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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