Table 4 Comparison of genetic diversity at MHC class II (segregating sites of amino acids (S_aa) and nucleotides (S_nt) and average nucleotide diversity (π)) in eight species of Charadriiformes, from six alleles randomly selected for each species (except for Black-tailed Godwit and Ruff where only four alleles were available). The measures of diversity and the synonymous and non-synonymous substitution rates were calculated for the complete sequences (All), the PBR and the non-PBR sites

Snowy Plover (Charadrius nivosus nivosus)

0.06 ± 0.01

0.10 ± 0.03

0.60

31

15

0.06

0.14 ± 0.05

0.10 ± 0.05

1.40

15

8

0.12

0.03 ± 0.01

0.11 ± 0.04

0.27

16

7

0.05

Common Murre (Uria aalge)

0.09 ± 0.02

0.05 ± 0.02

1.80

42

26

0.07

0.19 ± 0.05

0.11 ± 0.05

1.72

22

12

0.15

0.06 ± 0.02

0.04 ± 0.02

1.50

20

14

0.05

Razorbill (Alca torda)

0.03 ± 0.01

0.02 ± 0.01

1.50

17

10

0.02

0.07 ± 0.03

0.02 ± 0.02

3.50

10

6

0.05

0.02 ± 0.01

0.02 ± 0.01

1.00

7

4

0.01

Atlantic Puffin (Fratercula arctica)

0.10 ± 0.02

0.05 ± 0.02

2.00

44

26

0.08

0.26 ± 0.07

0.04 ± 0.03

6.50

24

14

0.16

0.05 ± 0.01

0.06 ± 0.02

0.83

20

12

0.05

Black-legged Kittiwake (Rissa tridactyla)

0.12 ± 0.02

0.06 ± 0.02

2.00

56

31

0.09

0.29 ± 0.06

0.05 ± 0.03

5.80

29

15

0.18

0.07 ± 0.02

0.07 ± 0.02

1.00

27

16

0.06

Great Snipe (Gallinago media)

0.03 ± 0.01

0.04 ± 0.01

0.75

20

10

0.03

0.08 ± 0.03

0.04 ± 0.03

2.00

10

6

0.06

0.02 ± 0.01

0.04 ± 0.02

0.50

10

4

0.02

Ruff (Philomachus pugnax)

0.17 ± 0.03

0.15 ± 0.04

1.13

67

36

0.14

0.33 ± 0.09

0.18 ± 0.01

1.83

29

15

0.23

0.12 ± 0.02

0.14 ± 0.03

0.85

38

21

0.11

Black-tailed Godwit (Limosa limosa)

0.18 ± 0.03

0.14 ± 0.03

1.28

68

40

0.15

0.31 ± 0.08

0.21 ± 0.08

1.47

27

16

0.23

0.14 ± 0.03

0.12 ± 0.04

1.16

41

24

0.12