Online Resource Table 1 Primers used to amplify the seven microsatellites located in the MHC class II region

Microsatellite / Forward / Reverse / Ref
D6S2892 / TGCATGTCCTGTGAGGTAAG / ACTCAACCCTGCTGTTGTAG / Wiseman et al. 2007
DRACA / TGGAATCTCATCAAGGTCAG / ACATTTGTATGCTTCAGATG / Bonhomme et al. 2005
D6S2876 / GGTAAAATTCCTGACTGGCC / GACAGCTCTTCTTAACCTGC / Wiseman et al. 2007
D6S2747 / AGGAATCTAGTGCTCTCTCC / CTCTAGCAAAAGGAAGAGCC / Wiseman et al. 2007
D6S2745 / CCTAGAGATTCCTCCACATTA / CCAATGTTTGATAGCAGACTGGGGT / Wiseman et al. 2007
D6S2741 / AGACTAGATGTAGGGCTAGC / CTGCACTTGGCTATCTCAAC / Wiseman et al. 20071
D6S2771 / ATTCCTTTCACTAGTTCTGG / CCACTTTAAGAAATTAGAAAAG / Wiseman et al. 2007

Online Resource Table 2: Heterozygosityobserved with theseven MHC microsatellites inthe Filippino cynomolgus macaque population sample.

Hea / Hob / Fis c / nA d
D6S2892 / 0.4128 / 0.3807 / 0.0792 / ns / 7
DRACA / 0.7571 / 0.6997 / 0.0772 / ns / 12
D6S2876 / 0.7121 / 0.5499 / 0.2292 / *** / 11
D6S2747 / 0.6881 / 0.5739 / 0.1675 / *** / 7
D6S2745 / 0.6708 / 0.6346 / 0.0555 / * / 5
D6S2741 / 0.8016 / 0.75 / 0.0658 / * / 18
D6S2771 / 0.5917 / 0.5581 / 0.0582 / ns / 4

aunbiased expected heterozygosity

b observed heterozygosity

cFis and significance of departure from Hardy-Weinberg proportions (ns = non significant, *= p<0.05, ***= p<0.001)

d number of alleles

Online Resource Table 3Allele frequencies of seven MHC microsatellites and DRB haplotypes in the Filipino population sample of Macaca fascicularis (N=353)

asize of amplified fragment (bp)

bthe number of animalshaving the allele. The number between brackets is the number of homozygous animal having the allele

cDRB haplotype nomenclature refers to that described in Blancher et al. 2012

dWe failed to amplify fragment.

Marker / Allelea / Animals numbers having the allele (HMZ) b
D6S2892 / 192 / 1 (0)
198 / 3 (0)
202 / 98 (11)
205 / 321 (203)
205;212 / 1 (0)
206 / 56 (3)
208 / 1 (0)
212 / 4 (1)
212;214 / 1 (0)
not determined d / 1 (1)
DRACA / 237 / 112 (16)
239 / 219 (79)
251 / 4 (0)
257 / 57 (2)
259 / 2 (0)
261 / 2 (0)
265 / 84 (6)
270 / 4 (0)
272 / 11 (0)
274 / 37 (2)
276 / 24 (0)
283 / 44 (1)
DRBc / #5 / 24 (0)
#7 / 196 (55)
#8a / 41 (1)
#8b / 7 (0)
#1b / 1 (0)
#2b / 4 (0)
#9 / 55 (3)
#18 / 8 (0)
#10 / 46 (1)
#11 / 96 (12)
#12 / 3 (0)
#19 / 10 (0)
#13ab / 45 (3)
#13c / 8 (0)
#14 / 22 (0)
#15 / 44 (6)
#16 / 3 (0)
#17 / 9 (1)
#20 / 2 (0)
D6S2876 / 182 / 34 (2)
197 / 41 (0)
200 / 1 (0)
204 / 161 (28)
205 / 9 (1)
211 / 242 (70)
213 / 49 (3)
215 / 2 (0)
217 / 49 (6)
225 / 2 (0)
236 / 2 (0)
not determined / 2 (2)
D6S2747 / 185 / 35 (1)
191 / 102 (12)
194 / 26 (1)
203 / 1 (0)
205 / 107 (18)
206 / 250 (98)
208 / 53 (0)
not determined / 1 (1)
D6S2745 / 299 / 235 (75)
303 / 112 (9)
304 / 5 (1)
311 / 184 (43)
313 / 41 (1)
D6S2741 / 250 / 4 (0)
252 / 3 (0)
256 / 103 (16)
258 / 19 (2)
260 / 1 (0)
262 / 22 (0)
264 / 98 (10)
266 / 4 (0)
268 / 3 (0)
270 / 172 (44)
272 / 32 (1)
274 / 139 (15)
276 / 7 (0)
278 / 1 (0)
282 / 1 (0)
284 / 5 (0)
288 / 1 (0)
290 / 1 (0)
not determined / 1 (1)
D6S2771 / 395 / 120 (14)
398 / 144 (23)
399 / 279 (118)
404 / 8 (0)

Online Resource Table 4Number of sequences used to calculate the Simpson’s variability indexes of alpha-1 and beta-1 domains of DQ and DP proteins presented in Figure 2.

Protein and domain / Hosa / Mafa / Filipino Mafa population
DQ alpha-1 / 48 / 46 / 13
DQ beta-1 / 300 / 66 / 12
DP alpha-1 / 27 / 39 / 9
DP beta-1 / 151 / 60 / 8