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Table 1 Log-likelihood values and parameter estimates for each gene of Echovirus E6 and some enterovirus B strains that could recombine with E6

From: Molecular evolution of two asymptomatic echovirus 6 strains that constitute a novel branch of recently epidemic echovirus 6 in China

Genes

Model codea

ℓb

Parameter estimatesc

Neutral sitesd

VP4

M1a(nearly neutral)

−1073.6

p0 = 0.963, p1 = 0.037

18 N, 64S

ω0 = 0.014, ω1 = 1.000

M2a(positive selection)

−1073.6

p0 = 0.963, p1 = 0.037, p2 = 0.000

 

ω0 = 0.014, ω1 = 1.000, ω2 = 4.752

M0(one ω)

−1076.3

ω = 0.021

 

Branch( ω changed )

−1076.2

ω = 0.021, ω(KM branch) = 0.0001

 

VP3

M1a(nearly neutral)

−3343.7

p0 = 0.984, p1 = 0.016

35 N, 80A, 232R

ω0 = 0.006, ω1 = 1.000

M2a(positive selection)

−3343.7

p0 = 0.984, p1 = 0.016, p2 = 0.000

 

ω0 = 0.006, ω1 = 1.000, ω2 = 5.550

M0(one ω)

−3353.0

ω = 0.010

 

Branch( ω changed )

−3351.5

ω = 0.009, ω(KM branch) = 0.048

 

VP2

M1a(nearly neutral)

−3769.9

p0 = 0.977, p1 = 0.023

55Q, 137 V, 163 T, 165G

ω0 = 0.010, ω1 = 1.000

M2a(positive selection)

−3769.9

p0 = 0.977, p1 = 0.023, p2 = 0.000

 

ω0 = 0.010, ω1 = 1.000, ω2 = 6.220

M0(one ω)

−3777.8

ω = 0.015

 

Branch( ω changed )

−3777.2

ω = 0.015, ω(KM branch) = 0.0001

 

VP1

M1a(nearly neutral)

−4171.4

p0 = 0.991, p1 = 0.009

139A

ω0 = 0.014, ω1 = 1.000

M2a(positive selection)

−4171.4

p0 = 0.991, p1 = 0.009, p2 = 0.000

 

ω0 = 0.014, ω1 = 1.000, ω2 = 33.127

M0(one ω)

−4177.0

ω = 0.016

 

Branch( ω changed )

−4177.0

ω = 0.016, ω(KM branch) = 0.023

 

2A

M1a(nearly neutral)

−2500.2

p0 = 0.962, p1 = 0.038

7A, 14I, 23 N, 49 T, 63 V

ω0 = 0.020, ω1 = 1.000

M2a(positive selection)

−2500.2

p0 = 0.962, p1 = 0.023, p2 = 0.015

 

ω0 = 0.014, ω1 = 1.000, ω2 = 1.000

M0(one ω)

−2533.4

ω = 0.032

 

Branch( ω changed )

−2532.3

ω = 0.031, ω(KM branch) = 0.090

 

2B

M1a(nearly neutral)

−1743.4

p0 = 0.994, p1 = 0.006

 

ω0 = 0.022, ω1 = 1.000

M2a(positive selection)

−1743.4

p0 = 0.994, p1 = 0.006, p2 = 0.000

 

ω0 = 0.022, ω1 = 1.000, ω2 = 5.357

M0(one ω)

−1743.6

ω = 0.023

 

Branch( ω changed )

−1743.4

ω = 0.023, ω(KM branch) = 0.0001

 

2C

M1a(nearly neutral)

−6875.4

p0 = 0.991, p1 = 0.009

34I, 48S

ω0 = 0.008, ω1 = 1.000

M2a(positive selection)

−6875.4

p0 = 0.991, p1 = 0.009, p2 = 0.000

 

ω0 = 0.008, ω1 = 1.000, ω2 = 17.307

M0(one ω)

−6889.1

ω = 0.010

 

Branch( ω changed )

−6882.4

ω = 0.009, ω(KM branch) = 0.1052

 

3AB

M1a(nearly neutral)

−2355.5

p0 = 0.977, p1 = 0.023

41K, 48I

ω0 = 0.020, ω1 = 1.000

M2a(positive selection)

−2355.5

p0 = 0.977, p1 = 0.029, p2 = 0.000

 

ω0 = 0.020, ω1 = 1.000, ω2 = 12.815

M0(one ω)

−2356.4

ω = 0.024

 

Branch( ω changed )

−2348.1

ω = 0.021, ω(KM branch) = 0.445

 

3C

M1a(nearly neutral)

−3926.0

p0 = 0.992, p1 = 0.008

57 V

ω0 = 0.016, ω1 = 1.000

M2a(positive selection)

−3926.0

p0 = 0.992, p1 = 0.008, p2 = 0.000

 

ω0 = 0.016, ω1 = 1.000, ω2 = 2.687

M0(one ω)

−3929.2

ω = 0.018

 

Branch( ω changed )

−3923.8

ω = 0.016, ω(KM branch) = 0.1411

 

3D

M1a(nearly neutral)

−8184.6

p0 = 0.989, p1 = 0.011

32H, 75R, 259S, 435S

ω0 = 0.014, ω1 = 1.000

M2a(positive selection)

−8184.6

p0 = 0.989, p1 = 0.011, p2 = 0.000

 

ω0 = 0.014, ω1 = 1.000, ω2 = 33.13

M0(one ω)

−8217.2

ω = 0.017

 

Branch( ω changed )

−8217.1

ω = 0.017, ω(KM branch) = 0.025

 
  1. aTwo types of hypotheses were tested for every gene. One is that positive selection happened at some sites (M2a) compared with its null model (M1a), which is that every site in the gene is nearly neutral. The likelihood values of this hypothesis were calculated using the site model in the PAML software. The other hypothesis is that the ω changed for the nonpathogenic branch (Branch Model) compared with its null model (M0), indicating the ω remained unchanged in the whole tree. The likelihood values of this hypothesis were calculated by using the branch model in the PAML software
  2. bThe bold ℓ means that there is a significantly different Log-likelihood value between the Branch and M0 models
  3. c ω is the ratio of nonsynonymous to synonymous substitutions (d N/d S) of sites. ω0, with the proportion of p0, comprises the sites at which nonsynonymous mutations are “slightly deleterious”; ω1 is the d N/d S of completely neutral sites (ω1 = 1) with a proportion of p1; ω2 is the d N/d S of positively selected sites with a proportion of p2
  4. dThe Naive Empirical Bayes (NEB) probabilities indicated that these sites are neutral with a possibility above 90%
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