Genetic diversity of MHC class I loci in six non-model frogs is shaped by positive selection and gene duplication
Karen M. Kiemnec-Tyburczy, Jonathan Q. Richmond, Anna E. Savage, Karen R. Lips, and Kelly R. Zamudio
Supplemental Files
Table S1 Sampling locations for Central and North American frogs.
Species / Locality / State/Province / CountryAgalychnis callidryas / El Copé / Province of Coclé / Panama
Espadarana prosoblepon / Serrania Maje / Province of Darien / Panama
Lithobates catesbeianus / Ithaca / New York / USA
Lithobates clamitans / Ithaca / New York / USA
Lithobates yavapaiensis / Seven Springs / Arizona / USA
Smilisca phaeota / El Copé / Province of Coclé / Panama
Table S2 GenBank accession numbers and frequencies of MHC class I sequences isolated from six species of frogs.
Species / Clone / Frequency / Accession no.A. callidryas / Agca-UA*01 / 2/5 / JQ679312
A. callidryas / Agca-UA*02 / 1/5 / JQ679313
A. callidryas / Agca-UA*03 / 1/5 / JQ679314
A. callidryas / Agca-UA*04 / 1/5 / JQ679315
A. callidryas / Agca-UA*05 / 1/5 / JQ679316
A. callidryas / Agca-UA*06 / 1/5 / JQ679317
A. callidryas / Agca-UA*07 / 1/5 / JQ679318
A. callidryas / Agca-UA*08 / 1/5 / JQ679319
A. callidryas / Agca-UA*09 / 1/5 / JQ679320
A. callidryas / Agca-UA*10 / 1/5 / JQ679321
A. callidryas / Agca-UA*11 / 1/5 / JQ679322
A. callidryas / Agca-UA*12 / 1/5 / JQ679323
A. callidryas / Agca-UA*13 / 1/5 / JQ679324
A. callidryas / Agca-UA*14 / 1/5 / JQ679325
A. callidryas / Agca-UA*15 / 1/5 / JQ679326
A. callidryas / Agca-UA*16 / 1/5 / JQ679327
A. callidryas / Agca-UA*17 / 1/5 / JQ679328
A. callidryas / Agca-UA*18 / 1/5 / JQ679329
A. callidryas / Agca-UA*19 / 1/5 / JQ679330
E. prosoblepon / Espr-UA*01 / 1/5 / JQ679331
E. prosoblepon / Espr-UA*02 / 3/5 / JQ679332
E. prosoblepon / Espr-UA*03 / 1/5 / JQ679333
E. prosoblepon / Espr-UA*04 / 1/5 / JQ679334
E. prosoblepon / Espr-UA*05 / 1/5 / JQ679335
E. prosoblepon / Espr-UA*06 / 2/5 / JQ679336
E. prosoblepon / Espr-UA*07 / 1/5 / JQ679337
E. prosoblepon / Espr-UA*08 / 1/5 / JQ679338
E. prosoblepon / Espr-UA*09 / 1/5 / JQ679339
E. prosoblepon / Espr-UA*10 / 1/5 / JQ679340
E. prosoblepon / Espr-UA*11 / 1/5 / JQ679341
E. prosoblepon / Espr-UA*12 / 1/5 / JQ679342
L. catesbeianus / Lica-UA*01 / 1/5 / JQ679343
L. catesbeianus / Lica-UA*02 / 1/5 / JQ679344
L. catesbeianus / Lica-UA*03 / 1/5 / JQ679345
L. catesbeianus / Lica-UA*04 / 1/5 / JQ679346
L. catesbeianus / Lica-UA*05 / 1/5 / JQ679347
L. catesbeianus / Lica-UA*06 / 1/5 / JQ679348
L. catesbeianus / Lica-UA*07 / 1/5 / JQ679349
L. catesbeianus / Lica-UA*08 / 1/5 / JQ679350
L. catesbeianus / Lica-UA*09 / 1/5 / JQ679351
L. catesbeianus / Lica- UA*10 / 2/5 / JQ679352
L. catesbeianus / Lica- UA*11 / 1/5 / JQ679353
L. catesbeianus / Lica-UA*12 / 1/5 / JQ679354
L. clamitans / Licl-UA*01 / 1/5 / JQ679355
L. clamitans / Licl-UA*02 / 1/5 / JQ679356
L. clamitans / Licl-UA*03 / 1/5 / JQ679357
L. clamitans / Licl-UA*04 / 1/5 / JQ679358
L. clamitans / Licl-UA*05 / 1/5 / JQ679359
L. clamitans / Licl-UA*06 / 1/5 / JQ679360
L. clamitans / Licl-UA*07 / 1/5 / JQ679361
L. clamitans / Licl-UA*08 / 1/5 / JQ679362
L. clamitans / Licl-UA*09 / 1/5 / JQ679363
L. clamitans / Licl-UA*10 / 1/5 / JQ679364
L. clamitans / Licl-UA*11 / 2/5 / JQ679365
L. clamitans / Licl-UA*12 / 1/5 / JQ679366
L. clamitans / Licl-UA*13 / 1/5 / JQ679367
L. clamitans / Licl-UA*14 / 1/5 / JQ679368
L. clamitans / Licl-UA*15 / 1/5 / JQ679369
L. clamitans / Licl-UA*16 / 1/5 / JQ679370
L. yavapaiensis / Liya-UA*01 / 1/5 / JQ679371
L. yavapaiensis / Liya-UA*02 / 1/5 / JQ679372
L. yavapaiensis / Liya-UA*03 / 3/5 / JQ679373
L. yavapaiensis / Liya-UA*04 / 1/5 / JQ679374
L. yavapaiensis / Liya-UA*05 / 1/5 / JQ679375
L. yavapaiensis / Liya-UA*06 / 1/5 / JQ679376
L. yavapaiensis / Liya-UA*07 / 3/5 / JQ679377
L. yavapaiensis / Liya-UA*08 / 1/5 / JQ679378
L. yavapaiensis / Liya-UA*09 / 1/5 / JQ679379
S. phaeota / Smph-UA*01 / 1/5 / JQ679380
S. phaeota / Smph-UA*02 / 1/5 / JQ679381
S. phaeota / Smph-UA*03 / 1/5 / JQ679382
S. phaeota / Smph-UA*04 / 1/5 / JQ679383
S. phaeota / Smph-UA*05 / 3/5 / JQ679384
S. phaeota / Smph-UA*06 / 2/5 / JQ679385
S. phaeota / Smph-UA*07 / 1/5 / JQ679386
S. phaeota / Smph-UA*08 / 1/5 / JQ679387
S. phaeota / Smph-UA*09 / 1/5 / JQ679388
S. phaeota / Smph-UA*10 / 3/5 / JQ679389
S. phaeota / Smph-UA*11 / 1/5 / JQ679390
Table S3Conservation of peptide-docking residues of MHC class Ia alleles. The amino acid found at that site inhuman compared with the sequences from six frog species(see text for details); amino acid position (subscript) is based on the alignment in Fig 2
Residue / Presumed function / Agca / Espr / Lica / Licl / Liya / SmphY52 / peptide-docking / H/L/Y* / H/Y* / Y / Y / Y / F/Y*
R/Y77 / peptide-docking / R / R / R / R / R / R
Y116 / peptide-docking / F*/L/Y / Y/F* / F/L/R / F/L/C / F / F
T136 / peptide-docking / I/S/T* / S/T* / S/T* / S/T* / S/T* / S/T
R139 / peptide-docking / K/R* / K/R*/T / K/R* / K/N/R* / R / K*/R
W140 / peptide-docking / I/W* / I/W* / L/W* / V/W* / W / I/W*
Y154 / peptide-docking / Y / Y / Y / S*/Y* / Y / Y
Y166 / peptide-docking / F/H/Y* / F/H*/Y / H/Y* / H/Y / F/H/Y* / H/Y*
Species: A. callidryas (Agca), E. prosoblepon (Espr), L. catesbeianus (Lica), L. clamitans (Licl), L. yavapaiensis (Liya), and S. phaeota (Smph). Underscored residues indicate non-conservative substitutions. ‘*’ = most common residue when multiple residues were recovered at the same site in different sequences (no ‘*’ means that alternative residues were recovered with roughly equal frequency)