Skip to main content

Table 2 Genetic diversity in MHCI and MHCII-DRB in the Lynx genus. Diversity at the nucleotide, amino acid and supertype levels are estimated as the number of observed alleles (allelic richness, AR), number (S) and proportion of segregating sites [S(%)], mean number (± standard error) of differences among alleles (K). The latter is calculated for all sites, ABS and non-ABS

From: Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

      Indice

Total

L. pardinus

L. lynx

L. canadensis

L. rufus

MHC Class

     

Diversity level

     

MHC Class I

DNA (299)

      AR

30

10

17

13

10

      Private

 

0

3

4

9

      S

86

72

73

76

76

      S (%)

37.55

31.44

31.88

33.19

33.19

      K

19.77 ± 0.52

24.11 ± 1.74

20.07 ± 1

21.51 ± 1.42

25.8 ± 1.64

      Gen. dist. All

0.094 ± 0.003

0.116 ± 0.009

0.096 ± 0.005

0.103 ± 0.007

0.125 ± 0.009

      Gen. dist. ABS

0.23 ± 0.01

0.27 ± 0.02

0.23 ± 0.01

0.24 ± 0.02

0.29 ± 0.02

      Gen. dist. Non-ABS

0.06 ± 0

0.08 ± 0.01

0.06 ± 0

0.07 ± 0.01

0.08 ± 0.01

Protein (76)

      AR

26

10

15

10

10

      Private

 

0

3

3

8

      S

45

38

39

39

40

      S (%)

59.21

50

51.32

51.32

52.63

      K

16.68 ± 0.4

19.97 ± 1.36

16.78 ± 0.79

17.27 ± 1.16

21.93 ± 1.28

      Gen. dist. All

0.189 ± 0.005

0.231 ± 0.018

0.191 ± 0.01

0.199 ± 0.015

0.256 ± 0.017

      Gen. dist. ABS

0.53 ± 0.01

0.58 ± 0.04

0.5 ± 0.02

0.54 ± 0.04

0.68 ± 0.04

  Gen. dist. Non-ABS

0.11 ± 0

0.15 ± 0.01

0.12 ± 0.01

0.13 ± 0.01

0.17 ± 0.01

Supertypes

      Number

11

7

8

7

8

      Private

 

0

1

0

3

MHC Class II-DRB

DNA (247)

     

      AR

13

7

8

3

5

      Private

 

2

2

0

3

      S

61

47

49

41

56

      S (%)

24.7

19.03

19.84

16.6

22.67

      K

23.71 ± 1.01

22.33 ± 1.81

23.39 ± 1.76

27.67 ± 4.37

29.1 ± 2.13

      Gen. dist. All

0.104 ± 0.005

0.097 ± 0.008

0.103 ± 0.008

0.122 ± 0.021

0.129 ± 0.01

      Gen. dist. ABS

0.19 ± 0.01

0.15 ± 0.01

0.16 ± 0.01

0.2 ± 0.04

0.26 ± 0.03

  Gen. dist. Non-ABS

0.07 ± 0

0.07 ± 0.01

0.08 ± 0.01

0.09 ± 0.01

0.08 ± 0.01

Protein (82)

      AR

12

7

7

3

5

      Private

 

2

1

0

3

      S

28

23

23

23

27

      S (%)

34.15

28.05

28.05

28.05

32.93

      K

16.17 ± 0.7

14.63 ± 1.23

15.72 ± 1.25

19.51 ± 3.73

20 ± 1.51

      Gen. dist. All

0.18 ± 0.008

0.161 ± 0.014

0.175 ± 0.015

0.221 ± 0.046

0.226 ± 0.018

      Gen. dist. ABS

0.38 ± 0.02

0.31 ± 0.03

0.36 ± 0.04

0.46 ± 0.15

0.5 ± 0.06

  Gen. dist. Non-ABS

0.11 ± 0.01

0.11 ± 0.01

0.11 ± 0.01

0.14 ± 0.02

0.14 ± 0.01

Supertypes

      Number

7

5

5

3

4

      Private

 

1

0

0

1