DOI: 10.5061/dryad.4xgxd25hf
title: Data from: Only rare classical MHC-I alleles are highly expressed in the European house sparrow

description: The exceptional polymorphism observed within genes of the major
 histocompatibility complex (MHC), a core component of the vertebrate
 immune system, has long fascinated biologists. The highly polymorphic
 classical MHC class-I (MHC-I) genes are maintained by pathogen-mediated
 balancing selection (PMBS), as shown by many sites subject to positive
 selection, while the more monomorphic MHC-I genes show signatures of
 purifying selection. In line with PMBS, at any point in time, rare
 classical MHC alleles are more likely than common classical MHC alleles to
 confer a selective advantage in host-pathogen interactions. Combining
 genomic and expression data from the blood of wild house sparrows Passer
 domesticus, we found that only rare classical MHC-I alleles were highly
 expressed, while common classical MHC-I alleles were lowly expressed or
 not expressed. Moreover, highly expressed rare classical MHC-I alleles had
 more positively selected sites, indicating exposure to stronger PMBS,
 compared with lowly expressed classical alleles. As predicted, the level
 of expression was unrelated to allele frequency in the monomorphic
 non-classical MHC-I alleles. Going beyond previous studies, we offer a
 fine-scale view of selection on classical MHC-I genes in a wild population
 by revealing differences in the strength of PMBS according to allele
 frequency and expression level.
description: Exon 3 of MHC class I was amplified and sequenced on the Illumina
 MiSeq platform from gDNA and cDNA originating from blood samples collected
 from 28 house sparrows (<em>Passer domesticus</em>) at four
 sites across Europe. Reads were trimmed and filtered to identify unique
 allele sequences in gDNA and cDNA. Alleles were classified as classical or
 non-classical, with non-classical alleles identified as having a 6 bp
 deletion. Filtered read counts were converted into allele presence/absence
 (1/0) for gDNA and cDNA, and cDNA read counts were designated as the
 expression levels for (i) nucleotide alleles
 (MHCI_cDNA_gDNA_nt_geno_pheno.txt) and (ii) amino acid alleles
 (MHCI_cDNA_gDNA_aa_geno_pheno.txt). Allele frequencies (i.e. number of
 individuals carrying each allele) were calculated. The numbers of unique
 genomic and expressed alleles were summed for each bird
 (MHCI_cDNA_gDNA_total_alleles_pheno.txt). Accompanying phenotypic data
 include country of origin (Bulgaria, Poland, Spain or Sweden) and season
 of sample collection (spring/autumn). For full methods, refer to the
 published article.
description: # Data from: Only rare classical MHC-I alleles are highly expressed in the
 European house sparrow 
 Datasets contain data on genomic and expressed diversity of the major
 histocompatibility (MHC) class I in European house sparrows (*Passer
 domesticus*). Data originates from amplicon sequencing of the exon 3
 region of MHC-I in gDNA and cDNA, originating from the blood of 28 house
 sparrows, sampled at four sites across Europe. MHC-I alleles are
 classified as classical or non-classical, with non-classical alleles
 identified as having a 6-bp deletion. Analyses conducted included
 investigation of the variation in genomic and expressed MHC-I diversity,
 variation in MHC-I expression (probability and level of expression) in
 relation to allele frequency (i.e. frequency of allele in the sampled
 population) and variation in MHC-I expression level according to the rank
 order of expression level within each individual's genotype. Analyses
 were conducted at the level of nucleotide alleles and amino acid alleles.
 Titles of datasets: MHCI_cDNA_gDNA_total_alleles_pheno.csv
 MHCI_cDNA_gDNA_nt_geno_pheno.csv MHCI_cDNA_gDNA_aa_geno_pheno.csv ##
 Description of the data and file structure Dataset:
 MHCI_cDNA_gDNA_nt_geno_pheno.csv Dataset: MHCI_cDNA_gDNA_aa_geno_pheno.csv
 Data description: The genomic (gDNA) and expressed (cDNA) genotypes, along
 with read counts, are given for each MHC-I allele and for each bird.
 Genotype is indicated by the presence (1) or absence (0) of alleles in
 gDNA or cDNA. Allele read counts from cDNA provide a measure of expression
 level. Total read counts for each sample are also given. All MHC-I alleles
 identified in the population (the sample of 28 birds) are included. The
 dataset named MHCI_cDNA_gDNA_nt_geno_pheno.csv contains data at the level
 of nucleotide (hence the notation, nt, in the file name) alleles. The 133
 unique nucleotide sequences detected in gDNA were translated to amino acid
 sequences, yielding 101 putative alleles. Data at the level of amino acid
 alleles can be found in the dataset named MHCI_cDNA_gDNA_aa_geno_pheno.csv
 (hence the notation, aa, in the file name). The two datasets allow
 separate analysis of nucleotide alleles and amino acid alleles. Data
 structure: Tabular data are organised in long format with one row for
 every allele (n = 133/101 nucleotide/amino acid alleles) and every bird (n
 = 28). The structure and variable names are almost identical for the two
 datasets, the difference being that one contains data for nucleotide
 alleles and the other contains data for amino acid alleles. Data
 definitions: * bird_ID = unique identifier for each bird/blood sample *
 Site = capture and sampling location (country) * Season = season of
 capture and sampling ("Spring" or "Autumn") *
 nt_allele_ID = unique identifier for each nucleotide allele, according to
 GenBank * GenBank_Accession_number = Genbank accession number for the
 corresponding nucleotide sequence * aa_allele_ID = unique identifier for
 the corresponding amino acid allele (the dataset
 MHCI_cDNA_gDNA_nt_geno_pheno.csv thus shows which nucleotide allele(s)
 translate to each amino acid allele since several nucleotide alleles can
 yield the same amino acid allele) * Allele_type = "Classical" or
 "Non-classical" * Allele_frequency = frequency of the
 corresponding nucleotide/amino acid allele in the population (i.e. sample
 of 28 birds) * gDNA_genotype = presence (1) or absence (0) of the
 corresponding nucleotide/amino acid allele in gDNA from the corresponding
 bird/blood sample * gDNA_read_count = number of (trimmed and filtered)
 gDNA reads corresponding to the nucleotide/amino acid allele from the
 corresponding bird/blood sample * gDNA_total_reads = total gDNA read count
 for the corresponding bird/blood sample * gDNA_NoAlleles = total number of
 genomic alleles for the corresponding bird/blood sample * cDNA_genotype =
 presence (1) or absence (0) of the corresponding nucleotide/amino acid
 allele in cDNA from the corresponding bird/blood sample * cDNA_read_count
 = number of (trimmed and filtered) cDNA reads corresponding to the
 nucleotide/amino acid allele from the corresponding bird/blood sample *
 cDNA_total_reads = total cDNA read count for the corresponding bird/blood
 sample * cDNA_NoAlleles = total number of expressed alleles for the
 corresponding bird/blood sample Dataset:
 MHCI_cDNA_gDNA_total_alleles_pheno.csv Data description: Dataset
 summarising the total number of genomic and expressed MHC-I alleles (both
 nucleotide and amino acid alleles) carried by each bird, separated between
 classical and non-classical alleles. Data structure: Tabular data are
 organised in long format with one row per bird (n = 28) and allele type (n
 = 2; i.e. classical or non-classical). Data definitions: * bird_ID =
 unique identifier for each bird/blood sample * Site = capture and sampling
 location (country) * Season = season of capture and sampling
 ("Spring" or "Autumn") * Allele_type =
 "Classical" or "Non-classical" * gDNA_NoAlleles_nt =
 total number of genomic nucleotide alleles for the corresponding
 bird/blood sample * gDNA_NoAlleles_aa = total number of genomic amino acid
 alleles for the corresponding bird/blood sample * cDNA_NoAlleles_nt =
 total number of expressed nucleotide alleles for the corresponding
 bird/blood sample * cDNA_NoAlleles_aa = total number of expressed amino
 acid alleles for the corresponding bird/blood sample ## Code/Software R
 code for performing the analyses and obtaining the summary statistics that
 are presented in the article is provided.