Table S1. GenBank Accession numbers for MHC sequences used to construct the phylogenetic tree.

Species / GenBank accession numbers / Reference
A. altamirani / KP408179-KP408181 / This study
A. andersoni / KP408182-KP408190 / This study
A. dumerilii / KP408191-KP408201 / This study
A. mexicanum / KP408202-KP408206
EF585229 -- EF585231, AF213378 / This study
(Laurens et al 2001; Richman et al 2007)
A. velasci / KP408207-KP408209 / This study
A. tigrinum / KP408210 and KP408211
DQ071907 -- DQ071913 / This study
(Bos and DeWoody 2005)
T. cristatus / FJ448027 / (Babik et al 2009)

Table S2. DAB genotypes of all individuals from our five focal Ambystoma species. Numbers given for genotypes are the number abbreviations for the full allele names given in Figures 2 and 4, and genotypes are given in the format allele number/allele number.

Individual / Genotype / Individual / Genotype
Altamirani_1 / 01/01 / Dumerilii_7 / 16/16
Altamirani_2 / 01/01 / Dumerilii_8 / 16/13
Altamirani_3 / 01/01 / Dumerilii_9 / 22/23
Altamirani_4 / 01/01 / Dumerilii_10 / 21/13
Altamirani_5 / 01/01 / Dumerilii_11 / 15/14
Altamirani_6 / 01/01 / Dumerilii_12 / 17/17
Altamirani_7 / 01/01 / Mexicanum_1 / 24/24
Altamirani_8 / 01/01 / Mexicanum_2 / 24/24
Altamirani_9 / 01/01 / Mexicanum_3 / 24/24
Altamirani_10 / 01/01 / Mexicanum_4 / 24/24
Altamirani_11 / 01/01 / Mexicanum_5 / 24/24
Altamirani_12 / 01/01 / Mexicanum_6 / 24/25
Altamirani_13 / 02/02 / Mexicanum_7 / 26/26
Altamirani_14 / 01/01 / Mexicanum_8 / 24/24
Altamirani_15 / 01/01 / Mexicanum_9 / 24/24
Altamirani_16 / 03/03 / Mexicanum_10 / 24/24
Altamirani_17 / 03/03 / Mexicanum_11 / 24/24
Altamirani_18 / 01/01 / Mexicanum_12 / 27/27
Altamirani_19 / 01/01 / Mexicanum_13 / 30/30
Andersoni_1 / 12/12 / Mexicanum_14 / 24/24
Andersoni_2 / 12/12 / Mexicanum_15 / 24/24
Andersoni_3 / 04/04 / Mexicanum_16 / 28/28
Andersoni_4 / 05/05 / Mexicanum_17 / 30/30
Andersoni_5 / 06/06 / Mexicanum_18 / 30/30
Andersoni_6 / 07/07 / Velasci_1 / 31/31
Andersoni_7 / 05/05 / Velasci_2 / 29/29
Andersoni_8 / 05/05 / Velasci_3 / 30/30
Andersoni_9 / 08/09 / Velasci_4 / 30/30
Andersoni_10 / 10/10 / Velasci_5 / 24/31
Andersoni_11 / 05/05 / Velasci_6 / 31/31
Andersoni_12 / 11/11 / Velasci_7 / 30/30
Andersoni_13 / 11/11 / Velasci_8 / 30/30
Dumerilii_1 / 13/13 / Velasci_9 / 30/31
Dumerilii_2 / 19/19 / Velasci_10 / 30/24
Dumerilii_3 / 13/20 / Velasci_11 / 10/10
Dumerilii_4 / 17/17 / Velasci_12 / 30/31
Dumerilii_5 / 18/18 / Velasci_13 / 24/31
Dumerilii_6 / 13/13

Table S3. A summary of the number of individuals in which each allele is found as well as allele pairs that differ by only a single allele. Alleles sequenced by previous investigators are given with GenBank accession numbers.

Allele / # Individuals / Single Nucleotide Different From:
Amal_DAB*01 / 16 / None
Amal_DAB*02 / 1 / None
Amal_DAB*03 / 2 / None
Aman_DAB*04 / 1 / Aman_DAB*10
Aman_DAB*05 / 4 / Aman_DAB*10
Aman_DAB*06 / 1 / None
Aman_DAB*07 / 1 / Amdu_DAB*21
Aman_DAB*08 / 1 / None
Aman_DAB*09 / 1 / None
Aman_DAB*10 / 2 / Aman_DAB*04; Aman_DAB*05
Aman_DAB*11 / 2 / None
Aman_DAB*12 / 2 / Amve_DAB*29
Amdu_DAB*13 / 4 / None
Amdu_DAB*14 / 1 / None
Amdu_DAB*15 / 1 / None
Amdu_DAB*16 / 2 / None
Amdu_DAB*17 / 2 / None
Amdu_DAB*18 / 1 / None
Amdu_DAB*19 / 1 / None
Amdu_DAB*20 / 1 / None
Amdu_DAB*21 / 1 / Aman_DAB*07
Amdu_DAB*22 / 1 / None
Amdu_DAB*23 / 1 / None
Amme_DAB*24 / 15 / Amme_DAB*42 (EF585231.1); Amme_DAB*44 (AF213378)
Amme_DAB*25 / 1 / None
Amme_DAB*26 / 1 / None
Amme_DAB*27 / 1 / None
Amme_DAB*28 / 1 / None
Amve_DAB*29 / 1 / Aman_DAB*12
Amve_DAB*30 / 10 / None
Amve_DAB*31 / 6 / None

Table S4. Results of additional codon-based maximum likelihood tests of selection (FEL, REL, SLAC, FUBAR) compared to MEME results. Codons are listed only if one of the methods showed positive selection or they correspond to a putative peptide binding residue. Asterisks indicate codons that are presumed to have undergone episodic selection. Numbering matches the alignment in Fig. 3.

Codon / MEME / FEL / FUBAR / REL / SLAC / Putative peptide binding?
1 / 0 / 0 / 0 / 0 / 0 / YES
3 / + / 0 / + / + / 0 / YES
5 / + / + / + / + / + / YES
18 / + / 0 / + / + / 0 / NO
20 / + / + / + / + / + / YES
22 / + / 0 / + / 0 / 0 / YES
23* / + / 0 / 0 / 0 / 0 / NO
29 / 0 / 0 / 0 / 0 / 0 / YES
30 / 0 / 0 / 0 / 0 / 0 / YES
43* / + / 0 / 0 / 0 / 0 / NO
44* / + / 0 / 0 / 0 / 0 / NO
49 / + / + / + / + / + / YES
52 / 0 / 0 / 0 / 0 / 0 / YES
53 / 0 / 0 / 0 / 0 / 0 / YES
59 / 0 / 0 / + / 0 / + / YES
62* / + / 0 / 0 / 0 / 0 / YES
63 / + / + / + / + / + / YES
66 / + / + / + / + / + / YES
70 / 0 / 0 / 0 / 0 / 0 / YES
73 / 0 / 0 / + / + / 0 / NO
74 / 0 / - / - / - / - / YES

Fig S1. Relationship of Ambystoma MHC alleles based on the supertyping method. Gray dashed boxes indicate alleles belonging to the same supertype. All four algorithms used produced similar trees and identified the same 17 supertypes; therefore only the tree generated with the paired correlation algorithm is shown here