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Table 4 Likelihood ratio tests comparing models of molecular evolution of MAT genes

From: Sex in the PAC: A hidden affair in dark septate endophytes?

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

  1. 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.
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BMC Ecology and Evolution

ISSN: 2730-7182

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