Variation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated European newts, Lissotriton montandoni and L. vulgaris, we demonstrated recent and ongoing MHC class I and II introgression in the Carpathian region. The extent of introgression correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded similarity between transects within species, implying pervasive introgression –  a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.

Dudek_et_al_ genotypes_haplotypes.xlsx: Genotypes of all individuals used in the study, composition of eight MHC class I and II haplotypes, expression status of MHC class I alleles

Dudek_et_al_MHCI_alleles.fas: Sequences of all MHC class I alleles described in the current study as well as these reported earlier by Fijarczyk et al. (2018, http://dx.doi.org/10.1098/rspb.2018.0819).

Dudek_et_al_MHCII_alleles.fas: Sequences of all MHC class II alleles described in the current study.