TABLE 2

Tests for selection among codons of SRY in Felidae using models implemented in PAML 315 using the likelihood method (see materials and methods)

CriteriaModelParameter estimatesLn likelihoodLRTSelected codon, BEB posterior probabilitya
AmongM0κ = 2.11751−1624.383NANA
    sites(one ratio)ω0 = 0.81556
M1aκ = 2.04609−1623.179NANA
(nearly neutral)ω0 = 0.21097 (p0 = 0.38216)
ω1 = 1.00000 (p1 = 0.61784)
M2aκ = 2.11857−1619.815M2a vs. M1aR46G (0.829)
(selection)ω0 = 0.63684 (p0 = 0.95861)6.729, P = 0.034, 2 d.f.G47S (0.910)
ω1 = 1 (p1 = 0)K125R (0.736)
ω2 = 5.98942 (p2 = 0.04139)D144E (0.569)
M187V, L (0.656)
M7κ = 2.06047−1623.196NANA
(β-distribution, neutral)β-distribution
p = 0.13573, q = 0.03540
M8κ = 2.11873−1619.819M8 vs. M7R46G (0.870)
(β-distribution, selection)ωs = 5.99456 (p1 = 0.04130)6.754, P = 0.034, 2 d.f.G47S (0.940)
β-distributionK125R (0.815)
p0 = 0.95870, p = 99.0, q = 56.358D144E (0.694)
M187V, L (0.759)
Y223H, C (0.588)
M8aκ = 2.04630−1623.181M8 vs. M8aNA
(β-distribution, ω = 1, fixed)ω1 = 1.00000 (p1 = 0.61804)6.724, P = 0.0047, 1 d.f.
β-distribution
p0 = 0.38196, p = 26.636, q = 99.0
  • P, proportion of sites; κ, transition:transversion ratio; ω = dN/dS for each proportion of sites; NA, not applicable;

  • a Corresponding codon (see Figure 1) of 36-species alignment.