Abstract
Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful tool for the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds.
Highlights
Genes of the Major Histocompatibility Complex (MHC) have become one of the most sought-after molecular markers for the investigation of adaptive genetic variation in vertebrates (e.g., Eizaguirre et al, 2012; Kamath & Getz, 2011; Kubinak et al, 2012; Radwan et al, 2012)
Versatile primers for songbirds: The primer pair MHCPasCI-Fw and MHCPasCI-Rv successfully amplified multiple MHC class I sequences in all 16 songbird species tested in the present study
Four out of the five MHC class I alleles that we isolated in the Common Yellowthroat are identical to some of the alleles previously isolated in the same species by Bollmer et al (2012)
Summary
Genes of the Major Histocompatibility Complex (MHC) have become one of the most sought-after molecular markers for the investigation of adaptive genetic variation in vertebrates (e.g., Eizaguirre et al, 2012; Kamath & Getz, 2011; Kubinak et al, 2012; Radwan et al, 2012). Given the extraordinary richness and diversity of continuously evolving pathogens in the environment, it is not surprising that the MHC harbors the most polymorphic genes described far, with some loci, such as the human HLA-B locus, possessing more than 2,000 alleles (de Bakker & Raychaudhuri, 2012) The maintenance of such astonishing diversity is believed to be driven primarily by two main types of balancing selection: heterozygote advantage, by which heterozygous individuals respond better to infection than homozygous individuals, and frequency-dependent selection, by which rare, low-frequency alleles might provide a selective advantage once pathogens have found a way to elude the most common immune defense alleles in the population. MHC genes have been of great interest in evolutionary biology and conservation genetics, as the capability of species and populations to counter and adapt to novel pathogen menaces is believed to be tightly linked to their degree of MHC variability (see Piertney & Oliver, 2006; Sommer, 2005; Spurgin et al, 2011), but see (Gangoso et al, 2012; Radwan, Biedrzycka & Babik, 2010; Westerdahl et al, 2012)
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