Extensive MHC class II B gene duplication in a passerine, the common Yellowthroat (Geothlypis trichas).

The major histocompatibility complex (MHC) is characterized by a birth and death model of evolution involving gene duplication, diversification, loss of function, and deletion. As a result, gene number varies across taxa. Birds have between one and 7 confirmed MHC class II B genes, and the greatest diversity appears to occur in passerines. We used multiple primer sets on both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the range of class II B genes present in a passerine, the common yellowthroat (Geothlypis trichas). We confirmed 39 exon 2 sequences from gDNA in a single individual, indicating the presence of at least 20 class II B loci. From a second individual, we recovered 16 cDNA sequences belonging to at least 8 transcribed loci. Phylogenetic analysis showed that common yellowthroat sequences fell into subgroups consisting of classical loci, as well as at least 4 different clusters of sequences with reduced sequence variability that may represent pseudogenes or nonclassical loci. Data from 2 additional common yellowthroats demonstrated high interindividual variability. Our results reveal that some passerines possess an extraordinary diversity of MHC gene duplications, including both classical and nonclassical loci.