MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion

Immunogenetics. 2017 Feb;69(2):101-111. doi: 10.1007/s00251-016-0953-7. Epub 2016 Oct 8.


The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. 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 influenced 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 signatures 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: Balancing selection; Gene conversion; Major histocompatibility complex; Pardalotus; Passerine; Recombination.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Evolution, Molecular
  • Exons / genetics*
  • Gene Conversion / genetics*
  • Histocompatibility Antigens Class II / genetics*
  • Passeriformes / genetics*
  • Phylogeny
  • Polymorphism, Genetic / genetics*
  • Recombination, Genetic / genetics*
  • Selection, Genetic / genetics*
  • Sequence Homology, Amino Acid
  • Species Specificity


  • Histocompatibility Antigens Class II