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Table 1 Parameter estimates for the one ratio and free-ratio branch models.

From: RPS4Ygene family evolution in primates

Data Set

Model

f

l

Estimated parameters

κ

RPS4Y1

One ratio (M0)

11

-1275.00

ω = 0.161

3.40

 

Free-ratio (FR)

19

-1269.87

Ggo ω = 1.27

3.39

RPS4Y2

One ratio (M0)

5

-1239.64

ω = 0.278

3.78

 

Free-ratio (FR)*

7

-1233.58

Hsaa

3.77

RPS4X

One ratio (M0)

7

-1100.83

ω = 0.0001

--- b

 

Free-ratio (FR)

11

-1100.83

Ptr ω = 15.81

--- b

RPS4Y1/Y2

One ratio (M0)

17

-1571.22

ω = 0.192

4.55

 

Free-ratio (FR)*

31

-1555.16

Ptr Y1 ω = 1.71;

Hsa Y2a;

Ggo/Mfu Y1 ω = 1.41

4.55

RPS4Y1/Y2/X

One ratio (M0)

25

-1994.26

ω = 0.069

2.95

 

Free-ratio (FR)*

47

-1961.77

Hsa Y2a;

Ggo/Mfu ω = 1.30

3.29

Y1Y2X

One ratio (M0)

23

-1937.8

ω = 0.058

2.95

No Hsa Y2

     
 

Free-ratio (FR)

43

-1917.62

Ggo/Mfu ω = 1.30

3.24

Y1Y2

One ratio (M0)

15

-1518.97

ω = 0.1520

4.55

No Hsa Y2

     
 

Free-ratio (FR)

27

-1510.59

Ppa ω = 1.25;

Ggo/Mfu Y1 ω = 1.46

4.56

Y1Y2X Hsa

One ratio (M0)

5

-1630.42

ω = 0.051

2.85

 

Free-ratio (FR)*

7

-1620.58

 

3.14

  1. f for the number of free parameters; l for likelihood values; and κ for transitions/transversions
  2. * Posterior probability >0.95.
  3. a ω cannot be estimated since there are no synonymous substitutions.
  4. b κ cannot be estimated since there are no transversions.