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Table 5 Results of Global Linkage Disequilibrium (GLD) significance test (PRS resampling procedure) between different pairs of MHC loci in chimpanzees (BPRC cohort) and humans (multiple populations, further subdivided into RGD and SGD 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

  Chimpanzees Humans
BPRCWB Multiple populations RGD SGD
Loci pairs N p k % significant results (after correction) k1 % significant results (after correction) k2 % significant results (after correction)
DPB1 ~ DQB1 25 0.106 40 30 (12.5) 15 47 (27) 25 24 (4)
DPB1 ~ DQA1 25 0.0697 33 27.3 (15.1) 16 44 (25) 17 12 (5.9)
DPB1 ~ DRB1 25 0.328 31 25.8 (9.7) 16 37 (12.5) 15 13 (6.7)
DPB1 ~ B 25 1 10 10 (10) 4 25 (25) 6 0
DPB1 ~ C 25 0.999 8 12.5 (0) 2 50 (0) 6 0
DPB1 ~ A 24 0.982 12 0 5 0 7 0
DQB1 ~ DQA1 29 <  10−4 46 97.8 (97.8) 20 95 (95) 26 100 (100)
DQB1 ~ DRB1 29 <  10−4 51 94.1 (94.1) 23 96 (96) 28 93 (93)
DQB1 ~ B 29 1 13 61.5 (53.8) 7 86 (86) 6 33 (16.7)
DQB1 ~ C 29 0.975 10 40 (40) 5 60 (60) 5 20 (20)
DQB1 ~ A 28 0.98 16 12.5 (12.5) 9 22 (22) 7 0
DQA1 ~ DRB1 29 <  10−4 38 97.4 (97.4) 21 100 (100) 17 94 (94)
DQA1 ~ B 29 1 9 44.4 (44.4) 5 80 (80) 4 0
DQA1 ~ C 29 1 6 33.3 (33.3) 3 67 (67) 3 0
DQA1 ~ A 28 0.831 12 8.3 (0) 7 14 (0) 5 0
DRB1 ~ B 29 1 39 51.3 (35.9) 22 73 (54.5) 17 23 (11.8)
DRB1 ~ C 29 0.998 30 63.3 (63.3) 18 78 (78) 12 42 (42)
DRB1 ~ A 28 0.991 39 28.2 (25.6) 24 33 (33) 15 20 (13.3)
B ~ C 29 0.0001 59 74.6 (74.6) 21 95 (95) 38 63 (63)
B ~ A 28 0.931 76 35.5 (25) 27 63 (40.7) 49 20 (16.3)
C ~ A 28 0.892 58 53.4 (37.9) 23 65 (47.8) 35 46 (31.4)
  1. The PRS resampling procedure was done with 10′000 simulations for the chimpanzee cohorts (significant results are in bold). The PRS resampling procedure was done with 1′000 simulations in each human population, and the table reports the percentage of significant results for each pair of loci (in brackets after Holm correction for multiple testing). Pairs in significant global linkage disequilibrium in more than 70% of human populations are in bold. N: number of chimpanzee individuals; p: p-value; k: total number of human populations; k1: number of RGD populations; k2: number of SGD populations. The table includes results obtained for the BPRCwb cohort, i.e. the cohort including the greatest number of animals and the only one for which all loci were tested. Results for the other cohorts are in Additional Table S5