Major Histocompatibility Complex immunogenetic diversity differs substantially across sea turtle species and genomic regions

Abstract Major histocompatibility complex (MHC) immune loci illustrate how natural selection shapes functional genetic diversity in wild populations. Balancing selection favors high MHC diversity within individuals and populations that persists beyond speciation, leading to shared allelic lineages among taxa. However, some vertebrates show markedly lower allelic diversity and even the loss of entire MHC gene classes. Variation in life history and disease prevalence makes sea turtles an important group for studying interspecific MHC diversity, but this has been minimally explored. We sequenced class I and class II MHC genes in over 300 individuals from loggerhead (Caretta caretta), green (Chelonia mydas), leatherback (Dermochelys coriacea), and Kemp’s ridley (Lepidochelys kempii) sea turtles. We recovered 141 class I and 308 class II functionally distinct alleles, many of which were shared among species. Codon usage analyses suggest that the shared alleles have been maintained through speciation. High allele counts and evidence of diversifying and positive selection suggest balancing selection maintains considerable MHC diversity in sea turtles. However, we found two notable exceptions: (1) D. coriacea had extremely low nucleotide and allelic diversity across all MHC loci, and (2) one MHC class II gene copy on a different chromosome from the core MHC genomic region showed little evidence of positive selection and almost no genetic variability among all four species, suggesting an atypical and potentially functionally distinct gene. Our study finds notably high allelic and nucleotide diversity in sea turtle MHC promoted by balancing selection, yet evolutionary pressures vary considerably between species and gene copies.