Salamanders reveal novel trajectories of amphibian MHC evolution

Genes of the Major Histocompatibility Complex (MHC) code for immune
proteins that are crucial for pathogen recognition in vertebrates. MHC
research in non-model taxa has long been hampered by its genomic
complexity that makes the locus-specific genotyping challenging. The
recent progress in sequencing and genotyping methodologies allows an
extensive phylogenetic coverage in studies of MHC evolution. Here, we
analysed the peptide-binding region of MHC class I in 30 species of
salamanders from six families representative of Urodela phylogeny. This
extensive dataset revealed an extreme diversity of MHC-I in salamanders,
both in terms of sequence diversity (ca. 3000 variants) and architecture
(2-22 gene copies per species). The signal of positive selection was
moderate and consistent between both peptide binding domains, but varied
greatly between genera. Positions of positively selected sites mostly
coincided with human Peptide Binding Sites, suggesting similar structural
properties of MHC-I molecules across distant vertebrate lineages. Finally,
we provided evidence for the common intra-exonic recombination at MHC-I
and for the role of life-history traits in the processes of MHC-I
expansion/contraction. Our study revealed novel evolutionary trajectories
of amphibian MHC and it contributes to the understanding of the mechanisms
that generated extraordinary MHC diversity throughout vertebrate
evolution.