ω₁ = 1
M2, selection	p₀ = 0.8433, ω₀ = 0.0452	-3567.8186
	p₁ = 0.1356, ω₁ = 1
	p₂ = 0.0212, ω₂ = 1
M3, discrete	p₀ = 0.5084, ω₀ = 0.0000	-3538.7336
	p₁ = 0.3169, ω₁ = 0.1063
	p₂ = 0.1747, ω₂ = 0.4661
M7, beta	p = 0.23059, q = 1.71469	-3540.0533	Not allowed
M8, beta and ω	p₀ = 1.0000, p = 0.23059, q = 1.71466	-3540.0535	25,36
	p₁ = 0.0000, ω = 2.02300
Branch specific models:
MA, foreground branch = *M. montanus*		-3567.8186	none
MA, foreground branch = *A. terrestris*		-3567.8187	none
MA, foreground branch = *C. glareolus*		-3567.8186	none
MA, foreground branch = *A. sylvaticus*		-3567.8186	none
MA, foreground branch = *M. musculus*		-3567.3630	none
MA, foreground branch = *R. norvegicus*		-3567.8186	none
MA, foreground branch = *O. aries*		-3563.2582	191,228,231,243,247,260
MA, foreground branch = *B. taurus*		-3567.3824	243
MA, foreground branch = *C. familiaris*		-3567.8186	191
MA, foreground branch = *M. mulatta*		-3567.8186	none
MA, foreground branch = *P. troglodytes*		-3567.5837	247
MA, foreground branch = *H. sapiens*		-3567.5242	259,274
MA, foreground branch = *M. domestica*		-3567.7818	none

Maximum likelihood methods were applied to compare models allowing for positive or negative selection (M2, M3, M8 and MA) with models without selection (M0, M1, M7). Parameters are represented as p₀ = proportion of sites where ω < 1 (ω₀), p₁ = proportion of sites where ω = 1 (ω₁), and for models with selection p₂ = proportion of sites where ω > 1 (ω₂). For models M7 and M8, p and q represent parameters of the beta distribution. The log likelihood l of each model is given as well as the position of positively selected codons (where ω > 1). A: Overall selection tests in Microtus species (M1 vs. M2, M7 vs. M8) and ratio heterogeneity (M0 vs. M3).B: Overall selection tests of avpr1a and tests for positive selection along specific mammal branches (M1 vs. MA).

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