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Table 4 Parameter estimates for INSL4 under different branch models, site models and branch-site models. Models implemented in Codeml from the PAML suite. Parameters in boldface indicate positive selection. Sites potentially under positive selection are numbered using the human INSL4 sequence in figure 1 as the reference.

From: Evolution of the relaxin-like peptide family

Model

ρ

Parameter est.

Positively selected sites

   1 ratio (R0)

1

-1460.1

ω = 0.7

 

Branch specific

   2 ratios (R2)

2

-1459.9

ω0 = 0.7(background),

ω 1 = 1.1 (branch A)

 

Site specific

   Neutral (M1)

1

-1424.4

ρ0 = 0.1, ρ1 = 0.8

not allowed

   Selection (M2)

3

-1416.6

ρ0 = 0.1, ρ1 = 0.6,

ρ 2 = 0.2, ω 2 = 2.9

15L (P >0.99)

14H, 27H, 28R, 36V (P >0.95)

   Discrete (M3) (k = 2)

3

-1421.4

ρ0 = 0.2, ω0 = 0.03,

ρ 1 = 0.8, ω 1 = 1.0

37 sitesa (P >0.99)

   Discrete (M3) (k = 3)

5

-1413.8

ρ0 = 0.1, ω0 = 0.01,

ρ1 = 0.5, ω1 = 0.6,

ρ 2 = 0.3, ω 2 = 2.0

15L, 27H, 28R (P >0.99)

14H, 25G, 26R, 30D, 36V

(P > 0.90)

   Beta (M7)

2

-1419.6

ρ0 = 0.2,q = 0.2

not allowed

   Beta&ω (M8)

4

-1414.6

ρ0 = 0.8,p = 0.3,

q = 0.06,

ρ 1 = 0.2, ω 1 = 2.6

15L, 28R (P > 0.95)

14H, 27H, 36V (P > 0.90)

Branch-Site

   Model A

3

-1418.4

ρ0 = 0.1, ρ1 = 0.6,

ρ 2 = 0.2, ω 2 = 3.0

In the foreground lineage:

13K, 37I (P > 0.95)

   Model B

5

-1416.4

ρ0 = 0.1, ω0 = 0.01,

ρ1 = 0.6, ω1 = 0.6,

ρ 2 = 0.3, ω 2 = 3.2

In the foreground lineage:

13K, 37I (P > 0.95)

In the background lineages:

no significant sites

  1. a1A, 2A, 3E, 5R, 6G, 10R, 11F, 12G, 14H, 15L, 16L, 17S, 18Y, 20P, 25G, 26R, 27H, 28R, 29F, 30D, 31P, 32F, 35E, 36V, 37I, 39D, 40D, 41G, 42T, 43S, 44V, 45K, 47L. Note that these sites should be treated with caution as ω under this model is not significantly higher than 1.