DOI: 10.5061/dryad.79t4b
title: Data from: Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer)

description: Background: The Major Histocompatibility Complex (MHC) plays a central
 role in immunity and has been given considerable attention by evolutionary
 ecologists due to its associations with fitness-related traits. Songbirds
 have unusually high numbers of MHC class I (MHC-I) genes, but it is not
 known whether all are expressed and equally important for immune function.
 Classical MHC-I genes are highly expressed, polymorphic and present
 peptides to T-cells whereas non-classical MHC-I genes have lower
 expression, are more monomorphic and do not present peptides to T-cells.
 To get a better understanding of the highly duplicated MHC genes in
 songbirds, we studied gene expression in a phylogenetic framework in three
 species of sparrows (house sparrow, tree sparrow and Spanish sparrow),
 using high-throughput sequencing. We hypothesize that sparrows could have
 classical and non-classical genes, as previously indicated though never
 tested using gene expression. Results: The phylogenetic analyses reveal
 two distinct types of MHC-I alleles among the three sparrow species, one
 with high and one with low level of polymorphism, thus resembling
 classical and non-classical genes, respectively. All individuals had both
 types of alleles, but there was copy number variation both within and
 among the sparrow species. However, the number of highly polymorphic
 alleles that were expressed did not vary between species, suggesting that
 the structural genomic variation is counterbalanced by conserved gene
 expression. Overall, 50% of the MHC-I alleles were expressed in sparrows.
 Expression of the highly polymorphic alleles was very variable, whereas
 the alleles with low polymorphism had uniformly low expression.
 Interestingly, within an individual only one or two alleles from the
 polymorphic genes were highly expressed, indicating that only a single
 copy of these is highly expressed. Conclusions: Taken together, the
 phylogenetic reconstruction and the analyses of expression suggest that
 sparrows have both classical and non-classical MHC-I genes, and that the
 evolutionary origin of these genes predate the split of the three
 investigated sparrow species seven million years ago. Because only the
 classical MHC-I genes are involved in antigen presentation, the function
 of different MHC-I genes should be considered in future ecological and
 evolutionary studies of MHC-I in sparrows and other songbirds.
description: Pado_Primercomb1_rawdataRaw (unfiltered) 454 amplicon sequence data for house sparrows using primer combination 1. Demultiplexed using the software jMHC (2011).Pahi_Primercomb1_rawdataRaw (unfiltered) 454 amplicon sequence data for Spanish sparrow using primer combination 1. Demultiplexed using the software jMHC (2011).Pamo_Primercomb1_rawdataRaw (unfiltered) 454 amplicon sequence data for tree sparrow using primer combination 1. Demultiplexed using the software jMHC (2011).Pado_Primercomb2_rawdataRaw (unfiltered) 454 amplicon sequence data for house sparrow using primer combination 2. Demultiplexed using the software jMHC (2011).Pahi_Primercomb2_rawdataRaw (unfiltered) 454 amplicon sequence data for Spanish sparrow using primer combination 2. Demultiplexed using the software jMHC (2011).Pamo_Primercomb2_rawdataRaw (unfiltered) 454 amplicon sequence data for tree sparrow using primer combination 2. Demultiplexed using the software jMHC (2011).Pado_primercomb_3_rawdataRaw (unfiltered) 454 amplicon sequence data for house sparrow using primer combination 3. Demultiplexed using the software jMHC (2011).Pahi_primer_comb_3_rawdataRaw (unfiltered) 454 amplicon sequence data for Spanish sparrow using primer combination 3. Demultiplexed using the software jMHC (2011).Pamo_primercomb_3_rawdataRaw (unfiltered) 454 amplicon sequence data for house sparrow using primer combination 3. Demultiplexed using the software jMHC (2011).Pado_Primercomb4_rawdataRaw (unfiltered) 454 amplicon sequence data for house sparrow using primer combination 4. Demultiplexed using the software jMHC (2011).Pahi_Primercomb4_rawdataRaw (unfiltered) 454 amplicon sequence data for Spanish sparrow using primer combination 4. Demultiplexed using the software jMHC (2011).Pamo_Primercomb4_rawdataRaw (unfiltered) 454 amplicon sequence data for tree sparrow using primer combination 4. Demultiplexed using the software jMHC (2011).Name_codeDetails of the samples included in the study. The column "Name in publication" indicates the name a samples has been given in the published article. The column "Name in 454 files" indicates the corresponding sample in the raw data files.Passer_concate_all_seqAlignment of the 129 concatenated exon 3 alleles identified. Alignment performed manually using BioEdit V.7.2.5 Sequence Alignment Editor (Hall 1999). In FASTA format.Tree_alignmentAlignment of all alleles identified with primer combination 1 and used for building the phylogenetic tree.