Table 4

Likelihood ratio tests comparing models of molecular evolution of MAT genes

Gene

Analysis

λ1

df1

2Δλ1

p-value

dN/dS

Parameters


MAT1-1-1

M0: one ratio

-2205.4733

4

5.9586

0.2023

0.4280

ω = 0.4280

M3: discrete (κ = 3)

-2202.4940

0.4462

p0 = 0.3732, ω0 = 0.7052; p1 = 0.3932, ω1 = 0.1117; p2 = 0.2336, ω2 = 0.7052

M1a: nearly neutral

-2202.6642

2

0.0000

1.0000

0.4599

p0 = 0.6556, ω0 = 0.1761; p1 = 0.3440, ω1 = 1

M2a: positive selection

-2202.6642

0.4599

p0 = 0.6556, ω0 = 0.1761; p1 = 0.2332, ω1 = 1; p2 = 0.1109, ω2 = 1

M7: β

-2202.5615

2

0.0000

1.0000

0.4507

p0 = 0.4117; q = 0.5019

M8: β & ω > 1

-2202.5615

0.4507

p0 = 0.1000 p = 0.4117 q = 0.5019; (p1 = 0.00001) ω = 1.0000

MAT1-1-3

M0: one ratio

-1706.3379

4

20.5175

0.0004*

0.295

ω = 0.2951

M3: discrete (κ = 3)

-1696.0792

0.3103

p0 = 0.0007, ω0 = 0.1116; p1 = 0.9232, ω1 = 0.1117; p2 = 0.0761, ω2 = 2.7212

M1a: nearly neutral

-1697.3663

2

2.5742

0.2761

0.2598

p0 = 0.7402, ω0 = 0; p1 = 0.2598, ω1 = 1

M2a: positive selection

-1696.0792

0.3103

p0 = 0.9239, ω0 = 0.1117; p1 = 0, ω1 = 1; p2 = 0.0761, ω2 = 2.7212

M7: β

-1697.6108

2

3.0594

0.2166

0.3000

p = 0.0050; q = 0.0119

M8: β & ω > 1

-1696.0811

0.3104

p0 = 0.9244 p = 12.5791 q = 99.0000; (p1 = 0.0756) ω = 2.7290

MAT1-2-1

M0: one ratio

-2133.8605

4

11.1677

0.0247*

0.3714

ω = 0.37135

M3: discrete (κ = 3)

-2128.2767

0.4212

p0 = 0.3531, ω0 = 0.2495; p1 = 0.6157, ω1 = 0.2496; p2 = 0.0312, ω2 = 5.7427

M1a: nearly neutral

-2129.6740

2

2.7948

0.2472

0.3528

p0 = 0.6472, ω0 = 0; p1 = 0.3528, ω1 = 1

M2a: positive selection

-2128.2767

0.4212

p0 = 0.9688, ω0 = 0.2496; p1 = 0, ω1 = 1; p2 = 0.0312, ω2 = 5.7428

M7: β

-2129.8169

2

3.0800

0.2144

0.3387

p = 0.0170; q = 0.0321

M8: β & ω > 1

-2128.2769

0.4212

p0 = 0.9690 p = 33.0717 q = 99.0000; (p1 = 0.0310) ω = 5.7612


Models of neutral evolution (M1a and M7) are tested against models that incorporate positive selection (M2a and M8). Comparison of M0 vs. M3 tests variable dN/dS rate ratios among sites. Model M3 classifies sites in the sequence into discrete classes (κ = 3) with both the dN/dS rate ratio ω0, ω1, ω3 and the proportions p0, p2 and p3 estimated from the data. For models M1a and M2a, values of p0, p1, and p2, are the proportions of sites inferred to be evolving under purifying selection, neutral evolution, and positive selection, respectively, and ω0, ω1 and ω2 are their corresponding dN/dS rate ratios. For models M7 and M8, the β distribution, β (p, q), describes the distribution of the dN/dS rate ratio between zero and one, and p0 is the proportion of sites within this distribution. In these models, p1 is the proportion of sites inferred to be under positive selection, and ω is the dN/dS rate ratio for those sites.

Zaffarano et al. BMC Evolutionary Biology 2011 11:282   doi:10.1186/1471-2148-11-282

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