ORIGINAL ARTICLE MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion Shandiya Balasubramaniam 1,2 & Raoul A. Mulder 2 & Paul Sunnucks 3 & Alexandra Pavlova 3 & Jane Melville 1 Received: 10 August 2016 /Accepted: 26 September 2016 # Springer-Verlag Berlin Heidelberg 2016 Abstract The high levels of polymorphism and allelic diver- sity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary pro- cesses. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influ- enced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signa- tures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes. Keywords Major histocompatibility complex . Passerine . Pardalotus . Balancing selection . Recombination . Gene conversion Introduction Classical genes of the major histocompatibility complex (MHC) encode molecules which are involved in the adaptive immune response of vertebrates. MHC class I and II molecules bind peptides derived from intracellular and extracellular path- ogens, respectively, and present them to T cells, whereupon the appropriate immune response is triggered (Klein 1986). High levels of polymorphism among MHC genes, especially in the peptide-binding region (PBR), have been found in a wide range of taxonomic groups (Hughes and Yeager 1998; Gaudieri et al. 2000; Garrigan and Hedrick 2003). Each PBR consists of a configuration of pockets and folds which only allows only spe- cific peptides to bind. Thus, variation in the sequence encoding the PBR affects the binding specificity of the MHC molecule, which in turn has significant implications for an individual’ s ability to recognise and respond to different pathogens (Westerdahl et al. 2005; Meyer-Lucht and Sommer 2005). Genetic variation in the MHC is generated through a num- ber of different processes, including point mutation, recombi- nation and gene conversion (Ohta 1995; Yeager and Hughes 1999; Miller and Lambert 2004). Point mutation acts on single sites and creates novel alleles, whereas recombination and gene conversion transfer stretches of nucleotide sequences between alleles and loci, generating new haplotypes in the process. The variation generated by these processes is thought to be maintained in individuals and populations by balancing selection, driven primarily by pathogen and parasite pressure (Hedrick 1999; Piertney and Oliver 2006; Spurgin and Richardson 2010). Balancing selection, which is a broad term * Shandiya Balasubramaniam sbalasubramaniam@museum.vic.gov.au 1 Department of Sciences, Museum Victoria, Melbourne, Victoria 3001, Australia 2 School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia 3 School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia Immunogenetics DOI 10.1007/s00251-016-0953-7