DOI: 10.5061/dryad.8g1bb
title: Data from: Birdsong signals individual diversity at the major histocompatibility complex

description: The major histocompatibility complex (MHC) plays a key role in vertebrate
 immunity, and pathogen-mediated selection often favours certain allelic
 combinations. Assessing potential mates' MHC profiles may provide
 receivers with genetic benefits (identifying MHC-compatible mates and
 producing optimally diverse offspring) and/or material benefits
 (identifying optimally diverse mates capable of high parental investment).
 Oscine songbirds learn songs during early life, such that song repertoire
 content can reflect population of origin while song complexity can reflect
 early life condition. Thus birdsong may advertise the singer's
 genetic dissimilarity to others in the population (and, presumably,
 compatibility with potential mates), or individual genetic diversity (and
 thus condition-dependent material benefits). We tested whether song
 repertoire content and/or complexity signal MHC class IIβ dissimilarity
 and/or diversity in male song sparrows (Melospiza melodia). Pairwise
 dissimilarity in repertoire content did not predict MHC dissimilarity
 between males, suggesting that locally rare songs do not signal rare MHC
 profiles. Thus, geographical variation in song may not facilitate
 MHC-mediated inbreeding or outbreeding. Larger repertoires were associated
 with intermediate MHC diversity, suggesting intermediate rather than
 maximal MHC diversity is optimal. This could reflect trade-offs between
 resisting infection and autoimmune disorders. Song complexity may
 advertise optimal MHC diversity, a trait affecting disease resistance and
 capacity for parental care.
description: Dryad1_PCRandSeqconditionsPCR and sequencing conditions for song sparrow MHC class IIßDryad2_FigS1_MHCalleletreeFigure S1. Phylogeny of MHC class IIß amino acid alleles amplified from 32 male song sparrows. Evolutionary history was inferred using the maximum likelihood method based on the WAG amino acid substitution model. The tree with the highest likelihood is shown. The percentage of replicate trees in which the associated alleles cluster together in the bootstrap test (500 replicates) is shown at each node. The tree is drawn to scale, with branch lengths corresponding to number of substitutions per site. The analysis involved 186 amino acid sequences (SOSP-DAB*#). Each vertical red line indicates a superallele (SA) composed of multiple similar sequences, and each black arrow indicates a single sequence that belonged to its own SA.Dryad3_RcodeAnnotated R code used in data analysis.Dryad4_MHC_composition_tableMHC composition table for 32 male song sparrows. Each row corresponds to an individual bird, and each column corresponds to a unique amino acid sequence at MHC IIß (allele). Presence or absence of each allele in each individual’s genotype is denoted by 1 or 0, respectively. Alleles are listed here as X1, X2, … and correspond to sequences SOSP-DAB*1, SOSP-DAB*2, … on Figure S1 and on GenBank.Dryad5_MHC_composition_table_with_IDsMHC composition table for 32 male song sparrows, including individual identifiers. Each row corresponds to an individual bird, and each column corresponds to a unique amino acid sequence at MHC IIß (“allele”). Presence or absence of each allele in each individual’s genotype is denoted by 1 or 0, respectively. Alleles are listed here as X1, X2, … and correspond to sequences SOSP-DAB*1, SOSP-DAB*2, … on Figure S1 and on GenBank.Dryad6_MHC_AA_sequencesAmino acid sequences for 32 male song sparrows genotyped at MHC IIß (FASTA format).Dryad7_MHC_AA_treeNewick tree topography for amino acid alleles characterized at MHC IIß. Evolutionary history was inferred as described in Figure S1 (file Dryad2).Dryad8_song_unifrac_matrixMatrix of UniFrac distances calculated for all pairwise combinations of 32 male song sparrows genotyped at MHC IIß.Dryad9_MHC_UniFrac_MatrixMatrix of UniFrac distances calculated for all pairwise combinations of 32 male song sparrows genotyped at MHC IIß. This file is identical to file Dryad8 except that it includes individual identity along the top row.Dryad10_syllable_jaccard_SIMILARITY_indexMatrix of Jaccard similarity based on syllable sharing, calculated for all pairwise combinations of 32 male song sparrows. A = syllables produced by individual A but not B; B = syllables produced by individual B but not A; C = syllables common to both individuals; D = difference in repertoire size (number of syllables) between individuals A and B.Dryad11_syllable_Jaccard_DissimilarityPairwise matrix of Jaccard DISSIMILARITY, calculated as 1-Jaccard similarity, for all pairwise combinations of 32 male song sparrows.Dryad12_MHC_SAs_and_Song_DataNumber of MHC superalleles (SA) and song repertoire size (Song) for each of 32 male song sparrows.Dryad13_Suppl_ analysisTables S1 and S2. Predictors of song sparrow song repertoire size, after excluding a potentially influential datapoint.