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Table 1 Summary of results for branch analysis and branch-site analysis of Prm2 domains of primates and rodents

From: Selective constraints on protamine 2 in primates and rodents

Sequence

cleaved Prm2

mature Prm2

Foreground

Primates

Rodentia

Primates

Rodentia

LRTs for selection at branches over whole sequence

 2Δ(M0-MC)

0.02

1.94

25.86

1.49

 p

ns

ns

<0.01

ns

 2Δ(MCfix-MC)

8.74

15.42

25.60

0.01

 p

0.01

<0.01

<0.01

ns

 M0 - ω

0.54

1.18

 MC - ω

0.530

0.420

3.120

0.980

LRTs for selection at branches on sites

 2Δ(M1-BS)

1.67

5.27

62.21

26.10

 p

ns

ns

<0.01

<0.01

 2Δ(BSfix-BS)

0.00

5.27

96.75

60.63

 p

ns

0.05

<0.01

<0.01

Proportion of sites in ω site classes

 0

0.23

0.23

0.18

0.21

 1

0.64

0.74

0.30

0.75

 2a

0.04

0.01

0.20

0.01

 2b

0.10

0.02

0.32

0.03

Positively selected sites (BEB p <0.05)

 PSS

-

26G

1Q, 4C, 5Y, 6G, 7Y, 11 L, 24Q, 25R, 29R, 44R, 45 N, 51R, 55 T, 61 T

64R,72H

Interpretation

 Selection at branches over whole sequence

conserved

conserved

positive

relaxed

 Selection at branches on sites

no signal

positive

positive

positive

 Sexual selection

not detected

not detected

not detected

not detected

  1. LRT: Likelihood ratio test (twice the difference (2Δ) between likelihood values of the tested models). ω: nonsynonymous/synonymous substitution rate ratio, evolutionary rate. When LRT of M0 versus MC is significant MC omega is reported. When LRT is non significant, M0 omega is reported
  2. PSS: positively selected sites. Ω site classes: 0: 0 < ω < 1 for foreground and background branches, 1: ω = 1 for foreground and background branches, 2a: 0 < ω < 1 for background and ω > 1 for foreground, 2b: ω = 1 for background and ω > 1 for foreground