SLA-DRB1*09

1. SLA-DRB1*09 AF272725 AF272725 02sp08 D87416 02ka05 EU039935 0201du02 L36571 0201br05 Z26641 0201 D87424 0201 AY247784 0201 AF464031 0201 EU432078 0201 AY135582 0201 D87421 02ka06 EU039936 02du03 D87425 02ka08 EU039934 02du01 SLA-DRB1*01 D87415 ka04 D87418 ka05 AB038989 oj02 AB016754 08hg09 SLA-DRB1*03 SLA-DRB1*06 AK236903 AB193509 0801 L36573 0801 Z26638 0801 AB016751 0801hg06 D78146 08ka83 D78149 08ka92 AF272728 08ka92 AF272728 08sp05 AF464034 EU039961 me02 AB038988 oj01 EU039940 La03 EU039942 La05 EU039938 du05 D87426 ka09 EU039939 La02 EU039941 La04 AF464050 0901 AY102480 0901 AB082382 0901 L08849 0901 L36570 0901br04 L08848 09sL48 AY243103 09ta01 AY962313 0301 AB016757 0301 M55165 0301 EU039957 Lu02 SLA-DRB1*07 EU039950 ha04 EU039948 ha01 AB215120 0101 AY135579 0101 BE232509 0101 DQ883227 0101 AF464046 0101 EU432072 0101 AY135580 0102 EU432076 0102 BF191401 0102 AB016746 0102 AB016755 0102 U10027 0102 SLA-DRB1*08 SLA-DRB1*02 EU039949 1301 U10032 1301 Z26640 1301 EU039954 er01 DQ883226 10jh01 EU039958 10Lu03 D87419 10ka06 D87410 1001 L36574 1001 CJ030292 1001 AF272730 10sp07 SLA-DRB1*10 EU039952 07yo02 D87412 07ka03 AY102481 0701 U10033 0701 SLA-DRB1*13 D87431 ka14 AB082385 kb04N SLA-DRB1*04 FJ169438 AB082384 kb03N AB082383 kb02 AB082383 AF464033 0601 Z26639 0601 U52526 06zs12 FJ169420 SLA-DRB1*05 BE232674 0603Q L08847 06sL47 L08847 AF464060 0602 AY135584 0602 D87423 0602 CB286464 0603Q SLA-DRB1*12 AY102479 05ch01 SLA-DRB1*14 D87411 0501 EU432074 0501 AF464032 0501 D87413 05ka03 D87409 05ka01 AF272729 05sp06 AF272729 EU087428 0502 U47277 0502 D78150 05np01 D78147 w12ka05 D78148 w12ka12 D78145 w12ka02 SLA-DRB1*11 U52528 02zs13 EU432075 1102 AF272724 w11sp01 L36568 w11br02 U46216 11zs10 AB180664 11ac21 AB211036 1101 DQ883225 1101 D87427 0402 AB205163 04ga01 AY191776 0402 DQ303220 1401 EU431322 1401 AY126721 0401 AY243107 04ta01 AF464051 0401 AF272727 0403 AF464037 0403 AB428522 0403 EU087426 0404 0.06 0.04 0.02 0.00 Domestication does not narrow MHC diversity in Sus scrofa Immunogenetics Katerina A. Moutou1, Evagelia Koutsogiannouli1, Costas Stamatis1, Charalambos Billinis2, Claudia Kalbe3, Massimo Scandura4, Zissis Mamuris1* *Laboratory of Cenetics, Evolutionary and Comparative Biology, Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos st, 41221 Larissa, Greece; zmamur@bio.uth.gr 64 52 54 50 65 73 68 74 73 79 64 81 78 66 87 71 51 82 90 76 88 59 65 90 92 78 94 A 83 50 94 89

2. AB215112 020202 EU195214 AY285934 020202 AY247777 020202 AY191777 020202 M29939 020201 AB215111 020201 AY285932 020201 AY906855 0201 AY285925 0201 EU195156 DQ159904 EU432059 02cs01 BP160216 0203 EU432058 0203 AY459303 0203 EU195213 DQ883217 02jh01 DQ159901 0204 AK236590 0204 SLA-DQA*08 DQ003300 02xu01 D17740 ka01 SLA-DQA*06 EU432060 0301 EU195199 AY285930 0301 AY243100 0301 SLA-DQA*05 EU195217 AY247776 03we01 SLA-DQA*09 AY285931 01my01 SLA-DQA*01 DQ883218 0101 AB215110 0101 SLA-DQA*02 AY962312 0102 M29938 0102 EU195144 SLA-DQA*03 AY285927 0103 DN595524 0103 AY102473 01ch01 AY102474 w05ch01 DQ159893 SLA-DQA*04 AY243104 04ta01 AY102475 0401 DN595570 0401 SLA-DQA*07 0.030 0.025 0.020 0.015 0.010 0.005 0.000 80 68 73 65 74 73 80 64 79 64 82 67 71 78 98 92 83 71 75 66 89 76 50 65 78 90 B FigureS2 Neighbour-joining phylogenetic trees of the (a) 14 SLA-DRB1 and (b) the nine SLA-DQA exon 2 alleles of Sus scrofa, together with sequences available from the Immuno Polymorphic Database (IPD)-MHC sequence database (http://www.ebi.ac.uk.ipd.mhc/sla/). Numbers indicate the percentage bootstrap support (10000 replicates). Numbers below 50 were ommited. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site.