Allelic diversity and selection at the MHC class I and class II in a long-distance migratory shorebird, the Hudsonian Godwit (Limosa haemastica).

The major histocompatibility complex (MHC) plays a central role in vertebrate adaptive immunity by encoding receptors that recognize pathogen-derived antigens. Migratory shorebirds, such as the Hudsonian Godwit (Limosa haemastica), encounter diverse pathogen landscapes across a wide range of habitats along their migratory routes. Therefore, migratory birds are expected to maintain a robust and effective immune system that minimizes the effects of infection without compromising their migration performance. We examined the genetic diversity of MHC class I exon 3 and MHC class IIB exon 2 across the species range. A total of 57 MHC-I and 13 MHC-IIB alleles were identified, with high polymorphisms observed in the peptide-binding regions (PBR). Signatures of positive selection were more pronounced in PBR sites from MHC-I than from MHC-IIB, suggesting stronger selective pressure from intracellular pathogens. In contrast, the relatively low allelic diversity and weaker selection signatures of MHC-IIB may reflect reduced exposure to extracellular pathogens. Despite broad geographic sampling, no evidence of an adaptive population structure was detected, indicating limited local adaptation and the likely influence of gene flow or neutral processes. Phylogenetic analyses revealed that some L. haemastica alleles clustered with those from closely related Scolopacidae species. These findings highlight the importance of pathogen-mediated selection in shaping MHC variation, providing valuable insights into the variability of a key group of adaptive immune genes in exceptional avian migratory species facing growing environmental pressure.