Skip to main content

Table 3 Genetic diversity at 7 MHC loci in chimpanzees (average on all chimpanzee cohorts and in the pooled cohort) and human populations (averaged on multiple populations)

From: Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution

 

Number of samples (k) & sample size (N)

Allelic richness (ar)

Heterozygosity (H)

Nucleotide diversity (П)

Chimpanzees

Humans

Chimpanzees

Humans

Chimpanzees

Humans

Chimpanzees

Humans

average

pooleda

average

pooleda

average

pooleda

k

NP

k

\( \overline{N} \)(s.d)

\( \overline{ar\ } \)(s.d)

arP

\( \overline{ar} \)P (s.d)

\( \overline{H}\% \)(s.d)

HP%

\( \overline{H}\% \)(s.d)

\( \overline{\varPi} \)x 10-2 (s.d)

ПP x 10-2

\( \overline{\varPi} \)x 10-2 (s.d)

DPB1

2

44

50

87.8 (45.2)

6.3 (1.8)

7.4

9.8 (3.7)

77.9 (0.4)

80.3

72.5 (17.1)

1.3 (0.1)

1.3

2.4 (0.9)

DQB1

3

48

79

100.6 (55.3)

5.0* (0.9)

5.6

9.6 (3.2)

63.7* (13.8)

55.8

79 (11.2)

4.0* (0.3)

3.9

6.0 (1.6)

DQA1

1

29

52

90.6 (45.5)

5 (-)

5

6.4 (1.6)

71.5 (-)

71.5

74.3 (10.9)

7.8 (-)

7.8

6.9 (1.3)

DRB1

3

46

89

105.5 (111.8)

10.1 (2.6)

9.7

14.3 (5.3)

84.7 (3.8)

84.6

86.4 (8.3)

8.1 (1.1)

7.0

7.0 (1.2)

B

3

51

80

124 (134.6)

13.9 (3.5)

17.1

19.2 (7.1)

84.1 (3.9)

86.4

90.3 (6.8)

5.0* (0.5)

5.2

4.2 (0.5)

C

2

51

59

127.9 (141.1)

9.7 (3.2)

11.5

12.4 (4.2)

79.6 (4.3)

81

85.2 (7.4)

2.1* (0.2)

2.1

2.6 (0.2)

A

3

50

81

127.6 (133.6)

13 (0.9)

14.2

11.9 (5.2)

88.6 (1.2)

90.3

79.7 (15.4)

2.7* (0.3)

2.7

3.4 (0.5)

  1. k: number of samples; Np: size of pooled cohort; \( \overline{N} \)(s.d): average size of human population samples and standard deviation
  2. \( \overline{ar} \)(s.d): average allelic richness in the chimpanzee samples and standard deviation; arP: allelic richness of the pooled cohort; \( \overline{ar} \)P (s.d): average allelic richness in human population samples (estimated relatively to the pooled cohort) and standard deviation. * value (in bold) significantly different between human populations and chimpanzee cohorts (Wilcoxon test, p = 0.0342) for allelic richness at DQB1. Test without the Texascb cohort: Wilcoxon two-sided test: p = 0.0604, single-sided test (“less”): p = 0.0302
  3. \( \overline{H}\% \)(s.d): average expected heterozygosity in the chimpanzee samples and in human population samples and standard deviation; HP%: expected heterozygosity of the pooled cohort. * value (in bold) significantly different between human populations and chimpanzee cohorts (Wilcoxon test, p = 0.0316) for heterozygosity at DQB1. Test without the Texascb cohort: Wilcoxon two-sided test: p = 0.0371, single-sided test (“less”): p = 0.0185
  4. \( \overline{\varPi} \)(s.d): average expected nucleotide diversity in the chimpanzee samples and in human population samples and standard deviation; ПP: expected nucleotide diversity of the pooled cohort. * values (in bold) significantly different between human populations and chimpanzee cohorts (Wilcoxon test, p = 0.0426, 0.0175, 0.0225,0.0371) for nucleotide diversity at DQB1, B, C and A, respectively. Test without the Texascb cohort: Wilcoxon two-sided test: p = 0.0825, 0.0255, 0.0944, single-sided test: p = 0.0412, 0.0128, 0.0472 at DQB1, B and A, respectively
  5. The order of loci corresponds to their position on the chromosome from centromere (top) to telomere (bottom)
  6. adoes not include Texascb (see Text)