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Table 5 Likelihood Values and Parameter Estimates for SULT1A Genes

From: Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example

Model

f.p.*

Log L

Parameter Estimates†

One-ratio

39

- 5,047.81

KA/KS = 0.15

  

Free-ratios

69

- 5,005.18

KA/KS ratios for each branch shown in Figure 2

  

Site-specific

Neutral

36

- 5,021.14

p0 = 0.48

(p1 = 0.52)

 
   

KA/KS 0 = 0

KA/KS 1 = 1

 

Selection

38

- 4,884.89

p0 = 0.41

p1 = 0.13

(p2 = 0.46)

   

KA/KS 0 = 0

KA/KS 1 = 1

KA/KS2 = 0.19

Discrete (k = 2)

37

- 4,931.05

p0 = 0.68

p1 = 0.32

 
   

KA/KS 0 = 0.06

KA/KS 1 = 0.77

 

Discrete (k = 3)

40

- 4,880.78

p0 = 0.59

p1 = 0.33

(p2 = 0.08)

   

KA/KS 0 = 0.02

KA/KS 1 = 0.31

K A /K S2 = 1.24

Beta

37

- 4,884.27

p = 0.27

q = 1.07

 

Beta+selection

39

- 4,879.97

p = 0.30

q = 1.33

 
   

p0 = 0.98

p1 = 0.02

K A /K S = > 2.0

Branch-site specific

Model A

38

- 5,013.29

p0 = 0.48

p1 = 0.49

(p2 = 0.03)

   

KA/KS 0 = 0

KA/KS 1 = 1

K A /K S2 = > 2.0

Model B

40

- 4,886.52

p0 = 0.68

p1 = 0.30

(p2 = 0.02)

   

KA/KS 0 = 0.04

KA/KS1 = 0.56

K A /K S2 = > 2.0

  1. *f.p. is the number of free parameters in each model. †Evidence for positive selection is shown in boldface. Proportions of sites in each KA/KS class, p0, p1, and p2, were not free parameters when in parentheses. Neutral site-specific model assumes two site classes having fixed KA/KS ratios of 0 and 1, with the proportion of sites in each class estimated as free parameters. Selection site-specific model assumes a third proportion of sites with KA/KS estimated from the data. Discrete model assumes 2 or 3 site classes (k) with the proportion of sites, and KA/KS ratios for each proportion, estimated as free parameters. Beta model assumes a beta distribution of sites, where the distribution is shaped by the parameters p and q. Beta+selection model assumes an additional class of sites having a KA/KS ratio estimated from the data. Model A, an extension of the neutral model, assumes a third site class on the 1A3/1A4 branch with KA/KS estimated from the data. Model B, an extension of the discrete model with two site classes (k = 2), also assumes a third site class on the 1A3/1A4 branch with KA/KS estimated from the data.