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Table 2 Sites potentially under selection according to BEB analysis of PAML M8 results for the most frequent haplotype.

From: Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus

Base position

P

aA

ω value

S.E.

P(ω > 1)

Exon

Bases

SNP alleles and amino acids

4429–31

3

T

9.983

0.878

0.998

1

ACA

V, F: CCA (P); B: GCA (A)

4435–37

5

F

10.002

0.772

1.000

1

TTT

Chicken, C: CTT (L); R, V, F: TTC (F); B TTG (F)

4477–79

19

L

9.996

0.807

0.999

1

CTG

V, F: CGC (R); B: CCA (P)

7453–56

23

V

9.951

1.029

0.995

2

GTT

V, F: TTT (F); B: CTT (L)

7534–36

50

E

10.003

0.77

1.000

2

GAA

V, F: CCA (P); B: CGA (R)

7582–84

66

L

10.000

0.786

1.000

2

CTT

V, F: TTT (F); B: AAT (N)

7594–5, 8394

70

R

9.984

0.871

0.998

2, 3

AGA

V: TCA (S); F: ATA (M)

9583–85

125

T

9.999

0.788

1.000

4

ACT

C, B: GCT (A); V, F: TCT (S)

9631–33

141

L

9.771

1.636

0.976

4

TTG

C, G, B: CTG (L); V, F: ATG (M)

9646–48

146

S

9.995

0.811

0.999

4

AGC

V, F: CGC (R); B: GGC (G)

9715–17

169

Q

9.972

0.933

0.997

4

CAA

V, F: CGC (R); B: CCC (P)

9721–23

171

E

9.970

0.942

0.997

4

GAA

V, F: GCA (A); B: GGA (G)

12367–69

418

M

9.661

1.904

0.964

9

ATG

V: CTG (L); B: GTG (V); F: TTG (L)

12628–30

509

A

9.895

1.253

0.989

9

GCA

V, F: GTA (V)

12631–33

510

R

9.966

0.963

0.996

9

AGA

V: AGT (S); B: AGG (R); F: AGC (S)

12652–54

517

H

9.995

0.811

0.999

9

CAC

Chicken, R: CAT (H); RJF, F, V: CAA (Q); B: AAC (N)

12661–63^

520

P

9.110

2.54

0.930

9

CCT

Chicken, R, RJF: CTT (L)

12742–44 *

547

I

9.619

2.097

0.954

9

ATA

R, C: TTA (L)

12823–25

574

H

9.941

1.07

0.994

9

CAT

V, F: CAC (H); B, F: CAT (H)

12844–46

581

V

9.976

0.914

0.997

9

GTG

V, F: ATG (M); B: CTG (L)

12871–73

590

G

9.580

2.076

0.956

9

GGC

Chicken, RJF, B, F, V: AGC (S)

12955–57 *

618

E

9.622

2.092

0.955

9

GAG

V, F, B: GCG (A)

12979–81

626

S

9.579

2.078

0.956

9

AGC

V: CGC (R); F: GGC (G)

12985–87

628

E

9.934

1.101

0.993

9

GAA

Chicken: GAG (E); RJF, R, G, C: GAC (D)

13042–44

647

A

9.661

1.902

0.964

9

GCC

V, B, F: GTC (V)

13078–80

659

N

9.727

1.746

0.971

9

AAT

V, F: AAA (K); B: AAC (N)

13096–98

665

R

9.981

0.889

0.998

9

CGA

Chicken: CAA (Q), TGA (stop); R, G, C: AGA (R): RJF, F: ATA (M); V: ACA (T); B: AAA (K)

13123–25

674

S

9.950

1.033

0.994

9

TCT

V: TGT (C); B: TTT (F); F: TAT (Y)

13138–40

679

A

9.994

0.82

0.999

9

GCA

V: GGC (G); B: GTG (V); F: GGT (G)

  1. P is the amino acid position. S.E. is the standard error for ω. B stands for bamboo partridge, F for grey francolin, V for green JF, C for Ceylon JF, R for red JF, G for grey JF and RJF for the genome sequence. * Significant in analysis with divergent sample FJ542675 only. ^Almost significant.