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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
  1. 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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BMC Ecology and Evolution

ISSN: 2730-7182

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