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Table 2 Parameter estimates for branch-site model A from maximum likelihood analyses.

From: RPS4Ygene family evolution in primates

Data Set

Foreground branch

f

l

Estimated parameters

κ

Positive selection (BEB)

RPS4Y1

Hsa Y1

14

-1275.00

p0 = 1 p1 = 0 (p2+p3 = 0), ω2 = 1

3.40

 

RPS4Y2

Hsa Y2

8

-1233.73

p0 = 0 p1 = 0 (p2+p3 = 1), ω2 = 139.62

3.78

68H*, 70L*, 87I*, 108C*, 185A*

RPS4X

Hsa X

10

-1100.83

p0 = 1 p1 = 0 (p2+p3 = 0), ω2 = 1

--- b

 

RPS4 Y1/Y2

Hsa Y2

20

-1562.15

p0 = 0 p1 = 0 (p2+p3 = 1), ω2 a

4.61

70I*, 185G*

 

Y2cluster

20

-1570.33

p0 = 0 p1 = 1 (p2+p3 = 1), ω2 = 139.62

4.59

 

RPS4 Y1/Y2/X

Hsa Y2

28

-1971.13

p0 = 0 p1 = 0 (p2+p3 = 1), ω2 a

3.21

68R*, 70I*, 87M*, 104D*, 108R*, 185G*

 

Y2cluster

28

-1986.19

p0 = 0.942 p1 = 0.058 (p2+p3 = 0), ω2 = 1

3.12

 

Y1Y2X No Hsa Y2

Y2cluster

26

-1925.91

p0 = 0.939 p1 = 0.061 (p2+p3 = 0), ω2 = 1

3.16

 

Y1Y2 No Hsa Y2

Y2cluster

18

-1516.95

p0 = 0.901 p1 = 0.099 (p2+p3 = 0), ω2 = 1

4.62

 

Y1Y2X Hsa

Hsa Y2

8

-1619.84

p0 = 0.647 p1 = 0.021 (p2+p3 = 0.332), ω2 = 1

3.03

68R, 70I, 87M, 104D, 108R, 180L, 185G, 205F, 222L (P > 0.71)

  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.