Data from: Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3

• Main Authors: Alcaide, Miguel, Liu, Mark, Edwards, Scott V.
• Format: Dataset
• Language: English
• Published: Dryad 2013
• Subjects: Dumetella carolinensis; Passeri; Vireo olivaceus; Bombycilla cedrorum; Haemorhous mexicanus; Thraupis episcopus; GC content; Sitta canadensis; Cardinalis cardinalis; adaptive variation; Agelaius phoeniceus; Diversifying selection; Thryothorus thoracicus; Geothlypis trichas; Passerina cyanea; Passerida; Sialia sialis; Passer domesticus; pathogen-mediated selection; Passeriformes; Major histocompatibility complex; 454 pyrosequencing; Polioptila plumbea; Sturnus vulgaris; Turdus migratorius; Corvida; Avian Studies
• Online Access: https://dx.doi.org/10.5061/dryad.jr583; http://datadryad.org/stash/dataset/doi:10.5061/dryad.jr583

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 toolfor the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds. : Alcaide_etal_PeerJ_MHC_classI_alignmentThis alignment was used in the analysis of the paper in PeerJ by M. Alcaide, M. Liu and S. Edwards entitled "Major Histocompatibility Complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3". The alignment begins on the first position of the codon and was made according to methods described in the paper. Taxa without Genbank numbers are original data; Genbank nubmers for these sequences can be found on Genbank. Taxa with Genbank numbers were taken from Genbank.