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. Author manuscript; available in PMC: 2013 Jul 4.
Published in final edited form as: Immunogenetics. 2006 Apr 26;58(0):362–373. doi: 10.1007/s00251-006-0112-7

Table 3.

Analysis of nucleotide differences for individual MDIR domains

A
  Type I and Type II 1 2 3 4 5 6 7 8 9
    1. MDIR1-IgD
    2. MDIR2-IgD1 0.715
    3. MDIR3-IgD1 0.674 0.177
    4. MDIR3-IgD2 0.683 0.172 0.027
    5. MDIR5-IgD1 0.703 0.170 0.027 0.027
    6. MDIR4-IgD1 0.745 0.217 0.159 0.167 0.146
    7. MDIR4-IgD3 0.723 0.222 0.185 0.186 0.191 0.247
    8. MDIR3-IgD4 0.685 0.191 0.141 0.139 0.171 0.198 0.115
    9. MDIR4-IgD5 0.672 0.189 0.104 0.115 0.134 0.176 0.127 0.067
    10. MDIR5-IgD3 0.676 0.185 0.142 0.153 0.158 0.206 0.122 0.082 0.067
  Type III and Type IV
1 2 3 4 5 6 7
    1. MDIR2-IgD2
    2. MDIR3-IgD5 0.245
    3. MDIR4-IgD6 0.264 0.131
    4. MDIR5-IgD4 0.327 0.201 0.139
    5. MDIR3-IgD3 0.318 0.399 0.405 0.418
    6. MDIR4-IgD2 0.327 0.417 0.420 0.421 0.051
    7. MDIR4-IgD4 0.275 0.389 0.385 0.368 0.078 0.077
    8. MDIR5-IgD2 0.283 0.367 0.396 0.406 0.051 0.063 0.091
B
  Type I and Type II
1 2 3 4 5 6 7 8 9
    1. MDIR1-IgD
    2. MDIR2-IgD1 0.423
    3. MDIR3-IgD1 0.441 0.207
    4. MDIR3-IgD2 0.443 0.187 0.060
    5. MDIR5-IgD1 0.454 0.200 0.104 0.060
    6. MDIR4-IgD1 0.453 0.158 0.173 0.154 0.178
    7. MDIR4-IgD3 0.444 0.214 0.195 0.182 0.176 0.180
    8. MDIR3-IgD4 0.443 0.185 0.171 0.154 0.152 0.161 0.101
    9. MDIR4-IgD5 0.441 0.198 0.196 0.179 0.182 0.185 0.128 0.052
    10. MDIR5-IgD3 0.458 0.217 0.209 0.192 0.191 0.193 0.133 0.060 0.086
  Type III and Type IV
1 2 3 4 5 6 7
    1. MDIR2-IgD2
    2. MDIR3-IgD5 0.218
    3. MDIR4-IgD6 0.186 0.071
    4. MDIR5-IgD4 0.218 0.097 0.061
    5. MDIR3-IgD3 0.290 0.298 0.266 0.279
    6. MDIR4-IgD2 0.260 0.278 0.247 0.273 0.071
    7. MDIR4-IgD4 0.256 0.293 0.268 0.292 0.133 0.089
    8. MDIR5-IgD2 0.249 0.260 0.229 0.261 0.080 0.058 0.093

A The proportion of synonymous nucleotide differences per synonymous site (Ps) estimated by Nei and Gojobori’s method (Nei and Gojobori 1986). B The proportion of non-synonymous nucleotide differences per non-synonymous site (Pn)

From Table 3, the following points can be made: The theoretical maximum value of Ps is 0.75, if the frequencies of the four different types of nucleotide are assumed to be equal. Therefore, the MDIR1 and MDIR2-MDIR5 sequences appear to have been diverged for a long period of time, as the proportion of synonymous nucleotide differences per synonymous sites are close to saturation

MDIR3-IgD1 and MDIR3-IgD2 are results of recent duplications, as the proportion of synonymous nucleotide differences per synonymous site is small

Two distinct types of MDIR intermediate (I)-type IgSF domains emerge: (a) Type I: MDIR1-IgD; (b1) Type II subtype 1: MDIR2-IgD1, MDIR3-IgD1, MDIR3-IgD2, MDIR5-IgD1, MDIR4-IgD1; (b2) Type II, subtype 2: MDIR3-IgD4, MDIR4-IgD3, MDIR4-IgD5, MDIR5-IgD3

Two distinct C2-types emerge: Type III: MDIR2-IgD2, MDIR3-IgD5, MDIR4-IgD6, MDIR5-IgD4; Type IV: MDIR3-IgD3, MDIR4-IgD2, MDIR4-IgD4, MDIR5-IgD2

Within the MDIR domain type II, subtype 1 or type III categories, the respective domains of MDIR2 show higher differences from MDIR3-5, indicating the MDIR2 may have diverged first from MDIR3-5. The proportion of synonymous nucleotide differences per synonymous site for MDIR3-IgD1/IgD2 vs MDIR5-IgD1, MDIR3-IgD3 vs MDIR5-IgD2, MDIR3-IgD4 vs MDIR5-IgD3, MDIR3-IgD5 vs MDIR5-IgD4 are 0.027, 0.051, 0.082, and 0.201, respectively. Simple duplication of Ig domains of MDIRs does not explain the observation, implying instead an exon shuffling or gene conversion-like event between ancestors of MDIR3 and MDIR5